bluuebunny/crossref_metadata_2025 huggingface dataset:
iDMer: an integrative and mechanism-driven response system for identifying compound interventions for sudden virus outbreak
Authors: Wei Zhiting , Gao Yuli , Meng Fangliangzi , Chen Xin , Gong Yukang , Zhu Chenyu , Ju Bin , Zhang Chao , Liu Zhongmin , Liu Qi
Published: October 2020

Emerging viral infections seriously threaten human health globally. Several challenges exist in identifying effective compounds against viral infections: (1) at the initial stage of a new virus outbreak, little information, except for its genome information, may be available; (2) although the identified compounds may be effective, they may be toxic in vivo and (3) cytokine release syndrome (CRS) triggered by viral infections is the primary cause of mortality. Currently, an integrative tool that takes all those aspects into consideration for identifying effective compounds to prevent viral infections is absent. In this study, we developed iDMer, as an integrative and mechanism-driven response system for addressing these challenges during the sudden virus outbreaks. iDMer comprises three mechanism-driven compound identification modules, that is, a virus-host interaction-oriented module, an autophagy-oriented module and a CRS-oriented module. As a one-stop integrative platform, iDMer incorporates compound toxicity evaluation and compound combination identification for virus treatment with clear mechanisms. iDMer was successfully tested on five viruses, including the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our results indicated that, for all five tested viruses, compounds that were reported in the literature or experimentally validated for virus treatment were enriched at the top, demonstrating the generalized effectiveness of iDMer. Finally, we demonstrated that combinations of the individual modules successfully identified combinations of compounds effective for virus intervention with clear mechanisms.
Calibrating variant-scoring methods for clinical decision making
Authors: Benevenuta Silvia , Capriotti Emidio , Fariselli Piero
Published: October 2020

Identifying pathogenic variants and annotating them is a major challenge in human genetics, especially for the non-coding ones. Several tools have been developed and used to predict the functional effect of genetic variants. However, the calibration assessment of the predictions has received little attention. Calibration refers to the idea that if a model predicts a group of variants to be pathogenic with a probability P, it is expected that the same fraction P of true positive is found in the observed set. For instance, a well-calibrated classifier should label the variants such that among the ones to which it gave a probability value close to 0.7, approximately 70% actually belong to the pathogenic class. Poorly calibrated algorithms can be misleading and potentially harmful for clinical decision making.

Avaliability and implementation

The dataset used for testing the methods is available through the DOI:10.5281/zenodo.4448197.

Supplementary information

Supplementary data are available at Bioinformatics online.
A robust computational pipeline for model-based and data-driven phenotype clustering
Authors: Simoni Giulia , Kaddi Chanchala , Tao Mengdi , Reali Federico , Tomasoni Danilo , Priami Corrado , Azer Karim , Neves-Zaph Susana , Marchetti Luca
Published: October 2020

Motivation

Precision medicine is a promising field that proposes, in contrast to a one-size-fits-all approach, the tailoring of medical decisions, treatments or products. In this context, it is crucial to introduce innovative methods to stratify a population of patients on the basis of an accurate system-level knowledge of the disease. This is particularly important in very challenging conditions, where the use of standard statistical methods can be prevented by poor data availability or by the need of oversimplifying the processes regulating a complex disease.

Results

We define an innovative method for phenotype classification that combines experimental data and a mathematical description of the disease biology. The methodology exploits the mathematical model for inferring additional subject features relevant for the classification. Finally, the algorithm identifies the optimal number of clusters and classifies the samples on the basis of a subset of the features estimated during the model fit. We tested the algorithm in two test cases: an in silico case in the context of dyslipidemia, a complex disease for which a large population of patients has been generated, and a clinical test case, in the context of a lysosomal rare disorder, for which the amount of available data was limited. In both the scenarios, our methodology proved to be accurate and robust, and allowed the inference of an additional phenotype division that the experimental data did not show.

Availability and implementation

The code to reproduce the in silico results has been implemented in MATLAB v.2017b and it is available in the Supplementary Material.

Supplementary information

Supplementary data are available at Bioinformatics online.
MiRKAT: kernel machine regression-based global association tests for the microbiome
Authors: Wilson Nehemiah , Zhao Ni , Zhan Xiang , Koh Hyunwook , Fu Weijia , Chen Jun , Li Hongzhe , Wu Michael C , Plantinga Anna M
Published: October 2020

Distance-based tests of microbiome beta diversity are an integral part of many microbiome analyses. MiRKAT enables distance-based association testing with a wide variety of outcome types, including continuous, binary, censored time-to-event, multivariate, correlated and high-dimensional outcomes. Omnibus tests allow simultaneous consideration of multiple distance and dissimilarity measures, providing higher power across a range of simulation scenarios. Two measures of effect size, a modified R-squared coefficient and a kernel RV coefficient, are incorporated to allow comparison of effect sizes across multiple kernels.

Availability and implementation

MiRKAT is available on CRAN as an R package.

Supplementary information

Supplementary data are available at Bioinformatics online.
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

Here 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

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

Brain-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

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

References

In 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

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

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

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

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

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

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

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

Background

Prior studies of dietary protein intake and breast cancer have been mixed and were limited by dietary self-report measurement error.

Methods

Biomarker-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.

Results

After 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 < .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.

Conclusions

Calibrated 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

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.
Short-Selling Bans and Bank Stability
Authors: Beber Alessandro , Fabbri Daniela , Pagano Marco , Simonelli Saverio
Published: October 2020

In both the subprime crisis and the eurozone crisis, regulators imposed bans on short sales mainly aimed at preventing stock price turbulence from destabilizing financial institutions. Contrary to the regulators’ intentions, financial institutions whose stocks were banned experienced greater increases in the probability of default and volatility than unbanned ones. Increases were larger for more vulnerable financial institutions. To take into account the endogeneity of short sales bans, we match banned financial institutions with unbanned ones with similar sizes and levels of riskiness and instrument the 2011 ban decisions with regulators’ propensity to impose a ban in the 2008 crisis. (JEL G01, G12, G14, G18)

Received July 8, 2020; editorial decision September 8, 2020 by Editor Isil Erel.
Gathering evidence of impact from research support services: Examining impact in the context of the Centre for Environmental Data Analysis
Authors: Townsend Poppy , Wilkinson Clare
Published: October 2020

The Centre for Environmental Data Analysis (CEDA) is a provider of two major services to the environmental science community; JASMIN and the CEDA Archive. CEDA is frequently required to evidence the impact it has on researchers and wider society. However, this is challenging as there are currently no formal or standard processes for collecting impact information. To understand how CEDA could collect impact information, and to allow its users to shape this monitoring, over 500 users provided their opinions, preferences and suggestions as to how to share impact, via six focus groups and an online survey. The results suggest that whilst there was a high degree of willingness to provide impact information to CEDA there remains confusion around what ‘impact’ is. Users are keen to share impact in ways which utilize existing processes, and at times which make sense to both the research and the impact, whilst also understanding the need and purpose for sharing that information.
Full-genome sequencing of German rabbit haemorrhagic disease virus uncovers recombination between RHDV (GI.2) and EBHSV (GII.1)
Authors: Szillat Kevin P , Höper Dirk , Beer Martin , König Patricia
Published: October 2020

Rabbit haemorrhagic disease virus (RHDV; genotypes GI.1 and GI.2) and European brown hare syndrome virus (EBHSV; genotype GII.1) are caliciviruses belonging to the genus Lagovirus. These viruses pose a serious threat to wild and domestic rabbit and hare populations around the world. In recent years, an expanding genetic diversity has been described within the genus, with recombination events occurring between the different genotypes. Here, we generated and analysed 56 full-genome sequences of RHDV and EBHSV from rabbit and hare livers, collected in Germany between the years 2013 and 2020. We could show that genotype Gl.2 (RHDV-2) almost entirely replaced Gl.1 (classical RHDV) in the German rabbit population. However, GI.1 is still present in Germany and has to be included into disease control and vaccination strategies. Three recombinant strains were identified from rabbit samples that contain the structural genes of genotype Gl.2 and the non-structural genes of genotype Gl.1b. Of special interest is the finding that sequences from two hare samples showed recombination events between structural genes of RHDV Gl.2 and non-structural genes of EBHSV GII.1, a recombination between different genogroups that has not been described before. These findings lead to the assumption that also a recombination of the non-structural genes of RHDV Gl.2 with the structural genes of EBHSV Gll.1 might be possible and therefore increase the potential genetic variability of lagoviruses immensely. Our findings underline the importance of whole genome analysis with next-generation sequencing technology as one of new tools now available for in-depth studies that allow in depth molecular epidemiology with continuous monitoring of the genetic variability of viruses that would otherwise likely stay undetected if only routine diagnostic assays are used.
Evaluating the Reliability and Validity Evidence of the RIME (Reporter–Interpreter–Manager–Educator) Framework for Summative Assessments Across Clerkships
Authors: Ryan Michael S. , Lee Bennett , Richards Alicia , Perera Robert A. , Haley Kellen , Rigby Fidelma B. , Park Yoon Soo , Santen Sally A.
Published: October 2020

Purpose

The ability of medical schools to accurately and reliably assess medical student clinical performance is paramount. The RIME (reporter–interpreter–manager–educator) schema was originally developed as a synthetic and intuitive assessment framework for internal medicine clerkships. Validity evidence of this framework has not been rigorously evaluated outside of internal medicine. This study examined factors contributing to variability in RIME assessment scores using generalizability theory and decision studies across multiple clerkships, thereby contributing to its internal structure validity evidence.

Method

Data were collected from RIME-based summative clerkship assessments during 2018–2019 at Virginia Commonwealth University. Generalizability theory was used to explore variance attributed to different facets through a series of unbalanced random-effects models by clerkship. For all analyses, decision (D-) studies were conducted to estimate the effects of increasing the number of assessments.

Results

From 231 students, 6,915 observations were analyzed. Interpreter was the most common RIME designation (44.5%–46.8%) across all clerkships. Variability attributable to students ranged from 16.7% in neurology to 25.4% in surgery. D-studies showed the number of assessments needed to achieve an acceptable reliability (0.7) ranged from 7 in pediatrics and surgery to 11 in internal medicine and 12 in neurology. However, depending on the clerkship each student received between 3 and 8 assessments.

Conclusions

This study conducted generalizability- and D-studies to examine the internal structure validity evidence of RIME clinical performance assessments across clinical clerkships. Substantial proportion of variance in RIME assessment scores was attributable to the rater, with less attributed to the student. However, the proportion of variance attributed to the student was greater than what has been demonstrated in other generalizability studies of summative clinical assessments. Overall, these findings support the use of RIME as a framework for assessment across clerkships and demonstrate the number of assessments required to obtain sufficient reliability.
End-of-Life-Care Quality in ICUs Is Associated With Family Surrogates’ Severe Anxiety and Depressive Symptoms During Their First 6 Months of Bereavement*
Authors: Tang Siew Tzuh , Huang Chung-Chi , Hu Tsung-Hui , Lo Mei-Ling , Chou Wen-Chi , Chuang Li-Pang , Chiang Ming Chu
Published: October 2020

OBJECTIVES:

Evidence linking end-of-life-care quality in ICUs to bereaved family members’ psychologic distress remains limited by methodological insufficiencies of the few studies on this topic. To examine comprehensively the associations of family surrogates’ severe anxiety and depressive symptoms with end-of-life-care quality in ICUs over their first 6 months of bereavement.

DESIGN:

Prospective, longitudinal, observational study.

SETTING/PARTICIPANTS:

Family surrogates (n = 278) were consecutively recruited from seven medical ICUs at two academically affiliated medical centers in Taiwan.

MEASUREMENTS AND STATISTICAL ANALYSIS:

Family surrogates’ anxiety and depressive symptoms were assessed 1, 3, and 6 months postloss using the Hospital Anxiety and Depression Scale. Family satisfaction with end-of-life care in ICUs was assessed 1-month postloss by the Family Satisfaction in the ICU questionnaire. Patients’ end-of-life care was documented over the patient’s ICU stay. Associations of severe anxiety and depressive symptoms (scores ≥ 8 for each subscale) with end-of-life-care quality in ICUs (documented by patient care received and family satisfaction with end-of-life care in ICUs) were examined by multivariate logistic regression models with generalized estimating equation.

MAIN RESULTS:

Prevalence of severe anxiety and depressive symptoms decreased significantly over time. Surrogates’ lower likelihood of severe anxiety or depressive symptoms 3–6 month postloss was associated with death without cardiopulmonary resuscitation, withdrawing life-sustaining treatments, and higher family satisfaction with end-of-life care in ICUs. Bereaved surrogates’ higher likelihood of these symptoms was associated with physician-surrogate prognostic communication and conducting family meetings before patients died.

CONCLUSIONS:

End-of-life-care quality in ICUs is associated with bereaved surrogates’ psychologic well-being. Enhancing end-of-life-care quality in ICUs by improving the process of end-of-life care, for example, promoting death without cardiopulmonary resuscitation, withdrawing life-sustaining treatments, and increasing family satisfaction with end-of-life care, can lighten bereaved family surrogates’ severe anxiety symptoms and severe depressive symptoms.
The Prevalence of Gastrointestinal Symptoms, Abnormal Liver Function, Digestive System Disease and Liver Disease in COVID-19 Infection
Authors: Dong Zi-yuan , Xiang Bing-Jie , Jiang Min , Sun Ming-jun , Dai Cong
Published: October 2020

Background:

The worldwide outbreak of COVID-19 infected millions of people. Some patients had gastrointestinal (GI) symptoms, abnormal liver function, digestive system disease and liver disease.

Aim:

To investigate the prevalence of GI symptoms, abnormal liver function, digestive system disease and liver disease in patients with COVID-19 by a systematic review and meta-analysis.

Methods:

We searched PubMed, Ovid Embase, Medline, and 2 Chinese databases. Primary outcomes were the prevalence of GI symptoms, abnormal liver function, digestive system disease, and liver disease. Different studies were included in different subset analysis. These outcomes were estimated with proportions, odds ratio, 95% confidence interval (CI) and P-value by Stata SE 15.1.

Results:

Thirty-one studies involving 4682 patients were included. The most significant GI symptoms were diarrhea (0.08, 95% CI: 0.06-0.11) and anorexia (0.17, 95% CI: 0.06-0.27). The most significant abnormal liver function was increased alanine aminotransferase (ALT) (0.25, 95% CI: 0.16-0.33). A total of 5% of the patients had digestive system disease (95% CI: 0.02-0.08). A total of 3% of the patients had liver disease (95% CI: 0.02-0.05). The prevalence of nausea and vomiting, diarrhea, abnormal liver function, digestive system disease, and liver disease was higher in Wuhan group. The prevalence of diarrhea was higher in non-China group. Patients in severe/intensive care unit group were more likely to have diarrhea, anorexia, abdominal pain increased aspartate aminotransferase, and increased ALT.

Conclusion:

The most significant GI symptoms were anorexia and diarrhea. The most significant abnormal liver function was increased ALT. Severe patients were more likely to have GI symptoms and abnormal liver function.
Acupuncture and Related Therapies for the Treatment of Gastrointestinal Diseases
Authors: Rabitti Stefano , Giovanardi Carlo M. , Colussi Dora
Published: October 2020

Gastrointestinal diseases are very common worldwide. Patients with gastroesophageal reflux disease, functional dyspepsia, irritable bowel syndrome, and inflammatory bowel diseases frequently recur to complementary medicine, including acupuncture, likely because of the recurrence of symptoms and the sometimes lack of efficacy of conventional treatments. Acupuncture is a medical practice used in Asian country with benefits for thousands years. In the last decades, growing attention has been given to acupuncture also in Western countries and many studies have investigated the role of acupuncture in gastroenterology. This review provided an overview of the effectiveness and potential mechanisms of action of acupuncture for the treatment of gastrointestinal diseases.
Psychological Comorbidity and Intervention in Inflammatory Bowel Disease
Authors: Kredentser Maia S. , Graff Lesley A. , Bernstein Charles N.
Published: October 2020

Inflammatory bowel disease (IBD) is associated with significant psychological comorbidities, with associated impacts on patient quality of life, disease course, and health care costs. The present article reviews the latest evidence on the etiology of psychological comorbidities in IBD, with a focus on shared inflammatory pathways. The current state of practice in managing and understanding psychological comorbidities from the perspective of both gastroenterology practice and psychological treatment is reviewed, with a focus on evidence-based treatments shown to be effective in managing depression, anxiety, stress, and improving IBD-related health outcomes.
Diagnostic accuracy of different blood cells-derived indexes in rheumatoid arthritis
Authors: Erre Gian Luca , Buscetta Giorgio , Mangoni Arduino Aleksander , Castagna Floriana , Paliogiannis Panagiotis , Oggiano Massimiliano , Carru Ciriaco , Passiu Giuseppe , Zinellu Angelo
Published: October 2020

To evaluate the performance of different blood cells-derived indexes in the diagnosis of rheumatoid arthritis (RA).

Neutrophil-to-lymphocyte ratio (NLR), lymphocyte to monocyte ratio, platelet to lymphocyte ratio (PLR), systemic inflammation response index (SIRI), and aggregate inflammation systemic index were calculated in 199 consecutive RA patients and 283 sex and age-matched controls (147 healthy donors and 136 patients with other rheumatic diseases). Area under the curve (AUCs), sensitivity and specificity were calculated to evaluate the accuracy of indexes in discriminating between RA and controls. Association between indexes and RA variables was explored by multiple linear regression analyses.

Blood cells-derived indexes did not demonstrate good accuracy in differentiating RA from controls with lymphocyte to monocyte ratio, the index with the best diagnostic performance, having 63.6% of sensitivity and 65.3% specificity [AUC (95%CI) = 0.67 (0.62–0.72]. The accuracy of the indexes in differentiating RA from healthy donors was significantly higher than that (AUCs < 0.6 for all comparisons) differentiating RA from rheumatic diseases. In RA, SIRI and aggregate inflammation systemic index showed significant association with C-reactive protein and erythrocyte sedimentation rate.

Our results do not support the use of blood cells-derived indexes for the diagnosis of RA, suggesting that they might reflect chronic inflammatory burden in rheumatic diseases rather than, specifically, in RA.
Characteristics and clinical outcomes in pituitary incidentalomas and non-incidental pituitary tumors treated with endoscopic transsphenoidal surgery
Authors: Morinaga Yusuke , Abe Ichiro , Nii Kouhei , Hanada Hayatsura , Takemura Yusuke , Takashi Yuichi , Sakamoto Kimiya , Inoue Ritsurou , Mitsutake Takafumi , Kobayashi Kunihisa , Higashi Toshio
Published: October 2020

Purpose:

In this retrospective study, we investigated the status and validity of endoscopic transsphenoidal surgery (eTSS) for pituitary incidentalomas (PIs) as well as the value of basing the indication for surgery on the PI guidelines.

Methods:

Patients who underwent eTSS at Fukuoka University Chikushi Hospital between 2012 and 2018 were divided into the PI group and the non-PI group in accordance with the PI guideline of the Endocrine Society and their clinicopathological characteristics and outcomes were compared and analyzed.

Results:

A total of 59 patients were enrolled, with 35 patients in the PI group and 24 patients in the non-PI group. The diagnoses in the PI group were of non-functioning pituitary adenoma (NFPA) (n = 12, 34%), gonadotropin-producing pituitary adenoma (n = 8, 23%), Rathke cleft cyst (n = 7, 20%), meningioma (n = 4, 11%), and growth hormone-producing pituitary adenoma (n = 3, 9%); those in the non-PI group were of NFPA (n = 6, 25%), gonadotropin-producing pituitary adenoma (n = 3, 13%), Rathke cleft cyst (n = 3, 13%), growth hormone-producing pituitary adenoma (n = 3, 13%), and prolactin producing pituitary adenoma (n = 3, 13%). Regarding the preoperative factors, 1 patient in the PI group with panhypopituitarism was diagnosed with pituitary apoplexy (pure infarction) of an NFPA. The rates of postoperative anterior pituitary hormonal deficiencies (14% vs 46%, P = .015), residual tumor size (2 ± 5 vs 6 ± 7 mm, P = .008), and reoperation (n = 0, 0% vs n = 5, 21%, P = .005) were significantly different between the PI and non-PI groups.

Conclusions:

This study showed that, postoperatively, the incidence of anterior pituitary hormonal deficiencies was lower in the PI than in the non-PI group, although it was comparable between the 2 groups before the operation. The patients in the PI group also had smaller residual tumors and a lower risk of reoperation than those in non-PI group. PIs could have a better postoperative clinical outcome than non-PIs when the indication for eTSS is based on preoperative scrutiny according to the PI guidelines and eTSS is performed by an experienced pituitary surgeon. Hence, more aggressive scrutiny and treatment for PIs might be desirable.