bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ten Years of Collaborative Progress in the Quest for Orthologs
Authors: Linard Benjamin , Ebersberger Ingo , McGlynn Shawn E , Glover Natasha , Mochizuki Tomohiro , Patricio Mateus , Lecompte Odile , Nevers Yannis , Thomas Paul D , Gabaldón Toni , Sonnhammer Erik , Dessimoz Christophe , Uchiyama Ikuo ,   QFO Consortium, Altenhoff Adrian , Ouangraoua Aida , Vesztrocy Alex Warwick , Linard Benjamin , Dessimoz Christophe , Szklarczyk Damian , Durand Dannie , Emms David , Moi David , Thybert David , Sonnhammer Erik , Kriventseva Evgenia , Tang Haiming , Chiba Hirokazu , Uchiyama Ikuo , Ebersberger Ingo , Huerta-Cepas Jaime , Fernandez-Breis Jesualdo Tomas , Blake Judith A , Pryszcz Leszek , Martin Maria-Jesus , Houben Marina Marcet , Patricio Mateus , Muffato Matthieu , Glover Natasha , Lecompte Odile , Thomas Paul D , Schiffer Philipp , Capella-Gutierrez Salvador , Cosentino Salvatore , McGlynn Shawn E , Kuraku Shigehiro , Forslund Sofia , Kelly Steven , Lewis Suzanna , Jones Tamsin , de Farias Tarcisio Mendes , Maeda Taro , Gabaldon Toni , Iwasaki Wataru , Pearson William , Wang Yan , Nevers Yannis , Hara Yuichiro 
Published: April 2021

AbstractAccurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology—evolutionary relatedness—is in many cases readily determined based on sequence similarity analysis. By contrast, whether or not two genes directly descended from a common ancestor by a speciation event (orthologs) or duplication event (paralogs) is more challenging, yet provides critical information on the history of a gene. Since 2009, this task has been the focus of the Quest for Orthologs (QFO) Consortium. The sixth QFO meeting took place in Okazaki, Japan in conjunction with the 67th National Institute for Basic Biology conference. Here, we report recent advances, applications, and oncoming challenges that were discussed during the conference. Steady progress has been made toward standardization and scalability of new and existing tools. A feature of the conference was the presentation of a panel of accessible tools for phylogenetic profiling and several developments to bring orthology beyond the gene unit—from domains to networks. This meeting brought into light several challenges to come: leveraging orthology computations to get the most of the incoming avalanche of genomic data, integrating orthology from domain to biological network levels, building better gene models, and adapting orthology approaches to the broad evolutionary and genomic diversity recognized in different forms of life and viruses.
An Examination of Day-to-Day and Intraindividual Pain Variability in Low Back Pain
Authors: Wesolowicz Danielle M , Bishop Mark D , Robinson Michael E 
Published: April 2021

AbstractObjectiveThis study aimed to capture day-to-day changes in pain intensity in individuals with low back pain (LBP), which may be indicative of patients’ ability to modulate their pain levels. A secondary aim was to explore the presence of latent subgroups characterized by pain level, intraindividual pain variability, and change in pain over a 14-day period.SubjectsParticipants were 54 adults with self-reported LBP recruited from outpatient physical therapy clinics and the community.MethodsOver the course of 14 days, participants completed daily measures of pain intensity, catastrophizing, pain self-efficacy, and negative affect. Change in pain intensity as well as total amount of intraindividual pain variability were also calculated.ResultsDaily increases in maladaptive coping and affective responses (i.e., higher catastrophizing, higher negative affect, lower pain self-efficacy) were associated with increases in pain intensity. A hierarchical cluster analysis revealed three subgroups: 1) moderate pain intensity, moderate pain variability, increase in pain over time; 2) low pain intensity, low pain variability, no change in pain over time; and 3) moderate pain intensity, high pain variability, decrease in pain over time. Cluster 2 demonstrated more adaptive coping and affective responses at baseline and during the 14-day period, and clusters 1 and 3 did not differ in their coping or affective responses.ConclusionsThese findings provide support that day-to-day changes in pain, coping, and affective responses are meaningful and provide additional evidence of pain variability as a potential phenotypic characteristic.
Protein-based lateral flow assays for COVID-19 detection
Authors: Mahmoudinobar Farbod , Britton Dustin , Montclare Jin Kim 
Published: April 2021

Abstract
To combat the enduring and dangerous spread of COVID-19, many innovations to rapid diagnostics have been developed based on proteinprotein interactions of the SARS-CoV-2 spike and nucleocapsid proteins to increase testing accessibility. These antigen tests have most prominently been developed using the lateral flow assay (LFA) test platform which has the benefit of administration at point-of-care, delivering quick results, lower cost, and does not require skilled personnel. However, they have gained criticism for an inferior sensitivity. In the last year, much attention has been given to creating a rapid LFA test for detection of COVID-19 antigens that can address its high limit of detection while retaining the advantages of rapid antibodyantigen interaction. In this review, a summary of these proteinprotein interactions as well as the challenges, benefits, and recent improvements to protein based LFA for detection of COVID-19 are discussed.
Correlates of COVID-19 vaccine hesitancy in Austria: trust and the government
Authors: Schernhammer Eva , Weitzer Jakob , Laubichler Manfred D , Birmann Brenda M , Bertau Martin , Zenk Lukas , Caniglia Guido , Jäger Carlo C , Steiner Gerald 
Published: April 2021

Abstract

Background
With the coronavirus disease 2019 (COVID-19) pandemic surging and new mutations evolving, trust in vaccines is essential.

Methods
We explored correlates of vaccine hesitancy, considering political believes and psychosocial concepts, conducting a non-probability quota-sampled online survey with 1007 Austrians.

Results
We identified several important correlates of vaccine hesitancy, ranging from demographics to complex factors such as voting behavior or trust in the government. Among those with hesitancy towards a COVID-19 vaccine, having voted for opposition parties (opp) or not voted (novote) were (95% Confidence Intervall (CI)opp, 1.44–2.95) to 2.25-times (95%CInovote, 1.53–3.30) that of having voted for governing parties. Only 46.2% trusted the Austrian government to provide safe vaccines, and 80.7% requested independent scientific evaluations regarding vaccine safety to increase willingness to vaccine.

Conclusions
Contrary to expected, psychosocial dimensions were only weakly correlated with vaccine hesitancy. However, the strong correlation between distrust in the vaccine and distrust in authorities suggests a common cause of disengagement from public discourse.
Dyslipidaemia and mortality in COVID-19 patients: a meta-analysis
Authors: Zuin M , Rigatelli G , Bilato C , Cervellati C , Zuliani G , Roncon L 
Published: April 2021

Summary

Background
The prevalence and prognostic implications of pre-existing dyslipidaemia in patients infected by the SARS-CoV-2 remain unclear.

Aim
To assess the prevalence and mortality risk in COVID-19 patients with pre-existing dyslipidaemia.

Design
Systematic review and meta-analysis.

Methods
Preferred reporting items for systematic reviews and meta-analyses guidelines were followed in abstracting data and assessing validity. We searched MEDLINE and Scopus to locate all the articles published up to 31 January 2021, reporting data on dyslipidaemia among COVID-19 survivors and non-survivors. The pooled prevalence of dyslipidaemia was calculated using a random-effects model and presenting the related 95% confidence interval (CI), while the mortality risk was estimated using the Mantel–Haenszel random-effect models with odds ratio (OR) and related 95% CI. Statistical heterogeneity was measured using the Higgins I2 statistic.

Results
Of about 18 studies, enrolling 74 132 COVID-19 patients (mean age 70.6 years), met the inclusion criteria and were included in the final analysis. The pooled prevalence of dyslipidaemia was 17.5% of cases (95% CI: 12.3–24.3%, P &lt; 0.0001), with high heterogeneity (I2 = 98.7%). Pre-existing dyslipidaemia was significantly associated with higher risk of short-term death (OR: 1.69, 95% CI: 1.19–2.41, P = 0.003), with high heterogeneity (I2 = 88.7%). Due to publication bias, according to the Trim-and-Fill method, the corrected random-effect ORs resulted 1.61, 95% CI 1.13–2.28, P &lt; 0.0001 (one studies trimmed).

Conclusion
Dyslipidaemia represents a major comorbidity in about 18% of COVID-19 patients but it is associated with a 60% increase of short-term mortality risk.
A Model of Endogenous Risk Intolerance and LSAPs: Asset Prices and Aggregate Demand in a “COVID-19” Shock
Authors: Caballero Ricardo J , Simsek Alp 
Published: April 2021

AbstractWe theoretically investigate the interaction of endogenous risk intolerance and monetary policy following a large recessionary shock. As asset prices dip, risk-tolerant agents’ wealth share declines. This decline reduces the market’s risk tolerance and triggers a downward loop in asset prices and aggregate demand when the interest rate policy is constrained. In this context, large-scale asset purchases are effective because they transfer unwanted risk to the government’s balance sheet. These effects are sizable when the model is calibrated to match the estimates of aggregate asset demand inelasticity. The COVID-19 shock illustrates the environment we seek to capture.
IMPROVEMENTS OF 111IN SPECT IMAGES RECONSTRUCTED WITH SPARSELY ACQUIRED PROJECTIONS BY DEEP LEARNING GENERATED SYNTHETIC PROJECTIONS
Authors: Rydén T , Emma W , Van Essen M , Svensson J , Bernhardt P 
Published: April 2021

Abstract
The aim was to improve single-photon emission computed tomography (SPECT) quality for sparsely acquired 111In projections by adding deep learning generated synthetic intermediate projections (SIPs). Method: The recently constructed deep convolutional network for generating synthetic intermediate projections (CUSIP) was used for improving 20 sparsely acquired 111In-octreotide SPECTs. Reconstruction was performed with 120 (120P) or 30 (30P) projections, or 120 projections with 90 SIPs generated from 30 projections (30–120SIP). The SPECT reconstructions were performed with attenuation, scatter and collimator response corrections. Postfiltered 30P reconstructed SPECT was also analyzed. Image quality were quantitatively evaluated with root-mean-square error, peak signal-to-noise ratio and structural similarity index metrics. Result: The 30–120SIP reconstructed SPECT had statistically significant improved image quality parameters compared to 30P reconstructed SPECT with and without post filtering. The images visual appearance was similar to slightly filtered 120P SPECTs. Thereby, substantial acquisition time reduction with SIPs seems possible without image quality degradation.
FREQUENCY RESPONSE AND DISTORTION PROPERTIES OF RECONSTRUCTION ALGORITHMS IN COMPUTED TOMOGRAPHY
Authors: Larsson Joel , Båth Magnus , Thilander-Klang Anne 
Published: April 2021

Abstract
Denoising reconstruction techniques can introduce nonlinear properties into computed tomography (CT) systems. These nonlinear algorithms introduce distortion which affects the assessment of the resolution of the system. The purpose of the present study was to decouple and investigate amplitude modulation and waveform distortion in reconstruction algorithms in CT. The methodology developed by Wells, J. R. and Dobbins, J. T. III [Frequency response and distortion properties of nonlinear image processing algorithms and the importance of imaging context. Med. Phys. 40, 091906 (2013)] was adapted to CT reconstruction algorithms. The CT simulating program ASTRA Toolbox© for MATLAB™ was used for the reconstruction of the sinusoidal wave functions. Filtered back projection and the simultaneous iterative reconstruction technique were investigated with simple nonlinear mechanisms: a median filter and a non-negative constraint, respectively. The native reconstruction algorithms were not free from nonlinear waveform distortion, however, none of the metrics showed any dependence on the contrast-to-noise ratio (CNR). Furthermore, the algorithms including nonlinear mechanisms showed a clear and specific CNR dependence, indicating the necessity for distortion analysis in nonlinear CT reconstruction.
Combining carbon and oxygen isotopic signatures to identify ozone-induced declines in tree water-use efficiency
Authors: Li Pin , Feng Zhaozhong , Shang Bo , Uddling Johan 
Published: April 2021

Abstract
Ground-level ozone (O3) pollution affects the plant carbon and water balance, but the relative contributions of impaired photosynthesis and the loss of stomatal functioning to the O3-induced reductions in water-use efficiency (WUE) remain unclear. We combined the leaf stable dual isotopic signatures of carbon (δ13C) and oxygen (δ18O) with related instantaneous gas exchange performance to determine the effects of O3 dose on the net photosynthetic rate (An), stomatal conductance (gs) and intrinsic WUE (iWUE = An/gs) in four tree species (one being a hybrid) exposed to five O3 levels. The iWUE declined for each step increase in O3 level, reflecting progressive loss of the coupling between leaf carbon gain and water loss. In ambient compared with charcoal-filtered air, the decreased iWUE was associated with reductions in both An and gs (i.e., decreased δ13C and increased δ18O). In elevated O3 treatments, however, the iWUE declines were caused by reduced An at constant or increased gs. The results show that the dual isotope approach provides a robust way to gather time-integrated information on how O3 pollution affects leaf gas exchange. Our study highlights that O3-induced decoupling between photosynthesis and stomatal regulation causes large and progressive declines in the WUE of forest trees, demonstrating the need for incorporating this hitherto unaccounted for effect into vegetation models.
Combining Ethics Inquiry and Clinical Experience in a Premedical Health Care Ethics Internship
Authors: McLean Margaret R. , Bottrell Melissa M. 
Published: April 2021

Problem
The professional formation of physicians begins in the premedical years, and educators are now recommending that medical ethics and humanities courses be considered essential components to becoming a physician rather than elective prerequisites for medical school admission. As a result, questions have arisen about how to teach students ethical reasoning skills before their professional training, as they have limited opportunities now to develop these skills and the related competencies in a real-world medical context.

Approach
The authors describe Santa Clara University’s Health Care Ethics Internship (HCEI), an undergraduate college experience that emphasizes ethical inquiry and immerses students in health care settings to foster deep learning. The HCEI includes mentored clinical rotations integrated with classroom inquiry into ethical theory, structured reflection, and professional development considerations. A survey of former students (academic years 2001–2002 to 2017–2018) explored their perceptions of these program components and the impact of the experience on their preprofessional readiness, career choice, and professional capabilities.

Outcomes
Of 185 former students who could be contacted, 89 (48.1%) completed the survey. Students reported that the HCEI: (1) assisted them in gaining admission to medical school, (2) had a positive influence on their career decisions, (3) increased their professional capabilities, (4) helped them develop preprofessional competencies, (5) gave them knowledge and experience they used in their personal and professional ethical decision making, and (6) increased their moral sensitivity and ethical responsibility.

Next Steps
Integrating clinical rotations into ethics education exposes premedical students to real-world ethical questions, helps them develop a nuanced understanding of a health care career, and prepares them for the medical school admissions process. Other universities should consider implementing a similar program to prime their students for continued professional and moral development during medical school and residency.
Medicine, Machines, and Medical Education
Authors: Wartman Steven A. 
Published: April 2021

While advances in science and technology continue to be at the forefront of the evolution of medical practice, the 21st century is also undergoing a unique and profound cultural shift that is changing the very nature of what it means to be a medical professional, namely humankind’s transition to an information-based internet society. Medical care will increasingly depend on computer-generated probabilities guided and supported by a growing variety of individuals in health care–related professions, including statisticians, technologists, and information managers. Perhaps the biggest challenge to the profession will come from the erosion of professional autonomy, driven by smart machines, social networks, and internet search engines. As a result of these and other changes, physicians are facing a systematic loss of control, often without the direct input and leadership of the profession itself.
In this commentary, the author urges the profession to adopt several strategies, including shifting its focus from reimbursement to the care patients value most, meaningfully addressing critical issues in health policy, becoming the definitive source for publicly available medical information, reimagining medical education, and overhauling the existing accreditation and licensing systems. Medical education must go beyond a focus on physicians whose professional identity revolves around being the exclusive source of medical knowledge. In the digitized 21st century, medical education should emphasize the centrality of the humanistic interface with patients such that the doctor–patient relationship is paramount in the complex medical world of machines and social media. Removing the roadblocks to successful professional reform is no small task, but the process can begin with a grassroots movement that empowers physicians and facilitates organizational and behavioral change. Failure to take action may well hasten the diminishment of patient care and the profession’s trusted role in society.
Efficacy and toxicity of intravesical Bacillus Calmette-Guérin therapy in elderly patients with non-muscle-invasive bladder cancer
Authors: Matsuoka Yuki , Taoka Rikiya , Kohashiguchi Kana , Tohi Yoichiro , Miyauchi Yasuyuki , Kato Takuma , Tsunemori Hiroyuki , Ueda Nobufumi , Sugimoto Mikio 
Published: April 2021

Abstract

Objectives:
This study aimed to compare the efficacy and toxicity of intravesical Bacillus Calmette-Guérin (BCG) therapy between elderly and younger patients with non-muscle-invasive bladder cancer (NMIBC).

Material and methods:
This retrospective study included 87 NMIBC patients who received intravesical BCG between January 2011 and December 2018. We compared the treatment outcomes of patients ≥75 and <75 years old. Our primary endpoint was intravesical recurrence-free survival after treatment. The secondary endpoint was the toxicity caused by intravesical BCG.

Results:
The elderly and younger patients included 38 and 49 patients with mean ages of 80.6 and 66.3 years (p < 0.01), respectively. Their baseline parameters were similar, aside from age. The elderly and younger patients’ 5-year recurrence-free survival rates were 59.4% and 51.6%, respectively, and were not significantly different (log-rank test, p = 0.72). Moderate to severe pain on micturition requiring prescription medications was observed more frequently in the elderly patients than in the younger patients (p < 0.01). No elderly patients required hospitalization for any adverse events. However, 3 (6.1%) younger patients were treated for urinary tract infection in the hospital.

Conclusions:
The efficacy and toxicity of intravesical BCG therapy for NMIBC patients are not associated with age. Therefore, elderly patients with high-risk NMIBC should be treated in the same manner as younger patients in clinical practice.
Comparison of the clinical usefulness of different urinary tests for the initial detection of bladder cancer: a systematic review
Authors: Sciarra Alessandro , Di Lascio Giovanni , Del Giudice Francesco , Leoncini Pier Paolo , Salciccia Stefano , Gentilucci Alessandro , Porreca Angelo , Chung Benjamin I. , Di Pierro Giovanni , Busetto Gian Maria , De Berardinis Ettore , Maggi Martina 
Published: April 2021

Abstract

Objectives:
The standard initial approach in patients with hematuria or other symptoms suggestive of bladder cancer (BC) is a combination of cystoscopy and urine cytology (UC); however, UC has low sensitivity particularly in low-grade tumors. The aim of the present review was to critically analyze and compare results in the literature of promising molecular urinary tests for the initial diagnosis of BC.

Methods:
We searched in the Medline and Cochrane Library databases for literature from January 2009 to January 2019, following the PRISMAguidelines.

Results:
In terms of sensitivity, ImmunoCyt showed the highest mean and median value, higher than UC. All tests analyses showed higher mean and median sensitivity when compared with UC. In terms of specificity, only UroVysion and Microsatellite analyses showed mean and median values similar to those of UC, whereas for all other tests, the specificity was lower than UC. It is evident that the sensitivity of UC is particularly low in low grade BC. Urinary tests mainly had improved sensitivity when compared to UC, and ImmunoCyt and UroVysion had the highest improvement in low grade tumors.

Conclusions:
Most of the proposed molecular markers were able to improve the sensitivity with similar or lower specificity when compared to UC. However, variability of results among the different studies was strong. Thus, as of now, none of these markers presented evidences so as to be accepted by international guidelines for diagnosis of BC.
Preliminary Study of Coping, Perceived Control, and Depressive Symptoms in Youth with Sickle Cell Anemia
Authors: Prussien Kemar V. , Siciliano Rachel E. , Ciriegio Abagail E. , Lee Chelsea A. , DeBaun Michael R. , Jordan Lori C. , Compas Bruce E. 
Published: April 2021

ABSTRACT:

Objective:
The primary objective of this study was to test perceived controllability of stressors as a moderator of the association between coping and depressive symptoms in children and adolescents with sickle cell anemia (SCA).

Method:
Twenty-eight children and adolescents (Mage = 11.71, SD = 4.31; 60.7% female) with SCA were enrolled. Caregivers provided reports of child and adolescent coping using the Response to Stress Questionnaire (RSQ), perceived control of stressors using the RSQ, and depressive symptoms using the Child Behavior Checklist. Children and adolescents also completed Wechsler assessments of working memory and verbal comprehension.

Results:
Secondary control coping (i.e., cognitive reappraisal, positive thinking, acceptance, and distraction) was a significant predictor of depressive symptoms such that greater use of secondary control coping was related to fewer reported depressive symptoms when accounting for perceived control of stress and neurocognitive variables. Furthermore, perceived control of peer-related stress was a significant moderator of the association between secondary control coping and depressive symptoms such that there was a significant negative association of secondary control coping with depressive symptoms only for low perceived control.

Conclusion:
Secondary control coping may be particularly helpful for reducing depressive symptoms when adolescents' peer-related stressors are perceived as uncontrollable. Interventions to reduce internalizing problems in this population should consider teaching children and adolescents secondary control coping skills in addition to skills in identifying uncontrollable sources of stress.