bluuebunny/crossref_metadata_2025_split huggingface dataset:
How representative are neuroimaging samples? Large-scale evidence for trait anxiety differences between fMRI and behaviour-only research participants
Authors: Charpentier Caroline J , Faulkner Paul , Pool Eva R , Ly Verena , Tollenaar Marieke S , Kluen Lisa M , Fransen Aniek , Yamamori Yumeya , Lally Níall , Mkrtchian Anahit , Valton Vincent , Huys Quentin J M , Sarigiannidis Ioannis , Morrow Kelly A , Krenz Valentina , Kalbe Felix , Cremer Anna , Zerbes Gundula , Kausche Franziska M , Wanke Nadine , Giarrizzo Alessio , Pulcu Erdem , Murphy Susannah , Kaltenboeck Alexander , Browning Michael , Paul Lynn K , Cools Roshan , Roelofs Karin , Pessoa Luiz , Harmer Catherine J , Chase Henry W , Grillon Christian , Schwabe Lars , Roiser Jonathan P , Robinson Oliver J , O’Doherty John P 
Published: May 2021

AbstractOver the past three decades, functional magnetic resonance imaging (fMRI) has become crucial to study how cognitive processes are implemented in the human brain. However, the question of whether participants recruited into fMRI studies differ from participants recruited into other study contexts has received little to no attention. This is particularly pertinent when effects fail to generalize across study contexts: for example, a behavioural effect discovered in a non-imaging context not replicating in a neuroimaging environment. Here, we tested the hypothesis, motivated by preliminary findings (N = 272), that fMRI participants differ from behaviour-only participants on one fundamental individual difference variable: trait anxiety. Analysing trait anxiety scores and possible confounding variables from healthy volunteers across multiple institutions (N = 3317), we found robust support for lower trait anxiety in fMRI study participants, consistent with a sampling or self-selection bias. The bias was larger in studies that relied on phone screening (compared with full in-person psychiatric screening), recruited at least partly from convenience samples (compared with community samples), and in pharmacology studies. Our findings highlight the need for surveying trait anxiety at recruitment and for appropriate screening procedures or sampling strategies to mitigate this bias.
Low competitive status elicits aggression in healthy young men: behavioural and neural evidence
Authors: Buades-Rotger Macià , Göttlich Martin , Weiblen Ronja , Petereit Pauline , Scheidt Thomas , Keevil Brian G , Krämer Ulrike M 
Published: May 2021

AbstractWinners are commonly assumed to compete more aggressively than losers. Here, we find overwhelming evidence for the opposite. We first demonstrate that low-ranking teams commit more fouls than they receive in top-tier soccer, ice hockey and basketball men’s leagues. We replicate this effect in the laboratory, showing that male participants deliver louder sound blasts to a rival when placed in a low-status position. Using neuroimaging, we characterize brain activity patterns that encode competitive status as well as those that facilitate status-dependent aggression in healthy young men. These analyses reveal three key findings. First, anterior hippocampus and striatum contain multivariate representations of competitive status. Second, interindividual differences in status-dependent aggression are linked with a sharper status differentiation in the striatum and with greater reactivity to status-enhancing victories in the dorsal anterior cingulate cortex. Third, activity in ventromedial, ventrolateral and dorsolateral prefrontal cortex is associated with trial-wise increases in status-dependent aggressive behaviour. Taken together, our results run counter to narratives glorifying aggression in competitive situations. Rather, we show that those in the lower ranks of skill-based hierarchies are more likely to behave aggressively and identify the potential neural basis of this phenomenon.
Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae)
Authors: Morales-Briones Diego F , Gehrke Berit , Huang Chien-Hsun , Liston Aaron , Ma Hong , Marx Hannah E , Tank David C , Yang Ya 
Published: May 2021

Abstract
Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common approaches for processing paralogs in target enrichment data sets include random selection, manual pruning, and mainly, the removal of entire genes that show any evidence of paralogy. These approaches are prone to errors in orthology inference or removing large numbers of genes. By removing entire genes, valuable information that could be used to detect and place WGD events is discarded. Here, we used an automated approach for orthology inference in a target enrichment data set of 68 species of Alchemilla s.l. (Rosaceae), a widely distributed clade of plants primarily from temperate climate regions. Previous molecular phylogenetic studies and chromosome numbers both suggested ancient WGDs in the group. However, both the phylogenetic location and putative parental lineages of these WGD events remain unknown. By taking paralogs into consideration and inferring orthologs from target enrichment data, we identified four nodes in the backbone of Alchemilla s.l. with an elevated proportion of gene duplication. Furthermore, using a gene-tree reconciliation approach, we established the autopolyploid origin of the entire Alchemilla s.l. and the nested allopolyploid origin of four major clades within the group. Here, we showed the utility of automated tree-based orthology inference methods, previously designed for genomic or transcriptomic data sets, to study complex scenarios of polyploidy and reticulate evolution from target enrichment data sets.[Alchemilla; allopolyploidy; autopolyploidy; gene tree discordance; orthology inference; paralogs; Rosaceae; target enrichment; whole genome duplication.]
Psychosocial correlates of objectively measured in-school and out-of-school physical activity among Brazilian adolescents
Authors: Lopes Marcus V V , da Costa Bruno G G , Knebel Margarethe T G , Matias Thiago S , Silva Kelly S 
Published: May 2021

Abstract
Physical activity is influenced by an interplay of time and setting, thus, the role of psychosocial factors on behavior is expected to vary across the day. This cross-sectional study identified the psychosocial correlates of time spent in physical activity during in-school (i.e., 08:00–11:59) and out-of-school (i.e., 12:00–22:00) time segments. The sample consisted of adolescents (7th to 9th grade) of two public schools in Florianópolis, Brazil. Accelerometer measured light-intensity (LPA) and moderate-to-vigorous-intensity physical activity (MVPA) were estimated. Psychosocial correlates of physical activity (i.e., outcome expectations, attitude, self-efficacy, support from parents, and support from peers) were self-reported. Linear mixed models were applied and interaction effects of gender and age were also analyzed. From a total of 194 participants, 138 and 112 provided in-school and out-of-school valid data, respectively. Outcome expectations were associated with out-of-school MVPA (β = 0.18; p = .006). Age interaction effects were observed for the associations between outcome expectations and out-of-school LPA (β = 0.21; p = .009) and between self-efficacy and out-of-school MVPA (β = 0.19; p = .009). In conclusion, psychosocial correlates were positively associated with out-of-school physical activity and the effects varied according to age. No psychosocial correlates were identified for LPA and MVPA performed during schooltime.
RETINAL FLUID AND THICKNESS AS MEASURES OF DISEASE ACTIVITY IN NEOVASCULAR AGE-RELATED MACULAR DEGENERATION
Authors: Kaiser Peter K. , Wykoff Charles C. , Singh Rishi P. , Khanani Arshad M. , Do Diana V. , Patel Hersh , Patel Nikhil 
Published: May 2021

Purpose:
Retinal fluid and thickness are important anatomical features of disease activity in neovascular age-related macular degeneration, as evidenced by clinical trials that have used these features for inclusion criteria, retreatment criteria, and outcome measures of the efficacy of intravitreal injections of anti–vascular endothelial growth factor agents.

Methods:
A literature review of anatomical measures of disease activity was conducted.

Results:
Treatment goals for neovascular age-related macular degeneration include improving/maintaining vision by drying the retina, and several analyses have evaluated the relationship between visual function and anatomy. The change in retinal thickness has been found to correlate with the change in the visual acuity, and variation in retinal thickness may predict visual acuity outcomes. In addition, specific fluid compartments may have different prognostic values. For example, the presence of intraretinal fluid has been associated with poorer visual acuity, whereas the presence of subretinal fluid has been associated with better visual acuity. Retinal fluid and thickness are important for selecting dosing interval durations in clinical trials and clinical practice.

Conclusion:
Retinal thickness and retinal fluid are common anatomical measures of disease activity in neovascular age-related macular degeneration. Further research is required to fully elucidate the relationship between anatomical features and visual outcomes in neovascular age-related macular degeneration.
Pharmacological Management of Heart Failure: A Century of Expert Opinions in Cecil Textbook of Medicine
Authors: Manu Peter , Rogozea Liliana M. , Dan Gheorghe-Andrei 
Published: May 2021

Background:
Drug therapy for heart failure influences quality of life and work potential of affected persons and has contributed to decrease in hospitalizations and cardiovascular mortality. The current approach is the result of incremental progress in understanding the pathophysiology of the syndrome, introduction of new molecules, and repurposing existing drugs.

Study Question:
What are the milestones of the changes in the expert clinicians' approach to the pharmacological management in the past century?

Study Design:
To determine the changes in the experts' approach to the management of heart failure, as presented in a widely used textbook in the United States.

Data Sources:
The chapters on the management of heart failure in the 26 editions of Cecil Textbook of Medicine published from 1927 through 2020.

Results:
In 1927, heart failure was treated with powdered leaf or tincture of digitalis, mercury chloride, and theophylline. Patients with acute pulmonary edema received injections of atropine, adrenaline, and ouabain. The therapeutic milestones in heart failure were the introduction of loop diuretics and aldosterone antagonists (1971), vasodilator treatment with hydralazine and nitroglycerine (1979–1985), angiotensin-converting enzyme inhibitors, angiotensin receptor blockers and selective beta-adrenergic blockers (1992–2000), and sacubitril–valsartan (2016). For acute pulmonary edema, the durable milestone was the treatment with morphine and furosemide (1971).

Conclusions:
The pharmacological management of heart failure in the past century has progressed in fits and starts, with latent periods between significant advances lasting 8–40 years. In chronological order, the major advances were efficient diuresis, afterload reduction, and blunting the neurohormonal response to hemodynamic stress and cardiac remodeling.
Design of a Randomized Controlled Trial of Percutaneous Posterior Tibial Nerve Stimulation for the Treatment of Refractory Fecal Incontinence in Women: The NeurOmodulaTion for Accidental Bowel Leakage Study
Authors: Zyczynski Halina M. , Arya Lily A. , Lukacz Emily S. , Richter Holly E. , Rahn David D. , Sung Vivian W. , Visco Anthony G. , Shaffer Amanda , Jelovsek J. Eric , Rogers Rebecca , Mazloomdoost Donna , Gantz Marie G. ,   for the Eunice Kennedy Shriver NICHD Pelvic Floor Disorders Network (PFDN)
Published: May 2021

Objectives
High-level evidence for second-line noninvasive treatments for fecal incontinence in women is limited. We present the rationale for and design of the NeuromOdulaTion for Accidental Bowel Leakage trial, a randomized controlled trial of percutaneous tibial nerve stimulation (PTNS) and validated sham stimulation in women with refractory accidental bowel leakage.

Methods
The rationale and goals for a 2-part study with a run-in phase, use of a generic pulse generator for PTNS and sham stimulation, masking, participant inclusion, primary and secondary outcome measures, and adverse event collection are described. A superiority design will be used to compare change from baseline in St. Mark’s score after 12 weekly stimulation sessions between PTNS and sham. Responders to initial treatment (PTNS or sham) will be assigned to scheduled or “as needed” intervention for up to 1 year. Secondary outcome measures include incontinence episodes and other bowel events recorded in a 14-day electronic bowel diary, general and condition-specific quality of life instruments, adaptive behavior, global impression of improvement, symptom control, and sexual function.

Results
Sample size calculations determined that 165 participants (110 PTNS and 55 sham) would provide 90% power to detect greater than or equal to 4-point difference between PTNS and sham in change from baseline in St. Mark’s score at 12 weeks.

Conclusions
The methods for the NeuromOdulaTion for Accidental Bowel Leakage trial will provide high-level evidence of the effectiveness and optimal maintenance therapy schedule of a low-cost PTNS protocol in community-dwelling women seeking second-line intervention for refractory accidental bowel leakage.
Prolonged SARS-CoV-2 RNA virus shedding and lymphopenia are hallmarks of COVID-19 in cancer patients with poor prognosis
Authors: Goubet Anne-Gaëlle , Dubuisson Agathe , Geraud Arthur , Danlos François-Xavier , Terrisse Safae , Alves Costa Silva Carolina , Drubay Damien , Touri Lea , Picard Marion , Mazzenga Marine , Silvin Aymeric , Dunsmore Garett , Haddad Yacine , Pizzato Eugenie , Ly Pierre , Flament Caroline , Melenotte Cléa , Solary Eric , Fontenay Michaela , Garcia Gabriel , Balleyguier Corinne , Lassau Nathalie , Maeurer Markus , Grajeda-Iglesias Claudia , Nirmalathasan Nitharsshini , Aprahamian Fanny , Durand Sylvère , Kepp Oliver , Ferrere Gladys , Thelemaque Cassandra , Lahmar Imran , Fahrner Jean-Eudes , Meziani Lydia , Ahmed-Belkacem Abdelhakim , Saïdani Nadia , La Scola Bernard , Raoult Didier , Gentile Stéphanie , Cortaredona Sébastien , Ippolito Giuseppe , Lelouvier Benjamin , Roulet Alain , Andre Fabrice , Barlesi Fabrice , Soria Jean-Charles , Pradon Caroline , Gallois Emmanuelle , Pommeret Fanny , Colomba Emeline , Ginhoux Florent , Kazandjian Suzanne , Elkrief Arielle , Routy Bertrand , Miyara Makoto , Gorochov Guy , Deutsch Eric , Albiges Laurence , Stoclin Annabelle , Gachot Bertrand , Florin Anne , Merad Mansouria , Scotte Florian , Assaad Souad , Kroemer Guido , Blay Jean-Yves , Marabelle Aurélien , Griscelli Frank , Zitvogel Laurence , Derosa Lisa 
Published: May 2021

AbstractPatients with cancer are at higher risk of severe coronavirus infectious disease 2019 (COVID-19), but the mechanisms underlying virus-host interactions during cancer therapies remain elusive. When comparing nasopharyngeal swabs from cancer and non-cancer patients for RT-qPCR cycle thresholds measuring acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in 1063 patients (58% with cancer, 89% COVID-19+), we found that malignant disease favors the magnitude and duration of viral RNA shedding concomitant with prolonged serum elevations of type 1 IFN that anticorrelated with anti-RBD IgG antibodies. Chronic viral RNA carriers exhibited the typical immunopathology of severe COVID-19 at the early phase of infection including circulation of immature neutrophils, depletion of non-conventional monocytes and a general lymphopenia that, however, was accompanied by a rise in plasmablasts, activated follicular T helper cells, and non-naive Granzyme B+ FasL+, EomehighTCF-1high, PD-1+CD8+ Tc1 cells. Virus-induced lymphopenia worsened cancer-associated lymphocyte loss, and low lymphocyte counts correlated with chronic SARS-CoV-2 RNA shedding, COVID-19 severity and a higher risk of cancer-related death in the first and second surge of the pandemic. Lymphocyte loss correlated with significant changes in metabolites from the polyamine and biliary salt pathways as well as increased blood DNA from Enterobacteriaceae and Micrococcaceae gut family members in long term viral carriers. We surmise that cancer therapies may exacerbate the paradoxical association between lymphopenia and COVID-19-related immunopathology, and that the prevention of COVID-19-induced lymphocyte loss may reduce cancer-associated death.
Manual curation of TCGA treatment data and identification of potential markers of therapy response
Authors: Moiso Enrico 
Published: May 2021

AbstractThe Cancer Genome Atlas (TCGA) represents a valuable source of genomic and clinical data across different tumor types. In this work, TCGA treatment response information have been manually curated in order to be computationally exploited. Drug names were manually corrected to remove typos and to unify commercial and molecule names. Moreover the drug therapy related information has been reorganized in a table to facilitate readability and analysis. The data were benchmarked with uni and multivariable statistical analyses to identify putative markers of response.
Smart Testing with Vaccination: A Bandit Algorithm for Active Sampling for Managing COVID-19
Authors: Wang Yingfei , Yahav Inbal , Padmanabhan Balaji 
Published: May 2021

AbstractThis paper presents methods to choose individuals to test for infection during a pandemic such as COVID-19, characterized by high contagion and presence of asymptomatic carriers. The smart-testing ideas presented here are motivated by active learning and multi-armed bandit techniques in machine learning. Our active sampling method works in conjunction with vaccination and quarantine policies and is adaptive to changes in real-time data. Using a data-driven agent-based model simulating New York City we show that the algorithm samples individuals to test in a manner that rapidly traces infected individuals. The results show that smart-testing is effective in significantly reducing infection and death rates as compared to current policies, with or without vaccination.
Does the Data Tell the True Story? A Modelling Study of Early COVID-19 Pandemic Suppression and Mitigation Strategies in Ghana
Authors: Frempong Nana Kena , Acheampong Theophilus , Apenteng Ofosuhene O. , Nakua Emmanuel , Amuasi John H. 
Published: May 2021

AbstractThis paper uses publicly available data and various statistical models to estimate the basic reproduction number (R0) and other disease parameters for the early COVID-19 pandemic outbreak in Ghana. We also test the effectiveness of government imposition of public health measures to reduce the risk of transmission and impact of the pandemic, especially in the early phase. R0 is estimated from the statistical model as 3.21 using a 0.147 estimated growth rate [95% C.I.: 0.137-0.157] and a 15-day time to recovery after COVID-19 infection. This estimate of the initial R0 is consistent with others reported in the literature from other parts of Africa, China and Europe. Our results also indicate that COVID-19 transmission reduced consistently in Ghana after the imposition of public health interventions - such as border restrictions, intra-city movement, quarantine and isolation - during the first phase of the pandemic from March to May 2020. However, the time-dependent reproduction number (Rt) beyond mid-May 2020 does not represent the true situation given there was not a consistent testing regime in place. This is also confirmed by our Jack-knife bootstrap estimates which show that the positivity rate over-estimates the true incidence rate from mid-May 2020. Given concerns about virus mutations, delays in vaccination and a possible new wave of the pandemic, there is a need for systematic testing of a representative sample of the population to monitor the reproduction number. There is also an urgent need to increase the availability of testing for the general population to enable early detection, isolation and treatment of infected individuals to reduce progression to severe disease and mortality.
ATLAS: An automated association test using probabilistically linked health records with application to genetic studies
Authors: Zhang Harrison G. , Hejblum Boris P. , Weber Griffin M. , Palmer Nathan P. , Churchill Susanne E. , Szolovits Peter , Murphy Shawn N. , Liao Katherine P. , Kohane Isaac S. , Cai Tianxi 
Published: May 2021

AbstractObjectiveLarge amounts of health data are becoming available for biomedical research. Synthesizing information across databases with no gold standard mappings between records may provide a more complete picture of patient health and enable novel research studies. To do so, researchers may probabilistically link databases and conduct inference using the linked data. However, previous inference methods for linked data are constrained to specific linkage settings and exhibit low power. Here, we present ATLAS, an automated, flexible, and robust association testing algorithm for probabilistically linked data.Materials and MethodsMissing variables are imputed at various thresholds using a weighted average method that propagates uncertainty from the linkage process. Next, an estimated effect size is obtained using a generalized linear model. ATLAS then conducts the threshold combination test by optimally combining p-values obtained from data imputed at varying thresholds using Fisher’s method and perturbation resampling.ResultsIn simulations, ATLAS controls for type I error and exhibits high power compared to previous methods. In a real-world application study, incorporation of linked data-enabled analyses using ATLAS yielded two additional signifigant associations between rheumatoid arthritis genetic risk score and biomarkers.DiscussionThe ATLAS weighted average imputation weathers false matches and increases contribution of true matches to mitigate linkage error induced bias. ATLAS’ threshold combination test avoids arbitrarily choosing a threshold to rule a match, thus automating linked data-enabled analyses and preserving power.ConclusionATLAS promises to enable novel and powerful research studies using linked data to capitalize on all available data sources.