bluuebunny/crossref_metadata_2025_split huggingface dataset:
LPTD: a novel linear programming-based topology determination method for cryo-EM maps
Authors: Behkamal Bahareh , Naghibzadeh Mahmoud , Pagnani Andrea , Saberi Mohammad Reza , Al Nasr Kamal 
Published: March 2022

Abstract

Summary
Topology determination is one of the most important intermediate steps toward building the atomic structure of proteins from their medium-resolution cryo-electron microscopy (cryo-EM) map. The main goal in the topology determination is to identify correct matches (i.e. assignment and direction) between secondary structure elements (SSEs) (α-helices and β-sheets) detected in a protein sequence and cryo-EM density map. Despite many recent advances in molecular biology technologies, the problem remains a challenging issue. To overcome the problem, this article proposes a linear programming-based topology determination (LPTD) method to solve the secondary structure topology problem in three-dimensional geometrical space. Through modeling of the protein’s sequence with the aid of extracting highly reliable features and a distance-based scoring function, the secondary structure matching problem is transformed into a complete weighted bipartite graph matching problem. Subsequently, an algorithm based on linear programming is developed as a decision-making strategy to extract the true topology (native topology) between all possible topologies. The proposed automatic framework is verified using 12 experimental and 15 simulated α–β proteins. Results demonstrate that LPTD is highly efficient and extremely fast in such a way that for 77% of cases in the dataset, the native topology has been detected in the first rank topology in &lt;2 s. Besides, this method is able to successfully handle large complex proteins with as many as 65 SSEs. Such a large number of SSEs have never been solved with current tools/methods.

Availability and implementation
The LPTD package (source code and data) is publicly available at https://github.com/B-Behkamal/LPTD. Moreover, two test samples as well as the instruction of utilizing the graphical user interface have been provided in the shared readme file.

Supplementary information
Supplementary data are available at Bioinformatics online.
(Re)-Emerging Challenges in Christian Bioethics: Leading Voices in Christian Bioethics
Authors: Iltis Ana 
Published: March 2022

AbstractThis is the third installment in a Christian Bioethics series that gathers leading voices in Christian bioethics to examine the themes and issues they find most pressing. The papers address fundamental theoretical questions about the nature of Christian bioethics itself, long-standing ethical issues that remain significant today, including physician-assisted suicide, euthanasia, the definition of death, the allocation of scarce resources, and finally, more futuristic questions regarding transhumanism. The contributions underscore the enduring significance of Christian engagement in bioethics.
Tragic Choices, Revisited: COVID-19 and the Hidden Ethics of Rationing
Authors: Ryan Maura A 
Published: March 2022

Abstract
Early in the COVID-19 pandemic in the United States, concern that there could be a shortage of ventilators raised the possibility of rationing care. Denying patients life-saving care captures our moral imagination, prompting the demand for a defensible framework of ethical principles for determining who will live and who will die. Behind the moral dilemma posed by the shortage of a particular medical good lies a broad moral geography encompassing important and often unarticulated societal values, as well as assumptions about the nature and purpose of health care and the consequences of long-standing choices about health care as a social good. This article explores what COVID-19 has exposed concerning values and choices around health care in the United States. Employing the lens of Catholic Social Thought, it argues for an approach to rationing that is grounded in respect for human dignity, committed to distributing social goods in light of the common good, and self-conscious about the construction of vulnerability to illness and death.
Evolution of anticipatory effects mediated by epigenetic changes
Authors: Kronholm Ilkka 
Published: March 2022

Abstract
Anticipatory effects mediated by epigenetic changes occur when parents modify the phenotype of their offspring by making epigenetic changes in their gametes, guided by information from an environmental cue. To investigate when do anticipatory effects mediated by epigenetic changes evolve in a fluctuating environment, I use an individual-based simulation model with explicit genetic architecture. The model allows for the population to respond to environmental changes by evolving plasticity, bet hedging, or by tracking the environment with genetic adaptation, in addition to the evolution of anticipatory effects. The results show that anticipatory effects evolve when the environmental cue provides reliable information about the environment and the environment changes at intermediate rates, provided that fitness costs of anticipatory effects are rather low. Moreover, evolution of anticipatory effects is quite robust to different genetic architectures when reliability of the environmental cue is high. Anticipatory effects always give smaller fitness benefits than within-generation plasticity, suggesting a possible reason for generally small observed anticipatory effects in empirical studies.
Multisystem inflammatory syndrome-related refractory cardiogenic shock in adults after coronavirus disease 2019 infection: a case series
Authors: Tonon David , Landrieux Clementine , Van Den Plas Soline , Harlé Jean-Robert , Lepidi Hubert , Bourenne Jérémy , Jaussaud Nicolas , Lagier David 
Published: March 2022

Abstract

Background
A novel multisystem inflammatory syndrome in children (MIS-C) temporally associated with the coronavirus disease 2019 (COVID-19) infection has been reported, arising weeks after the peak incidence of COVID-19 infection in adults. Patients with MIS-C have been reported to have cardiac involvement and clinical features overlapping with other acute inflammatory syndromes such as Kawasaki disease, toxic shock syndrome, and macrophage activation syndrome. Multisystem inflammatory syndrome in children may follow COVID-19 infection, most of the time after its asymptomatic form, even though it can lead to serious and life-threatening illness.

Case summary
In this case series, we discuss two cases of young adults with no former medical history who fit with the criteria defined in MIS-C. They both developed a refractory cardiogenic shock and required intensive care treatment including mechanical circulatory support, specifically the use of venous–arterial extracorporeal membrane oxygenation. They were both treated early with intravenous immune globulin and adjunctive high-dose steroids. They recovered ad integrum in less than 2 weeks.

Discussion
Multisystem inflammatory syndrome in children occurs 2–4 weeks after infection with severe acute respiratory syndrome coronavirus 2. Patients with MIS-C should ideally be managed in an intensive care environment since rapid clinical deterioration may occur. It would be preferable to have a multidisciplinary care to improve outcomes. Patients should be monitored for shock. Elucidating the mechanism of this new entity may have importance for understanding COVID-19 far beyond the patients who have had MIS-C to date. The pathogenesis seems to involve post-infectious immune dysregulation so early administration intravenous immune globulin associated with corticosteroids appears appropriate. It implies early recognition of the syndrome even in young adults.
An unusual pair: coronary artery fistula and coronary sinus ostium stenosis as a cause of refractory angina
Authors: Stefanescu Schmidt Ada C. , Redwood Tahira , Alonso-Gonzalez Rafael , Mezody Melitta , Horlick Eric M. 
Published: March 2022

Abstract

Background
Coronary fistula are rare and often present in early adulthood with symptoms of right heart overload from left to right shunting or ischaemia in the distal coronary bed due to coronary steal.

Case summary
A 73-year-old lady with prior history of supraventricular tachycardia, dyslipidemia and a right coronary artery (RCA) to coronary sinus (CS) fistula, presented with progressive angina. She did not have evidence of ischaemia in the RCA territory on nuclear imaging, and cardiac computed tomography (CT) did not show coronary artery disease but revealed a significantly dilated CS and coronary venous tree. She was found to have CS ostial stenosis and, under transesophageal echocardiographic guidance, underwent successful balloon angioplasty of the CS ostium, with decompression of the coronary venous circulation and resolution of her angina.

Discussion
Coronary fistula draining to the CS are rare, and association with CS ostial stenosis has been reported very infrequently. CS ostial stenosis can cause elevated coronary venous pressure, leading to decreased global coronary perfusion and symptoms of angina or heart failure. Previous case reports of coronary fistula and CS ostial stenosis were treated with either medical therapy or surgery, and our case is the first to our knowledge to report successful percutaneous treatment.
Rapid resolution of severe pericardial effusion using anakinra in a patient with COVID-19 vaccine-related acute pericarditis relapse: a case report
Authors: Perna Francesco , Verecchia Elena , Pinnacchio Gaetano , Gerardino Laura , Brucato Antonio , Manna Raffaele 
Published: March 2022

Abstract

Background
Pericarditis, along with myocarditis, is being increasingly reported after the coronavirus disease 2019 (COVID-19) vaccine, but the best treatment strategy in this specific setting is still unclear.

Case summary
We report a case of acute pericarditis after the second dose of mRNA COVID-19 vaccine with recurrence of large pericardial effusion after a previous pericardiocentesis and anti-inflammatory drugs tapering. The patient was successfully treated with the recombinant interleukin-1 receptor antagonist anakinra, with full reabsorption of the pericardial effusion and an abrupt drop of the inflammatory markers within 72 h. The patient was discharged a few days later, with a further decrease of the inflammatory markers and no residual symptoms.

Discussion
Anakinra is being increasingly used in the treatment of recurrent pericarditis due to its capability to interrupt the autoinflammatory response leading to deleterious cytokine storms. On account of its high efficacy and rapid onset, it has been reported to rapidly reverse large inflammatory pericardial effusions. Pericarditis and myocarditis have been reported after the COVID-19 vaccine, but this is the first case of COVID-19 vaccine-related pericarditis and pericardial effusion successfully treated with anakinra, avoiding a second pericardiocentesis.
Case report: paradoxically reversible perfusion defects on vasodilator stress imaging in a case of metastatic coronary compression
Authors: Kwiatkowski Sara G , Aulakh Vikrant S , Kapoor Kunal , Wei Xin , Grizzard John D , Hundley W Gregory , Gordon Sarah W , Trankle Cory R 
Published: March 2022

Abstract

Background
Patients with malignancy who experience metastasis to cardiac structures may exhibit ST-segment elevations and acute coronary syndrome (ACS) through poorly understood pathophysiologic mechanisms. We present a case in which vasodilator stress cardiovascular magnetic resonance provides unique insight into one such patient who suffered from recurrent episodes resembling ACS.

Case summary
A 58-year-old male with metastatic lung adenocarcinoma presented with refractory angina and dynamic inferior electrocardiogram changes. The patient was referred for adenosine stress cardiovascular magnetic resonance, revealing multiple territories of abnormal perfusion during rest with improvement during adenosine infusion. Subsequent computed tomography displayed tumour encasement of the right coronary artery. Taken together, vasodilator-responsive extrinsic compression of multiple epicardial coronary arteries was suspected. Outpatient oncology follow-up for chemoimmunotherapy initiation was arranged with the hope that reducing tumour burden might alleviate coronary compression. However, in the ensuing months, the patient’s disease advanced beyond the point of which his symptoms could be controlled medically, and he was ultimately enrolled in hospice care.

Discussion
Encasement of coronary arteries can result in anginal symptoms if their position impairs coronary arterial flow. The presented case highlights the unique manner in which these lesions might behave on stress cardiac magnetic resonance imaging. Clinicians who encounter such unusual findings on vasodilator stress imaging should consider metastatic lesions to the cardiac structures on the differential diagnosis.
An SPS Dispute without Science? The Fukushima Case and the Dichotomy of Science/Non-Science Obligations under the SPS Agreement
Authors: Lin Ching-Fu , Naiki Yoshiko 
Published: March 2022

Abstract
The interface between science and law has been much debated in various fields of international law and the World Trade Organization (WTO) has been one of the main forums. Notably, WTO disputes, such as EC – Hormones and EC – Biotech, have drawn controversies and criticisms over the role of science in WTO law. Korea – Radionuclides – also known as the Fukushima case – calls upon us to reconsider an under-analysed perspective regarding science and law. While the Fukushima accident marked the first massive radionuclide release into the ocean with significant uncertainties and complexities, Korea – Radionuclides did not touch upon any ‘science-based’ obligations under the Agreement on the Application of Sanitary and Phytosanitary Measures (SPS Agreement). Thus, it stands out as a unique dispute in the 25 years of the SPS case law. This article unpacks Korea – Radionuclides, challenging and rethinking the assumed dichotomy between science-based and non-science-based obligations under the SPS Agreement. Our critical examination of Korea – Radionuclides suggests that science plays an important role even in the discussions of non-science-based obligations. In contrast to the conventional wisdom of the science/non-science dichotomy, we further argue that the normative integrity and raison d’être of the SPS Agreement in fact rest upon the inextricable nexus and integration between science-based and non-science-based obligations.
The intestinal microbiota influences the microenvironment of metastatic colon cancer by targeting miRNAs
Authors: Zhou Shihai , Zhu Canhua , Jin Shaoqin , Cui Chunhui , Xiao Linghui , Yang Zhi , Wang Xi , Yu Jinlong 
Published: March 2022

Abstract
This study aimed to investigate the molecular mechanisms through which the intestinal microbiota and microRNAs (miRNAs) participate in colon cancer metastasis. Intestinal flora data, and the GSE29621 (messenger RNA/long non-coding RNA [mRNA/lncRNA]) and GSE29622 (miRNA) datasets, were downloaded from The Cancer Gene Atlas and Gene Expression Omnibus databases, respectively. Immune-related cells in M1 vs. M0 samples were analyzed using the Wilcoxon test. Furthermore, an lncRNA-miRNA-mRNA (competing endogenous RNA [ceRNA]) network was constructed, and survival analysis of RNAs in the network was performed. A total of 16 miRNA-genus co-expression pairs containing eight microbial genera and 15 miRNAs were screened; notably, Porphyromonas and Bifidobacterium spp. were found to be associated with most miRNAs, and has-miR-3943 was targeted by most microbial genera. Furthermore, five immune cell types, including activated natural killer cells, M1 macrophages, resting mast cells, activated mast cells and neutrophils, were differentially accumulated between the M1 and M0 groups. Enrichment analysis suggested that mRNAs related to colon cancer metastasis were mainly involved in pathways related to bacterial and immune responses. Survival analysis revealed that TMEM176A and PALM3 in the ceRNA network were significantly associated with the prognosis of patients with colon cancer. In conclusion, this study revealed a potential mechanism by which the intestinal microbiota influences the colon cancer microenvironment by targeting miRNAs.
Intestinal microbiota research from a global perspective
Authors: Wallenborn Jordyn T , Vonaesch Pascale 
Published: March 2022

Abstract
The intestinal microbiota plays a crucial role in health and changes in its composition are linked with major global human diseases. Fully understanding what shapes the human intestinal microbiota composition and knowing ways of modulating the composition are critical for promotion of life-course health, combating diseases, and reducing global health disparities. We aim to provide a foundation for understanding what shapes the human intestinal microbiota on an individual and global scale, and how interventions could utilize this information to promote life-course health and reduce global health disparities. We briefly review experiences within the first 1,000 days of life and how long-term exposures to environmental elements or geographic specific cultures have lasting impacts on the intestinal microbiota. We also discuss major public health threats linked to the intestinal microbiota, including antimicrobial resistance and disappearing microbial diversity due to globalization. In order to promote global health, we argue that the interplay of the larger ecosystem with intestinal microbiota research should be utilized for future research and urge for global efforts to conserve microbial diversity.
Insights into the underlying mechanisms and clinical management of microscopic colitis in relation to other gastrointestinal disorders
Authors: Liu Yuanbin , Chen Mingkai 
Published: March 2022

Abstract
Microscopic colitis (MC) is a chronic inflammatory disease of the large intestine and as a relatively late recognized condition, its relationship with other disorders of the gastrointestinal tract is gradually being understood and investigated. As a multifactorial disease, MC interacts with inflammatory bowel disease, celiac disease, and irritable bowel syndrome through genetic overlap, immunological factors, and gut microflora. The risk of colorectal cancer was significantly lower in MC, gastrointestinal infections increased the risk of developing MC, and there was an inverse association between Helicobacter pylori infection and MC. A variety of associations are found between MC and other gastrointestinal disorders, where aspects such as genetic effects, resemblance of immunological profiles, and intestinal microecology are potential mechanisms behind the relationships. Clinicians should be aware of these connections to achieve a better understanding and management of MC.
Development of an Electronic Frailty Index for Hospitalized Older Adults in Sweden
Authors: Mak Jonathan K L , Hägg Sara , Eriksdotter Maria , Annetorp Martin , Kuja-Halkola Ralf , Kananen Laura , Boström Anne-Marie , Kivipelto Miia , Metzner Carina , Bäck Jerlardtz Viktoria , Engström Malin , Johnson Peter , Lundberg Lars Göran , Åkesson Elisabet , Sühl Öberg Carina , Olsson Maria , Cederholm Tommy , Jylhävä Juulia , Religa Dorota 
Published: March 2022

Abstract

Background
Frailty assessment in the Swedish health system relies on the Clinical Frailty Scale (CFS), but it requires training, in-person evaluation, and is often missing in medical records. We aimed to develop an electronic frailty index (eFI) from routinely collected electronic health records (EHRs) and assess its association with adverse outcomes in hospitalized older adults.

Methods
EHRs were extracted for 18 225 patients with unplanned admissions between 1 March 2020 and 17 June 2021 from 9 geriatric clinics in Stockholm, Sweden. A 48-item eFI was constructed using diagnostic codes, functioning and other health indicators, and laboratory data. The CFS, Hospital Frailty Risk Score, and Charlson Comorbidity Index were used for comparative assessment of the eFI. We modeled in-hospital mortality and 30-day readmission using logistic regression; 30-day and 6-month mortality using Cox regression; and length of stay using linear regression.

Results
Thirteen thousand one hundred and eighty-eight patients were included in analyses (mean age 83.1 years). A 0.03 increment in the eFI was associated with higher risks of in-hospital (odds ratio: 1.65; 95% confidence interval: 1.54–1.78), 30-day (hazard ratio [HR]: 1.43; 1.38–1.48), and 6-month mortality (HR: 1.34; 1.31–1.37) adjusted for age and sex. Of the frailty and comorbidity measures, the eFI had the highest area under receiver operating characteristic curve for in-hospital mortality of 0.813. Higher eFI was associated with longer length of stay, but had a rather poor discrimination for 30-day readmission.

Conclusions
An EHR-based eFI has robust associations with adverse outcomes, suggesting that it can be used in risk stratification in hospitalized older adults.
Using a Nature-Based Virtual Reality Environment for Improving Mood States and Cognitive Engagement in Older Adults: A Mixed-Method Feasibility Study
Authors: Kalantari Saleh , Bill Xu Tong , Mostafavi Armin , Lee Angella , Barankevich Ruth , Boot Walter R , Czaja Sara J 
Published: March 2022

Abstract

Background and Objectives
Exposure to nature and nature-based imagery has been shown to improve mood states and stave off cognitive decline in older adults. Even “micro-doses” of natural scenery can provide beneficial effects in situations where more extensive interactions with nature are not feasible. In the current study, we evaluated the use of virtual reality (VR) for delivering interactive nature-based content with the goal of prompting active engagement and improving mood states in older adults.

Research Design and Methods
The researchers developed a novel VR environment that combined 360-degree videos of natural areas and botanical gardens with interactive digital features that allowed users to engage with aspects of the environment. We recruited 50 older adults to try out this VR environment and measured changes in mood states and attitudes toward VR from before versus after the sessions. We controlled for variables such as age, education level, and exposure to nature in everyday life, and we looked for differences in responses to the VR among participants with cognitive impairments (CIs) versus without, and participants with physical disabilities versus without.

Results
The findings indicated significant improvements in “good” mood and “calm” mood dimensions after exposure to the VR, as well as improvements in attitudes toward the technology. These positive outcomes were significantly greater for participants with physical disabilities compared to those without disabilities. No differences were found in the responses of participants with CIs versus those without. Exit interviews provided a variety of helpful suggestions about ways to improve the VR equipment design and content to meet the needs of an older adult population.

Discussion and Implications
The study demonstrates that VR can provide a cost-effective, noninvasive, and nonpharmaceutical approach for improving the lives of older adults in both clinical and recreational settings, particularly when real-world access to nature is limited.