bluuebunny/crossref_metadata_2025_split huggingface dataset:
Universal prediction of cell-cycle position using transfer learning
Authors: Zheng Shijie C. , Stein-O’Brien Genevieve , Augustin Jonathan J. , Slosberg Jared , Carosso Giovanni A. , Winer Briana , Shin Gloria , Bjornsson Hans T. , Goff Loyal A. , Hansen Kasper D. 
Published: January 2022

Abstract
Background
The cell cycle is a highly conserved, continuous process which controls faithful replication and division of cells. Single-cell technologies have enabled increasingly precise measurements of the cell cycle both as a biological process of interest and as a possible confounding factor. Despite its importance and conservation, there is no universally applicable approach to infer position in the cell cycle with high-resolution from single-cell RNA-seq data.

Results
Here, we present tricycle, an R/Bioconductor package, to address this challenge by leveraging key features of the biology of the cell cycle, the mathematical properties of principal component analysis of periodic functions, and the use of transfer learning. We estimate a cell-cycle embedding using a fixed reference dataset and project new data into this reference embedding, an approach that overcomes key limitations of learning a dataset-dependent embedding. Tricycle then predicts a cell-specific position in the cell cycle based on the data projection. The accuracy of tricycle compares favorably to gold-standard experimental assays, which generally require specialized measurements in specifically constructed in vitro systems. Using internal controls which are available for any dataset, we show that tricycle predictions generalize to datasets with multiple cell types, across tissues, species, and even sequencing assays.

Conclusions
Tricycle generalizes across datasets and is highly scalable and applicable to atlas-level single-cell RNA-seq data.
VirStrain: a strain identification tool for RNA viruses
Authors: Liao Herui , Cai Dehan , Sun Yanni 
Published: January 2022

AbstractViruses change constantly during replication, leading to high intra-species diversity. Although many changes are neutral or deleterious, some can confer on the virus different biological properties such as better adaptability. In addition, viral genotypes often have associated metadata, such as host residence, which can help with inferring viral transmission during pandemics. Thus, subspecies analysis can provide important insights into virus characterization. Here, we present VirStrain, a tool taking short reads as input with viral strain composition as output. We rigorously test VirStrain on multiple simulated and real virus sequencing datasets. VirStrain outperforms the state-of-the-art tools in both sensitivity and accuracy.
MOntelukast as a potential CHondroprotective treatment following Anterior cruciate ligament reconstruction (MOCHA Trial): study protocol for a double-blind, randomized, placebo-controlled clinical trial
Authors: Jacobs Cale A. , Conley Caitlin E. W. , Kraus Virginia Byers , Lansdown Drew A. , Lau Brian C. , Li Xiaojuan , Majumdar Sharmila , Spindler Kurt P. , Lemaster Nicole G. , Stone Austin V. 
Published: January 2022

Abstract
Background
After anterior cruciate ligament (ACL) reconstruction, patient-reported outcomes are improved 10 years post-surgery; however, cytokine concentrations remain elevated years after surgery with over 80% of those with combined ACL and meniscus injuries having posttraumatic osteoarthritis (PTOA) within 10–15 years. The purpose of this multicenter, randomized, placebo-controlled trial is to assess whether a 6-month course of oral montelukast after ACL reconstruction reduces systemic markers of inflammation and biochemical and imaging biomarkers of cartilage degradation.

Methods
We will enroll 30 individuals undergoing primary ACL reconstruction to participate in this IRB-approved multicenter clinical trial. This trial will target those at greatest risk of a more rapid PTOA onset (age range 25–50 with concomitant meniscus injury). Patients will be randomly assigned to a group instructed to take 10 mg of montelukast daily for 6 months following ACL reconstruction or placebo. Patients will be assessed prior to surgery and 1, 6, and 12 months following surgery. To determine if montelukast alters systemic inflammation following surgery, we will compare systemic concentrations of prostaglandin E2, monocyte chemoattractant protein-1, and pro-inflammatory cytokines between groups. We will also compare degradative changes on magnetic resonance imaging (MRI) collected 1 and 12 months following surgery between groups with reductions in early biomarkers of cartilage degradation assessed with urinary biomarkers of type II collagen breakdown and bony remodeling.

Discussion
There is a complex interplay between the pro-inflammatory intra-articular environment, underlying bone remodeling, and progressive cartilage degradation. PTOA affects multiple tissues and appears to be more similar to rheumatoid arthritis than osteoarthritis with respect to inflammation. There is currently no treatment to delay or prevent PTOA after ACL injury. Since there is a larger and more persistent inflammatory response after ACL reconstruction than the initial insult of injury, treatment may need to be initiated after surgery, sustained over a period of time, and target multiple mechanisms in order to successfully alter the disease process. This study will assess whether a 6-month postoperative course of oral montelukast affects multiple PTOA mechanisms. Because montelukast administration can be safely sustained for long durations and offers a low-cost treatment option, should it be proven effective in the current trial, these results can be immediately incorporated into clinical practice.

Trial registration
ClinicalTrials.govNCT04572256. Registered on October 1, 2020.
Baseline susceptibility of a wild strain of main vectors of leishmaniasis to WHO-recommended insecticides in southeastern Iran
Authors: Salim Abadi Yaser , Sanei-Dehkordi Alireza , Hakimi Parizi Maryam , Aghaei Afshar Abass , Sharifi Iraj , Gorouhi Mohammad Amin , Shirani-Bidabadi Leila , Alizadeh Ismaeil 
Published: January 2022

AbstractBackgroundIn Iran, both cutaneous leishmaniases (CL) and visceral leishmaniases (VL) are endemic, recording one of the 10 highest CL prevalence in the world. Parasites are transmitted by the bite of infectedPhlebotomussand fly females. Several sand fly species have been identified as vectors in the studied region of Kerman province. Residual spraying to control adult sand flies, is the only way to decrease the spreading of the diseases but, following control treatment against malaria vectors in endemic areas in Iran, resistance or tolerance to insecticides emerged in some sand fly species. The objective of this study was to survey insecticides susceptibility levels of 3 vector species in wild sand fly populations in different foci of the diseases in Kerman province.Ph. sergenti, andPh. papatasirespectively vectors of anthroponotic and zoonotic cutaneous leishmaniases and for the first timePh. alexandrione of the anthroponotic visceral leishmaniases vector were tested against: deltamethrin 0.05%, malathion 5%, dichloro-diphenyl-trichloroethane (DDT) 4%.Materials and methodsIn leishmaniases endemic areas species specific sand fly sites were selected in Kerman province, and specimens were collected by manual aspirators at different time intervals during the spring and summer 2019. All the susceptibility tests were performed according to the WHO tube test recommended procedure.ResultsTwenty five blood-fed female sand flies from the region's prevalent species were used in each pooled test replicates. All wild specimens died within 60 min of exposure to DDT 4%, malathion 5%, and deltamethrin 0.05%, but the mortality rate forPh. papatasiexposed to malathion and DDT was 91.6% and 66.6%, respectively.ConclusionAccording to current study results,Ph. sergentiandPh. alexandriare highly susceptible to all the evaluated insecticides in the study areas. However,Ph. papatasiwas susceptible to deltamethrin (100% mortality), possibly resistant or tolerant to malathion (91.6% mortality), and confirmed to be resistant to DDT (66.6% mortality).Graphical Abstract
Role of the S100 protein family in rheumatoid arthritis
Authors: Wu Yuan-yuan , Li Xiao-feng , Wu Sha , Niu Xue-ni , Yin Su-qin , Huang Cheng , Li Jun 
Published: January 2022

AbstractRheumatoid arthritis is a chronic systemic autoimmune disease characterized by synovial hyperplasia, inflammatory cell infiltration, and proliferation of inflammatory tissue (angiogranuloma). The destruction of joints and surrounding tissues eventually causes joint deformities and dysfunction or even loss. The S100 protein family is one of the biggest subtribes in the calcium-binding protein family and has more than 20 members. The overexpression of most S100 proteins in rheumatoid arthritis is closely related to its pathogenesis. This paper reviews the relationship between S100 proteins and the occurrence and development of rheumatoid arthritis. It will provide insights into the development of new clinical diagnostic markers and therapeutic targets for rheumatoid arthritis.
Differences between Staphylococcus aureus nasal carriage and IgE-sensitization to Staphylococcus aureus enterotoxin on risk factors and effects in adult population
Authors: Park Han-Ki , Yoo Seok-Ju , Kim Taek Soo , Kim Byung-Keun , Jang Sekyung , Kim Sung Yeon , Lee Kwan 
Published: January 2022

Abstract
Background
Staphylococcus aureus (SA) nasal carriage (SA carriage) and IgE-sensitization to SA enterotoxin (SE IgE-sensitization) are known to be associated with chronic airway disease.

Objective
This study aimed to evaluate the differences in risk factors, type 2 inflammation and respiratory symptoms between SA carriage and SE IgE-sensitization.

Methods
We conducted a cross-sectional study of a community-based adult population to evaluate the environmental exposure and health impact of the Pohang Industrial Complex, Korea. Participants were examined based on self-reported questionnaires, nasal swab, and blood sampling.

Results
There were 307 participants, and the overall prevalence of SA carriage and SE IgE-sensitization was 26.1% (80/307) and 25.7% (79/307), respectively. An urban environment was significantly correlated with SA carriage, whereas age and obesity were significantly correlated with SE IgE-sensitization. SA carriage was not associated with an increase in total IgE and blood eosinophil count, whereas SE IgE-sensitization was associated with an increased total IgE and blood eosinophil count. SA carriage was significantly correlated with cough persisting for more than three weeks (OR, 3.044; 95% CI, 1.137–8.153) and sputum (OR, 2.429; 95% CI, 1.008–5.854). SE IgE-sensitization was a significant correlation with only sputum (OR, 2.452; 95% CI, 1.066–5.640). SA carriage and SE IgE-sensitization showed a synergistic effect on the prevalence of cough and sputum.

Conclusion
SA carriage was associated with the urban environment, and SE IgE-sensitization was associated with the elderly and obesity. SA carriage and SE IgE-sensitization had different correlation with type 2 inflammation and airway symptoms.
Modified oral food challenge protocol approach in the diagnosis of Food Protein-Induced Enterocolitis Syndrome
Authors: Sultafa Jessica , McKibbon Lundy , Roberts Hannah , Sarraj Jumana , Kim Harold 
Published: January 2022

Abstract
Background
Food Protein-Induced Enterocolitis Syndrome (FPIES) is a non-IgE mediated food allergy most commonly presenting in infants. The most common food triggers include soy, cow’s milk and grains. Symptoms may include intractable vomiting, diarrhea, lethargy, pallor, abdominal distention, hypotension and/or shock. Oral food challenges (OFCs) given at food protein dose of 0.06–0.6 g/kg in 3 equivalent doses administered over a few hours are recommended in guidelines to confirm a diagnosis.

Case presentation
The patient is a 6-month-old girl with a history of severe FPIES symptoms to egg. In our clinic, we perform OFC with 1/100 serving dose on visit 1 and then increase the dose monthly. The patient takes the tolerated dose daily at home between visits. An OFC to baked egg at 1/100 of a serving was performed and was well-tolerated on her initial visit. The patient remained on the same dose upon returning home. Within 1-week, she developed FPIES symptoms including watery diarrhea and severe emesis requiring ondansetron. She required an Emergency Department visit for one of the reactions.

Conclusions
Our patient had severe FPIES symptoms with a small amount of egg. We believe that administration of three large food challenge doses on one clinic visit, as guidelines currently suggest, does not allow adequate time for symptoms to appear. Our patient likely would have suffered a severe reaction. Also, this guidelines protocol does not allow for monitoring of more delayed or chronic FPIES. We propose a modified protocol to OFCs with cautious up-dosing to allow for safer OFCs and monitoring of chronic FPIES. We have implemented an OFC approach where only one food challenge dose (starting with 1/100 of final dose) is given at each visit. The up-titration of the dose is completed every 4-weeks with one dose only. When the serving sized dose is reached and tolerated, the food can be maintained in the diet.
Cytomegalovirus pneumonitis amid COVID-19 chaos: the hidden enemy—a case report
Authors: Aldehaim Abdulkarim Yousef , Alfaifi Abrar Mohammed , Hussain Seham Nehdal , Alrajhi Abdulaziz Mohammed 
Published: January 2022

Abstract
Background
The effect of coronavirus disease 2019 on the immune system is increasingly recognized. When severe, it causes immune dysregulation that may favor other infections, including Herpesviridae. Cytomegalovirus shares many innate immune pathways with severe acute respiratory syndrome coronavirus 2, which may potentiate each other. We describe a case of cytomegalovirus pneumonitis complicating the course of coronavirus disease 2019 in a patient with systemic lupus erythematosus/systemic sclerosis overlap and usual interstitial pneumonia, mimicking interstitial lung disease exacerbation. To the best of the authors’ knowledge, this is the first case to be reported worldwide in the setting of connective tissue disease-associated interstitial lung disease.

Case description
We describe the case of a 47-year-old white/Yemeni female who is known to have systemic lupus erythematosus/scleroderma overlap and usual interstitial pneumonia who was initially admitted with severe coronavirus disease 2019 pneumonia mandating intensive care. After initial improvement, it was later complicated with cytomegalovirus pneumonitis, mimicking interstitial lung disease exacerbation. The case was successfully treated with ganciclovir.

Conclusion
Intriguingly, severe acute respiratory syndrome coronavirus 2 and cytomegalovirus may potentiate each other, since they share some innate immune pathways. Subjects with severe coronavirus disease 2019 and underlying connective tissue diseases and those who are immunosuppressed carry higher risk compared with other cohorts, which may mandate active surveillance for cytomegalovirus coinfection or reactivation. Among various immunosuppressive therapies that has been tried for cytokine storm, use of anti-interleukin-6 inhibitors in the aforementioned population may carry more harm than previously thought, which may suggest that is reasonable to omit its use in treating this group with coronavirus disease 2019. This case underlines an underrecognized and underreported cause of morbidity and mortality during the course of severe coronavirus disease 2019 and will help to alert clinicians of its occurrence.
Quality of care indicator performance was minimally changed in 2020 despite the COVID-19 pandemic
Authors: Konson Alexander , Kuniavsky Michael , Bronshtein Olga , Goldschmidt Nethanel , Hanhart Shuli , Mahalla Hannah , Peri Shir , Dollberg Shaul , Niv Yaron 
Published: January 2022

Abstract
Background
In 2020, the COVID-19 pandemic affected healthcare systems throughout the world, including the management of patients and compliance rates of quality indicators.

Objective
To measure the impact in Israel of the COVID-19 pandemic on the indicator-relevant caseload and compliance rates of the quality indicators reported by medical services providers within the Israeli National Program for Quality Indicators (NPQI).

Methods
Data was collected from the reports made to the NPQI by participating hospitals and medical service providers. The indicator results for the number of cases and compliance rates for 2019 were compared to those from 2020. We assessed and compared the results of the quality indicators in general hospitals, geriatric hospitals and departments, psychiatric hospitals and departments, emergency medical services (EMS), and Mother and Baby health centers.

Results
We found a decrease in measurable cases in 2020 relative to 2019, especially in geriatric hospitals. In most indicators, compliance rates rose in 2020. Few indicators had lower compliance rates associated with COVID-19 pandemic regulations.

Conclusions and policy implications
Routine medical activity decreased in Israel in 2020 in comparison to 2019, as reflected by a decrease in cases, but compliance rates were better in most indicators. The results of our study imply that the functioning of healthcare quality measurement programs should not be interrupted during a pandemic. This not only allows measuring of the healthcare system's performance during a crisis, but also may assist in maintaining a high level of healthcare quality.
Experiences of weight stigmatization in the Israeli healthcare system among overweight and obese individuals
Authors: Sagi-Dain Lena , Echar Moran , Paska-Davis Naama 
Published: January 2022

Abstract
Introduction
Weight stigmatization, a common phenomenon in the healthcare system, exerts numerous adverse consequences on patients' wellbeing. The objective of this study was to estimate the extent and characteristics of weight stigmatization in Israel, based on the reports of overweight and obese individuals.

Methods
This study was performed by distribution of a cross-sectional open anonymous survey in social media platforms, targeting respondents with body mass index over 25 kg/m2. The questionnaire consisted of Likert-scale based as well as open-ended questions, evaluating the experience during past medical appointments. Our primary outcome was the prevalence of disrespectful treatment. Subgroup analysis was performed by various demographic characteristics.

Results
Of the 1697 respondents, 59.0% reported frequent experiences of disrespectful approach, and 48.6% noted receiving suboptimal treatment related to excess weight. Insulting, insensitive and judgmental comments were noted by 58%, stemming from diverse healthcare disciplines, while 29.3% noted office equipment not suitable for overweight people. Avoidance of a needed medical appointment was reported by 40.5%, significantly associated with past adverse experiences of weight stigmatization in the healthcare system. The respondents offered numerous suggestions to improve the existing situation, including education of the medical personnel, thorough research of obesity, and establishment of specific guidelines for approach to patients with excess weight.

Conclusion
Weight stigmatization is prevalent in Israeli healthcare system; thus, decreasing the rates of this phenomenon should be an important national goal. Formal education about the wide prevalence and adverse effects of weight stigmatization should be practiced by academic institutions, professional organizations, and regulatory bodies. Straightforward policies with continuing supervision should be endorsed by the healthcare system to prevent weight-based discrimination. Finally, appropriate-size equipment for obese patients should become one of the requirements for accreditation of medical centers and facilities.
Snapshot compressive spectral - depth imaging based on light field
Authors: Ding Xiaoming , Yan QiangQiang , Hu Liang , Zhou Shubo , Wei Ruyi , Wang Xiaocheng , Li Yupeng 
Published: January 2022

AbstractThis paper proposes a snapshot Compressed Light Field Imaging Spectrometer based on compressed sensing and light field concept, which can acquire the two-dimensional spatial distribution, depth estimation and spectral intensity of input scenes simultaneously. The primary structure of the system contains fore optics, coded aperture, dispersion element and light field sensor. The detected data can record the coded mixture spatial-spectral information of the input scene with direction information of light rays. The datacube containing depth estimation can be recovered with the compressed sensing and digital refocus framework. We establish the mathematical model of the system and conduct simulations for verification. The reconstruction strategy is demonstrated for the simulation data.
From the Fan-KKM principle to extended real-valued equilibria and to variational-hemivariational inequalities with application to nonmonotone contact problems
Authors: Gwinner Joachim 
Published: January 2022

AbstractThis paper starts off by the celebrated Knaster–Kuratowski–Mazurkiewicz principle in the formulation by Ky Fan. We provide a novel variant of this principle and build an existence theory for extended real-valued equilibrium problems with general, then monotone and pseudomonotone bifunctions. We develop our existence theory first in general topological vector spaces, then in reflexive Banach spaces, where we investigate the issue of coerciveness for existence on unbounded sets. Thereafter we use the Clarke generalized differential calculus for locally Lipschitz functions and derive existence results for nonlinear variational-hemivariational inequalities and hemivariational quasivariational inequalities. As application, we treat a unilateral contact problem in solid mechanics with nonmonotone friction.
Intellectual capital factors at work in Dominican firms: understanding their influence
Authors: Gómez-Valenzuela Víctor 
Published: January 2022

AbstractFrom an empirical-based perspective, this paper explores the influence of intellectual capital factors on the performance of firms in the Dominican Republic. A Likert scale from one to seven was used to capture firms’ sensitivity to human, structural and relational capital factors. An exploratory factor analysis was carried out using the method of principal components with VARIMAX rotation. The final factorial scores were standardized to execute the regression analysis. Structural capital factors appear to be the dominant intellectual capital components within the Dominican context. Human capital factors play a vital role in performance in manufacturing and in-services firms, and relational capital factors are significant in determining their performance. This research contributes to the regional literature on intellectual capital studies in Latin America and the Caribbean. It puts forward some specific points related to the role of intellectual capital factors in explaining firms’ performance in small open economies such as that of the Dominican Republic.