bluuebunny/crossref_metadata_2025 huggingface dataset:
BRAWNIN: A sORF-encoded Peptide Essential for Vertebrate Mitochondrial Complex III Assembly
Authors: Zhang Shan , Liang Chao , Mary Camille , Kerouanton Baptiste , Francisco Joel , Jagannathan Narendra Suhas , Olexiouk Volodimir , Hou Peh Jih , Tang Claire , Fidelito Gio , Nama Srikanth , Cheng Ruey-Kuang , Wee Caroline Lei , Wang Loo Chien , Duek Roggli Paula , Sampath Prabha , Lane Lydie , Petretto Enrico , Sobota Radoslaw , Jesuthasan Suresh , Sun Lei , Tucker-Kellogg Lisa , Reversade Bruno , Menschaert Gerben , Stroud David A. , Ho Lena
Published: February 2020

The emergence of small open reading frame (sORF)-encoded peptides (SEPs) is rapidly expanding the known proteome at the lower end of the size distribution1,2. Here, we show that the mitochondria proteome is enriched for proteins smaller than 100 a.a. (defined as SEPs). Using a mitochondrial prediction and validation pipeline for small open-reading-frame (sORF)-encoded peptides (SEPs), we report the discovery of 16 endogenous mitochondrial SEPs (mito-SEPs) associated with oxidative phosphorylation (OXPHOS). Through functional prediction, proteomics, metabolomics and metabolic flux modeling, we demonstrate that BRAWNIN (BR), a 71 amino acid peptide encoded by theC12orf73gene, is essential for respiratory chain complex III (CIII) assembly. In human cells, BR is induced by the energy-sensing AMPK pathway, and its depletion impairs mitochondrial ATP production.In vivo, BR is enriched in muscle tissues and its maternal zygotic deletion in zebrafish causes complete CIII loss, resulting in severe growth retardation, lactic acidosis and early death. Our findings demonstrate that BR is essential for oxidative phosphorylation across vertebrate species. We propose that mito-SEPs are an untapped resource for essential regulators of oxidative metabolism.
Non-negative Independent Factor Analysis disentangles discrete and continuous sources of variation in scRNA-seq data
Authors: Mao Weiguang , Pouyan Maziyar Baran , Kostka Dennis , Chikina Maria
Published: February 2020

Motivation

Single-cell RNA-seq analysis has emerged as a powerful tool for understanding inter-cellular heterogeneity. Due to the inherent noise of the data, computational techniques often rely on dimensionality reduction (DR) as both a pre-processing step and an analysis tool. Ideally, dimensionality reduction should preserve the biological information while discarding the noise. However if the dimensionality reduction is to be used directly to gain biological insight it must also be interpretable – that is the individual dimensions of the reduction should correspond to specific biological variables such as cell-type identity or pathway activity. Maximizing biological interpretability necessitates making assumption about the data structures and the choice of the model is critical.

Results

We present a new probabilistic single-cell factor analysis model, Non-negative Independent Factor Analysis (NIFA), that incorporates different interpretability inducing assumptions into a single modeling framework. The key advantage of our NIFA model is that it simultaneously models uni- and multi-modal latent factors, and thus isolates discrete cell-type identity and continuous pathway activity into separate components. We apply our approach to a range of datasets where cell-type identity is known, and we show that NIFA-derived factors outperform results from ICA, PCA, NMF and scCoGAPS (an NMF method designed for single-cell data) in terms of disentangling biological sources of variation. Studying an immunotherapy dataset in detail, we show that NIFA is able to reproduce and refine previous findings in a single analysis framework and enables the discovery of new clinically relevant cell states.

Availability

NFIA is a R package which is freely available at GitHub (https://github.com/wgmao/NIFA).

Contact

mchikina@pitt.edu

Supplementary information

Supplementary data are available at Bioinformatics online.
Complex networks of miRNA-transcription factors mediate gene dosage compensation in aneuploid cancer
Authors: Acón ManSai , Oviedo Guillermo , Baéz Edwin , Vásquez-Vargas Gloriana , Guevara-Coto José , Segura-Castillo Andrés , Siles-Canales Francisco , Quirós-Barrantes Steve , Mendes Pedro , Mora-Rodríguez Rodrigo
Published: February 2020

Cancer complexity is consequence of enormous genomic instability leading to aneuploidy, a hallmark of most cancers. We hypothesize that dosage compensation of critical genes could arise from systems-level properties of complex networks of microRNAs (miRNA) and transcription factors (TF) as a way for cancer cells to withstand the negative effects of aneuploidy. We studied gene dosage compensation at the transcriptional level on data of the NCI-60 cancer cell line panel with the aid of computational models to identify candidate genes with low tolerance to variation in gene expression despite high variation in copy numbers. We identified a network of TF and miRNAs validated interactions with those genes to construct a mathematical model where the property of dosage compensation emerged for MYC and STAT3. Compensation was mediated by feedback and feed-forward motifs with 4 miRNAs and was dependent on the kinetic parameters of these TF-miRNA interactions, indicating that network analysis was not enough to identify this emergent property. The inhibition of miRNAs compensating MYC suggest a therapeutic potential of targeting gene dosage compensation against aneuploid cancer.
QDeep: distance-based protein model quality estimation by residue-level ensemble error classifications using stacked deep residual neural networks
Authors: Shuvo Md Hossain , Bhattacharya Sutanu , Bhattacharya Debswapna
Published: February 2020

Motivation

Protein model quality estimation, in many ways, informs protein structure prediction. Despite their tight coupling, existing model quality estimation methods do not leverage inter-residue distance information or the latest technological breakthrough in deep learning that has recently revolutionized protein structure prediction.

Results

We present a new distance-based single-model quality estimation method called QDeep by harnessing the power of stacked deep residual neural networks (ResNets). Our method first employs stacked deep ResNets to perform residue-level ensemble error classifications at multiple predefined error thresholds, and then combines the predictions from the individual error classifiers for estimating the quality of a protein structural model. Experimental results show that our method consistently out-performs existing state-of-the-art methods including ProQ2, ProQ3, ProQ3D, ProQ4, 3DCNN, MESHI, and VoroMQA in multiple independent test datasets across a wide-range of accuracy measures; and that predicted distance information significantly contributes to the improved performance of QDeep.

Availability

https://github.com/Bhattacharya-Lab/QDeep

Contact

bhattacharyad@auburn.edu
Transcriptomic analysis of dystonia-associated genes reveals functional convergence within specific cell types and shared neurobiology with psychiatric disorders
Authors: Mencacci Niccolò E. , Reynolds Regina , Ruiz Sonia Garcia , Vandrovcova Jana , Forabosco Paola ,   UK Brain Expression Consortium,   International Parkinson’s Disease Genomics Consortium, Weale Michael E. , Bhatia Kailash P. , Hardy John , Botía Juan A , Ryten Mina
Published: February 2020

Dystonia is a neurological disorder characterized by sustained or intermittent muscle contractions causing abnormal movements and postures, often occurring in absence of any structural brain abnormality. Psychiatric comorbidities, including anxiety, depression, obsessive-compulsive disorder and schizophrenia, are frequent in dystonia patients. While mutations in a fast-growing number of genes have been linked to Mendelian forms of dystonia, the cellular, anatomical, and molecular basis remains unknown for most genetic forms of dystonia, as does its genetic and biological relationship to neuropsychiatric disorders. Here we applied an unbiased systems-biology approach to explore the cellular specificity of all currently known dystonia-associated genes, predict their functional relationships, and test whether dystonia and neuropsychiatric disorders share a genetic relationship. To determine the cellular specificity of dystonia-associated genes in the brain, single-nuclear transcriptomic data derived from mouse brain was used together with expression-weighted cell-type enrichment. To identify functional relationships amongst dystonia-associated genes, we determined the enrichment of these genes in co-expression networks constructed from ten human brain regions. Stratified linkage-disequilibrium score regression was used to test whether co-expression modules enriched for dystonia-associated genes significantly contribute to the heritability of anxiety, major depressive disorder, obsessive-compulsive disorder, schizophrenia, and Parkinson’s disease. Dystonia-associated genes were significantly enriched in adult nigral dopaminergic neurons and striatal medium spiny neurons. Furthermore, four of the 220 gene co-expression modules tested were significantly enriched for the dystonia-associated genes. The identified modules were derived from the substantia nigra, putamen, frontal cortex, and white matter, and were all significantly enriched for genes associated with synaptic function. Finally, we demonstrated significant enrichments of the heritability of depression, obsessive-compulsive disorder and schizophrenia, but not anxiety and Parkinson’s disease, within the putamen and white matter modules. In conclusion, multiple dystonia-associated genes interact and contribute to pathogenesis likely through dysregulation of synaptic signalling in striatal medium spiny neurons, adult nigral dopaminergic neurons and frontal cortical neurons. Furthermore, the enrichment of the heritability of psychiatric disorders in the co-expression modules enriched for dystonia-associated genes indicates that psychiatric symptoms associated with dystonia are likely to be intrinsic to its pathophysiology.
A Novel Multiplex qPCR Assay for Detection ofPlasmodium falciparumwithHistidine-rich Protein 2 and 3 (pfhrp2 and pfhrp3)Deletions in Polyclonal Infections
Authors: Grignard Lynn , Nolder Debbie , Sepúlveda Nuno , Berhane Araia , Mihreteab Selam , Kaaya Robert , Phelan Jody , Moser Kara , van Schalkwyk Donelly A. , Campino Susana , Parr Jonathan B. , Juliano Jonathan J. , Chiodini Peter , Cunningham Jane , Sutherland Colin J. , Drakeley Chris , Beshir Khalid B.
Published: February 2020

Background

Rapid diagnostic tests (RDTs) that detect the malaria antigen histidine-rich protein 2 (HRP2) are widely used in endemic areas globally to confirmPlasmodium falciparuminfection in febrile patients. The emergence of parasites lacking the gene encoding HRP2 and escaping RDT detection threatens progress in malaria control and elimination. Many health facilities in malaria endemic countries are dependent on RDTs for diagnosis and some National Health Service hospitals without expert microscopists rely on them for diagnosis out of hours. It is vital to study the emergence and the extent of such parasites globally to guide diagnostic policy. Currently, verification of the presence of such parasites in a blood sample requires a series of PCR assays to confirm the presence ofP. falciparumand in the absence of amplicons frompfhrp2and/orpfhrp3, which encodes a cross-reactive protein isoform. These tests have different limits of detection and many laboratories have reported difficulty in confirming the absence ofpfhrp2andpfhrp3with certainty.

Methods

We developed and validated a novel and rapid multiplex real time quantitative (qPCR) assay to detectpfhrp2, pfhrp3,confirmatory parasite and human reference genes simultaneously. We also applied the assay to detectpfhrp2andpfhrp3deletion in 462 field samples from different endemic countries and UK travellers.

Results

The qPCR assay showed limit of detection and quantification of 0.76-1.5 parasites per μl. The amplification efficiency, coefficient of determination (R2) and slope for the genes were 96-1.07%, 0.96-0.98 and −3.375 2 to −3.416 respectively. The assay demonstrated diagnostic sensitivity of 100% (n=19, 95% CI= (82.3%; 100%)) and diagnostic specificity of 100% (n=31; 95% CI= (88.8%; 100%)) in detectingpfhrp2andpfhrp3in. In addition, the qPCR assay estimatesP. falciparumparasite density and can detectpfhrp2andpfhrp3deletions masked in polyclonal infections. We reportpfhrp2andpfhrp3deletions in parasite isolates from Kenya, Tanzania and in UK travellers.

Conclusion

The new qPCR assay is simple to use and offers significant advantages in speed and ease of interpretation. It is easily scalable to routine surveillance studies in countries whereP. falciparumparasites lackingpfhrp2andpfhrp3are a threat to malaria control.
A Pathoconnectome of Early Neurodegeneration
Authors: Pfeiffer Rebecca L. , Anderson James R. , Dahal Jeebika , Garcia Jessica C. , Yang Jia-Hui , Sigulinsky Crystal L. , Rapp Kevin , Emrich Daniel P. , Watt Carl B. , Morrison Hope , Houser Alexis R. , Marc Robert E. , Jones Bryan W.
Published: February 2020

Connectomics has demonstrated that synaptic networks and their topologies are precise and directly correlate with physiology and behavior. The next extension of connectomics is pathoconnectomics: to map neural network synaptology and circuit topologies corrupted by neurological disease in order to identify robust targets for therapeutics. In this report, we characterize the first pathoconnectome, in this case, generated from a retina with photoreceptor degeneration. We observe aberrant connectivity in the rod-network pathway and novel synaptic connections deriving from neurite sprouting. These observations reveal principles of neuron responses to the loss of network components and can be extended to other neurodegenerative diseases.
Meso-limbic Gene Expression Findings from Mouse Cocaine Self-Administration Recapitulate Human Cocaine Use Disorder
Authors: Huggett Spencer B. , Bubier Jason A. , Chesler Elissa J. , Palmer Rohan C.
Published: February 2020

Animal models of drug use have been employed for over 100 years to facilitate the identification of mechanisms governing human substance use and addiction. Most cross-species research on drug use/addiction examines behavioral overlap, but studies assessing neuro-molecular correspondence are lacking. Our study utilized transcriptome-wide data from the hippocampus and ventral tegmental area (VTA)/midbrain from a total of 35 human males with cocaine use disorder/controls and 49 male C57BL/6J cocaine/saline administering/exposed mice. We hypothesized that individual genes (differential expression) and systems of co-expressed genes (gene networks) would demonstrate appreciable overlap across mouse cocaine self-administration and human cocaine use disorder. We found modest, but significant associations between differentially expressed genes associated with cocaine self-administration (short access) and cocaine use disorder within meso-limbic circuitry, but non-robust associations with mouse models of acute cocaine exposure, (cocaine) context re-exposure and cocaine + context re-exposure. Investigating systems of co-expressed genes, we also found several validated gene networks with weak to moderate conservation between cocaine/saline self-administering mice and disordered cocaine users/controls. The most conserved hippocampal and VTA gene networks demonstrated substantial overlap (2,029 common genes) and included novel and previously implicated targets of cocaine use/addiction. Lastly, we conducted expression-based phenome-wide association studies of the ninecommonhub genes across conserved gene networks and found that they were associated with dopamine/serotonin function, cocaine self-administration and other relevant mouse traits. Overall, our study identified and characterized homologous transcriptional effects between mouse models of cocaine self-administration and human cocaine use disorder that may serve as a benchmark for future research.
Functional biological paths altered in Alzheimer’s disease: from genes to bile acids
Authors: Gorijala Priyanka , Nho Kwangsik , Risacher Shannon L. , Kaddurah-Daouk Rima , Saykin Andrew J. , Yan Jingwen
Published: February 2020

Large-scale genome wide association studies (GWASs) have been performed in search for risk genes for Alzheimer’s disease (AD). Despite the significant progress, replicability of genetic findings and their translation into targetable mechanisms related to the disease pathogenesis remains a challenge. Given that bile acids have been suggested in recent metabolic studies as potential age-related metabolic factors associated with AD, we integrated genomic and metabolomic data together with heterogeneous biological networks and investigated the potential cascade of effect of genetic variations to proteins, bile acids and ultimately AD brain phenotypes. Particularly, we leveraged functional protein interaction networks and metabolic networks and focused on the genes directly interacting with AD-altered bile acids and their functional regulators. We examined the association of all the SNPs located in those candidate genes with AD brain imaging phenotypes, and identified multiple AD risk SNPs whose downstream genes and bile acids were also found to be altered in AD. These AD related markers span from genetics to metabolomics, forming functional biological paths connecting across multiple-omics layers, and give valuable insights into the underlying mechanism of AD.
DELPHI: accurate deep ensemble model for protein interaction sites prediction
Authors: Li Yiwei , Ilie Lucian
Published: February 2020

Motivation

Proteins usually perform their functions by interacting with other proteins, which is why accurately predicting protein-protein interaction (PPI) binding sites is a fundamental problem. Experimental methods are slow and expensive. Therefore, great efforts are being made towards increasing the performance of computational methods.

Results

We propose DELPHI (DEep Learning Prediction of Highly probable protein Interaction sites), a new sequence-based deep learning suite for PPI binding sites prediction. DELPHI has an ensemble structure with data augmentation and it employs novel features in addition to existing ones. We comprehensively compare DELPHI to nine state-of-the-art programs on five datasets and show that it is more accurate.

Availability

The trained model, source code for training, predicting, and data processing are freely available athttps://github.com/lucian-ilie/DELPHI. All datasets used in this study can be downloaded athttp://www.csd.uwo.ca/~ilie/DELPHI/.

Contact

ilie@uwo.ca
Annotating Gene Ontology terms for protein sequences with the Transformer model
Authors: Duong Dat , Gai Lisa , Uppunda Ankith , Le Don , Eskin Eleazar , Li Jingyi Jessica , Chang Kai-Wei
Published: February 2020

Predicting functions for novel amino acid sequences is a long-standing research problem. The Uniprot database which contains protein sequences annotated with Gene Ontology (GO) terms, is one commonly used training dataset for this problem. Predicting protein functions can then be viewed as a multi-label classification problem where the input is an amino acid sequence and the output is a set of GO terms. Recently, deep convolutional neural network (CNN) models have been introduced to annotate GO terms for protein sequences. However, the CNN architecture can only model close-range interactions between amino acids in a sequence. In this paper, first, we build a novel GO annotation model based on the Transformer neural network. Unlike the CNN architecture, the Transformer models all pairwise interactions for the amino acids within a sequence, and so can capture more relevant information from the sequences. Indeed, we show that our adaptation of Transformer yields higher classification accuracy when compared to the recent CNN-based method DeepGO. Second, we modify our model to take motifs in the protein sequences found by BLAST as additional input features. Our strategy is different from other ensemble approaches that average the outcomes of BLAST-based and machine learning predictors. Third, we integrate into our Transformer the metadata about the protein sequences such as 3D structure and protein-protein interaction (PPI) data. We show that such information can greatly improve the prediction accuracy, especially for rare GO labels.
Estimates of autozygosity through runs of homozygosity in farmed coho salmon
Authors: Yoshida Grazyella M. , Cáceres Pablo , Marín-Nahuelpi Rodrigo , Koop Ben F. , Yáñez José M.
Published: February 2020

The characterization of runs of homozygosity (ROH), using high-density single nucleotide polymorphisms (SNPs) allows inferences to be made about the past demographic history of animal populations and the genomic ROH has become a common approach to characterize the inbreeding. We aimed to analyze and characterize ROH patterns and compare different genomic and pedigree-based methods to estimate the inbreeding coefficient in two pure lines (POP A and B) and one recently admixed line (POP C) of coho salmon breeding nuclei, genotyped using a 200K Affymetrix Axiom®myDesign Custom SNP Array. A large number and greater mean length of ROH were found for the two “pure” lines and the recently admixed line (POP C) showed the lowest number and smaller mean length of ROH. The ROH analysis for different length classes suggests that all three coho salmon lines the genome is largely composed of a high number of short segments (<4 Mb), and for POP C no segment >16 Mb was found. A high variable number of ROH, mean length and inbreeding values across chromosomes; positively the consequence of artificial selection. Pedigree-based inbreeding values tended to underestimate genomic-based inbreeding levels, which in turn varied depending on the method used for estimation. The high positive correlations between different genomic-based inbreeding coefficients suggest that they are consistent and may be more accurate than pedigree-based methods, given that they capture information from past and more recent demographic events, even when there are no pedigree records available.
Fast and accurate assembly of Nanopore reads via progressive error correction and adaptive read selection
Authors: Chen Ying , Nie Fan , Xie Shang-Qian , Zheng Ying-Feng , Bray Thomas , Dai Qi , Wang Yao-Xin , Xing Jian-feng , Huang Zhi-Jian , Wang De-Peng , He Li-Juan , Luo Feng , Wang Jian-Xin , Liu Yi-Zhi , Xiao Chuan-Le
Published: February 2020

Although long Nanopore reads are advantageous inde novogenome assembly, applying Nanopore reads in genomic studies is still hindered by their complex errors. Here, we developed NECAT, an error correction andde novoassembly tool designed to overcome complex errors in Nanopore reads. We proposed an adaptive read selection and two-step progressive method to quickly correct Nanopore reads to high accuracy. We introduced a two-stage assembler to utilize the full length of Nanopore reads. NECAT achieves superior performance in both error correction andde novoassembly of Nanopore reads. NECAT requires only 7,225 CPU hours to assemble a 35X coverage human genome and achieves a 2.28-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line showed an NG50 of 29 Mbp. The high-quality assembly of Nanopore reads can significantly reduce false positives in structure variation detection.
Extreme Genomic Makeover: Evolutionary History of Maternally-transmitted Clam Symbionts
Authors: Perez M , Breusing C , Angers B , Won YJ , Young CR
Published: February 2020

Given their recent switch to a vertically-transmitted intracellular lifestyle, the chemosynthetic bacteria associated with deep-sea vesicomyid clams are an excellent model system to study the processes underlying reductive genome evolution. In this study, we provide the first estimates of the relative contributions of drift, recombination and selection in shaping the ongoing reductive genome evolution in these symbionts. To do so, we compared the genomes of endosymbionts associated with 11 vesicomyid clam species to that of closely related free-living bacteria and their respective hosts’ mitochondria. Our investigation confirmed that neutral evolutionary processes were the dominant driver of reductive genome evolution in this group and highlighted the important role of horizontal gene transfer in mitigating genome erosion. Finally, a genome-wide screen for episodic positive selection across the symbiont phylogeny revealed the pervasive role of selective processes in maintaining symbiont functional integrity.
Phytochemical Content, Antibacterial and Antioxidant Potential of Endemic Plant Anabasis aretioïdes Coss. & Moq. (Chenopodiaceae)
Authors: Senhaji Souad , Lamchouri Fatima , Toufik Hamid
Published: February 2020

This study aims to investigate the biological activities of endemic plant Anabasis aretioïdes harvested in eastern Morocco. Various extracts were prepared from aerial part by aqueous and organic extraction using a Soxhlet and cold maceration. Preliminary phytochemical analysis was carried out on the powder and on the different extracts by standard phytochemical tests, and was confirmed by a quantitative analysis based on the determination of total polyphenols and cathechic tannins. Antioxidant activity was evaluated in vitro by five methods: H2O2, DPPH, ABTS, FRAP, and RP, and the antibacterial activity was carried out by disc diffusion method and the determination of MIC and MBC. Phytochemical screening revealed the presence of cathechic tannins, saponins, and sterols and quantitative analysis showed that Ethyl acetate extract presented the high level of phenolic and cathechic tannins contents (46.79 ± 0.75 µg GAE/mg E and 46.46 ± 0.67 µg CE/mg E). A highest hydrogen peroxide activity was observed in aqueous macerated extract (7.84 ± 0.44%) and the macerated methanol extract has the highest rates for the other four antioxidant activity tests: It was able to reduce DPPH with an IC50 of 52.91 ± 0.24 µg/ml, the highest ABTS•+ radical scavenging capacity (48.99 ± 1.316 µg TE/mg E), it showed also the highest antioxidant activity by the FRAP and reducing power test (99.73 ± 3.570 µg TE/mg E and 72.176 ± 0.540 µg AAE/mg E). Antibacterial screening showed that the maximum zone of inhibition was noted for ethyl acetate extract against Staphylococcus aureus (13.5 mm). The lowest MIC value was obtained with methanolic and macerated methanolic extracts against Protéus mirabilis strain (MIC = 3.125 mg/ml). Principal component analysis showed that the four methods ABTS, DPPH, FRAP, and RP are highly correlated and a correlation between the antioxidant activity and the total phenolic contents of the extracts indicated that phenolic compounds were the dominant contributors to the antioxidant activity of the plant.
Current Approach of Functioning Head and Neck Paragangliomas: Case Report of a Young Patient with Multiple Asynchronous Tumors
Authors: Terrones-Lozano Alejandro , Hernández-Hernández Alan , Nathal Vera Edgar , Guinto-Nishimura Gerardo Yoshiaki , Balderrama-Bañares Jorge Luis , Ramírez-Rentería Claudia , Serna-Soto Judith de la , Reza-Albarran Alfredo Adolfo , Portocarrero-Ortiz Lesly
Published: February 2020

Introduction. Pheochromocytomas (Pheo) and paragangliomas (PGL) are rare neuroendocrine tumors arising from chromaffin cells of the adrenal medulla and from the extra-adrenal autonomic paraganglia, respectively. Only 1–3% of head and neck PGL (HNPGL) show elevated catecholamines, and at least 30% of Pheo and PGL (PCPG) are associated with genetic syndromes caused by germline mutations in tumor suppressor genes and proto-oncogenes. Clinical Case. A 33-year-old man with a past medical history of resection of an abdominal PGL at the age of eleven underwent a CT scan after a mild traumatic brain injury revealing an incidental brain tumor. The diagnosis of a functioning PGL was made, and further testing was undertaken with a PET-CT with 68Ga-DOTATATE, SPECT-CT 131-MIBG, and genetic testing. Discussion and Conclusion. The usual clinical presentation of functioning PCPG includes paroxistic hypertension, headache, and diaphoresis, sometimes with a suggestive family history in 30–40% of cases. Only 20% of PGL are located in head and neck, of which only 1–3% will show elevated catecholamines. Metastatic disease is present in up to 50% of cases, usually associated with a hereditary germline mutation. However, different phenotypes can be observed depending on such germline mutations. Genetic testing is important in patients with PCPG since 31% will present a germline mutation. In this particular patient, an SDHB gene mutation was revealed, which can drastically influence the follow-up plan and the genetic counsel offered. A multidisciplinary approach is mandatory for every patient presenting with PCPG.
The correlation between score-based protocol for equine joint assessment and subsequent arthroscopic intervention outcomes
Authors: Silva Marilene Machado , Hagen Stefano Carlo Filippo , Vendruscolo Cynthia Do Prado , Baccarin Raquel Yvonne Arantes , Spagnolo Júlio David , Yamada Ana Lúcia Miluzzi , Stievani Fernanda De Castro , Correia da Silva Luis Claúdio Lopes
Published: February 2020

This study aimed to grade joint abnormalities in horses submitted to therapeutic arthroscopy using score-based protocols for equine joint assessment, correlated with arthroscopic treatment outcomes and owner satisfaction. In this prospective study, we evaluated 126 joints of athletic horses referred for arthroscopy. The joints were scored according to findings of medical history and physical, radiographic, ultrasonographic and arthroscopic examination. Lameness, positive response to flexion test and decreased maximum joint flexion angle were detected in more than 50% of joints. Soft tissue swelling, sclerosis, subchondral bone osteolysis and single osteochondral fragments were the most common radiographic findings. Ultrasonographic examination revealed changes in synovial fluid volume and appearance, and subchondral bone irregularities. Increased vascularity of the synovial villi, chondral fibrillation, chondral fissures and superficial cartilage erosions were the most significant arthroscopic findings. The approaches that demonstrated greater sensitivity and correlation with treatment outcome and owner satisfaction were medical history, ultrasonographic and arthroscopic examination. The scoring protocol employed to grade joint abnormalities enabled the creation of a joint score system for the objective assessment, thus determining the most frequent findings and establishing an injury severity score for each joint.
Radiographic and ultrasonographic imaging of a dystrophic mineralization on the oblique sesamoidean ligament in a jumping horse. Twenty months follow-up
Authors: Marsiglia Marilia Ferrari , Yamada Ana Lucia Miluzzi , Pinheiro Marcelo , Marcondes Geissiane Moraes , Paretsis Nicole Fidalgo , Da Silva Luis Cláudio Lopes Correia
Published: February 2020

Mineralization of the anatomical structures involved in the limb movement of horses has been reported to induce lameness and interfere with athletic performance. A 4-year-old jumping horse in sport activity was reported at Veterinary Hospital of University of São Paulo, with mild lameness and a mineralized oblique distal sesamoidean ligament (ODSL) of the left forelimb, revealed by a purchase radiographic and ultrasound examination. Mineralization is more common in tendons than ligaments. This report calls for attention to these structures when performing image exams, even in mild lameness. Long-term favorable follow-up by ultrasonographic and radiographic examination showed that the severe ligament injury in this case did not decrease the athletic activity until the present day.
Notas sobre poemas e imagens
Authors: Grazioli Fabiano Tadeu
Published: February 2020

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Festa da Raspa
Authors: Riscado Caio Arnizaut
Published: February 2020

A partir de poemas do livro haverá festa com o que restar (2018) o artigo apresenta uma leitura da produção bixa de Francisco Mallmann e relaciona seus gestos com os de outras autoras como, por exemplo, Ana Martins Marques e Maria Isabel Iorio. Para localizar a produção dissidente de Mallmann, o texto utiliza como referência o conceito de precariedade, articulado por Judith Butler, e passagens do pensamento de Paco Vidarte sobre a formulação de uma ética bixa. Além disso, propõe a festa como prática de autocuidado e possibilidade de celebração da vida.
A ilha
Authors: Almeida Daniel Manzoni de
Published: February 2020

Em 2018, publiquei o livro de ficção experimental “SetList”. Aqui continuou expandido a experimentação literária iniciada no romance com a escrita de mais um trecho (final?) da história. A identidade de um sujeito é um arquivo? A partir dessa pergunta escrevi uma pequena peça teatral que conta a história de Vicente um jovem homossexual que está intrigado com a morte do ex namorado ocorrida três anos atrás. O detalhe é que seu ex namorado foi irmão do candidato à reeleição da presidência da República do Brasil pelo partido ultraconservador comandado pela autoritária matriarca da família que é capaz de tudo, por meio de jogos de mídia e notícias falsas, para manter a família no poder político da nação brasileira.
Violências contra pergonagens travestis na literatura brasileira do século XX
Authors: Fernandes Carlos Eduardo Albuquerque
Published: February 2020

O presente trabalho discute sobre a representação da violência na construção de personagens centrais travestis na literatura brasileira do século XX. Faremos menção a alguns contos e romances brasileiros do século XX, para discutir a condição de subalternidade e abjeção dessas protagonistas a partir das violências que sofrem.  Nos baseamos em  pelo menos três aspectos teóricos para a análise em questão: estudos antropológicos sobre a experiência da travestilidade no Brasil, sobretudo em Silva (2007), Benedetti (2007) e Kulick (2008), os estudos culturais e de gênero, a partir de Butler (2010) e Spivak (2010), bem como a partir dos estudos literários de Fernandes (2015) e Silva (2010). O objetivo é chegar a um argumento crítico sobre a recorrente situação de subalternidade das protagonistas travestis na literatura brasileira, corroborando uma possível relação de mimetização ou de realismo nessa faceta da literatura homoerótica com o que se verifica no âmago de sociedades patriarcais e heteronormativas.
Figuras ex-cêntricas e uma heterotopia de desvio
Authors: Barili Renan Augusto
Published: February 2020

O presente artigo objetiva discutir o deslocamento de personagens marginais para o centro da trama do romance Pão de açúcar (2018), de Afonso Reis Cabral. Contudo, mesmo com esse movimento, percebe-se a inserção dessas personagens “ex-cêntricas” dentro de espaços que podem ser lidos como “heterotopias de desvio”, locais que enclausuram e retiram de circulação os seres que se afastam das normas e das convenções sociais que são impostas como obrigatórias.
A relação entre Eliná e Dona Lair em “Os objetos”, de Dinorath do Valle
Authors: Ramos Pâmela Coca dos Santos
Published: February 2020

Este artigo analisa a relação entre as personagens principais do conto "Os objetos", um dos finalistas do Concurso de Contos Eróticos da Revista Status em 1977 e publicado na coletânea de contos Idade da Cobra Lascada, de Dinorath do Valle em 1982. Este conto narra o conflito que se estabelece quando Eliná, pobre e assediada pelo pai em sua casa, recebe oferta de moradia de sua professora, Dona Lair, que também a assedia quando a menina, de 13 anos, visita sua casa.
A Arte é divina demais para ser normal
Authors: Thürler Djalma
Published: February 2020

Os autores discutem, dentro da cena transformista, o que seriam as Drag Queers, aquelas que buscariam performar a drag além da caricatura do feminino, trazendo em suas performances críticas sobre a norma, a normalidade e a normalização da própria cena, enquanto estética colonial, mas, também, marcas sociais da abjeção, da marginalidade e da invisibilidade. A drag queer, se utiliza do feio, do anormal e do monstruoso como positivação de subjetividades marginalizadas de quem são, quase sempre, representantes e desfruta da política queer enquanto modo de autoafirmação.
A dupla colonização da mulher nos romances O Alegre Canto da Perdiz, de Paulina Chiziane, e Jesusalém, de Mia Couto
Authors: Carvalho Keiliane Da Silva Araújo
Published: February 2020

O trabalho propõe uma reflexão concernente à dupla colonização da mulher, nos romances O Alegre Canto da Perdiz (2008), de Paulina Chiziane e Jesusalém (2009), de Mia Couto. Para tanto, as teorizações formuladas por Cristian Pagoto (2007); Thomas Bonnici (2000; 2005; 2007); Michele Perrot (2007); Deepika Bahri (2013); Katryn Woodword (2014), entre outras, servem como base de sustentação.
Amor e erotismo na obra Do desejo, de Hilda Hilst
Authors: Rosário Maria Do
Published: February 2020

O objetivo deste artigo é discorrer sobre os temas do amor e do erotismo na obra Do desejo, da escritora brasileira Hilda Hilst, publicada em 1992. Na referida coletânea de poemas, vislumbra-se a voz da poeta e da mulher, que reivindica sua posição como sujeito de seu próprio corpo e de seu próprio discurso, em um movimento transgressor da linguagem.
Em chave trans
Authors: Jimenez Rafael M. Merida
Published: February 2020

Neste trabalho, após traçar uma breve genealogia dos estudos trans, Rafael Mérida Jiménez mostra as significações ideológicas das representações de pessoas trans na história do século XX, assim como analisa as modalidades de autobiografias escritas por pessoas trans durante a segunda metade do século passado.
A Justiça Parcial e a Ganância enquanto virtude e vício do caráter na Ética a Nicômaco: ação interpessoal, emoção e prazer
Authors: Sousa André Luiz Cruz
Published: February 2020

The aim of this paper is to study a set of three issues related to the understanding of partial justice and partial injustice as character dispositions, namely the distinctive circumstance of action, the emotion involved therein and the pleasure or pain following it. Those points are treated in a relatively obscure way by Aristotle, especially in comparison with their treatment in the expositions of other character virtues in the Nicomachean Ethics. Building on the expression ‘capacity towards the other’ (δύναμις ἐν τῷ πρὸς ἕτερον), the paper highlights the interpersonal nature of the circumstances of just and unjust actions, and points how such nature is directly related to notions such as ‘profit’ (κέρδος) or ‘getting more’(πλεονεκτεῖν) as well as to the unusual conception of excess, defect and intermediacy in Nicomachean Ethics Book V. The interpersonal nature of just and unjust actions works also as the starting-point for the interpretation both of the pleasure briefly mentioned in 1130b4 as characterizing the greedy person and of the emotion involved in acting justly or greedy, which is mentioned in an extremely elliptical way in 1130b1-2: the paper argues, on the one hand, that the pleasure felt in acting justly or unjustly concerns not only the goods that are the object of just or unjust interactions, but also the way such interactions affect the people involved; on the other hand, it argues that the emotion actuated in just or unjust interactions relates to the agent’s concern or lack of concern with the good of those people.
Reconhecimento contábil nas operações em florestas nativas: o Caso Agrocortex
Authors: Graça Phillemon Telêmaco da , Pelucio Grecco Marta Cristina , Sales George Andre Willrich
Published: February 2020

O objetivo desse artigo foi analisar e propor uma solução para o reconhecimento contábil de operações em florestas nativas com base no caso Agrocortex. A empresa Agrocortex explora uma floresta nativa na região amazônica e sua operação está fora do escopo das normas contábeis, por isso suas demonstrações contábeis foram elaboradas sem reconhecimento das florestas nativas. Diante disso foi construída uma proposta de solução, pautada no CPC 23 - Políticas Contábeis, Mudança de Estimativa e Retificação de Erro, com duas vertentes: (1) elaboração de uma política contábil para que seja procedido o reconhecimento contábil das operações em florestas nativas de maneira semelhante às florestas plantadas, em conformidade com o CPC 29, com mensuração ao valor justo; e (2) elaboração do reconhecimento contábil nas operações em florestas nativas, por meio de manejo florestal sustentável, nas demonstrações contábeis. A segunda vertente é uma sugestão aos normatizadores e entidades da classe contábil, para que analisem, com base no caso demonstrado, os aspectos teóricos do reconhecimento contábil nas operações em florestas nativas, por meio de manejo florestal sustentável.
Como o volume de negociação reage ao sentimento do investidor?
Authors: Marschner Paulo Fernando , Ceretta Paulo Sergio
Published: February 2020

A economia comportamental ampliou a forma de entender as negociações no mercado de ações. Investidores com diferentes expectativas de otimismo (ou pessimismo) e confiança tendem a negociar de formas distintas no curto e longo prazo. Além disso, seus vieses comportamentais tendem a ser uma das causas subjacentes da não linearidade e da assimetria existente no mercado de ações, fator que dificulta uma análise precisa dessa relação. Por meio de uma abordagem não linear de atrasos distribuídos autorregressivos assimétricos foram analisadas detalhadamente as conexões não lineares e assimétricas de curto e longo prazo entre o sentimento do investidor e o volume de negociação no mercado americano entre 2004 a 2017. Os resultados, além de confirmarem que os vieses comportamentais influenciam o declínio do volume de negócios, indicam que o volume de negociação reage rapidamente à presença de investidores com menor nível de confiança e que essa relação é profundamente assimétrica no longo prazo. A partir destas evidências é presumível que em momentos de baixa liquidez a confiança dos investidores decline e sua aversão ao risco aumente, e por isso diminuam suas negociações para evitar resultados negativos.
The opportunistic approach of the Positive Accounting Theory (PAT) fails to explain choices made at OGX: An anomalous situation?
Authors: Silva Adolfo Henrique Coutinho e , Sancovschi Moacir , Santos Ariane Gabriela Chagas dos
Published: February 2020

This paper has two objectives: (1) to demonstrate that the main accounting choices made by accountants and managers of OGX Company throughout its full business life cycle were not opportunistic, as often suggested by the hypothesis of Positive Accounting Theory; and (2) to demonstrate that these accounting choices may be better explained by the Theory of Corporate Scandals, by the Monitoring Hypothesis and by the Corporate Reputation Hypothesis. The research was conducted using a longitudinal case study approach, from 2006-2015, in order to identify visible accounting decisions in annual financial statements reports. It was found that the analyzed Company had the incentives to preform opportunistic accounting choices, such as the ones predicted by the PAT hypothesis and had also done through several situations in its business life cycle that could have influenced it to perform opportunistic accounting choices. However, there is no evidence that the Company ever made use of either opportunistic increasing-income accounting changes to impact their financial debt-covenants and bonus plan, or decreasing-income accounting to avoid government intervention, as suggested by the opportunistic approach of PAT hypothesis.
"Atenta como uma antena"
Authors: Lessa Maria Silva Prado
Published: February 2020

“Arte poética II” de Sophia de Mello Breyner Andresen, como os demais textos da sequência homônima, apresenta uma teoria e uma interpretação da poesia que revelam sobretudo uma visão de mundo. Tratando-a não apenas como objeto sobre o qual tece suas considerações, Sophia transforma a poesia em um sujeito de exigências e pedidos lhe dirigidos, afirmando que “é da obstinação sem tréguas que a poesia exige que nasce o ‘obstinado rigor’ do poema”. Entre as demandas, sobressai o de que esteja voltada para o “universo” e, em formulação que se torna uma espécie de mote de sua produção, que “viva atenta como uma antena”. A ideia de que o poeta deve estar atento perpassará, assim, sua obra poética. A escuta emerge não apenas como uma “vibração com o exterior”, mas como algo que se dá antes por um ímpeto ou desejo de escutar. Como condição fundamental para a escrita, tal desejo tomará forma, em alguns poemas, em termos de um pedido, de uma prece ou, mais especificamente, de uma invocação a uma Musa. Apresenta-se, assim, um momento anterior à escuta e emerge, no rol das três ações andresenianas – escutar, nomear e fazer paisagens, como aponta Silvina Rodrigues Lopes –, uma quarta: invocar – isto é, pedir para escutar. Dedicamo-nos, portanto, a investigar as relações entre escuta e invocação que se apresentam num poema como “Musa”, de Livro Sexto (1962).
A voz e a vez da redação
Authors: Kneipp Valquíria Aparecida Passos
Published: February 2020

O cineasta João Batista de Andrade, apesar de já ser premiado e reconhecido, nos anos setenta atuou como repórter e diretor de documentários, em duas emissoras brasileiras. Primeiro foi na TV Cultura, produzindo reportagens diárias para o telejornal Hora da Notícia, e depois no Globo Repórter e na direção de reportagens especiais para diversos programas da emissora. A entrevista dele revela detalhes da passagem dos cineastas, pela televisão brasileira. Um momento histórico e significativo para a memória do telejornalismo, porque revela a influência dos cineastas e documentaristas no telejornalismo. João Batista de Andrade concedeu entrevista, no dia 12 de dezembro de 2006, na cidade de São Paulo, quando ocupava o cargo de Secretário Estadual de Cultura.
O diálogo como concepção para a entrevista jornalística retextualizada na legenda fotográfica
Authors: Santos Marcelo De Franceschi dos
Published: February 2020

Propor o diálogo de Freire (2016) como concepção para legenda de fotografias de entrevista é o objetivo deste artigo. Para isso, realiza uma revisão bibliográfica sobre a relação entre texto e fotografia, sintetizando quatro tipos de legenda: indicativa, descritiva, narrativa, e aditiva. Em seguida, defende juntamente a outros autores que a entrevista jornalística não pode ser confundida com história oral. Por fim, aponta que a entrevista, tendo como base o diálogo e a problematização, ao ser retextualizada na legenda aditiva, pode contribuir para a conscientização do fotografado e dos leitores.
Controle e “desvios de conduta” no Judiciário brasileiro
Authors: Vieira Moisés Lazzaretti , Engelmann Fabiano
Published: February 2020

O artigo esboça elementos para analisar os mecanismos de controle dos agentes judiciais no âmbito do poder Judiciário. Através de análise documental procuramos evidenciar as dimensões históricas e políticas da construção da ideia de controle sobre as atividades da magistratura com foco na disposição institucional pós-1988 e, particularmente, nas mudanças instituídas com a atuação do Conselho Nacional de Justiça. Procuramos relacionar a emergência de inovações jurídico-formais no contexto da relação entre os Poderes, enfatizando a dimensão corporativa e a atuação do Conselho da Magistratura. Para além dos limites das abordagens da problemática do controle da magistratura, a análise dos dados obtidos permitiu esboçar elementos sobre o perfil dos casos de “desvio de conduta” de magistrados, bem como, apontar os limites das fontes públicas disponíveis para apoiar esse tipo de estudo.