Variants in Candidate Genes for Phenotype Heterogeneity in Patients with the 22q11.2 Deletion Syndrome.

22q11.2 deletion syndrome (22q11.2DS) is a microdeletion syndrome with a broad and heterogeneous phenotype, even though most of the deletions present similar sizes, involving ∼3 Mb of DNA. In a relatively large population of a Brazilian 22q11.2DS cohort (60 patients), we investigated genetic variants that could act as genetic modifiers and contribute to the phenotypic heterogeneity, using a targeted NGS (Next Generation Sequencing) with a specific Ion AmpliSeq panel to sequence nine candidate genes (CRKL, MAPK1, HIRA, TANGO2, PI4KA, HDAC1, ZDHHC8, ZFPM2, and JAM3), mapped in and outside the 22q11.2 hemizygous deleted region. In silico prediction was performed, and the whole-genome sequencing annotation analysis package (WGSA) was used to predict the possible pathogenic effect of single nucleotide variants (SNVs). For the in silico prediction of the indels, we used the genomic variants filtered by a deep learning model in NGS (GARFIELD-NGS). We identified six variants, 4 SNVs and 2 indels, in MAPK1, JAM3, and ZFPM2 genes with possibly synergistic deleterious effects in the context of the 22q11.2 deletion. Our results provide the opportunity for the discovery of the co-occurrence of genetic variants with 22q11.2 deletions, which may influence the patients´ phenotype.

Diffuse Idiopathic Skeletal Hyperostosis (DISH)-Phagia: A Case Report and Review of Literature of a Rare Disease Manifestation.

Diffuse idiopathic skeletal hyperostosis (DISH), also called Forestier disease, is a clinical entity characterized by ossification of the anterolateral ligaments of the spine. DISH is more commonly diagnosed in older males, with an estimated prevalence of 42% in patients older than 65 years. As the disease affects predominantly the thoracic spine, dysphagia is a rare presentation of this entity observed in only 0.6-1.0% of the cases. We present a clinical case of an 84-year-old male with complaints of progressive dysphagia and foreign body sensation within one year of evolution. Computed tomography imaging revealed an anterior C4-C5 osteophyte compressing the posterior hypopharyngeal wall. Flexible endoscopy revealed a deformed and stenotic hypopharynx. The patient underwent surgical treatment with anterior cervical osteophyte resection using the Smith-Robinson approach. The patient showed significant improvement in preoperative symptoms, and no recurrence was detected at six months of follow-up. We also aim to discuss the clinical and radiological characteristics of the disease, as well as the crucial steps for a correct diagnosis and treatment of this rare disease.

Pelvic Ewing Sarcoma: The Great Mimicker.

Ewing sarcoma is the most common malignant bone tumor of the pelvis in children and young adults. Even with aggressive treatment, its survival rate is amongst the poorest. Classical presentation may not be the rule. It may simulate clinically, imagiologically and histopathologically other nonmalignant entities. Therefore, its suspicion should not be overlooked. We report two cases of pelvic Ewing sarcoma: the first mimicking eosinophilic granuloma, and the second mimicking osteomyelitis. In the latter, we also report an atypical finding of its natural history: an initial response to antibiotic and anti-inflammatory treatment. In both cases, we highlight the possibility of an inconclusive percutaneous bone biopsy and the importance of immunochemistry and cytogenetics for the definitive diagnosis.

Pelvic Ewing Sarcoma: The Great Mimicker / Sarcoma de Ewing pélvico: o grande imitador

Abstract Ewing sarcoma is the most common malignant bone tumor of the pelvis in children and young adults. Even with aggressive treatment, its survival rate is amongst the poorest. Classical presentation may not be the rule. It may simulate clinically, imagiologically and histopathologically other nonmalignant entities. Therefore, its suspicion should not be overlooked. We report two cases of pelvic Ewing sarcoma: the first mimicking eosinophilic granuloma, and the second mimicking osteomyelitis. In the latter, we also report an atypical finding of its natural history: an initial response to antibiotic and anti-inflammatory treatment. In both cases, we highlight the possibility of an inconclusive percutaneous bone biopsy and the importance of immunochemistry and cytogenetics for the definitive diagnosis.

Resumo O sarcoma de Ewing é o tumor ósseo maligno da pelve mais comum em crianças e adultos jovens. Mesmo com tratamento agressivo, sua taxa de sobrevivência está entre as piores. A apresentação clássica pode não ser a regra. Ele pode simular clinicamente, imaginologicamente e histopatologicamente outras entidades não malignas. Portanto, sua suspeita não deve ser negligenciada. Relatamos dois casos de sarcoma pélvico: o primeiro imitando granuloma eosinofílico e o segundo imitando osteomielite. Neste último, também relatamos um achado atípico de sua história natural: uma resposta inicial ao antibiótico e ao tratamento anti-inflamatório. Em ambos os casos, destacamos a possibilidade de uma biópsia óssea percutânea inconclusiva e a importância da imunoquímica e da citogenética para o diagnóstico definitivo.

Prevalence and clinical implications of germline pathogenic variants in cancer predisposing genes in young patients across sarcoma subtypes.

BACKGROUND: Sarcomas are a rare and diverse group of cancers occurring mainly in young individuals for which an underlying germline genetic cause remains unclear in most cases. METHODS: Germline DNA from 177 children, adolescents and young adults with soft tissue or bone sarcomas was tested using multigene panels with 113 or 126 cancer predisposing genes (CPGs) to describe the prevalence of germline pathogenic/likely pathogenic variants (GPVs). Subsequent testing of a subset of tumours for loss of heterozygosity (LOH) evaluation was performed to investigate the clinical and molecular significance of these variants. RESULTS: GPVs were detected in 21.5% (38/177) of the patients (15.8% in children and 21.6% in adolescents and young adults), with dominant CPGs being altered in 15.2% overall. These variants were found in genes previously associated with the risk of developing sarcomas (TP53, RB1, NF1, EXT1/2) but also in genes where that risk is still emerging/limited (ERCC2, TSC2 and BRCA2) or unknown (PALB2, RAD50, FANCM and others). The detection rates of GPVs varied from 0% to 33% across sarcoma subtypes and GPV carriers were more likely to present more than one primary tumour than non-carriers (21.1%×6.5%; p=0.012). Loss of the wild-type allele was detected in 48% of tumours from GPV carriers, mostly in genes definitively associated with sarcoma risk. CONCLUSION: Our findings reveal that a high proportion of young patients with sarcomas presented a GPV in a CPG, underscoring the urgency of establishing appropriate genetic screening strategies for these individuals and their families.

Artificial intelligence and statistical methods for stratification and prediction of progression in amyotrophic lateral sclerosis: A systematic review.

BACKGROUND: Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder characterised by the progressive loss of motor neurons in the brain and spinal cord. The fact that ALS's disease course is highly heterogeneous, and its determinants not fully known, combined with ALS's relatively low prevalence, renders the successful application of artificial intelligence (AI) techniques particularly arduous. OBJECTIVE: This systematic review aims at identifying areas of agreement and unanswered questions regarding two notable applications of AI in ALS, namely the automatic, data-driven stratification of patients according to their phenotype, and the prediction of ALS progression. Differently from previous works, this review is focused on the methodological landscape of AI in ALS. METHODS: We conducted a systematic search of the Scopus and PubMed databases, looking for studies on data-driven stratification methods based on unsupervised techniques resulting in (A) automatic group discovery or (B) a transformation of the feature space allowing patient subgroups to be identified; and for studies on internally or externally validated methods for the prediction of ALS progression. We described the selected studies according to the following characteristics, when applicable: variables used, methodology, splitting criteria and number of groups, prediction outcomes, validation schemes, and metrics. RESULTS: Of the starting 1604 unique reports (2837 combined hits between Scopus and PubMed), 239 were selected for thorough screening, leading to the inclusion of 15 studies on patient stratification, 28 on prediction of ALS progression, and 6 on both stratification and prediction. In terms of variables used, most stratification and prediction studies included demographics and features derived from the ALSFRS or ALSFRS-R scores, which were also the main prediction targets. The most represented stratification methods were K-means, and hierarchical and expectation-maximisation clustering; while random forests, logistic regression, the Cox proportional hazard model, and various flavours of deep learning were the most widely used prediction methods. Predictive model validation was, albeit unexpectedly, quite rarely performed in absolute terms (leading to the exclusion of 78 eligible studies), with the overwhelming majority of included studies resorting to internal validation only. CONCLUSION: This systematic review highlighted a general agreement in terms of input variable selection for both stratification and prediction of ALS progression, and in terms of prediction targets. A striking lack of validated models emerged, as well as a general difficulty in reproducing many published studies, mainly due to the absence of the corresponding parameter lists. While deep learning seems promising for prediction applications, its superiority with respect to traditional methods has not been established; there is, instead, ample room for its application in the subfield of patient stratification. Finally, an open question remains on the role of new environmental and behavioural variables collected via novel, real-time sensors.

Triclustering-based classification of longitudinal data for prognostic prediction: targeting relevant clinical endpoints in amyotrophic lateral sclerosis.

This work proposes a new class of explainable prognostic models for longitudinal data classification using triclusters. A new temporally constrained triclustering algorithm, termed TCtriCluster, is proposed to comprehensively find informative temporal patterns common to a subset of patients in a subset of features (triclusters), and use them as discriminative features within a state-of-the-art classifier with guarantees of interpretability. The proposed approach further enhances prediction with the potentialities of model explainability by revealing clinically relevant disease progression patterns underlying prognostics, describing features used for classification. The proposed methodology is used in the Amyotrophic Lateral Sclerosis (ALS) Portuguese cohort (N = 1321), providing the first comprehensive assessment of the prognostic limits of five notable clinical endpoints: need for non-invasive ventilation (NIV); need for an auxiliary communication device; need for percutaneous endoscopic gastrostomy (PEG); need for a caregiver; and need for a wheelchair. Triclustering-based predictors outperform state-of-the-art alternatives, being able to predict the need for auxiliary communication device (within 180 days) and the need for PEG (within 90 days) with an AUC above 90%. The approach was validated in clinical practice, supporting healthcare professionals in understanding the link between the highly heterogeneous patterns of ALS disease progression and the prognosis.

Expanding the Phenotype of 8p23.1 Deletion Syndrome: Eight New Cases Resembling the Clinical Spectrum of 22q11.2 Microdeletion.

OBJECTIVE: To report the effectiveness of early molecular diagnosis in the clinical management of rare diseases, presenting 8 patients with 8p23.1DS who have clinical features that overlap the phenotypic spectrum of 22q11.2DS. STUDY DESIGN: This report is part of a previous study that aims to provide a precocious molecular diagnosis of the 22q11.2 deletion syndrome in 118 infants with congenital heart disease. To confirm the clinical diagnosis, patients underwent comparative genomic screening by the multiplex ligation-dependent probe amplification (MLPA) assay with the SALSA MLPA probemix kits P064-B2, P036-E1, P070-B2, P356-A1, and P250- B1. Subsequently, the patients performed the genomic microarray using the Infinium CytoSNP-850K BeadChip to confirm the deletion, determine the breakpoints of the deletion, and search for genomic copy number variations. RESULTS: MLPA performed with 3 different kits revealed the 8p23.1 typical deletion involving the PPP1R3B, MSRA, and GATA4 genes in the 5 patients. The array analysis was performed on these 5 patients and 3 other patients (8 patients) who also had clinical suspicion of 22q11 deletion (8 patients) allowed a precise definition of the breakpoints and excluded other genomic abnormalities. CONCLUSIONS: Cytogenomic screening was efficient in establishing a differential diagnosis and ruling out the presence of other concomitant syndromes. The clinical picture of the 8p23.1 deletion syndrome is challenging; however, cytogenomic tools can provide an exact diagnosis and help to clarify the genotype-phenotype complexity of these patients. Our reports underline the importance of early diagnosis and clinical follow-up of microdeletion syndromes.

Learning prognostic models using a mixture of biclustering and triclustering: Predicting the need for non-invasive ventilation in Amyotrophic Lateral Sclerosis.

Longitudinal cohort studies to study disease progression generally combine temporal features produced under periodic assessments (clinical follow-up) with static features associated with single-time assessments, genetic, psychophysiological, and demographic profiles. Subspace clustering, including biclustering and triclustering stances, enables the discovery of local and discriminative patterns from such multidimensional cohort data. These patterns, highly interpretable, are relevant to identifying groups of patients with similar traits or progression patterns. Despite their potential, their use for improving predictive tasks in clinical domains remains unexplored. In this work, we propose to learn predictive models from static and temporal data using discriminative patterns, obtained via biclustering and triclustering, as features within a state-of-the-art classifier, thus enhancing model interpretation. triCluster is extended to find time-contiguous triclusters in temporal data (temporal patterns) and a biclustering algorithm to discover coherent patterns in static data. The transformed data space, composed of bicluster and tricluster features, capture local and cross-variable associations with discriminative power, yielding unique statistical properties of interest. As a case study, we applied our methodology to follow-up data from Portuguese patients with Amyotrophic Lateral Sclerosis (ALS) to predict the need for non-invasive ventilation (NIV) since the last appointment. The results showed that, in general, our methodology outperformed baseline results using the original features. Furthermore, the bicluster/tricluster-based patterns used by the classifier can be used by clinicians to understand the models by highlighting relevant prognostic patterns.

Costovertebral Osteoarthrosis: Rare Differential Diagnosis of Back pain in young patients. Case Report.

The differential diagnosis of dorsal thoracic pain can be a challange due to the proximity of the dorsal column to vital organs as well as to its unique anatomy, innervation, and rib joint. The patterns of referred visceral pain require, in most cases, extensive complementary diagnostic tests in order to exclude severe conditions. Referred pain patterns often result in numerous and expensive visceral workups in order to exclude serious conditions, and costovertebral joint osteoarthritis is usually only considered when the origin of the pain remains unexplained. The authors present the case of a 40-year-old man with disabling dorsal pain due to isolated costovertebral osteoarthrosis. The symptomatology was controlled after injection of methylprednisolone guided by computed tomography. This clinical case aims to describe the clinical presentation of a rare entity that should be considered in the differential diagnosis of back pain.

Costovertebral Osteoarthrosis: Rare Differential Diagnosis of Back pain in young patients. Case Report / Osteoartrose costovertebral: Diagnóstico diferencial raro de dorsalgia no paciente jovem. Relato de caso

Abstract The differential diagnosis of dorsal thoracic pain can be a challange due to the proximity of the dorsal column to vital organs as well as to its unique anatomy, innervation, and rib joint. The patterns of referred visceral pain require, in most cases, extensive complementary diagnostic tests in order to exclude severe conditions. Referred pain patterns often result in numerous and expensive visceral workups in order to exclude serious conditions, and costovertebral joint osteoarthritis is usually only considered when the origin of the pain remains unexplained. The authors present the case of a 40-year-old man with disabling dorsal pain due to isolated costovertebral osteoarthrosis. The symptomatology was controlled after injection of methylprednisolone guided by computed tomography. This clinical case aims to describe the clinical presentation of a rare entity that should be considered in the differential diagnosis of back pain.

Resumo O diagnóstico diferencial de dorsalgia revela-se um desafio pela proximidade da coluna dorsal a órgãos vitais assim como por sua anatomia única, inervação e articulação com as costelas. Os padrões de dor referida visceral obrigam, na maioria das vezes, a extensivos exames complementares de diagnóstico de forma a excluir condições graves. A osteoartrose da articulação costovertebral é um diagnóstico pouco reconhecido, e habitualmente é somente considerado quando a fonte de dor continua sem explicação após extensa investigação. Os autores apresentam o caso de um homem de 40 anos de idade com dor dorsal incapacitante devido a osteoartrose costovertebral isolada. A sintomatologia foi controlada após a injeção de metilprednisolona guiada por tomografia computadorizada. Este caso clínico tem como objetivo descrever a apresentação clínica de uma entidade rara que deverá ser considerada no diagnóstico diferencial de dorsalgia.

Function of Proneural Genes Ascl1 and Asense in Neurogenesis: How Similar Are They?

Proneural genes were initially identified in Drosophila, where pioneer work on these important regulators of neural development was performed, and from which the term proneural function was coined. Subsequently, their counterparts in vertebrates were identified, and their function in neural development extensively characterized. The function of proneural transcription factors in flies and vertebrates is, however, very distinct. In flies, proneural genes play an early role in neural induction, by endowing neural competence to ectodermal cells. In contrast, vertebrate proneural genes are expressed only after neural specification, in neural stem and progenitor cells, where they play key regulatory functions in quiescence, proliferation, and neuronal differentiation. An exception to this scenario is the Drosophila proneural gene asense, which has a late onset of expression in neural stem cells of the developing embryo and larvae, similar to its vertebrate counterparts. Although the role of Asense remains poorly investigated, its expression pattern is suggestive of functions more in line with those of vertebrate proneural genes. Here, we revise our current understanding of the multiple activities of Asense and of its closest vertebrate homologue Ascl1 in neural stem/progenitor cell biology, and discuss possible parallels between the two transcription factors in neurogenesis regulation.

Li-Fraumeni-associated pancreatic neuroendocrine tumour and XAF1 p.Glu134Ter risk modifier variant.

Studies have demonstrated that up to 17% of patients with pancreatic neuroendocrine tumours (pNETs) present pathogenic germline variants (PGVs) in several different genes, irrespective of family cancer history. Li-Fraumeni syndrome (LFS) is an autosomal dominant cancer predisposition syndrome related to PGVs in the TP53 gene. A previous case of a pNET associated with LFS (c.1009C > T, p.R337C) has been reported. Here we report the first case of a patient with pNET and TP53 p.R337H and XAF1 p.E134* germline variants, expanding the knowledge of LFS and germline mutations in neuroendocrine tumours.

Glyphosate Use, Toxicity and Occurrence in Food.

Glyphosate is a systemic, broad-spectrum and post-emergent herbicide. The use of glyphosate has grown in the last decades, and it is currently the most used herbicide worldwide. The rise of glyphosate consumption over the years also brought an increased concern about its possible toxicity and consequences for human health. However, a scientific community consensus does not exist at the present time, and glyphosate's safety and health consequences are controversial. Since glyphosate is mainly applied in fields and can persist several months in the soil, concerns have been raised about the impact that its presence in food can cause in humans. Therefore, this work aims to review the glyphosate use, toxicity and occurrence in diverse food samples, which, in certain cases, occurs at violative levels. The incidence of glyphosate at levels above those legally allowed and the suspected toxic effects of this compound raise awareness regarding public health.

An Energy-Saving Forwarding Mechanism Based on Clustering for Opportunistic Networks.

In Opportunistic Networks (OppNets), mobility of and contact between nodes are explored to create communication opportunities and exchange messages and information. A basic premise for a better performance of these networks is a collaboration of the nodes during communication. However, due to energy restriction factors, nodes may eventually fail to collaborate with message exchanges. In this work, we propose a routing mechanism called eGPDMI to improve message probability of delivery while optimizing nodes' energy consumption. Unlike other algorithms proposed in OppNets literature, eGPDMI groups nodes by energy level and nodes interests using clustering techniques. Our major assumption is that retaining messages in nodes with the highest energy levels can improve network performance, thus overcoming the problem of nodes' disconnection due to unwillingness to cooperate due to low energy values. Through questionnaire application and factorial design experiments, we characterize the impacts of energy levels in OppNets. Further, we apply performance evaluation of the eGPDMI mechanism in terms of effectiveness using mobility from real-world scenarios. The results show that our mechanism effectively reduces the degradation of the probability of delivery when the minimum energy level used for nodes to cooperate with communication increases.

Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cells.

During mitosis, chromatin condensation is accompanied by a global arrest of transcription. Recent studies suggest transcriptional reactivation upon mitotic exit occurs in temporally coordinated waves, but the underlying regulatory principles have yet to be elucidated. In particular, the contribution of sequence-specific transcription factors (TFs) remains poorly understood. Here we report that Brn2, an important regulator of neural stem cell identity, associates with condensed chromatin throughout cell division, as assessed by live-cell imaging of proliferating neural stem cells. In contrast, the neuronal fate determinant Ascl1 dissociates from mitotic chromosomes. ChIP-seq analysis reveals that Brn2 mitotic chromosome binding does not result in sequence-specific interactions prior to mitotic exit, relying mostly on electrostatic forces. Nevertheless, surveying active transcription using single-molecule RNA-FISH against immature transcripts reveals differential reactivation kinetics for key targets of Brn2 and Ascl1, with transcription onset detected in early (anaphase) versus late (early G1) phases, respectively. Moreover, by using a mitotic-specific dominant-negative approach, we show that competing with Brn2 binding during mitotic exit reduces the transcription of its target gene Nestin Our study shows an important role for differential binding of TFs to mitotic chromosomes, governed by their electrostatic properties, in defining the temporal order of transcriptional reactivation during mitosis-to-G1 transition.

Surgical outcome of a post-traumatic dystonic foot: Case report and literature review.

Post-traumatic dystonia is an underrecognized condition that can present with bizarre symptoms after trauma, usually out of proportion to the trigger event. We describe the case of a 31-year-old man with a severe lower extremity deformity, gradually developed after minor trauma. An interdisciplinary treatment was tried without any improvement and surgery was performed as a rescue approach. Tibialis anterior tendon transfer and hindfoot triple arthrodesis were carried out, successfully achieving a plantigrade foot and a functional gait. Despite the scarce literature available about functional results of surgery in dystonic feet, we present a step-by-step comprehensive approach to this disorder. LEVEL OF CLINICAL EVIDENCE: 4.

Lymphoproliferative disorder with polyautoimmunity and hypogammaglobulinemia: An unusual presentation of 22q11.2 deletion syndrome.

22q11.2 deletion syndrome (22q11.2DS) has a heterogeneous presentation that includes multiple congenital anomalies and immunodeficiency, one of the most striking features. Usually, it is characterized by T cell lymphopenia, B cell dysfunction and autoimmunity. Here, we describe an unusual case of 22q11.2DS in a patient with lymphoproliferative disorder, polyautoimmunity and hypogammaglobulinemia.

AGRASS Questionnaire: Assessment of Risk Management in Health Care.

OBJECTIVE: This study aims to assess the development and the validity analysis of the Assessment of Risk Management in Health Care Questionnaire (AGRASS). METHODS: This is a validation study of a measurement instrument following the stages: 1) Development of conceptual model and items; 2) Formal multidisciplinary assessment; 3) Nominal group for validity analysis with national specialists; 4) Development of software and national pilot study in 62 Brazilian hospitals 5) Delphi for validity analysis with the users of the questionnaire. In stages 3 and 5, the items were judged based on face validity, content validity, and utility and viability, by a 1-7 Likert scale (cut-off point: median < 6). Accuracy and reliability of the questionnaire were analyzed with the Confirmatory Factor Analysis and the Cronbach's alpha. RESULTS: The initial version of the instrument (98 items) was adapted during stages 1 to 3 for the final version with 40 items, which were considered relevant, of adequate content, useful, and viable. The instrument has 2 dimensions and 9 subdimensions, and the items have closed-ended questions (yes or no). The software for the automatic collection and analysis generates indicators, tables, and automatic graphs for the assessed institution and aggregated data. The adjustment indices confirmed a bi-dimensional model composed of structure and process (X2/gl = 1.070, RMSEA ≤ 0.05 = 0.847, TLI = 0.972), with high reliability for the AGRASS Questionnaire (α = 0.94) and process dimension (α = 0.93), and adequate for the structural dimension (α = 0.70). CONCLUSIONS: The AGRASS Questionnaire is a potentially useful instrument for the surveillance and monitoring of the risk management and patient safety in health services.