bluuebunny/crossref_metadata_2025_split huggingface dataset:
A customizable, open-source Winston-Lutz system for multi-target, single isocentre radiotherapy
Authors: Oliver P A K , Wood T R , Baldwin L N 
Published: September 2022

Abstract

Objective. To present and share an open-source system (phantom and software) for verifying the targeting accuracy of linac-based, single-isocenter, multi-target radiotherapy. This quality assurance test extends the traditional Winston-Lutz test, which considers a single target located at isocentre. Approach. Plans for a 3D-printed phantom are provided, which can be customized to accommodate various target (BB) positions. Given BB positions and gantry/collimator/couch combinations, the software generates multi-leaf collimator positions to facilitate multi-target Winston-Lutz (MTWL) plan creation. The software determines deviations between detected and expected BB positions on MV images resulting from MTWL plan delivery. BBs are located using a Hough circle detection algorithm, which is modified to favour the detection of circles: (1) having a reasonable size, (2) that are contained within the radiation field, and (3) having reasonable pixel intensities. Validation was performed in two ways: (1) using synthetic data with zero targeting errors and (2) by measuring real linac targeting errors and comparing against results obtained using a commercial system. Main results. Validation using the synthetic data yielded a mean (maximum) absolute discrepancy of 0.11 mm (0.21 mm), which is comparable to the synthetic phantom resolution (0.2 mm). The mean (maximum) absolute discrepancy compared to the commercial system is 0.13 mm (0.43 mm). These values are similar to results obtained with repeated deliveries of the same MTWL plan with the same phantom setup. Both validation tests yield reasonable results and are therefore considered successful. The MTWL test was performed independently by three physicists on two linacs to investigate repeatability, resulting in a mean (maximum) absolute discrepancy of 0.14 mm (0.51 mm) among the various attempts. Significance. Successful completion of this quality assurance test, using our customizable and open-source system, provides confidence that multi-target, single isocentre radiotherapy treatments can be delivered with sufficient geometric accuracy according to the chosen tolerance level.
Physics-based representations for machine learning properties of chemical reactions
Authors: van Gerwen Puck , Fabrizio Alberto , Wodrich Matthew D , Corminboeuf Clemence 
Published: September 2022

Abstract
Physics-based representations constructed using only atomic positions and nuclear charges (also known as quantum machine learning, QML) allow for the reliable and efficient inference of molecular properties from training data. Chemistry is a science rooted in chemical reactions, naturally involving multiple molecular species. Here, we extend QML’s capabilities to include the prediction of reaction properties by defining reaction representations: representations taking as input multiple molecules participating in a reaction, each represented by their corresponding atomic charges and three-dimensional coordinates. Several reaction representations are constructed from established molecular ones and benchmarked on four datasets representative of thermodynamic or kinetic reaction properties. One of these, the Hydroform-22-TS dataset (2350 energy barriers), is introduced as part of this work. The relevant ingredients for a high-performing reaction representation are extracted and used to construct the Bond-Based Reaction Representation (

B
2

R
2

) for the prediction of quantum-chemical properties of chemical reactions. Finally, variations of

B
2

R
2

with varying representation size vs. performance are provided.
Massively scalable wavelength diverse integrated photonic linear neuron
Authors: van Niekerk Matthew , Rizzo Anthony , Rubio Hector , Leake Gerald , Coleman Daniel , Tison Christopher , Fanto Michael , Bergman Keren , Preble Stefan 
Published: September 2022

Abstract
As computing resource demands continue to escalate in the face of big data, cloud-connectivity and the internet of things, it has become imperative to develop new low-power, scalable architectures. Neuromorphic photonics, or photonic neural networks, have become a feasible solution for the physical implementation of efficient algorithms directly on-chip. This application is primarily due to the linear nature of light and the scalability of silicon photonics, specifically leveraging the wide-scale complementary metal-oxide-semiconductor manufacturing infrastructure used to fabricate microelectronics chips. Current neuromorphic photonic implementations stem from two paradigms: wavelength coherent and incoherent. Here, we introduce a novel architecture that supports coherent and incoherent operation to increase the capability and capacity of photonic neural networks with a dramatic reduction in footprint compared to previous demonstrations. As a proof-of-principle, we experimentally demonstrate simple addition and subtraction operations on a foundry-fabricated silicon photonic chip. Additionally, we experimentally validate an on-chip network to predict the logical 2 bit gates AND, OR, and XOR to accuracies of 96.8%, 99%, and 98.5%, respectively. This architecture is compatible with highly wavelength parallel sources, enabling massively scalable photonic neural networks.
Evaluating Occupational Noise Exposure as a Contributor to Injury Risk among Miners
Authors: Shkembi Abas , Smith Lauren M , Bregg Sandar , Neitzel Richard L 
Published: September 2022

Abstract

Objectives
This study: (i) assessed the relationship between noise exposure and injury risk, comprehensively adjusting for individual factors, psychosocial stressors, and organizational influences; (ii) determined the relative importance of noise on injuries; (iii) estimated the lowest observed adverse effect level (LOAEL) of noise on injury risk to determine the threshold of noise considered hazardous to injuries; and (iv) quantified the fraction of injuries that could be attributed to hazardous noise exposure.

Methods
In this cross-sectional study at 10 US surface mine sites, traditional mixed effects, Poisson regression, and boosted regression tree (BRT) models were run on the number of reported work-related injuries in the last year. The LOAEL of noise on injuries was identified by estimating the percent increase in work-related injuries at different thresholds of noise exposure using a counterfactual estimator through the BRT model. A population attributable fraction (PAF) was quantified with this counterfactual estimator to predict reductions in injuries at the LOAEL.

Results
Among 18 predictors of work-related injuries, mine site, perceived job safety, age, and sleepiness were the most important predictors. Occupational noise exposure was the seventh most important predictor. The LOAEL of noise for work-related injuries was a full-shift exposure of 88 dBA. Exposure ≥88 dBA was attributed to 20.3% (95% CI: 11.2%, 29.3%) of reported work-related injuries in the last year among the participants.

Conclusions
This study further supports hypotheses of a dose–response relationship between occupational noise exposure and work-related injuries, and suggests that exposures ≥88 dBA may increase injury risk in mining.
Coryanthes macrantha(Orchidaceae: Stanhopeinae) and their floral and extrafloral secretory structures: an anatomical and phytochemical approach
Authors: Casique Jorgeane Valéria , Soares Marcos Vinícius Batista , da Silva Edilson Freitas , Kikuchi Tatiani Yuriko , Andrade Eloisa Helena de Aguiar , Mastroberti Alexandra Antunes 
Published: September 2022

AbstractCoryanthes is one of the most fascinating genera of Stanhopeinae (Orchidaceae) because of its complex pollination mechanism and the peculiar structures of its flowers. Although Coryanthes macrantha is widely studied, investigation of the secretory structures and floral biology is important to understand the mechanisms and ecology of pollination, which deserve attention despite the difficulties of collecting fertile material in nature. We conducted a morpho-anatomical analysis of the floral and extrafloral secretory structures of C. macrantha to better understand the secretory structures, contribute to the knowledge of its floral biology and/or pollination processes and understand the ecological function of these structures. The analysis revealed that C. macrantha has epidermal osmophores with unicellular papillae that were foraged by male Eulaema bees, floral nectaries in the sepals and extrafloral nectaries in the bracts. In both the floral and extrafloral nectaries, the nectar is exuded by the stomata. Azteca ants foraged the bract and sepal nectaries in pre-anthesis and post-anthesis. We also described the secretory epidermis of pleuridia, and the mode of secretion of osmophores and nectaries and found that they attract specific foraging agents.
Automatic Analysis of Constructional Diversity as a Predictor of EFL Students’ Writing Proficiency
Authors: Hwang Haerim , Kim Hyunwoo 
Published: September 2022

AbstractOne of the important components in second language (L2) development is to produce clause-level units of form–meaning pairings or argument structure constructions. Based on the usage-based constructionist approach that language development entails an ability to use more diverse, more complex, and less frequent constructions, this study tested whether constructional diversity and complexity predict L2 learners’ writing proficiency. Using a natural language processing tool called the Constructional Diversity Analyzer (CDA), we analyzed 3,284 essays produced by college EFL students in terms of the proportion of individual constructions and their diversity. Results from regression analyses showed that constructional diversity reliably predicted learner proficiency: essays with higher scores contained more diverse constructions. We also found that less frequent and more complex constructions made a stronger contribution to predicting the written proficiency levels. Based on the findings, we argue for the validity of constructional diversity and the use of individual constructions as reliable predictors of L2 writing proficiency and propose the application of the CDA for L2 writing assessment and instruction.
MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions
Authors: Thiele Ines , Preciat German , Fleming Ronan M T 
Published: September 2022

Abstract

Motivation
Genome-scale metabolic reconstructions have been assembled for thousands of organisms using a wide range of tools. However, metabolite annotations, required to compare and link metabolites between reconstructions, remain incomplete. Here, we aim to further extend metabolite annotation coverage using various databases and chemoinformatic approaches.

Results
We developed a COBRA toolbox extension, deemed MetaboAnnotator, which facilitates the comprehensive annotation of metabolites with database independent and dependent identifiers, obtains molecular structure files, and calculates metabolite formula and charge at pH 7.2. The resulting metabolite annotations allow for subsequent cross-mapping between reconstructions and mapping of, e.g., metabolomic data.

Availability and implementation
MetaboAnnotator and tutorials are freely available at https://github.com/opencobra.

Supplementary information
Supplementary data are available at Bioinformatics online.
Severe Mycobacterial Immune Reconstitution Inflammatory Syndrome (IRIS) in Advanced Human Immunodeficiency Virus (HIV) Has Features of Hemophagocytic Lymphohistiocytosis and Requires Prolonged Immune Suppression
Authors: Rocco Joseph M , Laidlaw Elizabeth , Galindo Frances , Anderson Megan , Rupert Adam , Higgins Jeanette , Sortino Ornella , Ortega-Villa Ana M , Sheikh Virginia , Roby Gregg , Kuriakose Safia , Lisco Andrea , Manion Maura , Sereti Irini 
Published: September 2022

Abstract

Background
People with HIV and mycobacterial infections can develop immune reconstitution inflammatory syndrome (IRIS) after starting antiretroviral therapy (ART). Severe mycobacterial IRIS has an overlapping clinical phenotype with hemophagocytic lymphohistiocytosis (HLH). We evaluated the pathophysiologic similarities between mycobacterial IRIS and HLH to identify clinical and immune predictors of mycobacterial IRIS severity.

Methods
HLH criteria were applied to a longitudinal cohort of 80 patients with HIV (CD4 &lt;100 cells/µL) and mycobacterial infections. Participants were subdivided into IRIS meeting HLH criteria (HLH-IRIS), IRIS without HLH (IRIS), and those without IRIS (non-IRIS). Clinical outcomes were evaluated by regression analyses. Soluble biomarkers and T-cell subsets were assessed at baseline and IRIS-equivalent time points.

Results
HLH-IRIS patients required corticosteroids more frequently (OR: 21.5; 95%CI: 5.6–114.8) and for longer duration (21.2; 95%CI: 10.7–31.7 weeks) than those not meeting HLH criteria. Utilizing decision tree analyses, hemoglobin &lt;9.2 g/dL was the best predictor of HLH-IRIS before ART, whereas ferritin, CXCL9 and sCD25 were most diagnostic for HLH at IRIS onset. At the IRIS timepoint, but not baseline, HLH-IRIS patients had lower regulatory and higher activated T cells along with greater production of IFNγ–IL-18 axis biomarkers compared with both IRIS and non-IRIS groups. Principal component analysis corroborated the distinct clustering of HLH-IRIS patients.

Conclusions
Severe mycobacterial IRIS and HLH have an overlapping pathogenesis involving IFNγ and unopposed T-cell activation causing severe inflammatory disease clinically distinguished by hyperferritinemia (hyperferritinemic IRIS [FIRIS]). Hemoglobin, ferritin, CXCL9, and sCD25 identify high-risk patients and may improve risk stratification and therapeutic strategies for mycobacterial IRIS.
Severely Restricting Abortion Threatens Equitable Health Outcomes for People With Human Immunodeficiency Virus
Authors: Hadley Megan , Powell Anna 
Published: September 2022

Abstract
Equitable access to abortion is a critical component of reproductive care. Women with human immunodeficiency virus (HIV) in the United States are disproportionately Black and will be disproportionately affected by abortion bans following the Supreme Court's decision to overturn Roe v Wade. We argue that this decision is directly in conflict with the National HIV/AIDS Strategies and Centers for Disease Control and Prevention's goals to eliminate perinatal HIV transmission.
ECCO Topical Review: Roadmap to Optimal Peri-Operative Care in IBD
Authors: Sebastian Shaji , Segal Jonathan P , Hedin Charlotte , Pellino Gianluca , Kotze Paulo Gustavo , Adamina Michel , Campmans-Kuijpers Marjo , Davies Justin , de Vries Annemarie C , Casbas Ana Gutiérrez , El-Hussuna Alaa , Juillerat Pascal , Meade Susanna , Millán Monica , Spinelli Antonino 
Published: September 2022

AbstractBackground and aimsDespite the advances in medical therapies, a significant proportion of patients with inflammatory bowel diseases [IBD] require surgical intervention. This Topical Review aims to offer expert consensus practice recommendations for peri-operative care to optimize outcomes of IBD patients who undergo surgery.MethodsA multidisciplinary panel of IBD healthcare providers systematically reviewed aspects relevant to peri-operative care in IBD. Consensus statements were developed using Delphi methodology.ResultsA total of 20 current practice positions were developed following systematic review of the current literature covering use of medication in the peri-operative period, nutritional assessment and intervention, physical and psychological rehabilitation and prehabilitation, and immediate postoperative care.ConclusionPeri-operative planning and optimization of the patient are imperative to ensure favourable outcomes and reduced morbidity. This Topical Review provides practice recommendations applicable in the peri-operative period in IBD patients undergoing surgery.
C4-dicarboxylate metabolons: interaction of C4-dicarboxylate transporters of Escherichia coli with cytosolic enzymes
Authors: Schubert Christopher , Kim Nam Yeun , Unden Gottfried , Kim Ok Bin 
Published: September 2022

Abstract
Metabolons represent the structural organization of proteins for metabolic or regulatory pathways. Here, the interaction of fumarase FumB, aspartase AspA, and L-tartrate dehydratase TtdAB with the C4-dicarboxylate (C4-DC) transporters DcuA, DcuB, DcuC, and the L-tartrate transporter TtdT of Escherichia coli was tested by a bacterial two-hybrid (BACTH) assay in situ, or by co-chromatography using mSPINE (membrane Streptavidin protein interaction experiment). From the general C4-DC transporters, DcuB interacted with FumB and AspA, DcuA with AspA, whereas DcuC interacted with neither FumB nor AspA. Moreover, TtdT did not interact with TtdAB. The fumB-dcuB, the dcuA-aspA, and the ttdAB-ttdT genes encoding the respective proteins colocalize on the genome and each pair of genes forms cotranscripts, whereas the dcuC gene lies alone. The data suggest the formation of DcuB/FumB and DcuB/AspA metabolons for the uptake of L-malate, or L-aspartate, and their conversion to fumarate for fumarate respiration and excretion of the product succinate. The DcuA/AspA metabolon catalyzes uptake and conversion of L-aspartate to fumarate coupled to succinate excretion. The DcuA/AspA metabolon provides ammonia at the same time for nitrogen assimilation (ammonia shuttle). On the other hand, TtdT and TtdAB are not organized in a metabolon. Reasons for the formation (DcuA/AspA, DcuB/FumB, and DcuB/AspA) or nonformation (DcuC, TtdT, and TtdAB) of metabolons are discussed based on their metabolic roles.
Concentrations of mesophilic bacteria in a poultry farm over two fattening periods focusing on the presence of staphylococci and enterococci
Authors: Haas Doris , Miskovic Tea , Fritz Theresa , Galler Herbert , Habib Juliana , Köck Sabine , Kropsch Michael , Pless Peter , Stonitsch Martin , Zentner Eduard , Reinthaler Franz F 
Published: September 2022

ABSTRACTThe increasing animal numbers have a potential impact on the air quality of stables. The aim of this study was to assess the microbial load in the barn air from the day of entry of the chickens to the day of removal for slaughter. A total of 10 measurements in two fattening periods were conducted in a poultry farm with a capacity of 400 chickens in Styria, Austria. The samples were collected with an Air-Sampling Impinger for the investigation of mesophilic bacteria, staphylococci and enterococci. Chicken skin swab samples were collected to detect Staphylococcus aureus. The total colony forming units per cubic meter of mesophilic bacteria of the first measurement series of period I was 7.8 × 104 and increased to 1.4 × 108 at the end and at the fattening period II it increased from 2.5 × 105 to 4.2 × 107. In the measurement series of the fattening period I, the concentration of Staphylococcus spp. increased from 0 to 4.9 × 107 CFUs/m3 and from 0 to 2.1 × 107 CFUs/m3 in the fattening period II. Staphylococcus aureus could not be found on the chicken skin. An interesting finding was the increase of staphylococci while the intestinal enterococci were not detectable in the air of the barn toward the end of both fattening periods.
Identification of 5 Potential Predictive Biomarkers for Alzheimer’s Disease by Integrating the Unified Test for Molecular Signatures and Weighted Gene Coexpression Network Analysis
Authors: Zhou Siquan , Ma Guochen , Luo Hang , Shan Shufang , Xiong Jingyuan , Cheng Guo 
Published: September 2022

AbstractBackgroundPrevious transcriptome-wide association study (TWAS) has documented 21 genes associated with Alzheimer’s disease (AD) risk, but the predictive biomarkers remain unexplored.MethodsTWAS leveraging the unified test for molecular signatures (UTMOST) was performed in 75,000 cases and 420,000 controls with 10 brain tissue gene expression references. Weighted gene coexpression network analysis (WGCNA) was conducted in GSE5281 and GSE48350 data sets containing 167 AD samples and 247 controls. Random forest (RF) analysis was applied to screen the potential predictive biomarkers based on overlapping genes identified by TWAS and WGCNA, followed by comprehensive bioinformatic analyses with differential gene expression, functional enrichment, and correlation with immune cells. A nomogram was established to verify the predictive power of the identified biomarkers.ResultsTWAS revealed 78 candidate genes (p &lt; 2.89 × 10−6). In WGCNA turquoise module, 3 718 AD-related genes were screened. RF identified 5 predictive biomarkers (FAM71E1, DDB2, AP4M1, GPR4, DOC2A), which are enriched in the global genome nucleotide excision repair pathway and associated with immune cell designations “Natural.killer.T.cell,” “Memory.B.cell,” “T.follicular.helper.cell,” “Neutrophil,” and “MDSC.” The nomogram based on the 5 markers showed a high predictive power.ConclusionFive potential predictive biomarkers for AD were identified, providing new insights into the pathogenesis and etiology of AD.
Insights into the antecedents of cyberchondria: a perspective from the USA
Authors: Afrin Rifat , Prybutok Gayle 
Published: September 2022

SummaryThis study establishes a theoretical framework for assessing antecedents of cyberchondria, which is a process of amplified anxiety about one’s health because of excessive online health information seeking. We examined the framework through partial least squares structural equation modeling after collecting data through a cross-sectional online survey. This research contributes to the literature by (i) evaluating the roles of health anxiety (HA) and affective responses (AR) on cyberchondria; (ii) equipping health strategists with understanding about ways to tailor their educational and communication strategies to specific segments by importance–performance map analysis and necessary condition analysis. Finally, by (iii) providing strategic tactics to curb cyberchondria so that it becomes possible to attain a better patient outcome. Findings suggest that the existing association between intolerance of uncertainty and cyberchondria is serially mediated by HA and AR. For healthcare educators and practitioners, the findings of this research deliver a blueprint for effectively controlling cyberchondria.
Engagement with the TCR induces plasticity in antigenic ligands bound to MHC class I and CD1 molecules
Authors: Morita Daisuke , Asa Minori , Sugita Masahiko 
Published: September 2022

Abstract
Complementarity-determining regions (CDRs) of αβ T-cell receptors (TCRs) sense peptide-bound MHC (pMHC) complexes via chemical interactions, thereby mediating antigen specificity and MHC restriction. Flexible finger-like movement of CDR loops contributes to the establishment of optimal interactions with pMHCs. In contrast, peptide ligands captured in MHC molecules are considered more static because of the rigid hydrogen-bond network that stabilizes peptide ligands in the antigen-binding groove of MHC molecules. An array of crystal structures delineating pMHC complexes in TCR-docked and TCR-undocked forms is now available, which enables us to assess TCR engagement-induced conformational changes in peptide ligands. In this short review, we overview conformational changes in MHC class I-bound peptide ligands upon TCR docking, followed by those for CD1-bound glycolipid ligands. Finally, we analyze the co-crystal structure of the TCR:lipopeptide-bound MHC class I complex that we recently reported. We argue that TCR engagement-induced conformational changes markedly occur in lipopeptide ligands, which are essential for exposure of a primary T-cell epitope to TCRs. These conformational changes are affected by amino acid residues, such as glycine, that do not interact directly with TCRs. Thus, ligand recognition by specific TCRs involves not only T-cell epitopes but also non-epitopic amino acid residues. In light of their critical function, we propose to refer to these residues as non-epitopic residues affecting ligand plasticity and antigenicity (NR-PA).