bluuebunny/crossref_metadata_2025_split huggingface dataset:
SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks
Authors: Csabai Luca , Fazekas Dávid , Kadlecsik Tamás , Szalay-Bekő Máté , Bohár Balázs , Madgwick Matthew , Módos Dezső , Ölbei Márton , Gul Lejla , Sudhakar Padhmanand , Kubisch János , Oyeyemi Oyebode James , Liska Orsolya , Ari Eszter , Hotzi Bernadette , Billes Viktor A , Molnár Eszter , Földvári-Nagy László , Csályi Kitti , Demeter Amanda , Pápai Nóra , Koltai Mihály , Varga Máté , Lenti Katalin , Farkas Illés J , Türei Dénes , Csermely Péter , Vellai Tibor , Korcsmáros Tamás 
Published: September 2021

Abstract
Signaling networks represent the molecular mechanisms controlling a cell's response to various internal or external stimuli. Most currently available signaling databases contain only a part of the complex network of intertwining pathways, leaving out key interactions or processes. Hence, we have developed SignaLink3 (http://signalink.org/), a value-added knowledge-base that provides manually curated data on signaling pathways and integrated data from several types of databases (interaction, regulation, localisation, disease, etc.) for humans, and three major animal model organisms. SignaLink3 contains over 400 000 newly added human protein-protein interactions resulting in a total of 700 000 interactions for Homo sapiens, making it one of the largest integrated signaling network resources. Next to H. sapiens, SignaLink3 is the only current signaling network resource to provide regulatory information for the model species Caenorhabditis elegans and Danio rerio, and the largest resource for Drosophila melanogaster. Compared to previous versions, we have integrated gene expression data as well as subcellular localization of the interactors, therefore uniquely allowing tissue-, or compartment-specific pathway interaction analysis to create more accurate models. Data is freely available for download in widely used formats, including CSV, PSI-MI TAB or SQL.
General one-loop contributions to the decay $H\rightarrow \nu_l\bar{\nu}_l\gamma$
Authors: Phan Khiem Hong , Hue Le Tho , Tran Dzung Tri 
Published: September 2021

Abstract
General one-loop contributions to the decay amplitudes $H\rightarrow \nu_l\bar{\nu}_l\gamma$ are presented, considering all possible contributions of additional heavy vector gauge bosons, fermions, and charged (and also neutral) scalar particles appearing in the loop diagrams. Moreover, the results can be applied directly when extra neutrinos (apart from three ones in the standard model) are taken into account in final states. Analytic results are expressed in terms of Passarino–Veltman scalar functions which can be evaluated numerically using $\texttt{LoopTools}$. In the standard model framework, these analytical results are generated and cross-checked with previous computations. We find that our results are well consistent with these computations. Within the standard model limit, phenomenological results for the decay channels are also studied using the present input parameters at the Large Hadron Collider. Lastly, the calculation is also applied to the Two Higgs Doublet Model framework as another example.
Asporin regulated by miR-26b-5p mediates chondrocyte senescence and exacerbates osteoarthritis progression via TGF-β1/Smad2 pathway
Authors: Liu Liangliang , Zhao Chang , Zhang Haiyan , Lu Yuheng , Luo Bingsheng , Yao Zihao , Shao Yan , Zeng Hua , Zeng Chun , Zhang Rongkai , Fang Hang , Pan Jianying , Bai Xiaochun , Cai Daozhang 
Published: September 2021

Abstract

Objectives
This study aimed to investigate the role and mechanism of asporin in modulating chondrocyte senescence in OA pathology.

Methods
Asporin and senescence-related hallmark expression were examined in human and experimental OA mouse cartilage samples. Twelve-week-old male C57 mice were administered with recombinant protein (rm-asporin)- or asporin-siRNA-expressing lentiviruses via intra-articular injection once a week after destabilization of the medial meniscus (DMM) surgery to induce OA. Cartilage damage was measured using the Osteoarthritis Research Society International score. Senescence-associated β-galactosidase (SA-β-Gal) staining, γH2AX, p21 and p16INK4a were analysed by immunofluorescence staining and western blot to assess the specific role of asporin in chondrocyte senescence. The TGF-β1–Smad2 signalling pathway and miR-26b-5p were further evaluated to explore the mechanism of asporin in OA.

Results
Asporin was upregulated in articular chondrocytes of OA patients and DMM mice and accompanied by accumulation of senescent cells. Asporin overexpression exaggerated OA progression, whereas silencing asporin restored chondrocyte homeostasis and deferred chondrocyte senescence, leading to markedly attenuated DMM-induced OA. Cellular and molecular analyses showed that asporin can be inhibited by miR-26b-5p, which was significantly downregulated in OA cartilage, leading to exacerbation of experimental OA partially through inhibition of TGF-β1–Smad2 signalling in chondrocytes.

Conclusions
Our findings indicate that asporin plays an essential role in chondrocyte senescence and OA pathogenesis. Upregulated by miR-26b-5p, asporin inhibits the TGF-β1–Smad2 pathway to accelerate chondrocyte senescence and exacerbate cartilage degeneration. Targeting the miR-26b-5p–asporin–Smad2 axis may serve as a practical therapeutic strategy to delay chondrocyte senescence and OA development.
Embedding Racism: City Government Credit Ratings and the Institutionalization of Race in Markets
Authors: Norris Davon 
Published: September 2021

Abstract
How does racism and racial inequality manifest in contemporary markets? Leveraging insights from the sociology of race and economic sociology, I highlight how ratings and scores operate as key mechanisms institutionalizing racism in markets according to an epistemology of racial ignorance. While ratings and scores give a veneer of individualized objectivity, their actual inputs reflect decades of racial disadvantage. The use of such racialized inputs embeds historical racism in ratings allowing racial inequality to persist and escape cognition as seemingly race-neutral inputs “explain away” racial disparities. I demonstrate this argument using an original dataset to approximate the evaluative criteria used in rating city government creditworthiness. I show that cities with larger proportions of Black residents receive worse credit ratings when controlling for the non-racialized inputs in the evaluative criteria. This racial disparity only attenuates after the inclusion of the criterion median family income, which I argue is a fundamentally racialized input owing to the legacy of racism in the United States. Establishing this point provides key theoretical takeaways at the intersection of race and economic sociology as scores and ratings pervade more corners of social life and push up against the epistemological seams of how we understand and identify inequality.
The Impact of Volunteering at a Family Camp for Children and Adolescents With Cancer: The Experience of Pediatric Intensive Care Nurses
Authors: Butterworth Lori , Nasr Annette , Pyke-Grimm Kimberly A. , Swisher Darcy , Johnson Kelly 
Published: September 2021

OBJECTIVE
This study explored the experience of pediatric ICU (PICU) nurses who volunteered at a camp for families of children and adolescents with cancer.

BACKGROUND
PICU nurses are at risk of developing symptoms of posttraumatic stress disorder, compassion fatigue, depression, and burnout due to exposure(s) to traumatic events. Spending time with patients, families, and nurse colleagues at camp may reduce the effects of this exposure.

METHODS
A qualitative descriptive study was conducted using content analysis. Fifteen nurse participants completed a precamp questionnaire and semistructured focus groups immediately following camp. Individual interviews were conducted 6 months after camp.

RESULTS
Three categories emerged: 1) personal factors, changes in the nurses themselves; 2) patient and family factors, changes in how nurses perceived patients and families; and 3) work-related factors, relationships with colleagues.

CONCLUSIONS
Supporting PICU nurses to participate with patients, families, and colleagues outside of the hospital may reduce burnout and support nurses' well-being.
Computational systematics of nutritional support of vaccination against viral and bacterial pathogens as prolegomena to vaccinations against COVID-19
Authors: Torshin Ivan Y. , Gromova Olga A. , Chuchalin Alexander G. 
Published: September 2021

AbstractA total of 6,628 PUBMED-registered publications on the relationships between the effects of vaccination and the provision of micronutrients have been studied by methods of topological analysis of text data. In case of insufficient intake of certain micronutrients, the functioning of the acquired immunity is disrupted resulting in an imbalance of populations of T-cells CD4+/CD8+ and of B-lymphocytes. Nutritional supplements of folate, vitamins A, D and B12, which are recognized regulators of cell division, support a wide range of lymphocyte populations. Trace elements zinc, iron, selenium, manganese and omega-3 polyunsaturated fatty acids are also important for supporting the mechanisms of acquired immunity. The data presented show that a course intake of these micronutrients by patients planning vaccination can significantly improve its effectiveness. In particular, these micronutrients can increase the titers of antibodies to pathogens, and to reduce the percentage of patients who still contract infection after vaccination. Supplements of these micronutrients can also contribute to the safety of vaccination: to prevent malaise and, in the unfortunate case of contracting infection despite the vaccine, to reduce the severity of the course and the mortality from the corresponding infection.
COVID-19 epidemics monitored through the logarithmic growth rate and SIR model
Authors: Konishi Tomokazu 
Published: September 2021

AbstractBackgroundThe SIR model is often used to analyse and forecast the expansion of an epidemic. In this model, the number of patients exponentially increases and decreases, resulting in two phases. Therefore, in these phases, the logarithm of infectious patients changes at a constant rate, the logarithmic growth rate K. However, in the case of the coronavirus disease 2019 (COVID19) epidemic, K never remains constant but increases and decreases linearly; therefore, the SIR model does not fit that seen in reality. We would like to clarify the cause of this phenomenon and predict the occurrence of COVID19 epidemics.MethodsWe simulated a situation in which smaller epidemics were repeated with short time intervals. The results were compared with the epidemic data from 279 countries and regions.ResultsIn the simulations, the K values increased and decreased linearly, similar to the real data. Because the previous peak covered the initial increase in the epidemic, K did not increase as much as expected; rather, the difference in the basic reproduction number R0 appeared in the slope of increasing K. Additionally, the mean infectious time τ appeared in the negative peaks of K. By using the R0 and τ estimated from the changes in K, changes in the number of patients could be approximated using the SIR model. This supports the appropriateness of the model for evaluating COVID-19 epidemics. By using the model, the distributions of the parameters were identified. On average, an epidemic started every eleven days in a country. The worldwide mean R0 was 2.9; however, this value showed an exponential character and could thus increase explosively. In addition, the average τ was 12 days; this is not the native value but represents a shortened period because of the isolation of patients. As τ represents the half-life, the infectious time varies among patients; hence, prior testing should be performed before isolation is lifted. The changes in K represented the state of epidemics and were several weeks to a month ahead of the changes in the number of confirmed cases. In the actual data, when K was positive on consecutive days, the number of patients increased a few weeks later. In addition, if the negative peaks of K could not be reduced to as small as 0.1, the number of patients remained high. Thus, the number of K-positive days and mean infectious time had a clear correlation with the total number of patients. In such cases, mortality, which was lognormally distributed, with a mean of 1.7%, increased. To control the epidemic, it is important to observe K daily, not to allow K to remain positive continuously, and to terminate a peak with a series of K-negative days. To do this, it was necessary to shorten τ by finding and isolating a patient earlier. The effectiveness of the countermeasures is apparent in τ. The effect of vaccination, in terms of controlling the epidemic, was limited.
Time-dependent prediction of mortality and cytomegalovirus reactivation after allogeneic hematopoietic cell transplantation using machine learning
Authors: Eisenberg Lisa ,   the XplOit consortium, Brossette Christian , Rauch Jochen , Grandjean Andrea , Ottinger Hellmut , Rissland Jürgen , Schwarz Ulf , Graf Norbert , Beelen Dietrich W. , Kiefer Stephan , Pfeifer Nico , Turki Amin T. 
Published: September 2021

AbstractAllogeneic hematopoietic cell transplantation (HCT) effectively treats high-risk hematologic diseases but can entail HCT-specific complications, which may be minimized by appropriate patient management, supported by accurate, individual risk estimation. However, almost all HCT risk scores are limited to a single risk assessment before HCT without incorporation of additional data. We developed machine learning models which integrate both baseline patient data and time-dependent laboratory measurements to individually predict mortality and cytomegalovirus (CMV) reactivation after HCT at multiple time points per patient. These gradient boosting machine models provide well-calibrated, time-dependent risk predictions and achieved areas under the receiver-operating characteristic of 0.92 and 0.83 and areas under the precision-recall curve of 0.58 and 0.62 for prediction of mortality and CMV reactivation, respectively, in a 21-day time window. Both models were successfully validated in a prospective, non-interventional study and performed on par with expert hematologists in a pilot comparison.
Vaccination or restriction?: COVID-19 vaccine hesitancy and vaccine passports
Authors: Okamoto Shohei , Kamimura Kazuki , Komamura Kohei 
Published: September 2021

AbstractObjectivesWhile the development of vaccines against the novel coronavirus (COVID-19) brought the hope of establishing herd immunity, which might help end the global pandemic, vaccine hesitancy can hinder the progress towards herd immunity. In this study, we assess the determinants of vaccine hesitancy, reasons for hesitation, and effectiveness of vaccine passports in relaxing public health restrictions.MethodsThrough an online survey that includes a conjoint experiment of a demographically representative sample of 5,000 Japanese adults aged 20–74, we assess the determinants of vaccine hesitancy, reasons for hesitation, and effectiveness of hypothetical vaccine passports.ResultsWe found that about 30% of respondents did not intend to vaccinate or have not yet decided, with major reasons for vaccine hesitancy being related to concerns about the safety and side effects of the vaccine. In line with previous findings, younger age, lower socioeconomic status, and psychological factors such as weaker COVID-19 fear were associated with vaccine hesitancy. The easing of public health restrictions such as travel, wearing face masks, and dining out at night was associated with an increase in vaccine acceptance by 4–10%.ConclusionVaccine hesitancy can be reduced by mitigating the concerns about vaccine safety and side effects, as well as by relaxing public health restrictions. However, the feasibility of vaccine passports needs to be sufficiently assessed, taking the ethical issues of passports and the public health impacts of the relaxation of restrictions into careful consideration.Strengths and limitations of this study□This study includes timely data on COVID-19 vaccine hesitancy, obtained from a demographically representative sample of 5,000 Japanese adults.□A conjoint experiment allows assessing the effectiveness of easing public health restrictions on vaccine acceptance.□Actual behaviour may diverge from the survey responses or fluctuate due to the pandemic situation and the timing of the survey.□Results may not be applicable in other countries, since the pandemic situation, government responses to the pandemic, and reasons for vaccine hesitancy can vary across countries.
Ontogeny of plasma lipid metabolism in pregnancy and early childhood: a longitudinal population study
Authors: Burugupalli Satvika , Smith Adam Alexander T. , Olshansky Gavriel , Huynh Kevin , Giles Corey , Paul Sudip , Nguyen Anh , Duong Thy , Mellett Natalie , Cinel Michelle , Mir Sartaj Ahmad , Chen Li , Wenk Markus R. , Karnani Neerja , Collier Fiona , Saffery Richard , Vuillermin Peter , Ponsonby Anne-Louise , Burgner David , Meikle Peter J. ,   Barwon Infant Study Investigator team
Published: September 2021

AbstractBackgroundThere is mounting evidence thatin uteroand early life exposures may predispose an individual to metabolic disorders in later life; and dysregulation of lipid metabolism is critical in such outcomes. However, there is limited knowledge about lipid metabolism and factors causing lipid dysregulation in early life that could result in adverse health outcomes in later life. In this study, we aim to understand the lipid metabolism in pregnancy, and from birth to four years.Methods and findingsWe performed comprehensive lipid profiling of 1074 mother-child dyads in the Barwon Infant Study (BIS), a population based pre-birth cohort and measured 776 distinct lipid species across 42 lipid classes using ultra high-performance liquid chromatography (UHPLC). We measured lipids in 1032 maternal serum samples at 28 weeks’ gestation, 893 cord serum samples at birth, 793, 735, and 511 plasma samples at six, twelve months, and four years, respectively. The lipidome differed between mother and newborn and changed markedly with increasing postnatal age. Cord serum was enriched with long chain poly-unsaturated fatty acids (LC-PUFAs), and corresponding cholesteryl esters relative to the maternal serum. Alkenyl-phosphatidylethanolamine species containing LC-PUFAs increased with postnatal age, whereas the corresponding lysophospholipids and triglycerides decreased. We performed regression analyses to investigate the associations of cord serum lipid species with birth factors: gestational age, birth weight, mode of birth and duration of labor. Majority of the cord serum lipids were strongly associated with gestational age and birth weight, with most lipids showing opposing associations. Each mode of birth showed an independent association with cord serum lipids.ConclusionsThere were marked changes in the plasma lipidome over the first four years of life. This study sheds light on lipid metabolism in infancy and early childhood and provide a framework to define the relationship between lipid metabolism and health outcomes in early childhood.Funding StatementThis work was supported by the A*STAR-NHMRC joint call funding (1711624031).
Toward Using Twitter Data to Monitor Covid-19 Vaccine Safety in Pregnancy
Authors: Klein Ari Z. , O’Connor Karen , Gonzalez-Hernandez Graciela 
Published: September 2021

AbstractBackgroundCoronavirus Disease 2019 (Covid-19) during pregnancy is associated with an increased risk of maternal death, intensive care unit (ICU) admission, and preterm birth; however, many people who are pregnant refuse to receive Covid-19 vaccination because of a lack of safety data.ObjectiveThe objective of this preliminary study was to assess whether we could identify (1) users who have reported on Twitter that they received Covid-19 vaccination during pregnancy or the periconception period, and (2) reports of their pregnancy outcomes.MethodsWe searched for reports of Covid-19 vaccination in a large collection of tweets posted by users who have announced their pregnancy on Twitter. To help determine if users were vaccinated during pregnancy, we drew upon a natural language processing (NLP) tool that estimates the timeframe of the prenatal period. For users who posted tweets with a timestamp indicating they were vaccinated during pregnancy, we drew upon additional NLP tools to help identify tweets that report their pregnancy outcomes.ResultsUpon manually verifying the content of tweets detected automatically, we identified 150 users who reported on Twitter that they received at least one dose of Covid-19 vaccination during pregnancy or the periconception period. Among the 60 completed pregnancies, we manually verified at least one reported outcome for 45 (75%) of them.ConclusionsGiven the limited availability of data on Covid-19 vaccine safety in pregnancy, Twitter can be a complementary resource for potentially increasing the acceptance of Covid-19 vaccination in pregnant populations. Directions for future work include developing machine learning algorithms to detect a larger number of users for observational studies.
Reduction of Major Adverse Cardiovascular Events (MACE) after Bariatric Surgery in Obese Patients with Cardiovascular Diseases: A Systematic Review and Meta-Analysis
Authors: Sutanto Andryanto , Sutanto Henry 
Published: September 2021

ABSTRACTCardiovascular diseases (CVDs) are the leading cause of death worldwide and obesity is a major risk factor which increases morbidity and mortality of CVDs. Lifestyle modifications (e.g., diet control, physical exercise and behavioral changes) have been the first-line managements of obesity for decades. Nonetheless, when such interventions fail, pharmacotherapies and bariatric surgery are considered. Interestingly, a sudden weight loss (e.g., due to bariatric surgery) could also increase mortality (i.e., “obesity paradox”). Thus, it remains unclear whether the bariatric-surgery-associated weight reduction in patients with obesity and CVDs is beneficial for the reduction of Major Adverse Cardiovascular Events (MACE). Here, we performed a systematic literature search and meta-analysis of published studies comparing the MACE in patients with obesity and CVDs underwent bariatric surgery with control patients (no surgery). Studies’ data, including odds ratio (OR), were pooled and analyzed in a meta-analysis using a random effect model. Ten studies with a total of 1,772,305 patients, consisted of 74,042 patients underwent any form of bariatric surgery and 1,698,263 patients with no-surgery, were included in the meta-analysis. A random effect model was employed for analysis and showed that bariatric surgery group had significantly lower odds of MACE as compared to no surgery (OR = 0.49; 95% CI 0.40-0.60;p<0.00001;I2=93%), suggesting the benefit of bariatric surgery in reducing the occurrence of MACE in obese patients with CVDs.