bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular systematics and phylogeography of a widespread Neotropical avian lineage: evidence for cryptic speciation with protracted gene flow throughout the Late Quaternary
Authors: Miranda Leonardo S , Prestes Bernardo O , Aleixo Alexandre 
Published: October 2020

AbstractHere we use an integrative approach, including coalescent-based methods, isolation–migration and species distribution models, to infer population structure, divergence times and diversification in the two species of the genus Cymbilaimus (Aves, Thamnophilidae). Our results support a recent and rapid diversification with both incomplete lineage sorting and gene flow shaping the evolutionary history of Cymbilaimus. The spatio-temporal pattern of cladogenesis suggests that Cymbilaimus originated in the north/western portion of cis-Andean South America and then diversified into the Brazilian Shield and Central America after consolidation of the modern Amazonian drainage and the Andean range. This evolutionary scenario is explained by cycles of range expansion and dispersal, followed by isolation, and recurrent gene flow, during the last 1.2 Myr. Our results agree with those recently reported for other closely related suboscine lineages, whereby the window of introgression between closely related taxa remains open for up to a few million years after their original split. In Cymbilaimus, introgression was recurrent between C. lineatus and C. sanctaemariae, even after they acquired vocal and ecological differentiation, supporting the claim that at least in Neotropical suboscines, full reproductive compatibility may take millions of years to evolve and cannot be interpreted as synonymous with a lack of speciation.
Transcriptome analysis of porcine endometrium after LPS-induced inflammation: effects of the PPAR-gamma ligands in vitro†
Authors: Mierzejewski Karol , Paukszto Łukasz , Kurzyńska Aleksandra , Kunicka Zuzanna , Jastrzębski Jan Paweł , Bogacka Iwona 
Published: October 2020

Abstract
Female fertility depends greatly on the capacity of the uterus to recognize and eliminate microbial infections, a major reason of inflammation in the endometrium in many species. This study aimed to determine the in vitro effect of peroxisome proliferator-activated receptor gamma (PPARγ) ligands on the transcriptome genes expression and alternative splicing in the porcine endometrium in the mid-luteal phase of the estrous cycle during LPS-stimulated inflammation using RNA-seq technology. The endometrial slices were incubated in vitro in the presence of LPS and PPARγ agonists—PGJ2 or pioglitazone and antagonist—T0070907. We identified 222, 3, 4, and 62 differentially expressed genes after LPS, PGJ2, pioglitazone, or T0070907 treatment, respectively. In addition, we detected differentially alternative spliced events: after treatment with LPS-78, PGJ2-60, pioglitazone-52, or T0070907-134. These results should become a basis for further studies explaining the mechanism of PPARγ action in the reproductive system in pigs.
The genetics of circulating BDNF: towards understanding the role of BDNF in brain structure and function in middle and old ages
Authors: Li Shuo , Weinstein Galit , Zare Habil , Teumer Alexander , Völker Uwe , Friedrich Nele , Knol Maria J , Satizabal Claudia L , Petyuk Vladislav A , Adams Hieab H H , Launer Lenore J , Bennett David A , De Jager Philip L , Grabe Hans J , Ikram M Arfan , Gudnason Vilmundur , Yang Qiong , Seshadri Sudha 
Published: October 2020

AbstractBrain-derived neurotrophic factor (BDNF) plays an important role in brain development and function. Substantial amounts of BDNF are present in peripheral blood, and may serve as biomarkers for Alzheimer’s disease incidence as well as targets for intervention to reduce Alzheimer’s disease risk. With the exception of the genetic polymorphism in the BDNF gene, Val66Met, which has been extensively studied with regard to neurodegenerative diseases, the genetic variation that influences circulating BDNF levels is unknown. We aimed to explore the genetic determinants of circulating BDNF levels in order to clarify its mechanistic involvement in brain structure and function and Alzheimer’s disease pathophysiology in middle-aged and old adults. Thus, we conducted a meta-analysis of genome-wide association study of circulating BDNF in 11 785 middle- and old-aged individuals of European ancestry from the Age, Gene/Environment Susceptibility-Reykjavik Study (AGES), the Framingham Heart Study (FHS), the Rotterdam Study and the Study of Health in Pomerania (SHIP-Trend). Furthermore, we performed functional annotation analysis and related the genetic polymorphism influencing circulating BDNF to common Alzheimer’s disease pathologies from brain autopsies. Mendelian randomization was conducted to examine the possible causal role of circulating BDNF levels with various phenotypes including cognitive function, stroke, diabetes, cardiovascular disease, physical activity and diet patterns. Gene interaction networks analysis was also performed. The estimated heritability of BDNF levels was 30% (standard error = 0.0246, P-value = 4 × 10−48). We identified seven novel independent loci mapped near the BDNF gene and in BRD3, CSRNP1, KDELC2, RUNX1 (two single-nucleotide polymorphisms) and BDNF-AS. The expression of BDNF was associated with neurofibrillary tangles in brain tissues from the Religious Orders Study and Rush Memory and Aging Project (ROSMAP). Seven additional genes (ACAT1, ATM, NPAT, WDR48, TTC21A, SCN114 and COX7B) were identified through expression and protein quantitative trait loci analyses. Mendelian randomization analyses indicated a potential causal role of BDNF in cardioembolism. Lastly, Ingenuity Pathway Analysis placed circulating BDNF levels in four major networks. Our study provides novel insights into genes and molecular pathways associated with circulating BDNF levels and highlights the possible involvement of plaque instability as an underlying mechanism linking BDNF with brain neurodegeneration. These findings provide a foundation for a better understanding of BDNF regulation and function in the context of brain aging and neurodegenerative pathophysiology.
Lack of Antibodies to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a Large Cohort of Previously Infected Persons
Authors: Petersen Lyle R , Sami Samira , Vuong Nga , Pathela Preeti , Weiss Don , Morgenthau Beth Maldin , Henseler Rebecca A , Daskalakis Demetre C , Atas Jenny , Patel Anita , Lukacs Susan , Mackey Lisa , Grohskopf Lisa A , Thornburg Natalie , Akinbami Lara J 
Published: October 2020

Abstract

Background
Reports suggest that some persons previously infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lack detectable immunoglobulin G (IgG) antibodies. We aimed to determine the proportion IgG seronegative and predictors for seronegativity among persons previously infected with SARS-CoV-2.

Methods
We analyzed serologic data collected from healthcare workers and first responders in New York City and the Detroit metropolitan area with a history of a positive SARS-CoV-2 reverse-transcription polymerase chain reaction (RT-PCR) test result and who were tested for IgG antibodies to SARS-CoV-2 spike protein at least 2 weeks after symptom onset.

Results
Of 2547 persons with previously confirmed SARS-CoV-2 infection, 160 (6.3%) were seronegative. Of 2112 previously symptomatic persons, the proportion seronegative slightly increased from 14 to 90 days post symptom onset (P = .06). The proportion seronegative ranged from 0% among 79 persons previously hospitalized to 11.0% among 308 persons with asymptomatic infections. In a multivariable model, persons who took immunosuppressive medications were more likely to be seronegative (31.9%; 95% confidence interval [CI], 10.7%–64.7%), while participants of non-Hispanic Black race/ethnicity (vs non-Hispanic White; 2.7%; 95% CI, 1.5%–4.8%), with severe obesity (vs under/normal weight; 3.9%; 95% CI, 1.7%–8.6%), or with more symptoms were less likely to be seronegative.

Conclusions
In our population with previous RT-PCR–confirmed infection, approximately 1 in 16 persons lacked IgG antibodies. Absence of antibodies varied independently by illness severity, race/ethnicity, obesity, and immunosuppressive drug therapy. The proportion seronegative remained relatively stable among persons tested up to 90 days post symptom onset.
Detecting Spam Product Reviews in Roman Urdu Script
Authors: Hussain Naveed , Mirza Hamid Turab , Iqbal Faiza , Hussain Ibrar , Kaleem Mohammad 
Published: October 2020

ReferencesIn recent years, online customer reviews have become the main source to determine public opinion about offered products and services. Therefore, manufacturers and sellers are extremely concerned with customer reviews, as these can have a direct impact on their businesses. Unfortunately, there is an increasing trend to write spam reviews to promote or demote targeted products or services. This practice, known as review spamming, has posed many questions regarding the authenticity and dependability of customers’ review-based business processes. Although the spam review detection (SRD) problem has gained much attention from researchers, existing studies on SRD have mostly worked on datasets of English, Chinese, Arabic, Persian, and Malay languages. Therefore, the objective of this research is to identify the spam in Roman Urdu reviews using different classification models based on linguistic features and behavioral features. The performance of each classifier is evaluated in a number of perspectives: (i) linguistic features are used to calculate accuracy (F1 score) of each classifier; (ii) behavioral features combined with distributional and non-distributional aspects are used to evaluate accuracy (F1 score) of each classifier; and (iii) the combination of both linguistic and behavioral features (distributional and non-distributional aspects) are used to evaluate the accuracy of each classifier. The experimental evaluations demonstrated an improved accuracy (F1 score: 0.96), which is the result of combinations of linguistic features and behavioral features with the distributional aspect of reviewers. Moreover, behavioral features using distributional characteristic achieve an accuracy (F1 score: 0.86) and linguistic features shows accuracy (F1 score: 0.69). The outcome of this research can be used to increase customers’ confidence in the South Asian region. It can also help to reduce spam reviews in the South Asian region, particularly in Pakistan.
How to measure left ventricular myocardial work by pressure–strain loops
Authors: Smiseth Otto A , Donal Erwan , Penicka Martin , Sletten Ole Jakob 
Published: October 2020

Abstract
Myocardial work is calculated from non-invasive left ventricular pressure and strain by speckle tracking echocardiography. Myocardial work provides diagnostic information beyond what is achieved from left ventricular ejection fraction and strain since it incorporates afterload, and provides a measure of myocardial efficiency. The method can be used to calculate global as well as segmental work. The work method was recently shown to be of clinical value in selection of patients for cardiac resynchronization therapy. Several other clinical applications are currently tested.
Pre-emptive extracorporeal membrane oxygenation to support endobronchial stenting for severe airway obstruction
Authors: Ni Fhlatharta Meadhbh , Khan Asad , Carton Edmund , Redmond Karen C 
Published: October 2020

Abstract
Tracheobronchial stent insertion is a common palliative intervention for the management of dynamic airway collapse due to severe tracheobronchomalacia or tracheal compression due to mass effect [1]. Airway stents are usually placed bronchoscopically with or without fluoroscopy. In more complex cases, airway stents are placed using a rigid bronchoscope under general anaesthesia with conventional or jet ventilation. In patients where advancement of a rigid bronchoscope into the distal airway or ventilation through a rigid bronchoscope may be difficult, pre-emptive awake veno-venous extracorporeal membrane oxygenation should be considered. This report is the first publication to describe a novel technique in a series of patients being treated for critical airway obstruction who would otherwise be at risk of respiratory arrest at the induction of anaesthesia.
Characteristics and implications of insurance-reimbursed inpatient care for gastric and oesophageal cancers in Anhui, China
Authors: Yao Anqi , Shen Xingrong , Chai Jing , Cheng Jing , Liu Rong , Feng Rui , Wang Debin 
Published: October 2020

Abstract

Background
This study aimed to identify characteristics and trends in insurance-reimbursed inpatient care (NRIC) for gastric and oesophageal cancers and inform evaluation of medical systems reform.

Methods
The study extracted routinely collected records of claims for reimbursement from the New Rural Cooperative Medical System (NRCMS) in Anhui Province, China and performed descriptive and regression discontinuity analysis.

Results
From 2013 to 2017, NRIC in terms of person-time per million people (pmp) increased 5.60 and 20.62 times for gastric and oesophageal cancers, respectively. Total expense per episode for gastric and oesophageal cancers increased from 1130.25 and 22 697.99 yuan to 12 514.98 and 24 639.37 yuan, respectively. The ratio of out-of-pocket expenses per inpatient care episode to annual disposable income per capita was 0.43 for gastric cancer and 0.91 for oesophageal cancer and decreased by 0.17 and 0.47, respectively. Regression discontinuity modelling revealed that, when controlled for disposable income, illiteracy rate and months from start time, the treatment variable was significantly associated with person-times of NRIC pmp (β=0.613, p=0.000), length of stay per 105 people (β=−52.990, p=0.000) and total expenses per NRIC episode (β=2.431, p=0.000).

Conclusions
The study period witnessed substantial achievements in benefits to patients, inpatient care efficiency and equity. These achievements may be attributed mainly to the recent reforms launched in Anhui province, China.
Health economic analyses of the Global Programme to Eliminate Lymphatic Filariasis
Authors: Turner Hugo C 
Published: October 2020

Abstract
The Global Programme to Eliminate Lymphatic Filariasis (GPELF) was established by the WHO in 2000. It aims to eliminate lymphatic filariasis as a public health problem. This paper summarises the key estimates of the cost-effectiveness and economic benefits related to the mass drug administration (MDA) provided by the GPELF. Several studies have investigated the cost-effectiveness of this MDA, estimating the cost per disability-adjusted life year (DALY) averted. These cost-effectiveness estimates have consistently classed the intervention as cost-effective and as favourable compared with other public health interventions conducted in low- and middle-income countries. Studies have also found that the MDA used for lymphatic filariasis control generates significant economic benefits. Although these studies are positive, there are still important gaps that warrant further health economic research (particularly, the evaluation of alternative interventions, further evaluation of morbidity management strategies and evaluation of interventions for settings coendemic with Loa loa). To conclude, health economic studies for a programme as large as the GPELF are subject to uncertainty. That said, the GPELF has consistently been estimated to be cost-effective and to generate notable economic benefits by a number of independent studies.
New improved Aggregator: predicting which clinical trial articles derive from the same registered clinical trial
Authors: Smalheiser Neil R , Holt Arthur W 
Published: October 2020

Abstract

Objectives
To identify separate publications that report outcomes from the same underlying clinical trial, in order to avoid over-counting these as independent pieces of evidence.

Materials and Methods
We updated our previous model by creating larger, more recent, and more diverse positive and negative training sets consisting of article pairs that were (or not) linked to the same ClinicalTrials.gov trial registry number. Features were extracted from PubMed metadata; pairwise similarity scores were modeled using logistic regression and used to form clusters of articles that are likely to arise from the same registered clinical trial.

Results
Articles from the same trial were identified with high accuracy (F1 = 0.859), nominally better than the previous model (F1 = 0.843). Predicted clusters showed a low error rate of splitting of 8–11% (ie, when 2 articles belonged to the same trial but were assigned to different clusters). Performance was similar whether only randomized controlled trial articles or a more diverse set of clinical trial articles were processed.

Discussion
Metadata are surprisingly accurate in predicting when 2 articles derive from the same underlying clinical trial.

Conclusion
We have continued confidence in the Aggregator tool which can be accessed publicly at http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/RCT_Tagger.cgi.
Application of Measurement Uncertainty on Conformity Assessment in Pharmaceutical Drug Products
Authors: Simabukuro Renan , Jeong Noh Ah , Lourenço Felipe Rebello 
Published: October 2020

Abstract

Background
Conformity assessment in pharmaceutical drug products usually are based on analytical results. An analytical result always is associated with an uncertainty which must be considered in a compliance assessment.

Objective
The objective of the present project aims to estimate the measurement uncertainty associated with the results of average weight, assay, uniformity of content, and dissolution testing in ranitidine tablets manufactured by two different companies (X and Y).

Methods
The uncertainty was evaluated using the Monte Carlo method. The particular and total risks of false acceptance decisions (consumers’ risks) were also estimated by the Monte Carlo method.

Results
The results for ranitidine tablets manufactured by company X were (359.2 ± 2.7) mg of average weight, (108.6 ± 1.6)% of assay, (11.4 ± 2.8) of acceptance value for uniformity of content, and (89.4 ± 1.3)% for dissolution testing. The results for company Y were (312.5 ± 0.9) mg, (107.0 ± 1.4)%, (7.2 ± 1.7), and (93.6 ± 1.3)%, respectively. A 95% confidence level was adopted. According to results obtained from the Monte Carlo simulations, the results of average weight, assay of ranitidine, and uniformity of content are significantly correlated due to shared analytical steps. The correlation between values significantly affected the risk of false decisions.

Conclusions
Consumers’ risks were estimated for both ranitidine tablets and their results ensure compliance for ranitidine tablets manufactured by companies X and Y.

Highlights
The use of measurement uncertainty is an important issue regarding the conformity/non-conformity assessment of pharmaceutical products.
Utilization of gastropod shells by hermit crabs (Decapoda: Anomura: Paguridae) in Japan as related to characteristics of domicile shell
Authors: Takeda Satoshi 
Published: October 2020

Abstract
The relative proportions of gastropod shells occupied by the hermit crabs Pagurus dubius (Ortmann, 1892), P. filholi (De Man, 1887), P. lanuginose De Haan, 1849, and P. nigrofascia Komai, 1996 on a boulder shore at Asamushi, northern Japan differ significantly from those of the living gastropods that leave behind their empty shells after death. There is a difference in the frequencies of the shells of Omphalius rusticus (Gmelin, 1791) and Chlorostoma turbinatum A. Adams, 1853, which resemble each other in shape, between the proportions of shells occupied by the living gastropods and those of their empty shells occupied by hermit crabs. The three species of hermit crabs that were dominant at the study site showed no difference in shell selectivity between the two gastropod species in the laboratory. This result indicates that shell selection by hermit crabs cannot be responsible for the difference in composition between availability and utilization observed in the field. The empty shells of O. rusticus are thicker and heavier than those of C. turbinatum, suggesting that the former last longer than the latter, as shell durability against compressive force decreases as shell thickness is reduced. These observations suggest that the difference in the period for which these empty gastropod shells remain intact accounts for the difference in composition between their availability and utilization by hermit crabs.
Protein Intake by Source and Breast Cancer Incidence and Mortality: The Women’s Health Initiative
Authors: Pan Kathy , Larson Joseph C , Prentice Ross L , Mortimer Joanne E , Neuhouser Marian L , Manson JoAnn E , Van Horn Linda , Rohan Thomas E , Lane Dorothy , Chlebowski Rowan T 
Published: October 2020

AbstractBackgroundPrior studies of dietary protein intake and breast cancer have been mixed and were limited by dietary self-report measurement error.MethodsBiomarker-calibrated total protein intake and estimated vegetable protein and animal protein intake were determined from baseline food frequency questionnaires in 100 024 Women’s Health Initiative participants. Associations between total, animal, and vegetable protein intake and breast cancer incidence, deaths from breast cancer, and deaths after breast cancer were estimated using Cox proportional hazards regression. Breast cancers were verified by medical record review and survival outcomes enhanced by National Death Index queries. All statistical tests were 2-sided.ResultsAfter 14 years of follow-up, there were 6340 incident breast cancers, 764 deaths from breast cancer, and 2059 deaths after breast cancer. In multivariable analyses, higher calibrated total protein intake was not associated with breast cancer incidence or deaths from or after breast cancer. Vegetable protein intake was associated with statistically significantly lower breast cancer incidence (hazard ratio [HR] = 0.98, 95% confidence interval [CI] = 0.96 to 0.99, Ptrend = .006) and statistically significantly lower risk of death after breast cancer (HR = 0.93, 95% CI = 0.91 to 0.97, Ptrend &lt; .001) but not with deaths from breast cancer. In contrast, higher animal protein intake was associated with statistically significantly higher breast cancer incidence (HR = 1.03, 95% CI = 1.01 to 1.06, Ptrend = .02) but not with deaths from or after breast cancer.ConclusionsCalibrated total protein intake was not associated with breast cancer incidence or mortality. Higher vegetable protein intake was associated with lower breast cancer incidence and lower risk of death after breast cancer. Higher animal protein intake was associated with higher breast cancer incidence.
Superclusters from velocity divergence fields
Authors: Peñaranda-Rivera J D , Paipa-León D L , Hernández-Charpak S D , Forero-Romero J E 
Published: October 2020

ABSTRACT
Superclusters are a convenient way to partition and characterize the large-scale structure of the Universe. In this Letter, we explore the advantages of defining superclusters as watershed basins in the divergence velocity field. We apply this definition on diverse data sets generated from linear theory and N-body simulations, with different grid sizes, smoothing scales, and types of tracers. From this framework emerges a linear scaling relation between the average supercluster size and the autocorrelation length in the divergence field, a result that holds for one order of magnitude from 10 up to 100 Mpc h−1. These results suggest that the divergence-based definition provides a robust context to quantitatively compare results across different observational or computational frameworks. Through its connection with linear theory, it can also facilitate the exploration of how supercluster properties depend on cosmological parameters, paving the way to use superclusters as cosmological probes.