bluuebunny/crossref_metadata_2025_split huggingface dataset:
A framework for predicting variable-length epitopes of human-adapted viruses using machine learning methods
Authors: Yin Rui , Zhu Xianghe , Zeng Min , Wu Pengfei , Li Min , Kwoh Chee Keong 
Published: July 2022

Abstract
The coronavirus disease 2019 pandemic has alerted people of the threat caused by viruses. Vaccine is the most effective way to prevent the disease from spreading. The interaction between antibodies and antigens will clear the infectious organisms from the host. Identifying B-cell epitopes is critical in vaccine design, development of disease diagnostics and antibody production. However, traditional experimental methods to determine epitopes are time-consuming and expensive, and the predictive performance using the existing in silico methods is not satisfactory. This paper develops a general framework to predict variable-length linear B-cell epitopes specific for human-adapted viruses with machine learning approaches based on Protvec representation of peptides and physicochemical properties of amino acids. QR decomposition is incorporated during the embedding process that enables our models to handle variable-length sequences. Experimental results on large immune epitope datasets validate that our proposed model’s performance is superior to the state-of-the-art methods in terms of AUROC (0.827) and AUPR (0.831) on the testing set. Moreover, sequence analysis also provides the results of the viral category for the corresponding predicted epitopes with high precision. Therefore, this framework is shown to reliably identify linear B-cell epitopes of human-adapted viruses given protein sequences and could provide assistance for potential future pandemics and epidemics.
BioRED: a rich biomedical relation extraction dataset
Authors: Luo Ling , Lai Po-Ting , Wei Chih-Hsuan , Arighi Cecilia N , Lu Zhiyong 
Published: July 2022

AbstractAutomated relation extraction (RE) from biomedical literature is critical for many downstream text mining applications in both research and real-world settings. However, most existing benchmarking datasets for biomedical RE only focus on relations of a single type (e.g. protein–protein interactions) at the sentence level, greatly limiting the development of RE systems in biomedicine. In this work, we first review commonly used named entity recognition (NER) and RE datasets. Then, we present a first-of-its-kind biomedical relation extraction dataset (BioRED) with multiple entity types (e.g. gene/protein, disease, chemical) and relation pairs (e.g. gene–disease; chemical–chemical) at the document level, on a set of 600 PubMed abstracts. Furthermore, we label each relation as describing either a novel finding or previously known background knowledge, enabling automated algorithms to differentiate between novel and background information. We assess the utility of BioRED by benchmarking several existing state-of-the-art methods, including Bidirectional Encoder Representations from Transformers (BERT)-based models, on the NER and RE tasks. Our results show that while existing approaches can reach high performance on the NER task (F-score of 89.3%), there is much room for improvement for the RE task, especially when extracting novel relations (F-score of 47.7%). Our experiments also demonstrate that such a rich dataset can successfully facilitate the development of more accurate, efficient and robust RE systems for biomedicine.Availability: The BioRED dataset and annotation guidelines are freely available at https://ftp.ncbi.nlm.nih.gov/pub/lu/BioRED/.
Immune infiltration and clinical significance analyses of the coagulation-related genes in hepatocellular carcinoma
Authors: He Qifan , Yang Jian , Jin Yonghai 
Published: July 2022

Abstract
Hepatocellular carcinoma (HCC) is one of the most common types of cancers and a global health challenge with a low early diagnosis rate and high mortality. The coagulation cascade plays an important role in the tumor immune microenvironment (TME) of HCC. In this study, based on the coagulation pathways collected from the KEGG database, two coagulation-related subtypes were distinguished in HCC patients. We demonstrated the distinct differences in immune characteristics and prognostic stratification between two coagulation-related subtypes. A coagulation-related risk score prognostic model was developed in the Cancer Genome Atlas (TCGA) cohort for risk stratification and prognosis prediction. The predictive values of the coagulation-related risk score in prognosis and immunotherapy were also verified in the TCGA and International Cancer Genome Consortium cohorts. A nomogram was also established to facilitate the clinical use of this risk score and verified its effectiveness using different approaches. Based on these results, we can conclude that there is an obvious correlation between the coagulation and the TME in HCC, and the risk score could serve as a robust prognostic biomarker, provide therapeutic benefits for chemotherapy and immunotherapy and may be helpful for clinical decision making in HCC patients.
Clair3-trio: high-performance Nanopore long-read variant calling in family trios with trio-to-trio deep neural networks
Authors: Su Junhao , Zheng Zhenxian , Ahmed Syed Shakeel , Lam Tak-Wah , Luo Ruibang 
Published: July 2022

Abstract
Accurate identification of genetic variants from family child–mother–father trio sequencing data is important in genomics. However, state-of-the-art approaches treat variant calling from trios as three independent tasks, which limits their calling accuracy for Nanopore long-read sequencing data. For better trio variant calling, we introduce Clair3-Trio, the first variant caller tailored for family trio data from Nanopore long-reads. Clair3-Trio employs a Trio-to-Trio deep neural network model, which allows it to input the trio sequencing information and output all of the trio’s predicted variants within a single model to improve variant calling. We also present MCVLoss, a novel loss function tailor-made for variant calling in trios, leveraging the explicit encoding of the Mendelian inheritance. Clair3-Trio showed comprehensive improvement in experiments. It predicted far fewer Mendelian inheritance violation variations than current state-of-the-art methods. We also demonstrated that our Trio-to-Trio model is more accurate than competing architectures. Clair3-Trio is accessible as a free, open-source project at https://github.com/HKU-BAL/Clair3-Trio.
Lyme neuroborreliosis: known knowns, known unknowns
Authors: Halperin John J , Eikeland Randi , Branda John A , Dersch Rick 
Published: July 2022

AbstractLyme borreliosis affects the nervous system in three principal ways—mononuclear cell meningitis, cranial neuropathies and radiculoneuropathies—the last a broad term encompassing painful radiculopathy, unifocal and multifocal peripheral nerve involvement. Diagnostic tools have been significantly refined—including improved peripheral blood and CSF serodiagnostics—and much has been learned about the interactions between the causative pathogen and the nervous system. Despite these advances in our understanding of this disease, a broad range of other disorders continue to be misattributed to nervous system Lyme borreliosis, supported by, at best, limited evidence. These misattributions often reflect limited understanding not only of Lyme neuroborreliosis but also of what constitutes nervous system disease generally. Fortunately, a large body of evidence now exists to clarify many of these issues, establishing a clear basis for diagnosing nervous system involvement in this infection and, based on well performed studies, clarifying which clinical disorders are associated with Lyme neuroborreliosis, which with non-neurologic Lyme borreliosis, and which with neither.
Near-infrared fluorescence imaging of thoracic duct in minimally invasive esophagectomy
Authors: Yang Feng , Gao Jian , Cheng Sida , Li Hao , He Kunshan , Zhou Jian , Chen Kezhong , Wang Zhenfan , Yang Fan , Zhang Zeyu , Li Jianfeng , Zhou Zuli , Chi Chongwei , Li Yun , Wang Jun 
Published: July 2022

Summary
Chylothorax is a serious complication after esophagectomy and there are unmet needs for new intraoperative navigation tools to reduce its incidence. The aim of this study is to explore the feasibility and effectiveness of near-infrared fluorescence imaging (NIR-FI) with indocyanine green (ICG) to identify thoracic ducts (TDs) and chyle leakage during video-assisted thoracoscopic esophagectomy. We recruited 41 patients who underwent thoraco-laparoscopic minimally invasive esophagectomy (MIE) for esophageal cancer in this prospective, open-label, single-arm clinical trial. ICG was injected into the right inguinal region before operations, after which TD anatomy and potential chyle leakage were checked under the near-infrared fluorescence intraoperatively. In 38 of 41 patients (92.7%) using NIR-FI, TDs were visible in high contrast. The mean signal-to-background ratio (SBR) value of all fluorescent TDs was 3.05 ± 1.56. Fluorescence imaging of TDs could be detected 0.5 hours after ICG injection and last up to 3 hours with an acceptable SBR value. The optimal observation time window is from about 1 to 2 hours after ICG injection. Under the guidance of real-time NIR-FI, three patients were found to have chylous leakage and the selective TD ligations were performed intraoperatively. No patient had postoperative chylothorax. NIR-FI with ICG can provide highly sensitive and real-time assessment of TDs as well as determine the source of chyle leakage, which might help reduce TD injury and direct selective TD ligation. It could be a promising navigation tool to reduce the incidence of chylothorax after minimally invasive esophagectomy.
Temperature-dependent Development, Survival, and Oviposition of Laricobius osakensis (Coleoptera: Derodontidae): A Specialist Predator of Adelges tsugae (Hemiptera: Adelgidae)
Authors: Foley Jeremiah R , McAvoy Thomas J , Saint-Amant Rémi , Régnière Jacques , Biggs Abby , Wright Erika , Mayfield Albert E , Brewster Carlyle , Salom Scott M 
Published: July 2022

Abstract
A predator, Laricobius osakensis Montgomery and Shiyake (Coleoptera: Derodontidae), is being mass-produced and released for the biological control of the invasive hemlock woolly adelgid (HWA), Adelges tsugae Annand (Hemiptera: Adelgidae). To better understand and predict the seasonality of this predator in North America, the development and reproduction of L. osakensis were evaluated at constant temperatures ranging from 5 to 22°C. The predicted seasonal biology was compared with data from field collections. L. osakensis did not complete development from egg to adult at the two lowest temperatures tested, 5 and 8°C, but did so at the highest temperature of 22°C. The minimum development thresholds were estimated for eggs (4.2°C), first (1.8°C), second (5.5°C), third (4.6°C), and fourth instar (4.1°C), prepupa (3.6°C), and pupa (7.5°C). Oviposition rates were significantly greater at 5 and 10°C than at 20 and 25°C. Head capsule width significantly increased for each of the four larval instars with a mean of 0.19, 0.26, 0.35, and 0.44 mm, respectively. Laboratory and field data were used to develop a phenology forecasting model to predict the occurrence of all developmental stages of L. osakensis. This model will allow land managers to more accurately predict the optimal timing for L. osakensis larval sampling throughout its established range.
Relation between the food environment and oral health—systematic review
Authors: Mackenbach Joreintje D , Ibouanga Elodie L , van der Veen Monique H , Ziesemer Kirsten A , Pinho Maria G M 
Published: July 2022

AbstractBackgroundThere is increasing evidence that the food environment, i.e. the availability, accessibility, price and promotion of foods and beverages, has a significant influence on oral health through food consumption. With this systematic literature review, we systematically summarize the available evidence on relations between the food environment and oral health outcomes in children and adults.MethodsEnglish-language studies were identified through a systematic literature search, executed by a medical information specialist, on OVID/Medline, Embase, Web of Science and CINAHL. Title and abstract screening, full-text screening and quality assessment [using the Quality Assessment with Diverse Studies (QuADS) tool] were done independently by two authors.ResultsTwenty-three studies were included, of which 1 studied the consumer food environment (food labeling), 3 the community food environment (e.g. number of food stores in the community), 5 the organizational food environment (availability of healthy foods and beverages in schools), 2 the information environment (television advertisements) and 13 government and industry policies related to the food environment (e.g. implementation of a sugar-sweetened beverage tax). Almost all studies found that unhealthy food and beverage environments had adverse effects on oral health, and that policies improving the healthiness of food and beverage environments improved—or would improve in case of a modeling study—oral health.ConclusionsThis systematic literature review provides evidence, although of low to moderate quality and available in a low quantity only, that several aspects of the food environment, especially policies affecting the food environment, are associated with oral health outcomes.
A GP’s clinical reasoning in the context of multimorbidity: beyond the perception of an intuitive approach
Authors: Sader Julia , Diana Alessandro , Coen Matteo , Nendaz Mathieu , Audétat Marie-Claude 
Published: July 2022

Abstract

Introduction
GP’s clinical reasoning processes in the context of patients suffering from multimorbidity are often a process which remains implicit. Therefore, the goal of this case study analysis is to gain a better understanding of the processes at play in the management of patients suffering from multimorbidity.

Methods
A case study analysis, using a qualitative thematic analysis was conducted. This case follows a 54-year-old woman who has been under the care of her GP for almost 10 years and suffers from a number of chronic conditions. The clinical reasoning of an experienced GP who can explicitly unfold his processes was chosen for this case analysis.

Results
Four main themes emerged from this case analysis: The different roles that GPs have to manage; the GP’s cognitive flexibility and continual adaptation of their clinical reasoning processes, the patient’s empowerment, and the challenges related to the collaboration with specialists and healthcare professionals.

Conclusion
This could help GPs gain a clearer understanding of their clinical reasoning processes and motivate them to communicate their findings with others during clinical supervision or teaching. Furthermore, this may emphasize the importance of valuing the role of the primary care physician in the management of multimorbid patients.
Limitations of microbial iron reduction under extreme conditions
Authors: Nixon Sophie L , Bonsall Emily , Cockell Charles S 
Published: July 2022

AbstractMicrobial iron reduction is a widespread and ancient metabolism on Earth, and may plausibly support microbial life on Mars and beyond. Yet, the extreme limits of this metabolism are yet to be defined. To investigate this, we surveyed the recorded limits to microbial iron reduction in a wide range of characterized iron-reducing microorganisms (n = 141), with a focus on pH and temperature. We then calculated Gibbs free energy of common microbially mediated iron reduction reactions across the pH–temperature habitability space to identify thermodynamic limits. Comparing predicted and observed limits, we show that microbial iron reduction is generally reported at extremes of pH or temperature alone, but not when these extremes are combined (with the exception of a small number of acidophilic hyperthermophiles). These patterns leave thermodynamically favourable combinations of pH and temperature apparently unoccupied. The empty spaces could be explained by experimental bias, but they could also be explained by energetic and biochemical limits to iron reduction at combined extremes. Our data allow for a review of our current understanding of the limits to microbial iron reduction at extremes and provide a basis to test more general hypotheses about the extent to which biochemistry establishes the limits to life.
Intersex Activism, Medical Power/Knowledge and the Scalar Limitations of the United Nations
Authors: Garland Fae , Lalor Kay , Travis Mitchell 
Published: July 2022

Abstract
This article considers the extent to which human rights mechanisms can ameliorate intersex rights at a sub-national, or medico-local, level. It engages with both intersex activism and the academy where the United Nations (UN) has become understood as a key mechanism through which to challenge day-to-day practices of healthcare practitioners and bring an end to nontherapeutic surgical and hormonal interventions on intersex infants and children. Using the UK as an example, this article examines how and why the UN’s engagement with intersex has had little effect on the medical regulation of intersex people. To do so, the article draws on legal geography to examine how scale prevents the UN from having a clear and lasting impact on domestic issues – particularly those in healthcare settings. The different ways in which intersex bodies are recognised and regulated at different scales, coupled with the UN’s inability to form dialogue with the institutions of the state, such as the healthcare profession, are problematic barriers to challenge practice at the medico-local scale.
Learning from three decades of Management Strategy Evaluation in South Africa
Authors: de Moor Carryn L , Butterworth Douglas S , Johnston Susan 
Published: July 2022

Abstract
South Africa is well known for being one of the first countries to implement management procedures that had been fully tested using Management Strategy Evaluation (MSE). Beginning in the early 1990s, Operational Management Procedures (OMPs) have been developed and implemented for the fisheries for seven important commercial species. Barring a few teething problems, for the first two decades, South Africa's track record of OMP implementation, with OMP-recommended catch limits being signed off by the responsible Minister without change, was exemplary. The sustainable management of some fisheries using OMPs continues without mishap, with regular reviews. However, the past decade has resulted in a number of deviations of decisions from OMP outputs following the declaration of “Exceptional Circumstances” (ECs). This occurred when a resource moved outside the range of scenarios tested at the time the OMP was developed. The reasons why ECs were declared, the methods used to recommend catch limits during ECs and whether ECs might have been avoided are reviewed. The experience gained over three decades of managing fisheries using MSE provides a basis to assess whether the highly time-intensive task of developing these OMPs has been worth the expected benefits, and to provide recommendations related to lessons learned.
Potential roles of community-based pharmacists in assisting home-quarantined patients with COVID-19 in a resource-challenged setting
Authors: Wibowo Yosi Irawati , Irawati Sylvi , Setiawan Eko , Halim Steven Victoria , Sunderland Bruce , Setiadi Adji Prayitno 
Published: July 2022

Abstract

Objectives
To present the experiences of community-based drug information centre (DIC) pharmacists assisting home-quarantined patients with COVID-19 in Indonesia.

Methods
A prospective case study included home-quarantined patients with suspected/confirmed COVID-19 contacting pharmacists at a DIC in Indonesia in July 2021. Patient characteristics, pharmacist interventions and outcomes were reported.

Key findings
Fifteen home-quarantined patients were screened for COVID-19 and were provided with follow-up services (i.e. medication review and monitoring). Worsening symptoms and/or reduction in oxygen saturation were reported in seven patients where a referral to medical services was made for them. Most patients recovered at follow-up (4–14 days).

Conclusions
Community-based DIC pharmacists potentially contributed to the frontline emergency response, as observed during the COVID-19 crisis in Indonesia.
Components in Meandric Systems and the Infinite Noodle
Authors: Féray Valentin , Thévenin Paul 
Published: July 2022

Abstract
We investigate here the asymptotic behaviour of a large, typical meandric system. More precisely, we show the quenched local convergence of a random uniform meandric system $\boldsymbol {M}_n$ on $2n$ points, as $n \rightarrow \infty $, towards the infinite noodle introduced by Curien et al. [3]. As a consequence, denoting by $cc( \boldsymbol {M}_n)$ the number of connected components of $\boldsymbol {M}_n$, we prove the convergence in probability of $cc(\boldsymbol {M}_n)/n$ to some constant $\kappa $, answering a question raised independently by Goulden–Nica–Puder [8] and Kargin [12]. This result also provides information on the asymptotic geometry of the Hasse diagram of the lattice of non-crossing partitions. Finally, we obtain expressions of the constant $\kappa $ as infinite sums over meanders, which allows us to compute upper and lower approximations of $\kappa $.
Local Systems on Diamonds and p-Adic Vector Bundles
Authors: Mann Lucas , Werner Annette 
Published: July 2022

Abstract
We use Scholze’s framework of diamonds to gain new insights in correspondences between $p$-adic vector bundles and local systems. Such correspondences arise in the context of $p$-adic Simpson theory in the case of vanishing Higgs fields. In the present paper, we provide a detailed analysis of local systems on diamonds for the étale, pro-étale, and the $v$-topology and study the structure sheaves for all three topologies in question. Applied to proper adic spaces of finite type over $\mathbb {C}_p$, this enables us to prove a category equivalence between $\mathbb {C}_p$-local systems with integral models, and modules under the $v$-structure sheaf that modulo each $p^n$ can be trivialized on a proper cover. The flexibility of the $v$-topology together with a descent result on integral models of local systems allows us to prove that the trivializability condition in the module category may be checked on any normal proper cover. This result leads to an extension of the parallel transport theory by Deninger and the second author to vector bundles with numerically flat reduction on a proper normal cover. 2020 MSC: 14G45, 14G22, 11G25.