From 8f9bbd49e93fbabcd0480709ae0d28be7088148a Mon Sep 17 00:00:00 2001 From: Juan Funez Date: Fri, 6 Jun 2014 17:33:14 -0300 Subject: [PATCH] Adicionar `packtools.stylechecker.validate_style` e melhorar msgs no template #820 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit [views.py] - fixes para o caso que o stylechecker não retorne todos os campos de erro (line, column, message, level) - ``notice_detail`` agora adiciona uma msg de erro explicativo para mostar no template, e também escreve mais informação sobre o erro no logger. - troca inocação do método ``validate`` pelo ``validate_style`` [articletrack/tests/xml_tests_files/with_style_errors.xml] - novo xml com erros para ser anotados. [test_pages.py] - ajustes nos tests. [notice_detail.html] - ajustes para mostrar a msg de error para o usuário. --- .../templates/articletrack/notice_detail.html | 7 +- .../articletrack/tests/tests_pages.py | 19 +- .../tests/xml_tests_files/to_be_annotated.xml | 1872 ----------------- .../xml_tests_files/with_style_errors.xml | 1235 +++++++++++ scielomanager/articletrack/views.py | 47 +- 5 files changed, 1276 insertions(+), 1904 deletions(-) delete mode 100644 scielomanager/articletrack/tests/xml_tests_files/to_be_annotated.xml create mode 100644 scielomanager/articletrack/tests/xml_tests_files/with_style_errors.xml diff --git a/scielomanager/articletrack/templates/articletrack/notice_detail.html b/scielomanager/articletrack/templates/articletrack/notice_detail.html index 5b6c1667..7c0dda9d 100644 --- a/scielomanager/articletrack/templates/articletrack/notice_detail.html +++ b/scielomanager/articletrack/templates/articletrack/notice_detail.html @@ -137,7 +137,7 @@

{% trans 'Notices' %}:

  • {% trans "Style Checking" %} - {% if not xml_data.can_be_analyzed %} + {% if not xml_data.can_be_analyzed.0 %} {# could not be analyzed #}   @@ -201,10 +201,11 @@

    {% trans 'Notices' %}:

    {# annotations #} - {% if not xml_data.can_be_analyzed %} + {% if not xml_data.can_be_analyzed.0 %} {# could not be analyzed #}
    - {% trans "The XML could not be analyzed" %} +

    {% trans "The XML could not be analyzed" %}

    +

    {{ xml_data.can_be_analyzed.1 }}

    {% elif not xml_data.annotations %} {# xml without annotations #} diff --git a/scielomanager/articletrack/tests/tests_pages.py b/scielomanager/articletrack/tests/tests_pages.py index 726831aa..a0950b39 100644 --- a/scielomanager/articletrack/tests/tests_pages.py +++ b/scielomanager/articletrack/tests/tests_pages.py @@ -244,7 +244,7 @@ def get_xml_uri(self, attempt_id, target_name): xml_data = response.context['xml_data'] self.assertEqual(response.status_code, 200) - self.assertTrue(xml_data['can_be_analyzed']) + self.assertTrue(xml_data['can_be_analyzed'][0]) self.assertIsNone(xml_data['annotations']) self.assertEqual(xml_data['uri'], expected_response['uri']) self.assertIsNone(xml_data['validation_errors']) @@ -276,7 +276,7 @@ def get_xml_uri(self, attempt_id, target_name): xml_data = response.context['xml_data'] self.assertEqual(response.status_code, 200) - self.assertFalse(xml_data['can_be_analyzed']) + self.assertFalse(xml_data['can_be_analyzed'][0]) self.assertIsNone(xml_data['annotations']) self.assertEqual(xml_data['uri'], expected_response['uri']) self.assertIsNone(xml_data['validation_errors']) @@ -287,7 +287,7 @@ def test_annotations_of_error(self): notice = self._makeOne() # MOCK/REPLACE/FAKE/PIMP MY BALAIO!!! - target_xml = "to_be_annotated.xml" + target_xml = "with_style_errors.xml" expected_response = { "filename": "1415-4757-gmb-37-0210.xml", "uri": self._get_path_of_test_xml(target_xml) @@ -306,19 +306,18 @@ def get_xml_uri(self, attempt_id, target_name): reverse('notice_detail', args=[notice.checkin.pk]), user=self.user) xml_data = response.context['xml_data'] - self.assertEqual(response.status_code, 200) - self.assertTrue(xml_data['can_be_analyzed']) + self.assertTrue(xml_data['can_be_analyzed'][0]) self.assertIsNotNone(xml_data['annotations']) self.assertEqual(xml_data['uri'], expected_response['uri']) self.assertEqual(xml_data['file_name'], expected_response['filename']) self.assertIsNotNone(xml_data['validation_errors']) - self.assertEqual('7', xml_data['validation_errors']['error_lines']) + self.assertEqual('', xml_data['validation_errors']['error_lines']) self.assertEqual(1, len(xml_data['validation_errors']['results'])) expected_validation_errors = { - 'column': 0, - 'line': 7, - 'message': u"Element 'article-meta': This element is not expected. Expected is ( journal-meta ).", + 'column': '--', + 'line': '--', + 'message': u"Element 'funding-group': This element is not filled-in correctly.", 'level': u'ERROR' } self.assertEqual([expected_validation_errors], xml_data['validation_errors']['results']) @@ -350,7 +349,7 @@ def get_xml_uri(self, attempt_id, target_name): xml_data = response.context['xml_data'] self.assertEqual(response.status_code, 200) - self.assertFalse(xml_data['can_be_analyzed']) + self.assertFalse(xml_data['can_be_analyzed'][0]) self.assertIsNone(xml_data['annotations']) self.assertEqual(xml_data['uri'], expected_response['uri']) self.assertEqual(xml_data['file_name'], expected_response['filename']) diff --git a/scielomanager/articletrack/tests/xml_tests_files/to_be_annotated.xml b/scielomanager/articletrack/tests/xml_tests_files/to_be_annotated.xml deleted file mode 100644 index b2abf468..00000000 --- a/scielomanager/articletrack/tests/xml_tests_files/to_be_annotated.xml +++ /dev/null @@ -1,1872 +0,0 @@ - - -
    - - - 1415-4757-gmb-37-0210 - - - Review Article - - - - - - - Nevado - Julián - - - 1 - - - 2 - - - * - - - - - Mergener - Rafaella - - - 3 - - - * - - - - - Palomares-Bralo - María - - - 1 - - - 2 - - - - - Souza - Karen Regina - - - 3 - - - - - Vallespín - Elena - - - 1 - - - 2 - - - - - Mena - Rocío - - - 1 - - - 2 - - - - - Martínez-Glez - Víctor - - - 1 - - - 2 - - - - - Mori - María Ángeles - - - 1 - - - 2 - - - - - Santos - Fernando - - - 1 - - - 4 - - - - - García-Miñaur - Sixto - - - 1 - - - 4 - - - - - García-Santiago - Fé - - - 1 - - - 5 - - - - - Mansilla - Elena - - - 1 - - - 5 - - - - - Fernández - Luis - - - 1 - - - 6 - - - - - de Torres - María Luisa - - - 1 - - - 5 - - - - - Riegel - Mariluce - - - 3 - - - 7 - - - $ - - - - - Lapunzina - Pablo - - - - 1 - - - 4 - - - 8 - - - $ - - - - - - Centro de Investigación Biomédica en Red de Enfermedades Raras, - - Instituto de Salud Carlos III - , - - - Madrid, - - Spain - . - - - Section of Functional and Structural Genomics, - - Instituto de Genética Médica y Molecular - , - - Hospital Universitario la Paz - , - - - Madrid, - - Spain - . - - - Programa de Pós-graduação em Genética e Biologia Molecular, - - Universidade Federal do Rio Grande do Sul - , - - - Porto Alegre - , - - RS, - - Brazil - . - - - Section of Clinical Genetics, - - Instituto de Genética Médica y Molecular - , - - Hospital Universitario la Paz - , - - - Madrid, - - Spain - . - - - Section of Cytogenetics, - - Instituto de Genética Médica y Molecular - , - - Hospital Universitario la Paz - , - - - Madrid, - - Spain - . - - - Section of Preanalytics, - - Instituto de Genética Médica y Molecular - , - - Hospital Universitario la Paz - , - - - Madrid, - - Spain - . - - - Serviço de Genética Médica, - - Hospital de Clínicas de Porto Alegre - , - - - Porto Alegre - , - - RS, - - Brazil - . - - - Section of Molecular Endocrinology, - - Overgrowth Disordes Laboratory - , - - Instituto de Genética Médica y Molecular - , - - Hospital Universitario la Paz - , - - - Madrid, - - Spain - . - - - -

    These authors contributed equally to this work.

    -     - - -

    These authors contributed equally to this work.

    -     - Send correspondence to Pablo Lapunzina. Instituto de Genética Médica y Molecular, Hospital Universitario la Paz, Paseo de la Castellana 261-28046, Madrid, Spain. E-mail: - plapunzina.hulp@salud.madrid.org - . -     - - 3 - 2014 - - - 20 - 03 - 2013 - - 37 - 1 (suppl) - 210 - 219 - - Copyright © 2014, Sociedade Brasileira de Genética. - 2014 - - License information: This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. - - - -

    Several new microdeletion and microduplication syndromes are emerging as disorders that have been proven to cause multisystem pathologies frequently associated with intellectual disability (ID), multiple congenital anomalies (MCA), autistic spectrum disorders (ASD) and other phenotypic findings. In this paper, we review the “new” and emergent microdeletion and microduplication syndromes that have been described and recognized in recent years with the aim of summarizing their main characteristics and chromosomal regions involved. We decided to group them by genomic region and within these groupings have classified them into those that include ID, MCA, ASD or other findings. This review does not intend to be exhaustive but is rather a quick guide to help pediatricians, clinical geneticists, cytogeneticists and/or molecular geneticists.

    -     - - microdeletion - microduplication - chromosome rearrangement - novel deletions - novel duplications - -     -     - - - Introduction -

    Alteration of gene dosage due to gains or deletions of large genomic regions causes many genetic disorders that are frequently associated with intellectual disability (ID), multiple congenital anomalies (MCA), autistic spectrum disorders (ASD) and other phenotypic findings ( - Lupski and Stankiewicz, 2005 - ) The advances in the use of microarrays for diagnosis and research in genomic disorders has permitted the discovery of infrequent genomic rearrangements in a variety of diseases and the report of several microdeletion and microduplication syndromes ( - - Deak - et al. - , 2011; - - Rafati - et al. - , 2012; - Vissers and Stankiewicz, 2012 - ;. - - Weise - et al. - , 2012).

    -

    The identification of novel syndromes is based on consistent, clinically recognizable features associated with a common chromosomal region; however, for some copy number variations (CNVs), variability in expression and penetrance of clinical manifestations have complicated the establishment of their clinical significance. Currently, the delineation of novel syndromes may start with the identification of overlapping genotypes, that is, a ‘genotype-first’ approach, in which patients are characterized by a similar genomic aberration before a common clinical presentation is delineated. This is referred to as “reverse genetics”. This approach has proven to be successful considering the growing list of microdeletion/microduplication syndromes that have been described in the past five years. Furthermore, the collection of clinical and genetic information in databases such as DECIPHER, ISCA, ECARUCA and other free databases has been crucial for discriminating between patients with rare aberrations and those with new micro-deletion/duplication syndromes.

    -

    In this paper, we systematically review the novel microdeletion and microduplication syndromes described in the past five years. We grouped these disorders by chromosome, with the intention of serving as a quick guide for clinicians and researchers.

    -     - - Chromosome 1 - - 1p34.2-p34.3 Deletion -

    This deletion is characterized by microcephaly, ID and ASD. The deletion spans approximately 3.3 Mb and involves approximately 43 genes, including RIMS3, which is the main candidate gene for this phenotype.

    -     - - 1p31.3-p32.2 Deletion -

    There are approximately 7 cases described to date. In five of these cases with an - NFIA - deletion, the patients show central nervous system (CNS) malformations (hypoplasia of the corpus callosum, macrocephaly, ventriculomegaly) and urinary tract defects.

    -     - - 1q21.1 Deletion/Duplication -

    Patients have a phenotype similar to 22q11.2 deletion syndrome (velocardio-facial syndrome-like phenotypic findings). They may have congenital heart disease, schizophrenia and ID. The micro-duplication of approximately 212 kb could be responsible for congenital heart disease in at least 2 patients. The phenotype of dup1q21.1 is variable due to incomplete penetrance and variable expression levels. Therefore, this microduplication is also observed in asymptomatic individuals. Patients with deletions (1.4–1.65 Mb) may also have microcephaly, epilepsy, ataxic gait, severe dysmorphic features of the face and ID. This deleted region comprises approximately 30 coding genes, including the cluster of genes encoding the ephrins ( - EFNA1, EFNA3 - and - EFNA4 - ), which are tyrosine kinase receptors.

    -     - - 1q24-q25 Deletion -

    This deletion is characterized by growth retardation, microcephaly, small hands and feet (with brachydactyly), dysmorphic facies, small ears, micrognathia, short nose with bulbous tip and severe ID. The deleted region is approximately 1.9 Mb (chr1: 170135865-172099327 coordinates hg18) and contains 13 genes including - DNM3 - and - CENPL - , which encodes a protein essential for centromeric function, mitotic progression and synaptic reaction.

    -     - - 1q32.2-q32.3 Deletion -

    Patients exhibit dysmorphic features and facial clefts due to deletion of the - IRF6 - gene, which is responsible for the Van der Woude syndrome (VWS). The deletion is approximately 2.98 Mb and includes 25 genes.

    -     - - 1q41-q42.12 Deletion -

    This deletion is characterized by moderate to severe ID, seizures, Pelger-Huet anomaly (leukocyte alteration), cleft lip and palate and agenesis of the corpus callosum. Patients may also have hypoglycemia, 13 pairs of ribs and a micropenis. - DISP1 - , in the sonic hedgehog pathway, has been proposed as the gene responsible for the alterations of the midline observed in this deletion. The deletions have a size of 777 kb to 6.87 Mb. It has been proposed that this would represent a locus for Fryns syndrome, a Fryns syndrome phenocopy, or congenital diaphragmatic hernia (CDH). It has also been observed in patients with the isolated 1q42 deletion (together with agenesis of the corpus callosum) or within a contiguous deletion, 1q41q42 syndrome ( - - Filges - et al. - , 2010).

    -     - - 1q43-q44 Deletion -

    Microcephaly, abnormalities of the corpus callosum, seizures, ID and speech disorder are observed in patients with this deletion. Deletion of the - AKT3 - gene appears to be correlated with microcephaly and alteration of the other 3 genes ( - FAM36A, C1ORF199 - and - HNRNPU - ) correlates with the epileptic phenotype.

    -     -     - - Chromosome 2 - - 2p14-p15 Deletion -

    This deletion is associated with ID, speech disorder, mild dysmorphic features, hearing loss and relative microcephaly. The deletion is approximately 2.23–2.84 Mb, with a minimal overlapping region of 10 genes.

    -     - - 2p15-q16.1 Deletion -

    This deletion is associated with ID, ASD and dysmorphic features. Eight patients described by three different groups have this deletion. The - OTX1 - and - XPO1 - genes have been associated with ASD. It has also been observed in patients with prenatal and postnatal growth retardation, ptosis of both eyelids and microcephaly. The deletions range from 2.6 Mb to 3.2 Mb.

    -     - - 2q13 Deletion -

    Patients with this deletion have CNS disorders and present with cortical disruption and Joubert syndrome. These phenotypes are associated with the deletion of the - NPHP1 - gene.

    -     - - 2q23.1 Deletion/Duplication -

    Seizures, speech disturbances, ataxia, short stature, ID and dysmorphic features (brachycephaly, proximal implementation of the hair, short nose, hypertelorism, everted lower lip, thick tongue, brachytelephalangy, clinodactyly and hypertrichosis) are observed. This deletion includes the - MBD5 - gene, which is implicated in the pathophysiology of seizures. Stereotyped behaviors are also present and these are similar to Rett syndrome or Angelman syndrome. Microduplications in this region present with ID, hypotonia, ASD and include the following genes: - MBD5, ACVR2A, ORC4L, EPC2, KIF5C, MIR1978, LYPD6B - and - LYPD6 - . ( - - Jaillard - et al - ., 2009).

    -     - - 2q31.1-q31.2. Deletion -

    This deletion is characterized by monodctylous hands, ectrodactyly, brachydactyly and clinodactyly with or without duplication of both halluces. This deletion is of the - HOXD - cluster. Mutations in - HOXD13 - and - HOXD10 - are associated with malformations of the limbs. Some patients may have ID, microcephaly and growth retardation.

    -     - - 2q32-33.1 Deletion -

    Patients with this deletion have ID, learning disabilities, growth retardation, thin and sparse hair, feeding difficulties, cleft lip/palate and multiple dysmorphic features. - SATB2 - haploinsufficiency has been suggested to be responsible for most of these findings. The deletions are between 35 kb to 10.4 Mb ( - - Rosenfeld - et al. - , 2009)].

    -     - - 2q37 Deletion -

    This deletion shows the Albright phenotype (hereditary osteodystrophy; brachydactyly, ID and short stature).

    -     -     - - Chromosome 3 - - 3p21.31 Deletion -

    Patients present with cortical blindness, CNS abnormalities, cleft lip and ID. The deletions are approximately 3.1 Mb, including approximately 80 genes.

    -     - - 3p25 interstitial Deletion -

    Patients present with low birth weight, mental retardation, telecanthus, ptosis and micrognathia and congenital heart disease, typically atrioventricular septal defect. - SRGAP3 - is the major determinant of ID.

    -     - - 3p11.2-p12.1 Deletion -

    This deletion includes - POU1F1 - , - CHMP2B - and - VGLL3 - . Patients have abnormalities in pituitary hormones similar to the hypothalamic Laron syndrome but are unresponsive to GH treatment.

    -     - - 3q13.31 Deletion -

    ID, postnatal overgrowth, hypoplastic genitalia (in men) and recognizable facial features (short philtrum and protruding lips) are observed in these patients. The deletion is 580 kb and includes - DRD3 - and - ZBTB20 - as candidate genes.

    -     - - 3q22.1-q25.2 Deletion -

    Patients with this deletion have multiple congenital anomalies and peculiar facial appearance. In particular, the phenotypes result from the variable combination of three recognizable patterns: Dandy-Walker malformation, BPES syndrome and Wisconsin syndrome.

    -     - - 3q27.3 Deletion -

    Patients shared a recognizable facial dysmorphism and Marfanoid habitus associated with psychosis and mild to severe ID. Most of these patients have severely impaired adaptive skills.

    -     - - 3q29 Deletion/Duplication -

    Facial dysmorphism, ASD, psychiatric disorders (bipolar disease), ID and MCA (cleft palate, congenital heart disease) are all associated with deletions in this region. There are reports of patients with deletions and parents with mosaic deletions. The microduplication is characterized by mild ID, microcephaly, dysmorphic features and musculoskeletal abnormalities. The minimum size of the rearrangement is 1.6 Mb ( - Figure 1A - ).

    -     -     - - Chromosome 4 - - 4q21 Deletion -

    Growth retardation, ID and absence of language are found in patients with this deletion. The smallest region of overlap in deletions is 1.37 Mb and contains five genes: - PRKG2, RASGEF1B, HNRNPD, HNRPDL - and - ENOPH1 - . It has been suggested that PRKG2 and RASGEF1B are the genes responsible for this clinical phenotype.

    -     - - 4q21.3 Deletion -

    Patients present ID, dysmorphic facial features, hypotonia and short stature.

    -     - - 4q34.1-q35.2 Deletion -

    The phenotype is somewhat similar to the 22q11.2 deletion syndrome.

    -     -     - - Chromosome 5 - - 5q14.3-q15 Deletion -

    ID (late Honest), epilepsy, hypotonia and dimples in the jugular region are found in patients with this deletion. Patients present with atypical clinical Rett syndrome features. The gene involved is - MEF2C - .

    -     - - 5q35.2-q35.3 Deletion/Duplication -

    The deletion is 1.63 Mb and sometimes includes - NSD1 - , the gene responsible for Sotos syndrome. Patients also have the Sotos phenotype, cleft palate, language delay, ID and macrocephaly. Microduplication of the Sotos syndrome region, which contains - NSD1 - , has been associated with microcephaly, short stature and development delay.

    -     -     - - Chromosome 6 - - 6p25 Deletion -

    Patients present with white matter abnormalities, hypotonia, ID, a dysmorphic face, hypoacusis, short stature, Axenfeld-Rieger anomaly and a bicuspid aortic valve.

    -     - - 6q13-q14 Deletion -

    ID and connective tissue abnormalities are found in patients with this deletion. The deletion is 3.7 Mb and affects 16 genes, including - COL12A1 - ,a good candidate for the anomaly in the connective tissue.

    -     - - 6q14.1-q15 Deletion -

    Obesity, ID and atypical facial phenotypic traits are observed among these patients. This deletion syndrome partly phenocopies patients with Prader-Willi syndrome. The haploinsufficiency of - SIM1 - is suggested to be responsible for the phenotype.

    -     - - 6q16.1 Deletion -

    Patients present with ID and characteristic facies. The deletion includes the haploinsufficiency of one gene (ephrin receptor 7; - EPHA7 - ) that has implications in cortical development.

    -     - - 6q25 Deletion -

    Patients usually show ID. Olfactory bulb aplasia and anosmia may also be observed. The syndrome is due to the haploinsufficiency of - ARID1B - , a member of the SWI/SNF chromatin-remodeling complex. Some patients with ID have point mutations in this gene.

    -     - - 6q25.2-q25.3 Deletion -

    Microcephaly, ID, hypoacusis and dysmorphic features are observed in patients with this deletion. The smallest region of overlap of the deletion in 4 patients is 3.52 Mb in size.

    -     -     - - Chromosome 7 - - 7p14.1 Deletion -

    This deletion is characterized by polysyndactyly, hypertelorism and microcephaly, having a phenotype similar to Greig syndrome.

    -     - - 7p22.1 Duplication -

    Speech delay and recognizable facial features are observed in these patients. The duplication is approximately 1.7 Mb. Macrocephaly, ocular hypertelorism and low-set ears can also occur. Fifteen genes are involved in the duplicated segment.

    -     - - 7q11.23 Duplication -

    It is the reciprocal duplication of the deletion observed in Williams Syndrome. Patients present with speech delay, epilepsy, ID, straight and thick eyebrows and ASD.

    -     - - 7q11.23 Deletion -

    This is the distal deletion of the Williams-Beuren region. The deletions are recurrent, 1.2 Mb in size and include the Huntingtin-interacting protein 1 ( - HIP1 - ) and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein gamma ( - YWHAG - ) genes. The deletion of - HIP1 - seems to be sufficient to cause ID.

    -     - - 7q21.3 Deletion -

    Myoclonus, dystonia, ID and psychosis have been observed in these patients. Two regions of 455 and 496 kb are critical for ID, which is where the gene - LOC253012 - ( - HEPACAM2 - ) is located.

    -     - - 7q22.2-q22.3 Deletion -

    Overgrowth, delayed bone age, epilepsy, ID, unusual face, hypoplasia of the corpus callosum and cerebellar hypoplasia are observed in patients with this deletion. The deletion spans 3.2 Mb and includes four of 15 genes involved in cell cycle ( - SRPK2, MLL5, RINT1 - and - LHFPL3 - ).

    -     - - 7q33-q35 Deletion -

    Patients with this deletion present with speech delay and ID. The deletion includes - CNTNAP2 - , a gene that has previously been found in children with speech disorders.

    -     -     - - Chromosome 8 - - 8p21 Deletion -

    ID and behavior disorder, with some features of autistic spectrum disorder occur in patients with this deletion.

    -     - - 8p23.1 Duplication -

    This duplication leads to a variable phenotype that may include one or more of the following: congenital heart disease (CHD), ID and mild dysmorphism with prominent forehead and arched eyebrows. The critical region is a duplication of 3.68 Mb that contains 31 genes and microRNAs, of which only - GATA4 - , - TNKS - , - SOX7 - and - XKR6 - are likely to be dosage-sensitive genes. Of the microRNAs, - MIR124-1 - and - MIR598 - have been implicated in neurocognitive phenotypes. A combination of the duplication of - GATA4 - , - SOX7 - and related genes may account for the variable penetrance of CHD.

    -     - - 8q12 Duplication -

    This duplication includes - CHD7 - . Patients present with hypotonia, ID, failure to thrive, Duane anomaly, Mondini malformation, hearing loss, malformations of the ear canal and atrial septal defects.

    -     - - 8q21.11 Deletion -

    ID, round face with full cheeks, eyelid ptosis, ocular malformations, hypoplastic nose, abnormal philtrum and vermillion and minimal hand anomalies (camptodactyly, syndactyly) are all observed in these patients. The smallest region of overlap is 539.7 kb, which includes three genes, including Zinc Finger Homeobox 4 ( - ZFHX4 - )( - Figure 1B - ).

    -     - - 8q22.1 Deletion -

    The phenotype of this deletion is similar to that of the Nablus mask syndrome, symptoms include ID, speech disorder and typical dysmorphic features. The deletion is approximately 1.6 Mb.

    -     - - 8q22.2 Deletion -

    Patients with this deletion have characteristic facial features, ID, absent speech, seizures, growth retardation and diaphragmatic hernia in some cases. The smallest region of deletion is 3.87 Mb (100.69 to 104.56 Mb, hg18), comprising at least 25 genes.

    -     -     - - Chromosome 9 - - 9p13.3-p13.1 interstitial Deletion -

    Patients with a 9p13 deletion have mild to moderate ID, social and interactive personality and behavioral problems, such as attention deficit-hyperactivity disorder. Short stature, prominent antihelices, hypoplastic nails and precocious/early puberty are also present ( - Figure 1C - ).

    -     - - 9q22.3 Deletion -

    ID, dysarthria, metopic craniosynostosis, hydrocephalus, macrosomia and seizures are associated with this deletion. Patients with a 9q22.3 microdeletion have the clinical findings of the Gorlin syndrome. The 9q22.3 microdeletions (352 kb to 20.5 Mb in size) include - PTCH1 - , the gene that is mutated in Gorlin syndrome (nevoid basal cell carcinoma syndrome).

    -     - - 9q31.1-q31.3 Deletion -

    Patients have a distinct clinical phenotype characterized by mild ID, short stature with high body mass index, thick hair, arched eyebrows, flat profile with broad chin, mild prognathism, broad and slightly overhanging tip of the nose and short neck with cervical gibbus.

    -     - - 9q34.3 Deletion (Kleefstra syndrome) -

    Patients have ID, behavior anomalies, hypotonia, epilepsy, congenital heart defect and renal anomalies. The highly recognizable facial features are hypertelorism, midface hypoplasia, prognathism, prominent eyebrows, cupid bow or tented upper lip and everted lower lip. The syndrome is either caused by a submicroscopic deletion in the chromosomal region 9q34.3 or an intragenic mutation of the - EHMT1 - gene causing haploinsufficiency of - EHMT1 - . There are some communications of mosaicism in parents of affected patients ( - Figure 1D - ).

    -     -     - - Chromosome 10 - - 10q22-q23 Deletion -

    The overlap of neuropathological phenotypes among patients described suggests that this region harbors genes important for function and neurodevelopment ( - NRG3, GRD1D1 - , BMPR1A, SNCG). Indeed, several genes in this region are candidates for neuropsychiatric disorders. - NRG3 and GRD1D1 - have been described as candidate genes associated with schizophrenia.

    -     -     - - Chromosome 11 - - 11q13.1 Deletion -

    Speech delay, autistic spectrum disorder, dysmorphic features, such as wide halluces and firsts digits and pancreatic gastrinoma. The deletion is 0.57 Mb.

    -     -     - - Chromosome 12 - - 12q13.11 Deletion -

    Severe ID, cleft palate and severe myopia. The deleted region contains 16 genes. It is hypothesized that haploinsufficiency of - AMIGO2 - is responsible for the ID and haploinsufficiency of - COL2A1 - in cleft palate and myopia.

    -     - - 12q13 Duplication -

    This syndrome may represent a phenocopy of the Wolf Hirschhorn syndrome ( - - Bertioli - et al. - , 2013)

    -     - - 12q14 Deletion -

    Microcephaly, short stature with similar clinical findings to the Russell Silver syndrome. Patients may have osteopoikilosis, low weight, failure to thrive and learning problems. The - HMGA2 - gene is involved in the growth deficiency.

    -     - - 12q24.31 Deletion -

    Hypoglycemia, macroglossia and overgrowth (similar to the Beckwith-Wiedemann syndrome at birth). The deleted region contains the gene - HNF1 - homeobox A (HNF1A) and others.

    -     -     - - Chromosome 14 - - 14q12-q22.1 Deletion -

    Patients present ID, failure to thrive, microcephaly and recognizable facial features (hypertelorism, epicanthic folds, peculiar eyebrows, depressed nose, receding forehead, CNS disorders, seizures, apnea, myoclonus and infection proneness).

    -     - - 14q32.2 Deletion -

    ID and many phenotypic abnormalities in two unrelated patients with identical deletions. The deletions are mediated by repetitions (TGG) (n)

    -     - - 14q32.33 Deletion -

    ID and minimal dysmorphic features. The deletion affects a small fragment of 0.3 Mb with 6 genes, including - NUDT14, BRF1, BTBD6, PACS2, MTA1 - and - TEX22 - . A 250-kb region critical for certain features of terminal 14q deletion syndrome has been proposed. Amongst them three potential candidate genes for intellectual disability: - CRIP2, MTA1 - and - TMEM121 - ( - - Engels - et al. - , 2012).

    -     -     - - Chromosome 15 - - 15q11.2 Deletion -

    ID, speech delay, behavioral problems, seizures and ASD. The deletion is between the - BP1 - and - BP2 - regions of the proximal portion of chromosome 15 that contains four genes ( - TUBGCP5, NIPA1, NIPA2 - and - CYFIP1 - ) not subjected to imprinting.

    -     - - 15q11-q13 Duplication -

    ASD, mild facial dysmorphism, sleep problems and unusual electroencephalogram findings ( - - Urraca - et al - ., 2013).

    -     - - 15q13.2-q13.3 Deletion -

    Phenotypic findings similar to the Angelman syndrome, with ASD, epilepsy and behavioral problems.

    -     - - 15q13.3 Deletion -

    Epilepsy, ID, psychiatric disorders (bipolar disorder), severe hypotonia and EEG abnormalities. Locus with incomplete penetrance for autism; may show retinal dysfunction and encephalopathy. One gene appears to be involved ( - CHRNA7 - ) ( - - Shinawi - et al. - , 2009).

    -     - - 15q14 Deletion -

    Dandy-Walker malformation, ID, macrocephaly, myopia and brachytelephalangy.

    -     - - 15q21.1-q21.2 Deletion -

    Clinical features similar to Marfan syndrome and with ID. The deletions involve the - FBN1 - gene.

    -     - - 15q24 Deletion/Duplication -

    Growth delay, ID, facial features (long face, anterior hairline, epicanthic folds, hypertelorism, long philtrum and thick lower lip). Other findings include ASD, hypotonia, behavioral problems, hearing loss, hernias and GH deficiency. Most deletions have breakpoints in five LCRs (LCR15q24A, -B, -C, -D and -E) and the minimum region of overlap is 1.2 Mb between LCR15q24B and LCR15q24C. Candidate genes within this deletion are - CYP11A1, SEMA7A, CPLX3, ARID3B, Stra6, Sin3A - and - CSK - . The duplication cases described share similar clinical features with the 15q24 deletion.

    -     - - 15q24.1 Deletion -

    Multiple cysts of the corpus callosum, ID, micropenis and strabismus. The deletion is approximately 3.1 Mb. The sizes of the deleted regions range from 1.7 Mb to 6.1 Mb. Most of the reported cases are male. Male genital abnormalities are frequently observed in 15q24 microdeletion patients. One candidate gene is - CYP11A1 - , which is highly expressed in the adrenal gland.

    -     - - 15q24.3- q25.2 Deletion -

    Cleft palate with or without cleft lip and hypotonia.

    -     - - 15q26 Deletion -

    Patients have mainly short stature due to haploinsufficiency of the - IGF1R - gene.

    -     - - 15q26.1 Deletion -

    Intractable epilepsy, ID and short stature.

    -     -     - - Chromosome 16 - - 16p11.2 Deletion/Duplication -

    The deletion is characterized by ID, ASD, epilepsy and other less common findings, such as obesity, microphthalmia, coloboma of the optic nerve, kidney and urinary tract abnormalities, Hirschsprung disease, endocardial fibroelastosis and hemivertebrae. Duplication is associated with autism, ID, CNS disorders and schizophrenia ( - - Rosenfeld - et al. - , 2010). A 600-kb 16p11.2 deletion containing 29 genes has been associated with several neurocognitive disorders, including autism, diabetes-independent obesity and microcephaly, whereas duplication of the same region is associated with autism, schizophrenia, anorexia and microcephaly. The 16p11.2 deletion is associated with increased head size, whereas 16p11.2 duplication is associated with decreased head size ( - - Golzio - et al. - , 2012) ( - Figure 1E - ).

    -     - - 16p11.2-p12.2 Deletion/Duplication -

    Minimal facial abnormalities, speech disorder, frequent ear infections and ID. It should be distinguished from the proximal deletion (see immediately above). Patients with duplications have severe ID, ASD and dysmorphic features ( - Figure 2A and B - ).

    -     - - 16p12.1 Deletion -

    ID and abnormal behavioral phenotype with behavioral disorders. It is a 520-kb deletion.

    -     - - 16q12-q13 Deletion -

    The phenotypic spectrum of microdeletions in 16q12-q13 region is broad with variable degrees of ID, craniofacial dysmorphic features, congenital brain abnormalities and limb and congenital heart disease.

    -     - - 16q22.1 Deletion/Duplication -

    Deletion presents ID and lobular breast cancer. The deletion is 0.24 MB and affects 3 genes ( - ZFP90, CDH3 - and - CDH1 - ). - ZFP90 - is expressed in the brain and is responsible for ID, while - CDH1 - may be responsible for cancer. Duplication is characterized by epilepsy and learning disabilities.

    -     - - 16q24.1 Deletion -

    Typically present persistent pulmonary hypertension in the newborn and sometimes atrioventricular canal, ureteral stenosis and annular pancreas. - FOXF1 - alterations would be responsible for alveolar capillary dysplasia and other alveolar malformations.

    -     - - 16q24.3 Deletion -

    ID, ASD, short stature and minimal facial anomalies. Deletions involve the - ANKRD11 - gene and cause KBG-like syndrome.

    -     -     - - Chromosome 17 - - 17p13.1 Deletion -

    ID, hypotonia and anomalies of the hands and feet but not cancer. Microdeletions affect the - TP53 - gene.

    -     - - 17p13.3 Deletion/Duplication -

    Short stature, ID and abnormal facial features. The microduplication includes autism and affects a region of 72 kb that includes a single gene ( - YWHAE - ). The microdeletion sometimes includes - CRK - , sometimes - YWHAE - and / or - TUSC5 - ( - Figure 2C and 2D - ).

    -     - - 17q11.2 Deletion/Duplication -

    The deletion and duplication affects the - NF1 - region. ID, facial dysmorphic features and seizures.

    -     - - 17q12 Deletion/Duplication -

    The deletion presents congenital diaphragmatic herniae and pulmonary and renal cysts. A case of Mayer-Rokitansky-Kuster-Hauser syndrome has been described with this deletion. The deletion is 1.4 Mb and affects 17 genes, including - AATF, ACACA, DDX52, DUSP14, GGNBP2, HNF- 1B, Lhx1, PIGW, SYNRG, TADA2A - and - ZNHIT3 - . Duplication is characterized by ASD ( - Figure 2E - ).

    -     - - 17q21.31 Deletion/Duplication -

    Deletions are associated with macrocephaly, ID, epilepsy, congenital anomalies and dysmorphic facial alterations of the pituitary. The skin lesions are characterized by nevi, abnormal skin pigmentation similar to cardiofaciocutaneous syndrome. Other findings include dilation of the aortic root, joint subluxation, hearing loss, recurrent otitis media and persistent digital pads. At least 6 genes are affected, including - MAPT - and - STH.

    -     - - 17q22-q23.2 Deletion -

    Microcephaly, thyroid duct cyst, sensorineural hearing loss and pulmonary hypertension. Includes the loss of - TBX2 - and - TBX4 - but not - NOG - .

    -     - - 17q23.1-q23.2 Deletion/Duplication -

    Duplication has been associated with pes cavus familiar. Duplication affects - PITX1 - and - TBX4 - . The deletion has congenital heart disease and limb abnormalities.

    -     - - 17q23.2 Deletion -

    Bilateral sensorineural hearing loss in two isolated patients.

    -     - - 17q24.2-q24.3 Deletion/Duplication -

    Duplication presents generalized hypertrichosis with gingival hyperplasia and deletions in general have less gingival hyperplasia.

    -     -     - - Chromosome 18 - - 18q12.3 Deletion -

    The deletion is 372 kb in size with haploinsufficiency of - SETBP1. - The clinical findings include ID and speech disorder. Missense heterozygous mutations in this gene cause Schinzel-Giedion syndrome (SGS). However, the phenotype of individual with partial chromosome 18q deletions does not resemble SGS.

    -     -     - - Chromosome 19 - - 19p13.11 Deletion -

    One patient presented with pontocerebellar hypoplasia and ID and haploinsufficiency of the helicase - DDX39 - . Another patient with a deletion in this region showed a deletion of 1.1 Mb involving - EPS15L1 - . The patient showed short stature, ID, severe hypotonia, ataxia, premature pubarche and dysmorphic features.

    -     - - 19p13.12 Deletion -

    Defects of the branchial arches (preauricular tags, ear canal stenosis), mild hearing loss and mild ID are due to the deletion of a region of 0.8 Mb of genomic DNA. The deletion extends 15300338-16064271 (hg18, NCBI build 36.1). One patient presented with ID, obesity and hypertrichosis.

    -     - - 19p13.13 Deletion/Duplication -

    The deletion is characterized by macrocephaly, overgrowth and ophthalmologic and gastrointestinal disturbances. Duplication has short stature and microcephaly. The smallest region of overlap is 311–340 Kb and has 16 genes including - MAST1, NFIX - and - CALR - .

    -     - - 19p13.2 Deletion -

    Patients present with ID, mild facial features, febrile seizures. The deletion is 834.2 kb in size and includes 32 genes.

    -     - - 19p13.3 Terminal Duplication -

    Patients’ phenotypes include severe psychomotor DD, skeletal malformations and a distinctive facial appearance.

    -     - - 19q13.2 Deletion -

    Patients present branchial arch defects. The critical region is approximately 0.8 Mb

    -     - - 19q12-q13.2 Duplication -

    It is an obesity-related syndrome, with ID and minor facial findings.

    -     - - 19q13.11 Deletion -

    Patients present a Diamond-Blackfan syndrome, pre and postnatal growth deficiency, tall stature, microcephaly, hypospadias, signs of ectodermal dysplasia and aplasia cutis vertex. The critical region is defined to 750 kb and is due to haploinsufficiency of - RPS19 - ( - - Malan - et al. - , 2009).

    -     -     - - Chromosome 20 - - 20p12.3 Deletion -

    Cleft palate / cleft lip, Pierre-Robin sequence. The deletion involves the - BMP2 - gene and has been implicated in Wolff-Parkinson-White (WPW) syndrome with neurocognitive deficits and with Alagille syndrome when the deletion includes the neighboring - JAG1 - gene in addition to - BMP2 - .

    -     - - 20p13 Deletion -

    Dysmorphic features, ID, epilepsy and brachydactyly. - SOX12 - and - NRSN2 - are the candidate genes that may be involved in the developmental defects.

    -     - - 20q13.33 Deletion -

    Severe limb malformations, skeletal abnormalities, ID, speech delay, seizures and other minimal dysmorphic features. The - ARFGAP1, CHRNA4 - and - KCNQ2 - genes have been associated with neurological deficits.

    -     -     - - Chromosome 21 - - 21q22 Deletion -

    Two patients with similar phenotype and overlapping deletions of the 21q22 region were observed. They had behavioral problems, no speech, microcephaly, feeding problems, regurgitation, obesity dysplastic ears and pointed chin. They also present with cerebral atrophy, thinned corpus callosum, epilepsy and ventricular septal defect. Another patient had microcephaly, ID, hypospadias and corneal opacity. Patients with chromosomal deletions of 21q show a variation in size and usually include the 21q22.12 region. The deleted region in most of these patients included, among other deleted genes, the - RUNX1 - gene (21q22.12), which is related with thrombocytopenia and platelet function and a predisposition to develop myeloid leukemia.

    -     -     - - Chromosome X - - Xq11.11 Deletion -

    Patients with this deletion have ID, epilepsy, macrosomia, macrocephaly, tall stature and dysmorphic features. The 1.3 Mb deletion includes - ARHGEF9 - , which is proposed to have a role in the cognitive development.

    -     -     - - Conclusions -

    The extensive use of high-resolution microarrays and the “genotype-first” experimental approach taken by genetic laboratories have allowed for the recognition and description of an important and growing number of new microdeletion and microduplication syndromes over the last three to five years ( - Figure 3 - ). Interestingly, most of these syndromes have phenotypic features that are similar to and overlapping with other previously described genetic syndromes. This review may be considered a quick guide to help pediatricians, clinical geneticists, cytogeneticists and/or molecular geneticists and emphasizes the necessity of a strong collaboration between clinical (pediatricians, geneticists) and molecular geneticists to assure new phenotype recognitions for these genomic aberrations.

    -     - - - - References - - - - - Bertoli - M - - - Alesi - V - - - Gullotta - F - - - Zampatti - S - - - Abate - MR - - - Palmieri - C - - - Novelli - A - - - Frontali - M - - - Nardone - AM - - - 2013 - Another patient with 12q13 microduplication - Am J Med Genet A - 161A - 2004 - 2008 - - Bertoli M, Alesi V, Gullotta F, Zampatti S, Abate MR, Palmieri C, Novelli A, Frontali M and Nardone AM (2013) Another patient with 12q13 microduplication. Am J Med Genet A 161A:2004–2008. - - - - - - Deak - KL - - - Horn - SR - - - Rehder - CW - - - 2011 - The evolving picture of microdeletion/microduplication syndromes in the age of microarray analysis: Variable expressivity and genomic complexity - Clin Lab Med - 31 - 543 - 564 - - Deak KL, Horn SR and Rehder CW (2011) The evolving picture of microdeletion/microduplication syndromes in the age of microarray analysis: Variable expressivity and genomic complexity. Clin Lab Med 31:543–564. - - - - - - Engels - H - - - Schüler - HM - - - Zink - AM - - - Wohlleber - E - - - Brockschmidt - A - - - Hoischen - A - - - Drechsler - M - - - Lee - JA - - - Ludwig - KU - - - Kubisch - C - - - - 2012 - A phenotype map for 14q32.3 terminal deletions - Am J Med Genet A. - 158A - 695 - 706 - - Engels H, Schüler HM, Zink AM, Wohlleber E, Brockschmidt A, Hoischen A, Drechsler M, Lee JA, Ludwig KU, Kubisch C, - et al. - (2012) A phenotype map for 14q32.3 terminal deletions. Am J Med Genet A.158A:695–706. - - - - - - Filges - I - - - Röthlisberger - B - - - Boesch - N - - - Weber - P - - - Wenzel - F - - - Huber - AR - - - Heinimann - K - - - Miny - P - - - 2010 - Interstitial deletion 1q42 in a patient with agenesis of corpus callosum: Phenotype-genotype comparison to the 1q41q42 microdeletion suggests a contiguous 1q4 syndrome - Am J Med Genet A - 152A - 987 - 993 - - Filges I, Röthlisberger B, Boesch N, Weber P, Wenzel F, Huber AR, Heinimann K and Miny P (2010) Interstitial deletion 1q42 in a patient with agenesis of corpus callosum: Phenotype-genotype comparison to the 1q41q42 microdeletion suggests a contiguous 1q4 syndrome. 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PLoS One 4:e6568. - - - - - - Rosenfeld - JA - - - Coppinger - J - - - Bejjani - BA - - - Girirajan - S - - - Eichler - EE - - - Shaffer - LG - - - Ballif - BC - - - 2010 - Speech delays and behavioral problems are the predominant features in individuals with developmental delays and 16p11.2 microdeletions and microduplications - J Neurodev Disord - 2 - 26 - 38 - - Rosenfeld JA, Coppinger J, Bejjani BA, Girirajan S, Eichler EE, Shaffer LG and Ballif BC (2010) Speech delays and behavioral problems are the predominant features in individuals with developmental delays and 16p11.2 microdeletions and microduplications J Neurodev Disord 2:26–38. - - - - - - Shinawi - M - - - Schaaf - CP - - - Bhatt - SS - - - Xia - Z - - - Patel - A - - - Cheung - SW - - - Lanpher - B - - - Nagl - S - - - Herding - HS - - - Nevinny-Stickel - C - - - - 2009 - A small recurrent deletion within 15q13.3 is associated with a range of neurodevelopmental phenotypes - Nat Genet - 41 - 1269 - 1271 - - Shinawi M, Schaaf CP, Bhatt SS, Xia Z, Patel A, Cheung SW, Lanpher B, Nagl S, Herding HS, Nevinny-Stickel C, - et al. - (2009) A small recurrent deletion within 15q13.3 is associated with a range of neurodevelopmental phenotypes. Nat Genet 41:1269–1271. - - - - - - Urraca - N - - - Cleary - J - - - Brewer - V - - - Pivnick - EK - - - McVicar - K - - - Thibert - RL - - - Schanen - NC - - - Esmer - C - - - Lamport - D - - - Reiter - LT - - - 2013 - The interstitial duplication 15q11.2–q13 syndrome includes autism, mild facial anomalies and a characteristic EEG signature - Autism Res - 6 - 268 - 279 - - Urraca N, Cleary J, Brewer V, Pivnick EK, McVicar K, Thibert RL, Schanen NC, Esmer C, Lamport D and Reiter LT (2013) The interstitial duplication 15q11.2–q13 syndrome includes autism, mild facial anomalies and a characteristic EEG signature. Autism Res 6:268–279. - - - - - - Vissers - LE - - - Stankiewicz - P - - - 2012 - Microdeletion and microduplication syndromes - Methods Mol Biol - 838 - 29 - 75 - - Vissers LE and Stankiewicz P (2012) Microdeletion and microduplication syndromes. Methods Mol Biol 838:29–75. - - - - - - Weise - A - - - Mrasek - K - - - Klein - E - - - Mulatinho - MV - - - Llerena - JC - Jr - - - Hardekopf - D - - - Pekova - S - - - Bhatt - S - - - Kosyakova - N - - - Liehr - T - - - 2012 - Microdeletion and Microduplication Syndromes - J Histochem Cytochem - 60 - 346 - 358 - - Weise A, Mrasek K, Klein E, Mulatinho MV, Llerena JC Jr, Hardekopf D, Pekova S, Bhatt S, Kosyakova N and Liehr T (2012) Microdeletion and Microduplication Syndromes. J Histochem Cytochem 60:346–358. - - - - Figures - - - -

    Chromosome microduplications and microdeletions. A: 3q29 microduplication. B: 8q21 microdeletion. C: Chromosome 9 profile showing a 9p13 microdeletion. D: Atypical microdeletion of 9q34. E: Partial aCGH in a patient with a 16p11.2 microdeletion.

    - - -     - - - -

    A: 16p12.2 deletion (array-cgh) and B: (FISH). C: 17p13.3 duplication (array-cgh) and D (FISH). E: 17q12 deletion (array-cgh).

    - - -     - - - -

    New microdeletion and microduplication syndromes discovered over the last three to five years. Red squares indicate reported microdeletions; blue circles indicate reported microduplications.

    - - -     -     -     -
    \ No newline at end of file diff --git a/scielomanager/articletrack/tests/xml_tests_files/with_style_errors.xml b/scielomanager/articletrack/tests/xml_tests_files/with_style_errors.xml new file mode 100644 index 00000000..bf844dae --- /dev/null +++ b/scielomanager/articletrack/tests/xml_tests_files/with_style_errors.xml @@ -0,0 +1,1235 @@ + + +
    + + + Rev Saude Publica + + Revista de Saúde Pública + Rev. Saúde Pública + + 0034-8910 + 1518-8787 + + Faculdade de Saúde Pública da Universidade de São Paulo + + + + S0034-8910.2014048004911 + 10.1590/S0034-8910.2014048004911 + + + Artigos Originais + + + + HIV/AIDS knowledge among men who have sex with men: applying the item response theory + + Conhecimento de HIV/Aids entre homens que fazem sexo com homens: teoria de resposta ao item + + + + + + Gomes + Raquel Regina de Freitas Magalhães + + + I + + + II + + + + + Batista + José Rodrigues + + + III + + + + + Ceccato + Maria das Graças Braga + + + II + + + IV + + + + + Kerr + Lígia Regina Franco Sansigolo + + + V + + + + + Guimarães + Mark Drew Crosland + + + II + + + VI + + + + + + Secretaria Municipal de Saúde de Belo Horizonte + + Belo Horizonte + MG + + Brasil + Secretaria Municipal de Saúde de Belo Horizonte. Belo Horizonte, MG, Brasil + + + + Faculdade de Medicina + Universidade Federal de Minas Gerais + + Belo Horizonte + MG + + Brasil + Grupo de Pesquisas em Epidemiologia e Avaliação em Saúde. Faculdade de Medicina. Universidade Federal de Minas Gerais. Belo Horizonte, MG, Brasil + + + + Faculdade de Educação + Universidade Federal de Minas Gerais + + Belo Horizonte + MG + + Brasil + Grupo de Avaliação e Medidas Educacionais. Faculdade de Educação. Universidade Federal de Minas Gerais. Belo Horizonte, MG, Brasil + + + + Departamento de Farmácia Social + Faculdade de Farmácia + Universidade Federal de Minas Gerais + + Belo Horizonte + MG + + Brasil + Departamento de Farmácia Social. Faculdade de Farmácia. Universidade Federal de Minas Gerais. Belo Horizonte, MG, Brasil + + + + Departamento de Saúde Comunitária + Faculdade de Medicina + Universidade Federal do Ceará + + Fortaleza + CE + + Brasil + Departamento de Saúde Comunitária. Faculdade de Medicina. Universidade Federal do Ceará. Fortaleza, CE, Brasil + + + + Departamento de Medicina Preventiva e Social + Faculdade de Medicina + Universidade Federal de Minas Gerais + + Belo Horizonte + MG + + Brasil + Departamento de Medicina Preventiva e Social. Faculdade de Medicina. Universidade Federal de Minas Gerais. Belo Horizonte, MG, Brasil + + + + : Raquel Regina de Freitas Magalhães Gomes Rua Virgílio Uchoa, 627 Belo Horizonte 30320-240 Belo Horizonte, MG, Brasil E-mail: quelfmg@gmail.com + + +

    This article was based on the doctorate thesis of Gomes RRFM, entitled: “Conhecimento sobre HIV/Aids entre homens que fazem sexo com homens em dez cidades brasileiras”, presented to the Universidade Federal de Minas Gerais, in 2014.

    +     + +

    The authors declare that there is no conflict of interest.

    +     +     + + 04 + 2014 + + 48 + 2 + 206 + 215 + + + 24 + 4 + 2013 + + + 12 + 11 + 2013 + + + + + This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. + + + + + OBJECTIVE +

    To evaluate the level of HIV/AIDS knowledge among men who have sex with men in Brazil using the latent trait model estimated by Item Response Theory.

    +     + + METHODS +

    Multicenter, cross-sectional study, carried out in ten Brazilian cities between 2008 and 2009. Adult men who have sex with men were recruited (n = 3,746) through Respondent Driven Sampling. HIV/AIDS knowledge was ascertained through ten statements by face-to-face interview and latent scores were obtained through two-parameter logistic modeling (difficulty and discrimination) using Item Response Theory. Differential item functioning was used to examine each item characteristic curve by age and schooling.

    +     + + RESULTS +

    Overall, the HIV/AIDS knowledge scores using Item Response Theory did not exceed 6.0 (scale 0-10), with mean and median values of 5.0 (SD = 0.9) and 5.3, respectively, with 40.7% of the sample with knowledge levels below the average. Some beliefs still exist in this population regarding the transmission of the virus by insect bites, by using public restrooms, and by sharing utensils during meals. With regard to the difficulty and discrimination parameters, eight items were located below the mean of the scale and were considered very easy, and four items presented very low discrimination parameter (< 0.34). The absence of difficult items contributed to the inaccuracy of the measurement of knowledge among those with median level and above.

    +     + + CONCLUSIONS +

    Item Response Theory analysis, which focuses on the individual properties of each item, allows measures to be obtained that do not vary or depend on the questionnaire, which provides better ascertainment and accuracy of knowledge scores. Valid and reliable scales are essential for monitoring HIV/AIDS knowledge among the men who have sex with men population over time and in different geographic regions, and this psychometric model brings this advantage.

    +     +     + + + OBJETIVO +

    Avaliar o nível de conhecimento de HIV/Aids entre homens que fazem sexo com homens no Brasil, utilizando o modelo de traço latente da Teoria de Resposta ao Item.

    +     + + MÉTODOS +

    Estudo multicêntrico, transversal, que ocorreu entre 2008 e 2009 em 10 cidades brasileiras. Foram recrutados 3.746 homens que fazem sexo com homens pela técnica amostral Respondent Driven Sampling. O conhecimento em HIV/Aids foi apurado a partir de dez afirmativas da entrevista realizada face a face e os escores foram obtidos utilizando o modelo logístico de dois parâmetros (discriminação e dificuldade) da Teoria de Resposta ao Item. O funcionamento diferencial dos itens foi verificado, analisando as curvas características dos itens pela idade e escolaridade.

    +     + + RESULTADOS +

    Os escores de conhecimento estimados pela Teoria de Resposta ao Item não ultrapassaram o valor 6,0 (escala de 0-10), com média e mediana de 5,0 (DP = 0,9) e 5,3, respectivamente, e com 40,7% da amostra com níveis de conhecimento abaixo da média. Algumas crenças ainda existem nessa população sobre a transmissão do vírus por picadas de insetos, pelo uso de banheiros públicos e pelo compartilhamento de utensílios durante as refeições. Com relação aos parâmetros dificuldade e discriminação, oito itens ficaram abaixo da média da escala de conhecimento e considerados muito fáceis, e quatro itens apresentaram parâmetros de discriminação muito baixos (< 0,34). A ausência de itens difíceis contribuiu para a imprecisão da medida do conhecimento entre aqueles com nível médio e superior.

    +     + + CONCLUSÕES +

    A análise da Teoria de Resposta ao Item, centrada nas propriedades individuais de cada item, permite a obtenção de medidas que não variam ou dependem do questionário utilizado, o que proporciona uma melhor apuração e precisão dos escores de conhecimento. Escalas válidas e confiáveis são fundamentais para monitorar o conhecimento em HIV/Aids nessa população ao longo do tempo e em diferentes regiões geográficas, vantagem que esse modelo psicométrico traz.

    +     +     + + Homosexuality, Male + Risk Groups + Health Knowledge, Attitudes, Practice + Acquired Immunodeficiency Syndrome, prevention & control + Multicenter Study + + + Homossexualidade Masculina + Grupos de Risco + Conhecimentos, Atitudes e Prática em Saúde + Síndrome de Imunodeficiência Adquirida, prevenção & controle + Estudo Multicêntrico + + + + + + + +     +     + + + INTRODUCTION +

    Brazil has adopted the Declaration of Commitment of the United Nations, which aimed at slowing the HIV/AIDS epidemic by 2015. HIV/AIDS knowledge is one of the indicators proposed by the United Nations General Assembly Special Session for monitoring AIDS among vulnerable subgroups including, sex workers, injection drug users and men who have sex with men (MSM). This indicator requires that adequate HIV/AIDS knowledge is an essential prerequisite for the adoption of behaviors that reduce the risk of infection. + a + Global estimates among low and middle income countries indicate that 56.0% of MSM did not have correct knowledge about HIV/AIDS, 70.0% had never been tested for HIV and 46.0% did not use condoms the last time they practiced anal sex. + 2 + +

    +

    In Brazil, the AIDS epidemic is concentrated in population subgroups with a markedly higher risk of acquiring HIV infection among MSM. + 4 + + , + + 6 + Recent data from a national survey found a worrisome HIV prevalence rate of 14.2% among this population. + 10 + The promotion of safer sex has been the main policy strategy for HIV prevention and access to information is a key element in reducing vulnerability to HIV/AIDS by providing an opportunity to change individual attitudes and increase safe practices. + b + +

    +

    Despite its importance, there is no standard instrument used to assess HIV/AIDS knowledge across different populations and many studies vary in their choice of the number and formulation of questions used. + 18 + + , + + 19 + Moreover, the knowledge score has been expressed as the sum of the correct responses to each item, based on Classical Test Theory (CTT), and an arbitrary cut-off point is established in order to classify good or adequate knowledge. + 9 + + , + + 11 + Thus, the total score is dependent on the set of items that compose the measuring instrument, which makes it difficult to compare results between different studies. + c + +

    +

    Recent studies assessed HIV/AIDS knowledge using the Item Response Theory (IRT). + 1 + + , + + 13 + + , + + 15 + IRT is considered the modern theory of psychometry, focuses on each item of the measuring instrument and assumes that the performance of a given test can be explained by individual characteristics, not directly observable, named latent traits. + 3 + + , + + 14 + Although IRT does not contradict classical methods, it is based on the assumption that the estimate of the latent trait is independent of sample items, which allows the equalization of scores on evaluations when using different instruments applied to the same population. + 14 + This is especially important when assessment of HIV/AIDS knowledge is used to monitor effectiveness of public health policies over time among vulnerable populations. More precise and accurate analysis of knowledge may allow proper planning of new prevention intervention strategies.

    +

    The objective of this study was to evaluate the level of HIV/AIDS knowledge among men who have sex with men from Brazil using the Item Response Theory.

    +     + + METHODS +

    This analysis is part of a cross-sectional study of MSM carried out in 10 Brazilian cities in 2008-2009. The main objectives of the national study were to estimate the prevalence of HIV and syphilis and to assess knowledge, attitudes and sexual practices of MSM. + 10 + +

    +

    Participants should be residents of the following cities: Manaus, Recife, Salvador, Campo Grande, Brasília, Curitiba, Itajaí, Santos, Rio de Janeiro and Belo Horizonte. These were a priori chosen by the Department of STD, AIDS and Viral Hepatitis of the Ministry of Health (STD/AIDS/MH). Eligibility criteria included adult MSM (18 years old or over), who reported at least one sexual contact with another man in the 12 months preceding the interview.

    +

    The sample size was previously calculated as 250 to 350 participants by city (α = 0.05, power = 0.90, estimated prevalence = 13.6%) + 10 + to provide independent estimates for each city and it was obtained using the Respondent Driven Sampling technique. + 12 + This technique is a chain link sampling method used to address hard to reach populations and their social networks, since the lack of a sampling base does not allow the application of traditional probabilistic method. The recruitment is carried out by participants themselves using a dual incentive system, and begins with a convenience sample of members of the target population, named seeds. In this study, these were selected during preliminary formative research, when individuals of different ages and socioeconomic classes were included. In each city, participants received three unique coupons, non-falsifiable, to distribute to their peers. Individuals who came to the study site with a valid coupon and who met the inclusion criteria were considered the first “wave” of the study. Each participant also received three coupons to invite new acquaintances, repeating this process thereafter until the desired sample size was reached in each city.

    +

    Data were collected in face-to-face interviews, composed of questions regarding sociodemographic data, behavior, social context, health care and HIV/AIDS knowledge. Participants were also invited for HIV and syphilis testing.

    +

    HIV/AIDS knowledge was assessed using 10 statements to which participants should indicate whether each one was true, false or “did not know”. The statements were chosen from previously used instrument by the STD/AIDS/MH at face value. For this analysis, correct responses were categorized as 1 and those which were considered incorrect or to which respondents replied “did not know” were categorized as 0.

    +

    Descriptive analysis of the sample was carried out and HIV/AIDS knowledge was assessed by IRT using the two-parameter logistic model, difficulty and discrimination. Because our main interest was to assess the overall result and the quality of the instrument using the methodology of IRT, we conducted the analysis considering the 10 cities simultaneously, since the parameter estimates do not depend on the recruitment sampling method. + 8 + This model makes the assumption of unidimensionality, i.e., that a given test should measure one single latent trait, which indicates a dominant skill responsible for the performance of a set of items of the test. In this study, HIV/AIDS knowledge was the dominant latent trait measured by the 10 items.

    +

    The logistic model represents the probability that the participants correctly responded to a given item as a function of their level of HIV/AIDS knowledge and the difficulty and discrimination parameters of the item. The responses to the different items are independent (local independence). It is described as a non-linear logistic function and expressed by the item characteristic curve (ICC) defined by the parameters of the item. The probability of a correct answer varies from 0 to 1 and the knowledge scale assumes a normal distribution pattern (-∞ to +∞) with mean = 0 and standard deviation = 1, but in practice -3 to +3 is used, corresponding to 99.97% of all individuals in a population. It is assumed that every individual has a specific level of knowledge, score theta, which places him on the scale. The discrimination parameter of each item (a + + i + ) is expressed by the slope of the ICC at the inflection point when the probability of a correct response is 0.5. In general, the metric for this parameter is 0 to 3, where higher values produce steeper curves and indicate items with high discrimination power. + 14 + Baker’s scale was used to interpret this parameter. + d + The difficulty parameter of each item (b + + i + ) corresponds to the point on the scale of knowledge where the probability of correct response is 0.5. Typically, the values are between -3 to +3 and higher values indicate the most difficult items. For a better understanding of our results, the parameters and the knowledge scores were transformed so that the knowledge scores were presented on a scale of 0 to 10. + 14 + +

    +

    The item parameters were estimated by marginal maximum likelihood, proposed by Bock & Aitkin, + 5 + and the knowledge score (theta) was estimated by the expected a posteriori method based on Bayesian statistical principles. BILOG-MG software for Windows 3.0.2 was used for these analyses and the convergence criterion used was 0.0001. + 18 + +

    +

    Full-information factor analysis was carried out to test the unidimensionality of the knowledge scale, i.e., the items must share only one underlying variable if they are to be combined into a scale. Full-information factor analysis takes into account all the empirical data and it is based on the tetrachoric correlation matrix using TESTFACT software, version 4.0. + e + The marginal maximum likelihood was used to estimate the probabilities of all possible response patterns that occurred in the sample according to the different levels of knowledge.

    +

    The differential item functioning (DIF) was assessed by the likelihood ratio test for age and years of schooling, using the IRTLRDIF software, version 2.0b. + f + When individuals with the same level of knowledge in different groups do not have the same probability of correctly answering a given item, this is taken as an indicator of DIF. Differences in parameters were tested by chi-squared statistic and the significance level considered was 0.05. The characteristic curves of the items which presented with DIF were analyzed and differentiated between uniform DIF (parallel ICC) and non-uniform (crossover ICC). + g + +

    +

    This study was approved by the National Research Ethical Committee (CONEP 14,494) and all participants signed the informed consent form.

    +     + + RESULTS +

    On average, there were 15 (range 8-20) waves of recruitment in each city, resulting in 3,859 participants, with 3,746 (97.1%) responding to the ten items on HIV/AIDS knowledge. Most of the participants was more than 25 years old (52.1%), had more than eight years of schooling (69.7%), were single or separated (83.4%) and non-white (72.4%). Only 19.0% was living alone, and 28.8% were classified as economic class AB (higher).

    +

    Overall, the proportion of correct answers varied from 34.5% to 98.5%, with the lowest proportions shown for items 1 and 2 (35.5% and 34.5%, respectively). Some beliefs still exist in this population regarding the transmission of the virus by insect bites, by using public restrooms, and by sharing utensils during meals (Table).

    +

    + + + + Proportion of correct HIV/AIDS knowledge responses as reported by the men who have sex with men, the difficulty and discrimination parameters for each item, estimated by Item Response Theory. Brazil, 2008-2009. (N = 3,746) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Item% Correct responseDifficulty (b + + i + )Discrimination (a + + i + )
    1. The risk of transmitting HIV is small if one follows the treatment correctly.35.514.450.04
    2. People are using less condoms because of AIDS treatment.34.514.230.04
    3. A person can get the AIDS virus by using public toilets.78.13.720.95
    4. A person can get the AIDS virus through insect bites.75.53.700.72
    5. A person can become infected by sharing eating utensils, cups or food.85.73.281.01
    6. The risk of HIV + mothers infecting their babies is small if she receives treatment in pregnancy and childbirth.75.82.700.32
    7. The risk of HIV infection can be reduced if you have relations only with an uninfected partner.72.62.030.20
    8. A healthy person can be infected with the AIDS virus.94.11.610.59
    9. A person can get the virus from sharing a syringe or needle.96.91.510.78
    10. Anyone can get the AIDS virus if condoms are not used.98.51.270.95
    + +

    + b + + i + : Difficulty parameter of each item; a + + i + : Discrimination parameter of each item

    + + +

    +

    The crude mean and median total score of correct items were 7.5 (SD = 1.5) and 8.0, respectively, with 43.2% of the sample falling below the average. On the other hand, the mean and median overall HIV/AIDS knowledge score using IRT were 5.0 (SD = 0.9) and 5.3, respectively, with 40.7% of the sample with knowledge levels below the average.

    +

    The parameters for each item, estimated by IRT, can also be seen in the Table, in descending order of the parameter of difficulty. Items 1 and 2 stood out as the most difficult items, with the larger values of difficulty parameter (b = 14) exceeding the scale (0 to 10). This points to potential problems in these items, as indicated by the low percentage of correct responses for these items. The eight remaining items showed low degree of difficulty, with values below the average of the scale, ranging from 1.0 to 4.0. The average difficulty of the set of items, excluding items 1 and 2, was 2.48 (SD = 1.0). The discrimination parameters ranged from 0.04 to 1.01. Item 5 was considered the best item, with the highest discrimination parameter (a5 = 1.01), capable of differentiating individual HIV/AIDS knowledge. According to Baker’s classification, five items (3, 4, 5, 9 and 10) showed moderate discrimination, one item showed low discrimination (8), and four items (1, 2, 6 and 7) had very low discrimination (values lower than 0.34). The overall average of all items was 0.56 (SD = 0.38), and it can be considered of low discriminatory value.

    +

    One item of each type of discrimination is shown in Figure 1, represented on the left by the ICC and on the right by the curve of the item information. As observed, the ICC of item 5 is the steepest curve, gently sloping to the right of the knowledge scale. This indicates that a slight increase in the level of knowledge is capable of significantly increasing the probability of a correct response to this item. Because item 5 had the highest degree of discrimination, it is capable of distinguishing individual knowledge at much closer levels, as compared to the remaining items. On the other hand, ICC for item 1 is almost a straight line parallel to the scale of knowledge, indicating that an increase in the theta values does not significantly change the probability of correctly answering the item, i.e., low discriminatory power of this item. The item information curve shows how much the item contributes to the measure of knowledge, i.e., it indicates precisely which levels of theta were better discriminated. Usually the item brings best information about a few theta levels than others, and its representation resembles a normal curve type. The information curve of item 5 brought more information for measuring the levels of knowledge around value 3.0. Outside this amplitude, the item starts producing incorrect information on the level of knowledge, since the standard error curve is inversely proportional to the information curve. On the other hand, the information curve of item 1 showed that this item hardly contributed with any information for measuring HIV/AIDS knowledge.

    +

    + + + + Graphical representation of the characteristic and information curves of the items selected. + + + +

    +

    + Figure 2 presents a graphical representation of the total information curve, i.e., the sum of all information functions, for all the ten items. Overall, the curve indicates that the 10 items provided better differentiation among individuals who are below the midpoint on the knowledge scale. For individuals with levels above the average, the items have little discrimination, producing most of the information error, as seen by the standard error curve (dotted line). In addition, there was no measurable knowledge score above six on the scale.

    +

    + + + + Total Information curve (10 items). + + + +

    +

    A macroscopic view of the item analysis in our sample is shown in Figure 3, which simultaneously provides the total information curve, the curve of HIV/AIDS knowledge scores (IRT), and the total observed scores (CTT). In summary, the estimated latent knowledge among MSM was limited by the parameters of the items, i.e., it more accurately measured individuals with lower knowledge but little differentiation was obtained among those with median or high knowledge levels.

    +

    + + + + Graphical representation of the items and HIV/AIDS knowledge scores. + + + +

    +

    Regarding the existence of the unidimensionality, Full-information factor analysis indicated four factors with the following variance partition: 31.0%, 10.0%, 5.2% and 3.8%. The first component is predominant in relation to the other factors, which confirms that the set of analyzed items presents a unidimensional structure, explained by a variance of 31.0%.

    +

    The DIF by age and schooling was identified in six items (1, 2, 3, 5, 6 and 7) whose ICC are shown in Figure 4. Items 3 and 5 presented uniform DIF in the two variables, producing parallel curves that differ between the two groups only in the difficulty parameter. This indicates that individuals who are younger than 25 years old and those with more than eight years of schooling have a greater probability of correctly responding to these items compared to those 25 years old or more and with eight or fewer years of education, respectively. On the other hand, crossover DIF has been found for items 2 and 6 with respect to age, and for items 1 and 7 with respect to schooling. This indicates that the ICC of these items differ with respect to both parameters difficulty and discrimination.

    +

    + + + + Items characteristic curves with differential item functioning. + + + +

    +     + + DISCUSSION +

    Currently, there is no validated instrument capable of measuring HIV/AIDS knowledge across different populations in Brazil. This study applied IRT for the analysis of HIV/AIDS knowledge among MSM, as it offers important advantages, particularly by the individual analysis of the items and the reliability of the measure, supplementing information provided by the CTT. In addition, IRT psychometrics offers a suitable approach to studying an instrument’s ability to detect change. + 17 + In particular, IRT offers both the potential for new ways of interpreting individual change and improving scale properties in order to better ascertain the measurement scores.

    +

    Initially, both analyses (CTT and IRT) showed that a large proportion (43.2% and 40.7%, respectively) of participants did not reach the average level of HIV/AIDS knowledge, and this is of public health concern. It also indicates that myths about HIV transmission are still present in this population, also reported in other studies. + 11 + +

    +

    On the other hand, the IRT analysis provided more useful information with regard to the knowledge score as well as the individual analysis of the items, including the characteristic curves, the item information curves, the identification of items with problems, their distribution on a scale, and how much information each item brought to the measurement of knowledge.

    +

    We should note that the most problematic items were those related to AIDS treatment (items 1 and 2). Both require knowledge on two distinct issues, risk or prevention and treatment, and therefore, presented higher degree of difficulty, low discrimination power and also the lowest percentage of correct answers. Most likely, the respondents did not completely distinguish or understood their contents, casting doubt on where the lack of knowledge predominated and also indicating an excessive difficulty for a correct response. On the other hand, item 6, which is also related to the risk of HIV positive mothers infecting their babies and AIDS treatment, did not seem to be totally unknown by the respondents.

    +

    The absence of difficult items in this study contributed to the inaccuracy of the measurement of knowledge among those with median level and above, as accurately shown by the total information curve. A recent study that examined the psychometric properties of an HIV/AIDS knowledge scale among adolescents reported that in order to improve the precision of the instrument, new items should be added, particularly those more difficult to answer which provide information about higher trait values. Moreover, in order to improve the overall performance of the knowledge scale, this should include a greater number of items, with higher discriminatory power and different degrees of difficulty, which can provide information along the whole scale. + 1 + +

    +

    The analysis of the DIF identified items that tend to benefit one group more than others. Items 3 and 5 were shown to be more favorable to MSM under age 25 and those with higher schooling, showing higher chances of correct answers of these items. The domain of items 3 and 5 with uniform DIF refers to the indirect transmission of HIV (using public restrooms and the sharing of meals). Studies show that the analysis of patterns of items that display DIF is a useful tool to identify and better understand the differences between ethnic and racial groups. + 7 + + , + + 16 + The analysis of the DIF items may contribute to the development of educational strategies in the approach of the domain of items in which DIF was detected. However, it becomes more complex when trying to understand crossover DIF, as in the case of items 1, 2, 6 and 7. As these items also showed low discrimination power, further analysis is warranted for a better understanding of the DIF effects. We suggest they should be reviewed with regard to content, language and format, since they contain words (e.g., small, less, reduced) that may have caused ambiguity, bringing confusion, indecision and insecurity for respondents.

    +

    Although there are substantial problems in the structure of some items, the results of the unidimensional analysis led us to admit the existence of a dominant trait or factor (i.e., HIV knowledge) responsible for the performance of the set of items and that the instrument used was able to measure the levels of latent knowledge. Ideally, one should pursue a higher percentage of total variance accounted for by the first principle component, indicating that the set of items is more associated with the dominant factor, which is the latent trait measured. + h + We emphasize the need to review items 1, 2, 6 and 7 in order to better compose the scale with large loading values in the first factor. In addition, in order to promote unidimensionality, it is recommended to use constructs that are in the same direction, i.e., a set of items strictly negative or positive. + i + +

    +

    In conclusion, the IRT model was shown to be adequate to measure the level of HIV/AIDS knowledge among MSM and brought important information that can contribute to improving the properties of the items in order to build a knowledge scale suitable for this population. The high proportion (40.7%) of participants with a knowledge score below the average is of concern, considering that the evaluated items are basic and well publicized information about the modes of HIV transmission, particularly among MSM populations. Furthermore, the results revealed some weaknesses of the measuring instrument, and improvement in the quality of the instrument is essential to better ascertain the levels of knowledge of HIV/AIDS.

    +

    The results of IRT analyses should be considered before carrying out other evaluations or interventions in this population. It is essential to review the items with lower discrimination, to incorporate new and more difficult items, and to add other relevant topics. Calibration of items and checking differential item functioning should be assessed in preliminary pilot studies. Comparisons between scores of different samples are possible with IRT methodology because item parameters are invariant to the various groups, and both parameters and latent trait are measured in the same metric scale. + b + This way, monitoring the level of knowledge of this MSM population, or others, over time could be measured in different samples, allowing to accurately detect the progress made by the population, as well as assisting in the development of prevention programs and of new interventions.

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    This study was supported by the Brazilian Ministry of Health/Secretariat of Health Surveillance/Department of STD, AIDS and Viral Hepatitis, through the Project of International Technical Cooperation AD/BRA/03/H34 between the Brazilian Government and the United Nations Office on Drugs and Crime (Process CSV 234/07).

    +     +     +     +
    diff --git a/scielomanager/articletrack/views.py b/scielomanager/articletrack/views.py index d8f561e5..30cf6a71 100644 --- a/scielomanager/articletrack/views.py +++ b/scielomanager/articletrack/views.py @@ -40,13 +40,14 @@ def extract_validation_errors(validation_errors): error_lines = [] # only to simplify the line's highlights of prism.js plugin on template for error in validation_errors: error_data = { - 'line': error.line, - 'column': error.column, - 'message': error.message, - 'level': error.level_name, + 'line': error.line or '--', + 'column': error.column or '--', + 'message': error.message or '', + 'level': error.level_name or 'ERROR', } results.append(error_data) - error_lines.append(str(error.line)) + if error.line: + error_lines.append(str(error.line)) return { 'results': results, 'error_lines': ", ".join(error_lines) @@ -280,7 +281,7 @@ def notice_detail(request, checkin_id): xml_data = { 'file_name': None, 'uri': None, - 'can_be_analyzed': False, + 'can_be_analyzed': (False, ''), 'annotations': None, 'validation_errors': None, } @@ -294,27 +295,35 @@ def notice_detail(request, checkin_id): files_list += [{'ext': file_extension, 'name': f} for f in files[file_extension]] xml_data['file_name'] = files['xml'][0] # assume only ONE xml per package + xml_data['can_be_analyzed'] = (True, '') - except ValueError: + except ValueError as e: # Service Unavailable - pass + logger.error('ValueError while requesting: list_files_members_by_attempt(%s) for checkin.pk == %s. Traceback: %s' % (checkin.attempt_ref, checkin.pk, e)) + xml_data['can_be_analyzed'] = (False, "The package's files could not requested") # get stylechecker annotations - try: - xml_data['uri'] = balaio.get_xml_uri(checkin.attempt_ref, xml_data['file_name']) if xml_data['file_name'] else None - except ValueError: - # Service Unavailable - xml_data['can_be_analyzed'] = False - else: - xml_data['can_be_analyzed'] = bool(xml_data['uri']) + if xml_data['can_be_analyzed'][0]: + try: + xml_data['uri'] = balaio.get_xml_uri(checkin.attempt_ref, xml_data['file_name']) if xml_data['file_name'] else None + except ValueError as e: + # Service Unavailable + logger.error('ValueError while requesting: get_xml_uri(%s, %s) for checkin.pk == %s. Traceback: %s' % (checkin.attempt_ref, xml_data['file_name'], checkin.pk, e)) + xml_data['can_be_analyzed'] = (False, 'Could not obtain the XML with this file name %s' % xml_data['file_name']) + else: + if bool(xml_data['uri']): + xml_data['can_be_analyzed'] = (True, "") + else: + xml_data['can_be_analyzed'] = (False, "XML's URI is invalid (%s)" % xml_data['uri']) - if xml_data['can_be_analyzed']: + if xml_data['can_be_analyzed'][0]: try: xml_check = stylechecker.XML(xml_data['uri']) - except Exception: # any exception will stop the process - xml_data['can_be_analyzed'] = False + except Exception as e: # any exception will stop the process + xml_data['can_be_analyzed'] = (False, "Error while starting Stylechecker.XML()") + logger.error('ValueError while creating: Stylechecker.XML(%s) for checkin.pk == %s. Traceback: %s' % (xml_data['file_name'], checkin.pk, e)) else: - status, errors = xml_check.validate() + status, errors = xml_check.validate_style() if not status: # have errors xml_check.annotate_errors() xml_data['annotations'] = str(xml_check)