bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensitivity of Antemortem Imaging for Pericarditis
Authors: Kostelecky Nicolas , Kreutz Kasey , Lin Chieh-Yu 
Published: December 2022

Abstract
Pericarditis is a challenging diagnosis with nonspecific manifestations, significant clinical implications, and possible mortality. The advancement of imaging, such as echocardiography, computed tomography (CT), and magnetic resonance imaging (MRI), has improved the sensitivity of diagnosis, although limitations remain. In this study, we investigated the prevalence of pericarditis identified at autopsy and correlated these findings with antemortem imaging studies and clinical information. Thirty-four decedents were identified in our archival autopsy records (prevalence, 1.23%) from 2010 to 2021 with a postmortem diagnosis of pericarditis. Thirty-five antemortem imaging studies were performed on 32 decedents, of which CT was the most common (18/35, 51.4%). The sensitivity of antemortem imaging was poor, with CT showing the highest sensitivity at 16.7% (3/18), while echocardiography studies, transthoracic (TTE) and transesophageal (TEE), each had a sensitivity of 0.0%. Pericarditis was determined as the immediate cause of death by autopsy in 13 decedents, of which 3 were diagnosed antemortem. It was considered contributory to the death in 6 decedents, none of which were diagnosed antemortem. In summary, antemortem imaging has limited utility in the diagnosis of pericarditis. It is imperative to examine the pericardium during autopsy to identify a possible cause of death or contributing factor.
Guidelines for Triage of COVID-19 Patients Presenting With Multisystemic Symptoms
Authors: Alemi Farrokh , Guralnik Elina , Vang Jee , Wojtusiak Janusz , Peterson Rachele , Roess Amira , Jain Praduman 
Published: December 2022

Background and Objectives:
This article describes how multisystemic symptoms, both respiratory and nonrespiratory, can be used to differentiate coronavirus disease-2019 (COVID-19) from other diseases at the point of patient triage in the community. The article also shows how combinations of symptoms could be used to predict the probability of a patient having COVID-19.

Methods:
We first used a scoping literature review to identify symptoms of COVID-19 reported during the first year of the global pandemic. We then surveyed individuals with reported symptoms and recent reverse transcription polymerase chain reaction (RT-PCR) test results to assess the accuracy of diagnosing COVID-19 from reported symptoms. The scoping literature review, which included 81 scientific articles published by February 2021, identified 7 respiratory, 9 neurological, 4 gastrointestinal, 4 inflammatory, and 5 general symptoms associated with COVID-19 diagnosis. The likelihood ratio associated with each symptom was estimated from sensitivity and specificity of symptoms reported in the literature. A total of 483 individuals were then surveyed to validate the accuracy of predicting COVID-19 diagnosis based on patient symptoms using the likelihood ratios calculated from the literature review. Survey results were weighted to reflect age, gender, and race of the US population. The accuracy of predicting COVID-19 diagnosis from patient-reported symptoms was assessed using area under the receiver operating curve (AROC).

Results:
In the community, cough, sore throat, runny nose, dyspnea, and hypoxia, by themselves, were not good predictors of COVID-19 diagnosis. A combination of cough and fever was also a poor predictor of COVID-19 diagnosis (AROC = 0.56). The accuracy of diagnosing COVID-19 based on symptoms was highest when individuals presented with symptoms from different body systems (AROC of 0.74-0.81); the lowest accuracy was when individuals presented with only respiratory symptoms (AROC = 0.48).

Conclusions:
There are no simple rules that clinicians can use to diagnose COVID-19 in the community when diagnostic tests are unavailable or untimely. However, triage of patients to appropriate care and treatment can be improved by reviewing the combinations of certain types of symptoms across body systems.
Figure-ground segmentation based on motion in the archerfish
Authors: Volotsky Svetlana , Segev Ronen 
Published: December 2022

AbstractObject detection and recognition is a complex computational task that is thought to rely critically on the ability to segment an object from the background. Mammals exhibit varying figure-ground segmentation capabilities, ranging from primates that can perform well on figure-ground segmentation tasks to rodents that perform poorly. To explore figure-ground segmentation capabilities in teleost fish, we studied how the archerfish, an expert visual hunter, performs figure-ground segmentation. We trained archerfish to discriminate foreground objects from the background, where the figures were defined by motion as well as by discontinuities in intensity and texture. Specifically, the figures were defined by grating, naturalistic texture, and random noise moving in counterphase with the background. The archerfish performed the task well and could distinguish between all three types of figures and grounds. Their performance was comparable to that of primates and outperformed rodents. These findings suggest the existence of a complex visual process in the archerfish visual system that enables the delineation of figures as distinct from backgrounds, and provide insights into object recognition in this animal.
Crystal structure of theArabidopsisSPIRAL2 C-terminal domain reveals a p80-Katanin-like domain
Authors: Bolhuis Derek L. , Dixit Ram , Slep Kevin C. 
Published: December 2022

AbstractEpidermal cells of dark-grown plant seedlings reorient their cortical microtubule arrays in response to blue light from a net lateral orientation to a net longitudinal orientation with respect to the long axis of cells. The molecular mechanism underlying this microtubule array reorientation involves katanin, a microtubule severing enzyme, and a plant-specific microtubule associated protein called SPIRAL2. Katanin preferentially severs longitudinal microtubules, generating seeds that amplify the longitudinal array. Upon severing, SPIRAL2 binds nascent microtubule minus ends and limits their dynamics, thereby stabilizing the longitudinal array while the lateral array undergoes net depolymerization. To date, no experimental structural information is available for SPIRAL2 to help inform its mechanism. To gain insight into SPIRAL2 structure and function, we determined a 1.8 Å resolution crystal structure of theArabidopsis thalianaSPIRAL2 C-terminal domain. The domain is composed of seven core α-helices, arranged in an α-solenoid. Amino-acid sequence conservation maps primarily to one face of the domain involving helices α1, α3, α5, and an extended loop, the α6-α7 loop. The domain fold is similar to, yet structurally distinct from the C-terminal domain of Ge-1 (an mRNA decapping complex factor involved in P-body localization) and, surprisingly, the C-terminal domain of the katanin p80 regulatory subunit. The katanin p80 C-terminal domain heterodimerizes with the MIT domain of the katanin p60 catalytic subunit, and in metazoans, binds the microtubule minus-end factors CAMSAP3 and ASPM. Structural analysis predicts that SPIRAL2 does not engage katanin p60 in a mode homologous to katanin p80. The SPIRAL2 structure highlights an interesting evolutionary convergence of domain architecture and microtubule minus-end localization between SPIRAL2 and katanin complexes, and establishes a foundation upon which structure-function analysis can be conducted to elucidate the role of this domain in the regulation of plant microtubule arrays.
Mechanical coupling with the nuclear envelope shapes theS. pombemitotic spindle
Authors: Begley Marcus A , Pagán Medina Christian , Couture Taylor , Zareiesfandabadi Parsa , Rapp Matthew B , Tirfe Mastawal , LeBlanc Sharonda , Betterton Meredith D. , Elting Mary Williard 
Published: December 2022

SUMMARYThe fission yeastS. pombedivides via closed mitosis, meaning that spindle elongation and chromosome segregation transpire entirely within the complete nuclear envelope. Both the spindle and nuclear envelope must undergo significant conformation changes and exert varying forces on each other during this process. Previous work has demonstrated that nuclear envelope expansion1,2and spindle pole body (SPB) embedding in the nuclear envelope3are required for normalS. pombemitosis, and mechanical modeling has described potential contributions of the spindle to nuclear morphology4,5. However, it is not yet fully clear how and to what extent the nuclear envelope and mitotic spindle each directly shape each other during closed mitosis. Here, we investigate this relationship by observing the behaviors of spindles and nuclei in live mitotic fission yeast following laser ablation. First, we characterize these dynamics in molecularly typicalS. pombespindles, finding them to be stabilized by dense crosslinking, before demonstrating that the compressive force acting on the spindle poles is higher in mitotic cells with greater nuclear envelope tension and that spindle compression can be relieved by lessening nuclear envelope tension via laser ablation. Finally, we use a quantitative model to interpret how these data directly demonstrate that fission yeast spindles and nuclear envelopes are a mechanical pair that can each shape the other’s morphology.
Glucocorticoid and adrenergic receptor distribution across human organs and tissues: a map for stress transduction
Authors: Basarrate Sophia , Monzel Anna S. , Smith Janell , Marsland Anna , Trumpff Caroline , Picard Martin 
Published: December 2022

AbstractObjectivePsychosocial stress is transduced into disease risk through energy-dependent release of hormones that affect target organs, tissues, and cells. The magnitude of the physiological stress responses reflects both systemic levels of these hormones and the sensitivity of target tissues to their effects. Thus, differential expression of receptors across organs likely contributes to stress transduction. Here we provide a quantitative whole-body map of glucocorticoid and adrenergic receptor expression.MethodsWe systematically examined gene expression levels for the glucocorticoid receptor (GR), α- and β-adrenergic receptors (AR-α1B, AR-α2B AR-β2, and AR-β3), across 55 different organs using the Human Protein Atlas dataset. We also leveraged the Human Proteome Map and MitoCarta3.0 data to examine receptor protein levels and, given the energy-dependence of the stress response, the link between stress hormone receptor density and mitochondrial pathways. Finally, we tested the functional interplay between GR activation and AR expression in living human cells.ResultsThe GR was expressed ubiquitously across all investigated organ systems. Immune tissues and cells expressed the highest GR RNA and protein levels. In contrast, AR subtypes showed lower and more localized expression patterns. Co-regulation was found between GR and AR-α1B, as well as between AR-α1B and AR-α2B. In human fibroblasts, activating the GR selectively increased AR-β2 (3.6-fold) and AR-α1B (2.2-fold) expression, confirming their interaction. Consistent with the energetic cost of stress responses, GR and AR expression were positively associated with the expression of key mitochondrial pathways.ConclusionOur results provide a cartography of GR and AR expression across the human body. Tissue-specific stress hormone receptor expression patterns could make specific organ systems more responsive to the sustained, energetically expensive, neuroendocrine signaling pathways triggered by chronic psychosocial stress.
PACESS: Practical AI-based Cell Extraction and Spatial Statistics for large 3D bone marrow tissue images
Authors: Adams George , Tissot Floriane S. , Liu Chang , Brunsdon Chris , Duffy Ken R. , Lo Celso Cristina 
Published: December 2022

ABSTRACT/SUMMARYDespite much being known about the molecular regulation of hematopoiesis, little is understood about how hematopoietic cells are organized within bone marrow (BM) tissue. Recent advances in microscopy have led to the creation of increasingly detailed images of murine hematopoietic tissue. Accurate, efficient, and informative methodologies to extract and analyze the large amount of data generated are, however, still lacking. Indeed, cells are very densely packed in the bone marrow and therefore difficult to efficiently and accurately segment. In addition, currently employed statical analyses of cellular localization are generally unsuitable for the investigation of interactions between more than two cell types. To overcome these limitations, we developed PACESS, a readily applicable method based on neural network classification of hundreds of thousands of cells in thick 3D bone marrow samples, and a combination of statistical techniques to assess the spatial interactions between multiple cell types. To validate this approach, we used it to investigate the spatial organization of T cells, megakaryocytes and leukemic cells. We demonstrate that the presence of large clusters of leukemic cells affects the distribution of both T cells and megakaryocytes, albeit differently, resulting in the generation of previously unrecognized, unique microenvironments adjacent to each other within the same bone marrow cavity. We believe that this approach can contribute to unravel the BM cellular organization.MOTIVATIONThe organization of diverse hematopoietic cells within bone marrow tissue remains unclear. Recently developed tissue clearing methods enable the generation of large, 3D, single cell resolution microscopy images datasets, but the bottleneck in their analysis lies in both the identification and classification of cells, and in statistical analyses to probe their spatial relationships. We present a workflow (PACESS) that takes advantage of a convoluted neural network to identify and classify cells in 2D coupled with an automated method that extrapolates to 3D, followed by a combination of spatial statistics to classify tissue regions based on each cell type’s density, and logistic regression to test whether the relative abundance of cell types may be explained by reciprocal dependencies. Finally, we provide a combined measurement of the abundance of all cell types in a 3D map, highlighting regional variations found within the tissue.Graphical Abstract
A robust deep learning platform to predict CD8+ T-cell epitopes
Authors: Lee Chloe H. , Huh Jaesung , Buckley Paul R. , Jang Myeongjun , Pereira Pinho Mariana , Fernandes Ricardo A. , Antanaviciute Agne , Simmons Alison , Koohy Hashem 
Published: December 2022

AbstractT-cells play a crucial role in the adaptive immune system by inducing an anti-tumour response, defending against pathogens, and maintaining tolerance against self-antigens, which has sparked interest in the development of T-cell-based vaccines and immunotherapies. Because screening antigens driving the T-cell response is currently low-throughput and laborious, computational methods for predicting CD8+ T-cell epitopes have emerged. However, most immunogenicity algorithms struggle to learn features of peptide immunogenicity from small datasets, suffer from HLA bias and are unable to reliably predict pathology-specific CD8+ T-cell epitopes. Therefore, we developed TRAP (T-cell recognition potential of HLA-I presented peptides), a robust deep learning platform for predicting CD8+ T-cell epitopes from MHC-I presented pathogenic and self-peptides. TRAP uses transfer learning, deep learning architecture and MHC binding information to make context-specific predictions of CD8+ T-cell epitopes. TRAP also detects low-confidence predictions for peptides that differ significantly from those in the training datasets to abstain from making incorrect predictions. To estimate the immunogenicity of pathogenic peptides with low-confidence predictions, we further developed a novel metric, RSAT (relative similarity to autoantigens and tumour-associated antigens), as a complementary to ‘dissimilarity to self’ from cancer studies. We used TRAP to identify epitopes from glioblastoma patients as well as SARS-CoV-2 peptides, and it outperformed other algorithms in both cancer and pathogenic settings. Thus, this study presents a novel computational platform for accurately predicting CD8+ T-cell epitopes to foster a better understanding of antigen-specific T-cell response and the development of effective clinical therapeutics.HighlightsHLA bias and out-of-distribution problem are causes of poor performance of current state-of-the-art algorithmsTransfer learning, deep learning architecture, context-specific and HLA-generalised approaches improve CD8+ T-cell epitope predictionTRAP reports degree of correctness to improve reliability of the predictionA novel metric termed RSAT estimates immunogenicity of pathogenic peptides, as a complementary to ‘dissimilarity to self’ from cancer studies
Immunogenicity of COVID-eVax Is Moderately Impacted by Temperature and Molecular Isoforms
Authors: D’Alessio Federico , Lione Lucia , Salvatori Erika , Bucci Federica , Muzi Alessia , Roscilli Giuseppe , Conforti Antonella , Compagnone Mirco , Pinto Eleonora , Battistuzzi Gianfranco , Aurisicchio Luigi , Palombo Fabio 
Published: December 2022

AbstractDNA integrity is a key issue in gene therapy and genetic vaccine approaches based on plasmid DNA. In contrast to messenger RNA that requires a controlled cold chain for efficacy, DNA molecules are considered to be more stable. In this study, we challenged this concept by characterizing the immunological response induced by a plasmid DNA vaccine delivered using electroporation. As a model, we used COVID-eVax, which is a plasmid DNA vaccine that targets the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Increased nicked DNA was produced by using either an accelerated stability protocol or a lyophilization protocol. Surprisingly, the immune response induced in vivo was only minimally affected by the percentage of open circular DNA. This result suggests that plasmid DNA vaccines, such as COVID-eVax that has completed a phase I clinical trial, retain their efficacy upon storage at higher temperatures and this feature may facilitate their use in low-/middle-income countries.
Optimization of energy production and central carbon metabolism in a non-respiring eukaryote
Authors: Alam Sara , Gu Ying , Reichert Polina , Bähler Jürg , Oliferenko Snezhana 
Published: December 2022

SummaryMost eukaryotes respire oxygen, using it to generate biomass and energy. Yet, a few organisms lost the capacity to respire. Understanding how they manage biomass and energy production may illuminate the critical points at which respiration feeds into central carbon metabolism and explain possible routes to its optimization. Here we use two related fission yeasts,Schizosaccharomyces pombeandSchizosaccharomyces japonicus, as a comparative model system. We show that althoughS. japonicusdoes not respire oxygen, unlikeS. pombe, it is capable of efficient NADH oxidation, amino acid synthesis and ATP generation. We probe possible optimization strategies using stable isotope tracing metabolomics, mass isotopologue distribution analysis, genetics, and physiological experiments.S. japonicusappears to have optimized cytosolic NADH oxidation via glycerol-3-phosphate synthesis. It runs a fully bifurcated TCA ‘cycle’, supporting higher amino acid production. Finally, it uses the pentose phosphate pathway both to support faster biomass generation and as a shunt to optimize glycolytic flux, thus producing more ATP than the respiro-fermentingS. pombe. By comparing two related organisms with vastly different metabolic strategies, our work highlights the versatility and plasticity of central carbon metabolism in eukaryotes, illuminating critical adaptations supporting the preferential use of glycolysis over oxidative phosphorylation.
Performance of conical hydrodynamic journal bearing under the worn-out condition
Authors: Kamble Dinesh Haribhau , Phalle Vikas M. , Mantha Shankar S. , Pawar Sanjay Rangrao 
Published: December 2022

Purpose
Where combined radial and axial loads act on the bearing, the conical journal bearing is best suited. Large turbines, generators, compressors and other machinery perform better while using conical hydrodynamic journal bearings (CHJBs). The bearings worn out and the performance suffered because of regular use and numerous start and stop operations.

Design/methodology/approach
The performance of CHJB is evaluated using both analytical and experimental methods in this paper. The analytical method for resolving Reynolds equation uses spherical coordinate system and finite element analysis. On the CHJB test rig, data is collected for different radial loads with 10°, 20° and 30° semi-cone angles using hydraulic oil of viscosity grade ISO VG46.

Findings
The findings of this paper demonstrate that at various semi-cone angles for worn-out bearings, the maximum pressure developed increases with increasing radial load.

Originality/value
This paper provides analytical and experimental performance of CHJBs considering the effect of abrasive wear that is caused because of frequent start and stop operations of machine. The results of wear impact on CHJBs will be helpful for researchers and design engineers.
Supply chain coordination in sustainable agribusiness development: an investigation from coffee exporters
Authors: Nguyen Hoang , Mai Thanh Lan , Pham Thi Thu Thuy , Binh Do 
Published: December 2022

PurposeThis study intends to investigate drivers and consequences of supply chain coordination (SCC) towards green to highlight some convincing evidence for an emerging country's exporters to promote sustainable coffee development.Design/methodology/approachData were gathered from surveying 189 managers of coffee exporters in Vietnam and then applied PLS-SEM for analysis.FindingsThis study demonstrates that top management sensitivity, along with institutional forces of regulation, market and competition, strongly stimulate exporters' supply chain coordination towards green. Additionally, that coordination boosts the export financial and market performance.Research limitations/implicationsThe findings may not be generalizable because the current study only included data from Vietnamese coffee exporters.Originality/valueThis study contributes to the current literature by looking from the perspective of coffee exporters – leading players in supply chains for export. The research findings represent the first solid argument for Vietnam coffee exporters to encourage SCC towards green and reveal several implications for managers and policymakers to support sustainable development in an emerging country.