bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fake dark matter from retarded distortions
Authors: Re Federico 
Published: April 2021

AbstractWe push ahead the idea developed in a previous work, that some fraction of the dark matter and the dark energy can be explained as a relativistic effect. The inhomogeneity matter generates gravitational distortions, which are general relativistically retarded. These combine in a magnification effect since the past matter density, which generated the distortion we feel now, is greater than the present one. The non negligible effect on the averaged expansion of the universe contributes both to the estimations of the dark matter and to the dark energy, so that the parameters of the Cosmological Standard Model need some corrections. In this second work we apply the previously developed framework to relativistic models of the universe. It results that one parameter remain free, so that more solutions are possible, as function of inhomogeneity. One of these fully explains the dark energy, but requires more dark matter than the Cosmological Standard Model ($$91\%$$

91
%

of the total matter). Another solution fully explains the dark matter, but requires more dark energy than the Cosmological Standard Model ($$15\%$$

15
%

more). A third noteworthy solution explains a consistent part of the dark matter ($$63\%$$

63
%

of the total matter) and also some of the dark energy ($$4\%$$

4
%

).
SummEval: Re-evaluating Summarization Evaluation
Authors: Fabbri Alexander R. , Kryściński Wojciech , McCann Bryan , Xiong Caiming , Socher Richard , Radev Dragomir 
Published: April 2021

AbstractThe scarcity of comprehensive up-to-date studies on evaluation metrics for text summarization and the lack of consensus regarding evaluation protocols continue to inhibit progress. We address the existing shortcomings of summarization evaluation methods along five dimensions: 1) we re-evaluate 14 automatic evaluation metrics in a comprehensive and consistent fashion using neural summarization model outputs along with expert and crowd-sourced human annotations; 2) we consistently benchmark 23 recent summarization models using the aforementioned automatic evaluation metrics; 3) we assemble the largest collection of summaries generated by models trained on the CNN/DailyMail news dataset and share it in a unified format; 4) we implement and share a toolkit that provides an extensible and unified API for evaluating summarization models across a broad range of automatic metrics; and 5) we assemble and share the largest and most diverse, in terms of model types, collection of human judgments of model-generated summaries on the CNN/Daily Mail dataset annotated by both expert judges and crowd-source workers. We hope that this work will help promote a more complete evaluation protocol for text summarization as well as advance research in developing evaluation metrics that better correlate with human judgments.
An Error Analysis Framework for Shallow Surface Realization
Authors: Shimorina Anastasia , Parmentier Yannick , Gardent Claire 
Published: April 2021

Abstract
The metrics standardly used to evaluate Natural Language Generation (NLG) models, such as BLEU or METEOR, fail to provide information on which linguistic factors impact performance. Focusing on Surface Realization (SR), the task of converting an unordered dependency tree into a well-formed sentence, we propose a framework for error analysis which permits identifying which features of the input affect the models’ results. This framework consists of two main components: (i) correlation analyses between a wide range of syntactic metrics and standard performance metrics and (ii) a set of techniques to automatically identify syntactic constructs that often co-occur with low performance scores. We demonstrate the advantages of our framework by performing error analysis on the results of 174 system runs submitted to the Multilingual SR shared tasks; we show that dependency edge accuracy correlate with automatic metrics thereby providing a more interpretable basis for evaluation; and we suggest ways in which our framework could be used to improve models and data. The framework is available in the form of a toolkit which can be used both by campaign organizers to provide detailed, linguistically interpretable feedback on the state of the art in multilingual SR, and by individual researchers to improve models and datasets.1
Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels
Authors: Zanti Maria , Michailidou Kyriaki , Loizidou Maria A. , Machattou Christina , Pirpa Panagiota , Christodoulou Kyproula , Spyrou George M. , Kyriacou Kyriacos , Hadjisavvas Andreas 
Published: April 2021

Abstract
Background
Next-generation sequencing (NGS) represents a significant advancement in clinical genetics. However, its use creates several technical, data interpretation and management challenges. It is essential to follow a consistent data analysis pipeline to achieve the highest possible accuracy and avoid false variant calls. Herein, we aimed to compare the performance of twenty-eight combinations of NGS data analysis pipeline compartments, including short-read mapping (BWA-MEM, Bowtie2, Stampy), variant calling (GATK-HaplotypeCaller, GATK-UnifiedGenotyper, SAMtools) and interval padding (null, 50 bp, 100 bp) methods, along with a commercially available pipeline (BWA Enrichment, Illumina®). Fourteen germline DNA samples from breast cancer patients were sequenced using a targeted NGS panel approach and subjected to data analysis.

Results
We highlight that interval padding is required for the accurate detection of intronic variants including spliceogenic pathogenic variants (PVs). In addition, using nearly default parameters, the BWA Enrichment algorithm, failed to detect these spliceogenic PVs and a missense PV in the TP53 gene. We also recommend the BWA-MEM algorithm for sequence alignment, whereas variant calling should be performed using a combination of variant calling algorithms; GATK-HaplotypeCaller and SAMtools for the accurate detection of insertions/deletions and GATK-UnifiedGenotyper for the efficient detection of single nucleotide variant calls.

Conclusions
These findings have important implications towards the identification of clinically actionable variants through panel testing in a clinical laboratory setting, when dedicated bioinformatics personnel might not always be available. The results also reveal the necessity of improving the existing tools and/or at the same time developing new pipelines to generate more reliable and more consistent data.
Transcriptome regulation of carotenoids in five flesh-colored watermelons (Citrullus lanatus)
Authors: Yuan Pingli , Umer Muhammad Jawad , He Nan , Zhao Shengjie , Lu Xuqiang , Zhu Hongju , Gong Chengsheng , Diao Weinan , Gebremeskel Haileslassie , Kuang Hanhui , Liu Wenge 
Published: April 2021

Abstract
Background
Fruit flesh color in watermelon (Citrullus lanatus) is a great index for evaluating the appearance quality and a key contributor influencing consumers’ preferences. But the molecular mechanism of this intricate trait remains largely unknown. Here, the carotenoids and transcriptome dynamics during the fruit development of cultivated watermelon with five different flesh colors were analyzed.

Results
A total of 13 carotenoids and 16,781 differentially expressed genes (DEGs), including 1295 transcription factors (TFs), were detected in five watermelon genotypes during the fruit development. The comprehensive accumulation patterns of carotenoids were closely related to flesh color. A number of potential structural genes and transcription factors were found to be associated with the carotenoid biosynthesis pathway using comparative transcriptome analysis. The differentially expressed genes were divided into six subclusters and distributed in different GO terms and metabolic pathways. Furthermore, we performed weighted gene co-expression network analysis and predicted the hub genes in six main modules determining carotenoid contents. Cla018406 (a chaperone protein dnaJ-like protein) may be a candidate gene for β-carotene accumulation and highly expressed in orange flesh-colored fruit. Cla007686 (a zinc finger CCCH domain-containing protein) was highly expressed in the red flesh-colored watermelon, maybe a key regulator of lycopene accumulation. Cla003760 (membrane protein) and Cla021635 (photosystem I reaction center subunit II) were predicted to be the hub genes and may play an essential role in yellow flesh formation.

Conclusions
The composition and contents of carotenoids in five watermelon genotypes vary greatly. A series of candidate genes were revealed through combined analysis of metabolites and transcriptome. These results provide an important data resource for dissecting candidate genes and molecular basis governing flesh color formation in watermelon fruit.
Developing and validating a risk algorithm to diagnose Neisseria gonorrhoeae and Chlamydia trachomatis in symptomatic Rwandan women
Authors: Wall Kristin M. , Nyombayire Julien , Parker Rachel , Ingabire Rosine , Bizimana Jean , Mukamuyango Jeannine , Mazzei Amelia , Price Matt A. , Unyuzimana Marie Aimee , Tichacek Amanda , Allen Susan , Karita Etienne 
Published: April 2021

AbstractBackgroundAlgorithms that bridge the gap between syndromic sexually transmitted infection (STI) management and treatment based in realistic diagnostic options and local epidemiology are urgently needed across Africa. Our objective was to develop and validate a risk algorithm forNeisseria gonorrhoeae(NG) andChlamydia trachomatis(CT) diagnosis among symptomatic Rwandan women and to compare risk algorithm performance to the current Rwandan National Criteria for NG/CT diagnosis.MethodsThe risk algorithm was derived in a cohort (n = 468) comprised of symptomatic women in Kigali who sought free screening and treatment for sexually transmitted infections and vaginal dysbioses at our research site. We used logistic regression to derive a risk algorithm for prediction of NG/CT infection. Ten-fold cross-validation internally validated the risk algorithm. We applied the risk algorithm to an external validation cohort also comprised of symptomatic Rwandan women (n = 305). Measures of calibration, discrimination, and screening performance of our risk algorithm compared to the current Rwandan National Criteria are presented.ResultsThe prevalence of NG/CT in the derivation cohort was 34.6%. The risk algorithm included: age < =25, having no/primary education, not having full-time employment, using condoms only sometimes, not reporting genital itching, testing negative for vaginal candida, and testing positive for bacterial vaginosis. The model was well calibrated (Hosmer-Lemeshowp = 0.831). Higher risk scores were significantly associated with increased prevalence of NG/CT infection (p < 0.001). Using a cut-point score of > = 5, the risk algorithm had a sensitivity of 81%, specificity of 54%, positive predictive value (PPV) of 48%, and negative predictive value (NPV) of 85%. Internal and external validation showed similar predictive ability of the risk algorithm, which outperformed the Rwandan National Criteria. Applying the Rwandan National Criteria cutoff of > = 2 (the current cutoff) to our derivation cohort had a sensitivity of 26%, specificity of 89%, PPV of 55%, and NPV of 69%.ConclusionsThese data support use of a locally relevant, evidence-based risk algorithm to significantly reduce the number of untreated NG/CT cases in symptomatic Rwandan women. The risk algorithm could be a cost-effective way to target treatment to those at highest NG/CT risk. The algorithm could also aid in sexually transmitted infection risk and prevention communication between providers and clients.
Indoor nocturnal noise is associated with body mass index and blood pressure: a cross-sectional study
Authors: Li Sha , Fong Daniel Yee Tak , Wong Janet Yuen Ha , McPherson Bradley , Lau Esther Yuet Ying , Huang Lixi , Mary Sau Man I. P. 
Published: April 2021

Abstract
Background
Studies have demonstrated that noise is associated with various health problems, such as obesity and hypertension. Although the evidence of the associations of noise with obesity and hypertension is inconsistent, there seems to be a stronger association of the latter. This study aimed to investigate the associations of noise with body mass index (BMI) and blood pressure in adults living in multi-story residential buildings.

Methods
A cross-sectional study was conducted in Hong Kong from February 2018 to September 2019. The Weinstein Noise Sensitivity Scale, Pittsburgh Sleep Quality Index, ENRICHD Social Support Instrument, Patient Health Questionnaire, Perceived Stress Scale, and Hospital Anxiety and Depression Scale were administered to the participants. BMI and blood pressure were assessed. Nocturnal noise exposure and total sleep duration were measured for a week.

Results
Five hundred adults (66.4% female), with an average age of 39 years (range: 18–80), completed the study. The average levels of nocturnal noise, BMI, systolic blood pressure (SBP), and diastolic blood pressure (DBP) were 51.3 dBA, 22.2 kg/m2, 116.0 mmHg, and 75.4 mmHg, respectively. After adjusting for sociodemographic characteristics, nocturnal noise was associated with BMI (b = 0.54, 95% CI: 0.01 to 1.06, p = 0.045) and SBP (b = 2.90, 95% CI: 1.12 to 4.68, p = 0.001). No association was detected between nocturnal noise and DBP (b = 0.79, 95% CI: − 0.56 to 2.13, p = 0.253). Specifically, higher nocturnal noise was associated with higher BMI (b = 0.72, 95% CI: 0.07 to 1.38, p = 0.031) and SBP (b = 3.91, 95% CI: 2.51 to 5.31, p < 0.001) in females but only higher SBP (b = 3.13, 95% CI: 1.35 to 4.92, p < 0.001) in males. The association between noise and SBP remained significant (b = 2.41, 95% CI: 0.62 to 4.20, p = 0.008) after additionally adjusting for lifestyle, diagnosis of hypertension, psychometric constructs, and sleep.

Conclusions
Indoor nocturnal noise was associated with BMI and blood pressure in females but only blood pressure in males. It is important to control nocturnal noise or use soundproofing materials in buildings to reduce noise exposure.
Trust in health information sources and its associations with COVID-19 disruptions to social relationships and health services among people living with HIV
Authors: Kalichman Seth C. , Shkembi Bruno , Kalichman Moira O. , Eaton Lisa A. 
Published: April 2021

Abstract
Background
SARS-CoV-2 infection (COVID-19) is potentially severe for individuals with compromised immune systems, including people living with HIV. Along with the direct health threats of COVID-19, there are disruptions to social relationships and health services resulting from mitigation efforts instituted by public health authorities. This study examined the relationship between trust in the government and trust in COVID-19 health information from the US CDC, state health departments, and social media on the experience of COVID-19 social and health services-related disruptions.

Methods
People living with HIV (N = 459) recruited through social media advertisements and chain referrals completed confidential surveys delivered through an online platform.

Results
Participants experienced high-levels of disruptions to social relationships and health services attributable to COVID-19 mitigation efforts. We also observed high-rates of inaccurate information and low-levels of trust in government and sources of COVID-19 information. Greater disruptions to social relationships were predicted by more concern about oneself and others contracting COVID-19, whereas disruptions to health services were predicted by greater concern for oneself contracting COVID-19, greater general medical mistrust, and less trust in information from the CDC.

Conclusions
Findings have implications for the necessity of rebuilding public trust in credible sources of health information and stepping up efforts to counter sources of inaccurate information.
Individual and social determinants of COVID-19 vaccine uptake
Authors: Viswanath K. , Bekalu Mesfin , Dhawan Dhriti , Pinnamaneni Ramya , Lang Jenna , McLoud Rachel 
Published: April 2021

Abstract
Background
COVID-19 has had a devastating impact and efforts are being made to speed up vaccinations. The growing problem of vaccine hesitancy may affect the uptake of COVID-19 vaccine. We examined the individual, communication and social determinants associated with vaccines uptake.

Methods
Data come from a nationwide online probability-based panel of 1012 representative adults in the United States and the survey was conducted before the vaccines were available. People under the federal poverty level and racial and ethnic minorities were oversampled. Our outcome variables of interest were likelihood of vaccinating self and likelihood of vaccinating people under one’s care (such as children) measuring behavioral intentions. Independent variables included perceptions of risk, exposure to different media for COVID-19 news, political party identification, confidence in scientists and social determinants of health. Logistic regression analysis was used to ascertain the effects of independent variables on the two outcome variables.

Results
The results indicated that 68 and 65% agreed to get the vaccine for themselves and people under their care, respectively. Risk perceptions (severity of and susceptibility to COVID-19) were significantly associated with vaccine uptake. People who relied on “conservative” news outlets, Republicans, and who had low confidence in scientists are least likely to vaccinate self or children. Non-Hispanic Blacks and those with least schooling were also less likely to receive vaccine for themselves or people in their care.

Conclusions
Our study identified race/ethnicity, risk perceptions, exposure to different media for COVID-19 news, party identification and confidence in scientists as factors that would be affecting COVID-19 vaccine uptake. The good news is that these are addressable through strategic public health communications, but a lot of work remains to be done with some urgency.
Occupational burnout and job satisfaction among physicians in times of COVID-19 crisis: a convergent parallel mixed-method study
Authors: Alrawashdeh Hamzeh Mohammad , Al-Tammemi Ala’a B. , Alzawahreh Mohammad Kh. , Al-Tamimi Ashraf , Elkholy Mohamed , Al Sarireh Fawaz , Abusamak Mohammad , Elehamer Nafisa M. K. , Malkawi Ahmad , Al-Dolat Wedad , Abu-Ismail Luai , Al-Far Ali , Ghoul Imene 
Published: April 2021

Abstract
Background
Healthcare professionals including physicians were subjected to an increased workload during the COVID-19 crisis, leaving them exposed to significant physical and psychological distress. Therefore, our present study aimed to (i) assess the prevalence of burnout and levels of job satisfaction among physicians in Jordan, and (ii) explore physicians’ opinions, experiences, and perceptions during the pandemic crisis.

Methods
This was a mixed-method study that utilized a structured web-based questionnaire and semi-structured individual interviews. The 10-Item Burnout Measure-Short version (BMS), and the 5-Item Short Index of Job Satisfaction (SIJS) were adopted to assess occupational burnout and job satisfaction, respectively. Semi-structured interviews were conducted, based on a conceptual framework that was developed from Herzberg’s Two-Factor Theory of Motivation and Job Demands-Resources Model. Descriptive statistics and regression models, as well as inductive thematic analysis, were used to analyze quantitative and qualitative data, respectively.

Results
A total of 973 survey responses and 11 interviews were included in our analysis. The prevalence of burnout among physicians was (57.7%). Several significant factors were positively associated with burnout, including female gender, working at highly loaded hospitals, working for long hours, doing night shifts, lack of sufficient access to personal protective equipment, and being positively tested for SARS-CoV-2. Regarding job satisfaction, regression analysis revealed that age was positively associated with higher levels of job satisfaction. On contrary, being a general practitioner or specialist, working at highly loaded hospitals, low salaries, and suffering from burnout have predicted lower levels of job satisfaction.
Besides, four themes have emerged from the thematic analysis: (i) Work-induced psychological distress during the pandemic, (ii) Decision-driven satisfactory and dissatisfactory experiences, (iii) Impact of the pandemic on doctor-patient communication and professional skills, and (iv) Economic impacts of the pandemic crisis and lockdown.

Conclusion
A significant physical and psychological burden was associated with the COVID-19 pandemic. Reliable efforts should be implemented aiming at protecting physicians’ physical and mental wellbeing, enhancing their working conditions, and raising awareness about burnout. Evidence-based decisions and proper utilization of financial and human resources at institutional and national levels are believed to be crucial for the sustainability of the health workforce, especially in crises.
Stem retention and survival in revision of anatomical convertible shoulder arthroplasty to reverse arthroplasty: a Dutch registry study
Authors: Theelen Luuk M. A. , Mory Ben , Venkatesan Sharmila , Spekenbrink-Spooren Anneke , Janssen Loes , Lambers Heerspink Frederik O. 
Published: April 2021

Abstract
Background
Convertible stem designs allow for stem retention during revision from anatomical to reverse shoulder arthroplasty. In some cases conversion is not possible for example due to excessive soft tissue tensioning. In these cases a total revision is necessary. The primary aim of this Dutch registry study was to evaluate the unforeseen stem reversion percentages in revision of convertible anatomical shoulder arthroplasty to reverse shoulder arthroplasty.

Methods
Shoulder arthroplasties (n = 2834) performed between 2014 and 2016 registered in the Dutch Arthroplasty Registry were selected. In 2016 94% of primary arthroplasties and 92% of revision arthroplasties were registered in the database. Arthroplasties were selected on convertibility. Mean follow-up was 2.4 years. We analysed the number of revisions for convertible and non-convertible designs. Cases with obligatory revisions as periprosthetic joint infections, stem loosening and periprosthetic fractures were excluded. Kaplan-Meier analysis was used to calculate humeral stem survival. Multivariate cox-regression analysis was used to determine risk factors for stem revision.

Results
The majority of procedures (respectively 90.9 and 72.1% for the convertible and non-convertible group) concerned a conversion to reverse shoulder arthroplasty (p = .02). In the convertible group, the stem was retained in 29 out of 40 patients (72.5%). Overall implant survival was 94.5% after a mean follow-up of 2.4 years. Hemiartroplasty, fracture as primary indication, previous shoulder surgery and lower age were risk factors for revision.

Conclusions
Although convertible designs are gaining popularity due to their expected advantage in revision arthroplasty, surgeons should be aware that during a revision procedure in 27.5% of the patients an unforeseen stem revision is necessary.