bluuebunny/crossref_metadata_2025_split huggingface dataset:
Asymptomatic Spinal Cord Compression: Is Surgery Necessary to Return to Play
Authors: Lee Yunsoo , Selverian Stephen , Hsu Wellington K , Watkins Robert G , Vaccaro Alexander R , Hecht Andrew C 
Published: November 2020

Abstract
Advising athletes with asymptomatic cervical canal stenosis on their return to active play is a topic of considerable debate, with no definitive guidelines in place. Once cervical canal stenosis is identified, often through imaging following other injuries, it is difficult to predict the risk of future injury upon return to play in both contact and collision sports. Consequently, the decision can be a complicated one for the athlete, family, and physician alike. In this article, we identify radiographical and magnetic resonance imaging (MRI)-based criteria that may distinguish athletes “at-risk” for more severe consequences due to asymptomatic cervical canal stenosis from those who are safe to return to play. Using a Torg-Pavlov ratio <0.7 and MRI metrics, namely a minimal disc-level canal diameter <8 mm, a cord-to-canal area ratio >0.8, or space available for the cord <1.2 mm, can help when making these difficult decisions. Counseling can be a critical asset to patients with cervical stenosis who have had a previous episode of cervical cord neuropraxia, especially when they are involved in high-risk sports such as American football and rugby. We believe that while this remains an area of continued concern and controversy, improved MRI criteria will be a useful springboard for further studies, especially in the elite athlete population.
Cerebrospinal Fluid-Venous Fistulas: A Systematic Review and Examination of Individual Patient Data
Authors: Shlobin Nathan A , Shah Vinil N , Chin Cynthia T , Dillon William P , Tan Lee A 
Published: November 2020

Abstract

BACKGROUND
Spontaneous intracranial hypotension (SIH) is usually caused by a spinal cerebrospinal fluid (CSF) leak. CSF-venous fistula is an underdiagnosed cause of spinal CSF leak, as it is challenging to identify on myelography.

OBJECTIVE
To review existing literature to summarize common presentations, diagnostic imaging modalities, and current treatment strategies for CSF-venous fistulas.

METHODS
We conducted a systematic review using PubMed, Embase, Scopus, and Web of Science databases to identify studies discussing CSF-venous fistulas. Titles and abstracts were screened. Studies meeting prespecified inclusion criteria were reviewed in full.

RESULTS
Of 180 articles identified, 16 articles met inclusion criteria. Individual patient data was acquired from 7 studies reporting on 18 patients. CSF-venous fistula most frequently presented as positional headache. Digital subtraction myelography provided greatest detection of CSF-venous fistula in the lateral decubitus position and detected CSF-venous fistula in all individual patient cases. Dynamic computed tomography (CT) myelogram enabled detection and differentiation of CSF-venous fistulas from low-flow epidural leaks. The majority of fistulas were in the thoracic spine and slightly more common on the right. Epidural blood patch (EBP) provided temporary or no relief in all individual patients. Resolution or improvement of clinical symptoms and radiologic normalization were observed in all surgically treated patients.

CONCLUSION
Although rare, CSF-venous fistula is an important cause of spinal CSF leak contributing to SIH. Dynamic CT myelogram and digital subtraction myelography, particularly in the lateral decubitus position, are the most accurate and effective diagnostic imaging modalities. EBPs often provide only transient relief, while surgical management is preferred.
More is different: how aggregation turns on the light
Authors: Ball Philip 
Published: November 2020

Abstract
The reductionist approach to science seeks to understand the behaviour of systems by studying their individual components. It has been an enormously productive approach, but it is also widely acknowledged now that in some systems the behaviour of interest is an emergent property that cannot be discerned in the separate parts. Biology is replete with such examples, from the flocking of birds to the way metabolic processes in cells rely on a dynamic interplay of proteins and other components.
Yet molecular systems do not have to be particularly complex before their properties become more than the sum of the parts. A classic example is the appearance of bulk-like metallic behaviour in small clusters of metal atoms only once they exceed a certain critical size. One of the most striking instances became apparent in 2001, when Ben Zhong Tang of the Hong Kong University of Science and Technology and his co-workers found that heterocyclic silicon-containing molecules called siloles become luminescent as nanoscopic aggregates even though the individual molecules in dilute solution do not emit light [1]. This looked like the opposite of the well-known phenomenon of concentration quenching, in which energy transfer between fluorescent (generally organic) molecules quenches the emission, an effect explained in 1955 [2]. Aggregation-induced ‘switching off’ is intuitively understandable, but ‘switching on’ due to aggregation was more surprising.
Yet this effect of ‘aggregation-induced emission’ (AIE), as Tang and colleagues called it, was apparently seen, but not understood, much earlier [3]. In the 1850s, George Stokes noted that some inorganic complexes were fluorescent in the condensed, solid state but not in solution. At first, AIE was seen as a curiosity and deemed likely to be rare. However, subsequent research has shown not only that it is a rather common effect but also that it can be considered just one manifestation of a wide range of behaviours that arise from aggregation—leading to the proposed field of ‘aggregate science’, manifesting at the supramolecular level of small clusters or groups of molecules held together by relatively weak interactions. The field might be considered to illustrate George Whitesides’ notion of a chemistry ‘beyond the molecule’ [4], which bridges disciplines ranging from colloid science to crystal growth, nanotechnology, liquid crystals, photochemistry and molecular biology. At the same time, it echoes the famous insight of physicist Philip Anderson about emergent phenomena and the hierarchical nature of science: ‘More is different’ [5]. An ability to switch properties on and off by controlling intermolecular interactions and aggregation suggests various applications, from optical device technologies to targeted drugs for cancer therapy [6].
NSR spoke to Ben Zhong Tang about the origins and possibilities of the field.
Cure of Limb-Threatening XDR Pseudomonas aeruginosa Infection: Combining Genome Sequencing, Therapeutic Drug Level Monitoring, and Surgical Debridement
Authors: Narayanasamy Shanti , Nation Roger L , Mahony Andrew A , Grayson M Lindsay , Kwong Jason C , Sherry Norelle L , Khumra Sharmila , Ellis Andrew G , Frauman Albert G , Holmes Natasha E 
Published: November 2020

Abstract
We describe a case of limb-threatening osteomyelitis and metalware infection with carbapenemase-producing extensively drug-resistant Pseudomonas aeruginosa successfully cured with aggressive surgical debridement and combined intravenous fosfomycin and colistin. Real-time therapeutic drug monitoring was used to maximize probability of efficacy and minimize potential for toxicity.
Diagnostic and Prognostic Utility Compared Among Different Sepsis Scoring Systems in Adult Patients With Sepsis in Thailand: A Prospective Cohort Study
Authors: Pairattanakorn Prat , Angkasekwinai Nasikarn , Sirijatuphat Rujipas , Wangchinda Walaiporn , Tancharoen Lalita , Thamlikitkul Visanu 
Published: November 2020

Abstract

Background
The diagnostic and prognostic utility of various sepsis scores varied among different cohorts and settings.

Methods
A prospective cohort study in adult patients with sepsis at Siriraj Hospital (Bangkok, Thailand) was conducted during January to July 2019. The performance of sepsis assessments, including systemic inflammatory response syndrome (SIRS) score, sequential organ failure assessment (SOFA) score, quick sepsis-related organ failure assessment (qSOFA) score, modified early warning score (MEWS), and national early warning score (NEWS), for sepsis detection and mortality prediction were compared with agreement between 2 infectious disease (ID) specialists to determine their sepsis and septic shock status as the reference standard.

Results
Among the 470 subjects included in this study, 206 patients (43.8%) were determined by 2 ID specialists to have sepsis. Systemic inflammatory response syndrome ≥2, qSOFA ≥2, and NEWS ≥5 yielded the highest sensitivity (93.2%), specificity (81.3%), and accuracy (72.6%), respectively, for detecting sepsis. The SIRS ≥2 had the highest sensitivity (97.8%), whereas qSOFA ≥2 had the highest specificity (61%) and accuracy (69.7%) for predicting mortality among sepsis patients. Receiver operating characteristic (ROC) curve showed MEWS to have the highest discriminatory power for sepsis detection (area under the ROC curve [AUROC], 0.79; 95% confidence interval [CI], 0.74–0.83), whereas SOFA had the highest discriminatory power for predicting hospital mortality (AUROC, 0.76; 95% CI, 0.69–0.79).

Conclusions
The NEWS ≥5 and qSOFA ≥2 were the most accurate scoring systems for sepsis detection and mortality prediction, respectively. Each scoring system is useful for different specific purposes relative to early detection and mortality prediction in sepsis patients.
Clinical Symptoms Among Ambulatory Patients Tested for SARS-CoV-2
Authors: Chung Jessie R , Kim Sara S , Jackson Michael L , Jackson Lisa A , Belongia Edward A , King Jennifer P , Zimmerman Richard K , Nowalk Mary Patricia , Martin Emily T , Monto Arnold S , Gaglani Manjusha , Smith Michael E , Patel Manish , Flannery Brendan 
Published: November 2020

Abstract
We compared symptoms and characteristics of 4961 ambulatory patients with and without laboratory-confirmed severe acute respiratory syndrome coronavirus 2 infection. Findings indicate that clinical symptoms alone would be insufficient to distinguish between coronavirus disease 2019 and other respiratory infections (eg, influenza) and/or to evaluate the effects of preventive interventions (eg, vaccinations).
High-resolution mapping and characterization of epitopes in COVID-19 patients
Authors: Haynes Winston A. , Kamath Kathy , Bozekowski Joel , Baum-Jones Elisabeth , Campbell Melissa , Casanovas-Massana Arnau , Daugherty Patrick S. , Dela Cruz Charles S. , Dhal Abhilash , Farhadian Shelli F. , Fitzgibbons Lynn , Fournier John , Jhatro Michael , Jordan Gregory , Kessler Debra , Klein Jon , Lucas Carolina , Luchsinger Larry L. , Martinez Brian , Muenker Mary C. , Pischel Lauren , Reifert Jack , Sawyer Jaymie R. , Waitz Rebecca , Wunder Elsio A. , Zhang Minlu ,   Yale IMPACT Team, Iwasaki Akiko , Ko Albert I. , Shon John C. 
Published: November 2020

AbstractFine scale delineation of epitopes recognized by the antibody response to SARS-CoV-2 infection will be critical to understanding disease heterogeneity and informing development of safe and effective vaccines and therapeutics. The Serum Epitope Repertoire Analysis (SERA) platform leverages a high diversity random bacterial display library to identify epitope binding specificities with single amino acid resolution. We applied SERA broadly, across human, viral and viral strain proteomes in multiple cohorts with a wide range of outcomes from SARS-CoV-2 infection. We identify dominant epitope motifs and profiles which effectively classify COVID-19, distinguish mild from severe disease, and relate to neutralization activity. We identify a repertoire of epitopes shared by SARS-CoV-2 and endemic human coronaviruses and determine that a region of amino acid sequence identity shared by the SARS-CoV-2 furin cleavage site and the host protein ENaC-alpha is a potential cross-reactive epitope. Finally, we observe decreased epitope signal for mutant strains which points to reduced antibody response to mutant SARS-CoV-2. Together, these findings indicate that SERA enables high resolution of antibody epitopes that can inform data-driven design and target selection for COVID-19 diagnostics, therapeutics and vaccines.
Skin Lesion Classification Using Convolutional Neural Network for Melanoma Recognition
Authors: Dutta Aishwariya , Hasan Md. Kamrul , Ahmad Mohiuddin 
Published: November 2020

AbstractSkin cancer, also known as melanoma, is generally diagnosed visually from the dermoscopic images, which is a tedious and time-consuming task for the dermatologist. Such a visual assessment, via the naked eye for skin cancers, is a challenging and arduous due to different artifacts such as low contrast, various noise, presence of hair, fiber, and air bubbles, etc. This article proposes a robust and automatic framework for the Skin Lesion Classification (SLC), where we have integrated image augmentation, Deep Convolutional Neural Network (DCNN), and transfer learning. The proposed framework was trained and tested on publicly available IEEE International Symposium on Biomedical Imaging (ISBI)-2017 dataset. The obtained average area under the receiver operating characteristic curve (AUC), recall, precision, and F1-score are respectively 0.87, 0.73, 0.76, and 0.74 for the SLC. Our experimental studies for lesion classification demonstrate that the proposed approach can successfully distinguish skin cancer with a high degree of accuracy, which has the capability of skin lesion identification for melanoma recognition.
Translatomic profiling of the acute stress response: It’s a TRAP
Authors: von Ziegler Lukas , Bohacek Johannes , Germain Pierre-Luc 
Published: November 2020

AbstractThe impact of stress on gene expression in different cell types of the brain remains poorly characterized. Three pioneering studies have recently used translating ribosome affinity purification followed by RNA sequencing (TRAP-seq) to assess the response to stress in CA3 pyramidal neurons of the hippocampus. The results suggest that acute stress alters the translation of thousands of genes in CA3 pyramidal neurons, and that this response is strongly modulated by factors such as sex, genotype and a history of early life stress. However, our reanalysis of these datasets leads to different conclusions. We confirm that acute stress induces robust translational changes in a small set of genes. However, we found no evidence that either early life stress or sex have an effect on gene translation induced by acute stress. Our findings highlight the need for additional studies with adequate sample sizes and proper methods of analysis to assess the impact of stress across cell types in the brain.
Optimization of Spectral Library Size Improves DIA-MS Proteome Coverage
Authors: Ge Weigang , Liang Xiao , Zhang Fangfei , Xu Luang , Xiang Nan , Sun Rui , Liu Wei , Xue Zhangzhi , Yi Xiao , Wang Bo , Zhu Jiang , Lu Cong , Zhan Xiaolu , Chen Lirong , Wu Yan , Zheng Zhiguo , Gong Wangang , Wu Qijun , Yu Jiekai , Ye Zhaoming , Teng Xiaodong , Huang Shiang , Zheng Shu , Liu Tong , Yuan Chunhui , Guo Tiannan 
Published: November 2020

AbstractEfficient peptide and protein identification from data-independent acquisition mass spectrometric (DIA-MS) data typically rely on an experiment-specific spectral library with a suitable size. Here, we report a computational strategy for optimizing the spectral library for a specific DIA dataset based on a comprehensive spectral library, which is accomplished bya priorianalysis of the DIA dataset. This strategy achieved up to 44.7% increase in peptide identification and 38.1% increase in protein identification in the test dataset of six colorectal tumor samples compared with the comprehensive pan-human library strategy. We further applied this strategy to 389 carcinoma samples from 15 tumor datasets and observed up to 39.2% increase in peptide identification and 19.0% increase in protein identification. In summary, we present a computational strategy for spectral library size optimization to achieve deeper proteome coverage of DIA-MS data.
SequenceBouncer: A method to remove outlier entries from a multiple sequence alignment
Authors: Dunn Cory D. 
Published: November 2020

AbstractPhylogenetic analyses can take advantage of multiple sequence alignments as input. These alignments typically consist of homologous nucleic acid or protein sequences, and the inclusion of outlier or aberrant sequences can compromise downstream analyses. Here, I describe a program, SequenceBouncer, that uses the Shannon entropy values of alignment columns to identify and remove outlier entries in a manner responsive to overall alignment context. I demonstrate the utility of this software using alignments of mammalian reference mitochondrial genomes, bird cytochromecoxidase-derived sequence barcodes, and COVID-19 sequences.
Using seasonal genomic changes to understand historical adaptation: parallel selection on stickleback in highly-variable estuaries
Authors: Garcia-Elfring Alan , Paccard Antoine , Thurman Timothy J. , Wasserman Ben A. , Palkovacs Eric P. , Hendry Andrew P. , Barrett Rowan D. H. 
Published: November 2020

AbstractParallel evolution is considered strong evidence for natural selection. However, few studies have investigated the process of parallel selection as it plays out in real time. The common approach is to study historical signatures of selection in populations already well adapted to different environments. Here, to document selection in action under natural conditions, we study six populations of threespine stickleback (Gasterosteus aculeatus) inhabiting bar-built estuaries that undergo seasonal cycles of environmental changes. Estuaries are periodically isolated from the ocean due to sandbar formation during dry summer months, with concurrent environmental shifts that resemble the long-term changes associated with postglacial colonization of freshwater habitats by marine populations. We used pooled whole-genome sequencing (Pool-WGS) to track seasonal allele frequency changes in these populations and search for signatures of natural selection. We found consistent changes in allele frequency across estuaries, suggesting a potential role for parallel selection. Functional enrichment among candidate genes included transmembrane ion transport and calcium binding, which are important for osmoregulation and ion balance. The genomic changes that occur in threespine stickleback from bar-built estuaries could provide a glimpse into the early stages of adaptation that have occurred in many historical marine to freshwater transitions.
SABRE populates ER domains essential for cell plate maturation and cell expansion influencing cell and tissue patterning
Authors: Cheng Xiaohang , Bezanilla Magdalena 
Published: November 2020

AbstractThe SABRE protein, originally identified in plants, is found throughout eukaryotes. In plants, SABRE has been implicated in cell expansion, division plane orientation and planar polarity. However, how SABRE mediates these processes remains an open question. Here, we have taken advantage of the fact that the bryophytePhyscomitrium patenshas a single copy ofSABRE, is an excellent model for cell biology and is readily amenable to precise genetic alterations to investigate SABRE’s mechanism of action. We discovered that SABRE null mutants were stunted in both polarized growing and diffusely growing tissues, similar to reported phenotypes in seed plants. However, in polarized growing cells, we observed significant delays in cell plate formation and sometimes catastrophic failures in cell division. We generated a functional SABRE fluorescent fusion protein and determined that it forms dynamic puncta on regions of the endoplasmic reticulum (ER) both in the cytoplasm during interphase and at the new cell plate during division. In the absence ofSABRE, ER morphology was severely compromised with large aggregates accumulating in the cytoplasm and abnormal buckling along the developing cell plate late in cytokinesis. In fact, SABRE and the ER maximally accumulated on the developing plate specifically during cell plate maturation, coincident with the timing of the onset of failures in cell plate formation in cells lacking SABRE. Further we discovered that callose deposition is delayed inΔsabrecells, and in cells that failed to divide, abnormal callose accumulations formed at the cell plate. Our findings demonstrated that SABRE functions by influencing the ER and callose deposition, revealing a surprising and essential role for the ER in cell plate maturation. Given that SABRE is conserved, understanding how SABRE influences cell and tissue patterning has profound significance across eukaryotes.
An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology
Authors: Young Colin , Meng Sarah , Moshiri Niema 
Published: November 2020

AbstractThe use of computational techniques to analyze viral sequence data and ultimately inform public health intervention has become increasingly common in the realm of epidemiology. These methods typically attempt to make epidemiological inferences based on multiple sequence alignments and phylogenies estimated from the raw sequence data. Like all estimation techniques, multiple sequence alignment and phylogenetic inference tools are error-prone, and the impacts of such imperfections on downstream epidemiological inferences are poorly understood. To address this, we executed multiple commonly-used workflows for conducting viral phylogenetic analyses on simulated viral sequence data modeling HIV, HCV, and Ebola, and we computed multiple methods of accuracy motivated by transmission clustering techniques. For multiple sequence alignment, MAFFT consistently outperformed MUSCLE and Clustal Omega in both accuracy and runtime. For phylogenetic inference, FastTree 2, IQ-TREE, RAxML-NG, and PhyML had similar topological accuracies, but branch lengths and pairwise distances were consistently most accurate in phylogenies inferred by RAxML-NG. However, FastTree 2 was orders of magnitude faster than the other tools, and when the other tools were used to optimize branch lengths along a fixed topology provided by FastTree 2 (i.e., no tree search), the resulting phylogenies had accuracies that were indistinguishable from their original counterparts, but with a fraction of the runtime. Our results indicate that an ideal workflow for viral phylogenetic inference is to (1) use MAFFT to perform MSA, (2) use FastTree 2 under the GTR model with discrete gamma-distributed site-rate heterogeneity to quickly obtain a reasonable tree topology, and (3) use RAxML-NG to optimize branch lengths along the fixed FastTree 2 topology.