bluuebunny/crossref_metadata_2025_split huggingface dataset:
Objectively Measured Sedentary Levels and Bouts by Day Type in Australian Young Children
Authors: Pereira João R. , Cliff Dylan P. , Sousa-Sá Eduarda , Zhang Zhiguang , McNeill Jade , Veldman Sanne L.C. , Santos Rute 
Published: April 2021

Background: This study aimed to understand whether a higher number of sedentary bouts (SED bouts) and higher levels of sedentary time (SED time) occur according to different day types (childcare days, nonchildcare weekdays, and weekends) in Australian toddlers (1–2.99 y) and preschoolers (3–5.99 y). Methods: The SED time and bouts were assessed using ActiGraph GT3X+ accelerometers. The sample was composed of 264 toddlers and 343 preschoolers. The SED bouts and time differences were calculated using linear mixed models. Results: The toddlers’ percentage of SED time was higher on nonchildcare days compared with childcare days (mean difference [MD] = 2.3; 95% confidence interval, 0.7 to 3.9). The toddlers had a higher number of 1- to 4-minute SED bouts on nonchildcare days compared with childcare days. The preschoolers presented higher percentages of SED time during nonchildcare days (MD = 3.1; 95% confidence interval, 1.6 to 4.5) and weekends (MD = 1.9; 95% confidence interval, 0.4 to 3.4) compared with childcare days. The preschoolers presented a higher number of SED bouts (1–4, 5–9, 10–19, and 20–30 min) during nonchildcare days and weekends compared with childcare days. No SED times or bout differences were found between nonchildcare days and weekends, neither SED bouts >30 minutes on toddlers nor on preschoolers. Conclusion: The SED time and bouts seem to be lower during childcare periods, which means that interventions to reduce sedentary time should consider targeting nonchildcare days and weekends.
Diagnostic value of culture results from aqueous tap versus vitreous tap in cases of bacterial endophthalmitis
Authors: AlBloushi Abdulrahman F , Ajamil-Rodanes Sofia , Testi Ilaria , Wagland Catherine , Grant-McKenzie Nadine , Pavesio Carlos 
Published: April 2021

ObjectiveTo investigate the concordance between aqueous and vitreous tap culture results among different types of bacterial endophthalmitis.Methods and analysisThis retrospective cohort analysis included all cases diagnosed with endophthalmitis at Moorfields Eye Hospital between January 2008 and March 2020. Aqueous and vitreous samples obtained simultaneously at presentation. Samples were evaluated for sensitivity, specificity, negative and positive predictive values.ResultsA total of 217 patients (217 eyes) were included in the study. Postsurgical endophthalmitis was the most common type of endophthalmitis and diagnosed in 35.9% of the cases. The rate of positive culture results was 32.2% from vitreous tap and 21.7% from aqueous tap. The culture yield through vitreous sampling was 15.7% when aqueous culture results were negative, and in 5.1%, the aqueous sample was positive when the vitreous tap results were negative. Considering the vitreous tap as the gold standard, aqueous sample culture results showed a statistically significant high specificity and positive predictive values in cases of postsurgical endophthalmitis, late-onset endophthalmitis associated with glaucoma procedures, postintravitreal injection and endophthalmitis associated with bacterial keratitis. Coagulase Negative Staphylococcus was the most common organism isolated from vitreous and aqueous samples.ConclusionsEven though the sensitivity and specificity of aqueous tap are low, our results show that in a few cases it identified important organisms, otherwise missed by vitreous sampling alone. Culture of vitreous sample remains the gold standard for isolation of pathogen in bacterial endophthalmitis, but aqueous samples should also be obtained as an adjunct for the diagnosis.
Cultivation of compound ability of postgraduates with medical professional degree: the importance of double tutor system
Authors: Xiao Yu , Wu Xiao-Hong , Huang Yu-Hong , Zhu Shao-Yi 
Published: April 2021

AbstractAs we all know, medical postgraduate education is very important for training high-quality clinicians, and can have a long-term impact on the promotion of the global health service system. In recent years, following the example of developed countries in Europe and America, the Chinese government has reformed the training mode of medical postgraduates and implemented the double tutor system. Although this system will bring many positive effects in theory, the difficulties encountered in implementing this system are real and need the joint efforts of schools, tutors and students to solve them. This article closely follows the background of the current era, compares the differences between Chinese and foreign graduate training modes, and emphatically discusses the significance and problems of the double tutor system in the postgraduate education reform in China.
Genetically Proxied Inhibition of Coagulation Factors and Risk of Cardiovascular Disease: A Mendelian Randomization Study
Authors: Yuan Shuai , Burgess Stephen , Laffan Mike , Mason Amy M. , Dichgans Martin , Gill Dipender , Larsson Susanna C. 
Published: April 2021

Background
We conducted Mendelian randomization analyses investigating the linear associations of genetically proxied inhibition of different coagulation factors with risk of common cardiovascular diseases.

Methods and Results

Genetic instruments proxying coagulation factor inhibition were identified from genome‐wide association studies for activated partial thromboplastin time and prothrombin time in BioBank Japan (up to 58 110 participants). Instruments were identified for 9 coagulation factors (fibrinogen alpha, beta, and gamma chain; and factors II, V, VII, X, XI, and XII). Age‐ and sex‐adjusted estimates for associations of the instruments with the outcomes were derived from UK Biobank and the FinnGen, CARDIoGRAMplusC4D (Coronary Artery Disease Genome‐wide Replication and Meta‐analysis), and MEGASTROKE consortia with numbers of incident and prevalent cases of 820 to 60 810. Genetically proxied inhibition of fibrinogen alpha, beta, and gamma chain, factor II, and factor XI were associated with reduced risk of venous thromboembolism (
P
<0.001). With the exception of fibrinogen beta and factor II, inhibition of these factors was also associated with reduced risk of any ischemic stroke and cardioembolic stroke (
P
≤0.002). Genetically proxied inhibition of fibrinogen beta and gamma were associated with reduced large‐artery stroke risk (
P
=0.001). There were suggestive protective associations of genetically proxied inhibition of factors V, VII, and X with ischemic stroke (
P
<0.05), and suggestive adverse associations of genetically proxied inhibition of factors II and XII with subarachnoid hemorrhage.

Conclusions
This study supports targeting fibrinogen and factor XI for reducing venous thromboembolism and ischemic stroke risk, and showed suggestive evidence that inhibition of factors V, VII, and X might reduce ischemic stroke risk.
Greater Acculturation is Associated With Poorer Cardiovascular Health in the Multi‐Ethnic Study of Atherosclerosis
Authors: Osibogun Olatokunbo , Ogunmoroti Oluseye , Mathews Lena , Okunrintemi Victor , Tibuakuu Martin , Michos Erin D. 
Published: April 2021

Background
Greater acculturation is associated with increased risk of cardiovascular disease. However, little is known about the association between acculturation and ideal cardiovascular health (CVH) as measured by the American Heart Association's 7 CVH metrics. We investigated the association between acculturation and ideal CVH among a multi‐ethnic cohort of US adults free of clinical cardiovascular disease at baseline.

Methods and Results

This was a cross‐sectional analysis of 6506 men and women aged 45 to 84 years of 4 races/ethnicities. We examined measures of acculturation(birthplace, language spoken at home, and years lived in the United States [foreign‐born participants]) by CVH score. Scores of 0 to 8 indicate inadequate, 9 to 10 average and 11 to 14 optimal CVH. We used multivariable regression to examine associations between acculturation and CVH, adjusting for age, sex, race/ethnicity, education, income and health insurance. The mean (SD) age was 62 (10) years, 53% were women, 39% non‐Hispanic White‐, 26% non‐Hispanic Black‐, 12% Chinese‐ and 22% Hispanic‐Americans. US‐born participants had lower odds of optimal CVH (odds ratio [OR]: 0.63 [0.50–0.79],
P
<0.001) compared with foreign‐born participants. Participants who spoke Chinese and other foreign languages at home had greater odds of optimal CVH compared with those who spoke English (1.91 [1.08–3.36],
P
=0.03; and 1.65 [1.04–2.63],
P
=0.03, respectively). Foreign‐born participants who lived the longest in the United States had lower odds of optimal CVH (0.62 [0.43–0.91],
P
=0.02).

Conclusions
Greater US acculturation was associated with poorer CVH. This finding suggests that the promotion of ideal CVH should be encouraged among immigrant populations since more years lived in the United States was associated with poorer CVH.
Philological Notes on the Letter Rho in a New Greek-English Dictionary
Authors: Olson S. Douglas 
Published: April 2021

Abstract
Two generations ago, Robert Renehan published a series of articles expanding, refining, and correcting entries in the 9th edition of the monumental Liddell-Scott-Jones Greek-English Lexicon (1940) as supplemented by Barber and his fellow editors (1968). The following notes on the letter rho in the new Brill Dictionary of Ancient Greek are offered in a similar spirit.
Epicurus’ Non-Propositional Theory of Truth
Authors: Hahmann Andree , Robitzsch Jan Maximilian 
Published: April 2021

Abstract
Scholars typically distinguish at least two different Epicurean conceptions of truth: (1) an account that pertains to the truth of perceptions or impressions and (2) an account that pertains to the truth of opinions. This paper addresses the relationship between the truth of perceptions (and by extension: preconceptions and feelings), on the one hand, and the truth of opinions, on the other. It offers an account of what these determinations of truth amount to and how they interact with each other. In doing so, the paper rejects a propositional understanding of Epicurean truth. It instead argues that the Epicurean conception of truth can be explained by relying on images and their combination.
Review of Article 27.3(b) and the Patenting of Life Forms: Hitting a BRIC Wall in the WTO?
Authors: Plahe Jagjit , Kukreja Nitesh , Ponnamperuma Sunil 
Published: April 2021

Abstract
Under Article 27.3(b) of the Trade-Related Aspects of Intellectual Property Rights (TRIPS) Agreement of the World Trade Organization (WTO), all members are required to extend private property rights to life forms. Using official WTO documents, this article analyzes the negotiating positions of WTO members on life patents during a review of Article 27.3(b) which commenced in 1999 and is currently ongoing. Initially, developing countries raised serious ethical concerns regarding life patents, creating a clear North-South divide. However, over time the position of Brazil and India moved away from the ethics of life patents to the prevention of bio-piracy, a position supported by China. Russia too is supportive of life patents. A group of small developing countries have, however, continued to question the morality of life patents despite this “BRIC wall,” changing the dynamics of the negotiations from a North-South divide to one which now includes a South-South divide.
A theory of Spring Persistence Barrier on ENSO. Part II: Persistence Barriers in SST and ocean heat content
Authors: Jin Yishuai , Liu Zhengyu 
Published: April 2021

AbstractIn this paper, we investigate the potential factors that control the relationship between the El Niño-Southern Oscillation (ENSO) persistence barriers (PB) in sea surface temperature (SST) and ocean heat content (OHC) and apply it to explain observational ENSO PBs. With the addition of seasonal growth rate in SST in the neutral recharge oscillator (NRO) model, approximate analytical solutions of autocorrelation functions for SST and OHC suggest strictly that the timing of PB for OHC leads that of SST by half a year and the strength of the two PBs are the same. The numerical solutions of the NRO model also show a similar relationship. The role of ENSO growth rate to PBs in SST and OHC is then identified in the damped and unstable ENSO regime. Therefore, it is suggested that for the observational ENSO, the seasonally varying ENSO growth rate in SST controls PBs in SST and OHC simultaneously.
All in one, a rare case presentation of genitourinary tuberculosis
Authors: Singh Vishwajeet , Kumar Manoj , Pavan Kumar S. K. , Jain Mayank 
Published: April 2021

Abstract
Background
The kidneys are the most common site of urogenital tuberculosis. Tuberculosis of the urethra and bladder is caused by a descending infection through the urinary collecting system. Urogenital tuberculosis affects 2% to 10% of pulmonary tuberculosis cases in developed countries, but 15% to 20% in developing countries.

Case presentation
A 55-year-old male referred to us with bilateral percutaneous nephrostomy, which was done for obstructive uropathy with raised creatinine of 4.5 mg/dl. He was diagnosed with pulmonary tuberculosis two years back and took antitubercular therapy for one year. His routine blood parameters were within normal limits. On evaluation with bilateral nephrostograms, he was found to have right-sided pelvic ureteric junction stricture and left-sided vesicoureteric junction stricture. On retrograde urethrography, there was evidence of 4-cm stricture at proximal bulbar urethra. On contrast-enhanced CT whole abdomen, he was found to have small-sized right kidney and findings in par with nephrostogram with thickened, small capacity bladder (thimble bladder). Patient underwent urethroscopy and urethral dilatation followed by augmentation ileocystoplasty with left ureteric reimplantation and right nephrectomy done at 3 months of follow-up.

Conclusion
Only 1.9 percent to 4.5 percent of all cases of urogenital tuberculosis are urethral tuberculosis, and it never happens alone. For urogenital tuberculosis diagnosis, imaging techniques are up to 91.4 percent sensitive, with intravenous urography and abdominal computerised tomography being the most widely used. Diagnosis relies on a range of signs such as “caliceal irregularities; infundibular stenosis; pseudotumor or renal scarring; nonfunctioning kidney; renal cavitation; urinary tract calcification (present in 7% to 19% of cases); collecting system thickening, stenosis, or dilatation; contracted bladder”.
Improving protein domain classification for third-generation sequencing reads using deep learning
Authors: Du Nan , Shang Jiayu , Sun Yanni 
Published: April 2021

AbstractBackgroundWith the development of third-generation sequencing (TGS) technologies, people are able to obtain DNA sequences with lengths from 10s to 100s of kb. These long reads allow protein domain annotation without assembly, thus can produce important insights into the biological functions of the underlying data. However, the high error rate in TGS data raises a new challenge to established domain analysis pipelines. The state-of-the-art methods are not optimized for noisy reads and have shown unsatisfactory accuracy of domain classification in TGS data. New computational methods are still needed to improve the performance of domain prediction in long noisy reads.ResultsIn this work, we introduce ProDOMA, a deep learning model that conducts domain classification for TGS reads. It uses deep neural networks with 3-frame translation encoding to learn conserved features from partially correct translations. In addition, we formulate our problem as an open-set problem and thus our model can reject reads not containing the targeted domains. In the experiments on simulated long reads of protein coding sequences and real TGS reads from the human genome, our model outperforms HMMER and DeepFam on protein domain classification.ConclusionsIn summary, ProDOMA is a useful end-to-end protein domain analysis tool for long noisy reads without relying on error correction.
Development and validation of genome-wide InDel markers with high levels of polymorphism in bitter gourd (Momordica charantia)
Authors: Cui Junjie , Peng Jiazhu , Cheng Jiaowen , Hu Kailin 
Published: April 2021

Abstract
Background
The preferred choice for molecular marker development is identifying existing variation in populations through DNA sequencing. With the genome resources currently available for bitter gourd (Momordica charantia), it is now possible to detect genome-wide insertion-deletion (InDel) polymorphisms among bitter gourd populations, which guides the efficient development of InDel markers.

Results
Here, using bioinformatics technology, we detected 389,487 InDels from 61 Chinese bitter gourd accessions with an average density of approximately 1298 InDels/Mb. Then we developed a total of 2502 unique InDel primer pairs with a polymorphism information content (PIC) ≥0.6 distributed across the whole genome. Amplification of InDels in two bitter gourd lines ‘47–2–1-1-3’ and ‘04–17,’ indicated that the InDel markers were reliable and accurate. To highlight their utilization, the InDel markers were employed to construct a genetic map using 113 ‘47–2–1-1-3’ × ‘04–17’ F2 individuals. This InDel genetic map of bitter gourd consisted of 164 new InDel markers distributed on 15 linkage groups with a coverage of approximately half of the genome.

Conclusions
This is the first report on the development of genome-wide InDel markers for bitter gourd. The validation of the amplification and genetic map construction suggests that these unique InDel markers may enhance the efficiency of genetic studies and marker-assisted selection for bitter gourd.
Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics
Authors: Karp Peter D. , Midford Peter E. , Caspi Ron , Khodursky Arkady 
Published: April 2021

AbstractBackgroundEnrichment or over-representation analysis is a common method used in bioinformatics studies of transcriptomics, metabolomics, and microbiome datasets. The key idea behind enrichment analysis is: given a set of significantly expressed genes (or metabolites), use that set to infer a smaller set of perturbed biological pathways or processes, in which those genes (or metabolites) play a role. Enrichment computations rely on collections of defined biological pathways and/or processes, which are usually drawn from pathway databases. Although practitioners of enrichment analysis take great care to employ statistical corrections (e.g., for multiple testing), they appear unaware that enrichment results are quite sensitive to the pathway definitions that the calculation uses.ResultsWe show that alternative pathway definitions can alter enrichmentp-values by up to nine orders of magnitude, whereas statistical corrections typically alter enrichmentp-values by only two orders of magnitude. We present multiple examples where the smaller pathway definitions used in the EcoCyc database produces stronger enrichmentp-values than the much larger pathway definitions used in the KEGG database; we demonstrate that to attain a given enrichmentp-value, KEGG-based enrichment analyses require 1.3–2.0 times as many significantly expressed genes as does EcoCyc-based enrichment analyses. The large pathways in KEGG are problematic for another reason: they blur together multiple (as many as 21) biological processes. When such a KEGG pathway receives a high enrichmentp-value, which of its component processes is perturbed is unclear, and thus the biological conclusions drawn from enrichment of large pathways are also in question.ConclusionsThe choice of pathway database used in enrichment analyses can have a much stronger effect on the enrichment results than the statistical corrections used in these analyses.
Transcriptomic, proteomic and ultrastructural studies on salinity-tolerant Aedes aegypti in the context of rising sea levels and arboviral disease epidemiology
Authors: Ramasamy Ranjan , Thiruchenthooran Vaikunthavasan , Jayadas Tibutius T. P. , Eswaramohan Thampoe , Santhirasegaram Sharanga , Sivabalakrishnan Kokila , Naguleswaran Arunasalam , Uzest Marilyne , Cayrol Bastien , Voisin Sebastien N. , Bulet Philippe , Surendran Sinnathamby N. 
Published: April 2021

AbstractBackgroundAedes aegyptimosquito, the principal global vector of arboviral diseases, lays eggs and undergoes larval and pupal development to become adult mosquitoes in fresh water (FW). It has recently been observed to develop in coastal brackish water (BW) habitats of up to 50% sea water, and such salinity tolerance shown to be an inheritable trait. Genomics of salinity tolerance inAe. aegyptihas not been previously studied, but it is of fundamental biological interest and important for controlling arboviral diseases in the context of rising sea levels increasing coastal ground water salinity.ResultsBW- and FW-Ae. aegyptiwere compared by RNA-seq analysis on the gut, anal papillae and rest of the carcass in fourth instar larvae (L4), proteomics of cuticles shed when L4 metamorphose into pupae, and transmission electron microscopy of cuticles in L4 and adults. Genes for specific cuticle proteins, signalling proteins, moulting hormone-related proteins, membrane transporters, enzymes involved in cuticle metabolism, and cytochrome P450 showed different mRNA levels in BW and FW L4 tissues. The salinity-tolerantAe. aegyptiwere also characterized by altered L4 cuticle proteomics and changes in cuticle ultrastructure of L4 and adults.ConclusionsThe findings provide new information on molecular and ultrastructural changes associated with salinity adaptation in FW mosquitoes. Changes in cuticles of larvae and adults of salinity-tolerantAe. aegyptiare expected to reduce the efficacy of insecticides used for controlling arboviral diseases. Expansion of coastal BW habitats and their neglect for control measures facilitates the spread of salinity-tolerantAe. aegyptiand genes for salinity tolerance. The transmission of arboviral diseases can therefore be amplified in multiple ways by salinity-tolerantAe. aegyptiand requires appropriate mitigating measures. The findings inAe. aegypti have attendant implications for the development of salinity tolerance in other fresh water mosquito vectors and the diseases they transmit.