bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tree decompositions of real-world networks from simulated annealing
Authors: Klemm Konstantin 
Published: June 2020

Abstract
Decompositions of networks are useful not only for structural exploration. They also have implications and use in analysis and computational solution of processes (such as the Ising model, percolation, SIR model) running on a given network. Tree and branch decompositions considered here directly represent network structure as trees for recursive computation of network properties. Unlike coarse-graining approximations in terms of community structure or metapopulations, tree decompositions of sufficiently small width allow for exact results on equilibrium processes. Here we use simulated annealing to find tree decompositions of narrow width for a set of medium-size empirical networks. Rather than optimizing tree decompositions directly, we employ a search space constituted by so-called elimination orders being permutations on the network’s node set. For each in a database of empirical networks with up to 1000 edges, we find a tree decomposition of low width.
Frailty among middle-aged and older Canadians: population norms for the frailty index using the Canadian Longitudinal Study on Aging
Authors: Pérez-Zepeda Mario Ulises , Godin Judith , Armstrong Joshua J , Andrew Melissa K , Mitnitski Arnold , Kirkland Susan , Rockwood Kenneth , Theou Olga 
Published: June 2020

Abstract

Background
frailty is a public health priority now that the global population is ageing at a rapid rate. A scientifically sound tool to measure frailty and generate population-based reference values is a starting point.

Objective
in this report, our objectives were to operationalize frailty as deficit accumulation using a standard frailty index (FI), describe levels of frailty in Canadians ≥45 years old and provide national normative data.

Design
this is a secondary analysis of the Canadian Longitudinal Study on Aging (CLSA) baseline data.

Setting/participants
about 51,338 individuals (weighted to represent 13,232,651 Canadians), aged 45–85 years, from the tracking and comprehensive cohorts of CLSA.

Methods
after screening all available variables in the pooled dataset, 52 items were selected to construct an FI. Descriptive statistics for the FI and normative data derived from quantile regressions were developed.

Results
the average age of the participants was 60.3 years (95% confidence interval [CI]: 60.2–60.5), and 51.5% were female (95% CI: 50.8–52.2). The mean FI score was 0.07 (95% CI: 0.07–0.08) with a standard deviation of 0.06. Frailty was higher among females and with increasing age, and scores &gt;0.2 were present in 4.2% of the sample. National normative data were identified for each year of age for males and females.

Conclusions
the standardized frailty tool and the population-based normative frailty values can help inform discussions about frailty, setting a new bar in the field. Such information can be used by clinicians, researchers, stakeholders and the general public to understand frailty, especially its relationship with age and sex.
Epidemiology of COVID-19 in older persons, Wuhan, China
Authors: Guo Yan , Liu Xinghua , Deng Mengyao , Liu Pulin , Li Fang , Xie Nianhua , Pang Yanhui , Zhang Xiaoxia , Luo Wen , Peng Ying , Yan Yaqiong , Li Gang , Yang Mei 
Published: June 2020

Abstract

Background
the epidemiological characteristics of older patients with COVID-19 was far from clear.

Objective
to explore the epidemiology of older patients with COVID-19 in Wuhan, China.

Design
a retrospective cross-sectional study.

Setting
a population-based study.

Subjects
the resident older patients (&gt;65 years) diagnosed with COVID-19.

Methods
city-wide case series reported to Wuhan Center for Disease Control and Prevention from 12 December 2019 to 17 March 2020 were included. The epidemic curves were constructed by dates of disease onset.

Results
14,238 confirmed COVID-19 cases were older persons. The number of male cases were slightly less than female cases (1:1.01). The attack rate of COVID-19 in the older persons was 11.49‰ in Wuhan. There was a rapid increase of disease at the early stage of the epidemic and then a gradual and steady decrease was performed. 3,723 (26.15%) and 734 (5.16%) patients were diagnosed as severe and critical cases, respectively. The attributable crude fatality ratio of COVID-19 in the older population was 222.57/100,000, and the crude fatality ratio of COVID was 19.37%. The proportion of severe and critical cases, and fatality ratio were both higher in downtown area and increased with age.

Conclusions
the older persons are sensitive to COVID-19. The proportion of severe and critical cases and fatality ratio are higher than that in children and younger adults. Strengthen the protection and control strategies for the older adults are of priorities. More detailed epidemiological and clinical information should be measured in further studies.
Social context and noise affect within and between male song adjustments in a common passerine
Authors: Grabarczyk Erin E , Vonhof Maarten J , Gill Sharon A 
Published: June 2020

AbstractAcross populations, animals that inhabit areas with high anthropogenic noise produce vocalizations that differ from those inhabiting less noisy environments. Such patterns may be due to individuals rapidly adjusting their songs in response to changing noise, but individual variation is seldom explored. Therefore, we tested the hypothesis that male house wrens (Troglodytes aedon) immediately adjust their songs according to changing noise and that social context further modifies responses. We recorded songs, quantified noise, and defined social context within pairs as female fertile status and between males as number of conspecific neighbors. We used a reaction-norm approach to compare song trait intercepts (between-male effects) and slopes (within-male effects) as a function of noise. Individuals immediately adjusted song duration in response to changing noise. How they achieved adjustments varied: some sang shorter and others longer songs with greater noise, and individuals varied in the extent to which they adjusted song duration. Variation in song duration could be affected by competition as between-male noise levels interacted with number of neighbors to affect syllable duration. Neither within- nor between-male noise effects were detected for frequency traits. Rather, males with fertile mates sang lower-frequency songs and increased peak frequency with more neighbors. Among males, social context but not noise affected song frequency, whereas temporal structure varied between and within individuals depending on noise and social factors. Not all males adjusted signals the same way in response to noise, and selection could favor different levels of variation according to noise.
Detecting and correcting misclassified sequences in the large-scale public databases
Authors: Bagheri Hamid , Severin Andrew J , Rajan Hridesh 
Published: June 2020

Abstract

Motivation
As the cost of sequencing decreases, the amount of data being deposited into public repositories is increasing rapidly. Public databases rely on the user to provide metadata for each submission that is prone to user error. Unfortunately, most public databases, such as non-redundant (NR), rely on user input and do not have methods for identifying errors in the provided metadata, leading to the potential for error propagation. Previous research on a small subset of the NR database analyzed misclassification based on sequence similarity. To the best of our knowledge, the amount of misclassification in the entire database has not been quantified. We propose a heuristic method to detect potentially misclassified taxonomic assignments in the NR database. We applied a curation technique and quality control to find the most probable taxonomic assignment. Our method incorporates provenance and frequency of each annotation from manually and computationally created databases and clustering information at 95% similarity.

Results
We found more than two million potentially taxonomically misclassified proteins in the NR database. Using simulated data, we show a high precision of 97% and a recall of 87% for detecting taxonomically misclassified proteins. The proposed approach and findings could also be applied to other databases.

Availability and implementation
Source code, dataset, documentation, Jupyter notebooks and Docker container are available at https://github.com/boalang/nr.

Supplementary information
Supplementary data are available at Bioinformatics online.
More Mind Games: How ‘The Action’ and ‘The Odds’ have Changed in Prison
Authors: Liebling Alison , Williams Ryan , Lieber Elinor 
Published: June 2020

Abstract
Surviving prison has always involved ‘action’ and game playing. Higher stakes—‘life-trashing sentences’, the fear and risk of radicalization, increased incidences of homicide and labyrinth routes out—have compounded the experience of struggle: to be heard, for dignity, against exposure to violent injustice, and for release; the wrestling of ‘the self’ against a bleak and unyielding bureaucracy. In this article, we revisit McDermott and King’s Mind Games: Where the Action is in Prison showing how long-term prisoners are exposed to unregulated, unfathomable forms of power and action, and how long-term imprisonment feels increasingly like being ‘abandoned by humanity.’
Is China Playing by the Rules? — Assessing China’s Reservations to International Human Rights Treaties
Authors: Wu Jingjing 
Published: June 2020

Abstract
In this paper, I examine two substantive reservations China has made to international human rights treaties, namely China’s reservation to Article 8.1(a) of the International Covenant on Economic, Social and Cultural Rights (ICESCR) and Article 6 of the Convention on the Rights of the Child (CRC), as well as the arguments China adopted to support them in the constructive dialogue between China and the two treaty committees. By positioning China’s reservations and its supporting arguments against the current criteria on making reservations to international human rights treaties, I argue that these two reservations are permissible and the arguments that support them are in general justifiable, all things considered. In conclusion, I reflect on China’s relationship with international human rights treaty bodies through the lens of reservations.
The Disproportionate Impact of COVID-19 on Racial and Ethnic Minorities in the United States
Authors: Tai Don Bambino Geno , Shah Aditya , Doubeni Chyke A , Sia Irene G , Wieland Mark L 
Published: June 2020

Abstract
The coronavirus disease 2019 (COVID-19) pandemic has disproportionately affected racial and ethnic minority groups, with high rates of death in African American, Native American, and LatinX communities. Although the mechanisms of these disparities are being investigated, they can be conceived as arising from biomedical factors as well as social determinants of health. Minority groups are disproportionately affected by chronic medical conditions and lower access to healthcare that may portend worse COVID-19 outcomes. Furthermore, minority communities are more likely to experience living and working conditions that predispose them to worse outcomes. Underpinning these disparities are long-standing structural and societal factors that the COVID-19 pandemic has exposed. Clinicians can partner with patients and communities to reduce the short-term impact of COVID-19 disparities while advocating for structural change.
Superiority of a Novel Mp1p Antigen Detection Enzyme Immunoassay Compared to Standard BACTEC Blood Culture in the Diagnosis of Talaromycosis
Authors: Thu Nguyen T M , Chan Jasper F W , Ly Vo Trieu , Ngo Hoa T , Hien Ha T A , Lan Nguyen P H , Chau Nguyen V V , Cai Jian-Piao , Woo Patrick C Y , Day Jeremy N , van Doorn Rogier , Thwaites Guy , Perfect John , Yuen Kwok , Le Thuy 
Published: June 2020

Abstract

Background
Talaromycosis is an invasive mycosis endemic in Southeast Asia and causes substantial morbidity and mortality in individuals with advanced human immunodeficiency virus (HIV) disease. Current diagnosis relies on isolating Talaromyces marneffei in cultures, which takes up to 14 days and is detectable only during late-stage infection, leading to high mortality.

Methods
In this retrospective case-control study, we assessed the accuracy of a novel Mp1p antigen-detecting enzyme immunoassay (EIA) in stored plasma samples of 372 patients who had culture-proven talaromycosis from blood or sterile body fluids (reference standard) and 517 individuals without talaromycosis (338 healthy volunteers; 179 with other infections). All participants were recruited between 2011 and 2017 in Vietnam.

Results
Of cases and controls, 66.1% and 75.4%, respectively, were male; the median age was 33 and 37, respectively. All cases were HIV infected; median CD4 count was 10 cells/μL. At an optical density cutoff of 0.5, the specificity was 98.1% (95% CI, 96.3%–99.0%); the sensitivity was superior to blood culture (86.3% [95% CI, 82.3%–89.5%] vs 72.8% [95% CI, 68.0%–77.2%]) (P &lt; .001, McNemar test). The time to diagnosis was 6 hours vs 6.6 ± 3.0 days for blood culture. Paired plasma and urine testing in the same patients (n = 269) significantly increased sensitivity compared to testing plasma alone or testing urine alone (P &lt; .001 and P = .02, respectively, McNemar test).

Conclusions
The Mp1p EIA is highly specific and is superior in sensitivity and time to diagnosis compared to blood culture for the diagnosis of talaromycosis. Paired plasma and urine testing further increases sensitivity, introducing a new tool for rapid diagnosis, enabling early treatment and potentially reducing mortality.
Clinical Presentation and Outcomes of Pregnant Women With Coronavirus Disease 2019: A Systematic Review and Meta-analysis
Authors: Matar Reem , Alrahmani Layan , Monzer Nasser , Debiane Labib G , Berbari Elie , Fares Jawad , Fitzpatrick Fidelma , Murad Mohammad H 
Published: June 2020

AbstractBackgroundDescriptions of coronavirus disease 2019 (COVID-19) have focused on the nonpregnant adult population. This study aims to describe the clinical characteristics and perinatal outcomes of COVID-19 in pregnancy.MethodsWe searched databases from December 2019 to 30 April 2020. Eligible studies reported clinical characteristics, radiological findings, and/or laboratory testing of pregnant women during infection. Data were pooled across studies using a random-effects model.ResultsTwenty-four studies (136 women) were included. The most common symptoms were fever (62.9%) and cough (36.8%). Laboratory findings included elevated C-reactive protein (57%) and lymphocytopenia (50%). Ground-glass opacity was the most common radiological finding (81.7%). Preterm birth rate was 37.7% and cesarean delivery rate was 76%. There was 1 maternal death. There were 2 fetal COVID-19 cases.ConclusionsThe clinical picture in pregnant women with COVID-19 did not differ from the nonpregnant population; however, the rate of preterm birth and cesarean delivery are considerably higher than international averages.
Thomas Carlyle and Stoicism
Authors: Jordan Alexander 
Published: June 2020

AbstractRecent studies have pointed to the importance of Thomas Carlyle’s engagement with classical thought, especially Epicureanism and Cynicism. However, in these recent studies, Carlyle’s debts to Stoicism have received only passing attention. Previous scholars hardly considered the question at all, and those who did argued that Carlyle could never have accepted the passive withdrawal and indifference of the Stoics. By way of corrective, the current article offers a comprehensive account of Carlyle’s engagement with Stoicism, showing that he subscribed to an active interpretation of the latter that emphasized will, duty, and heroic action. Indeed, contemporaries were well aware of Carlyle’s debts to Stoicism, pointing out that his thought stood in stark contradiction to Christian doctrines of original sin. Thus, while Carlyle’s Stoicism was compatible with his hereditary Calvinism insofar as divine providence and duty were concerned, there was a significant contradiction regarding the question of sin. In this sense, Carlyle’s Stoicism made an important contribution to the ‘meliorist’ revolt against orthodox Christianity.
Complex relationships between physiological stress and endoparasite infections in natural populations
Authors: Romeo Claudia , Wauters Lucas A , Santicchia Francesca , Dantzer Ben , Palme Rupert , Martinoli Adriano , Ferrari Nicola 
Published: June 2020

AbstractShort-term elevation of glucocorticoids (GCs) is one of the major physiological mechanisms by which vertebrates cope with challenging environmental or social factors (stressors). However, when exposure to stressors occurs repeatedly or over a prolonged period of time, animals may experience chronic elevation of GCs, which reduces the immune response efficiency and can lead to higher intensity of parasitic infection. Here, we used invasive gray squirrels Sciurus carolinensis introduced in Northern Italy and their 2 most prevalent gastrointestinal parasites, the nematode Strongyloides robustus and coccidia of the genus Eimeria, as a model to investigate relationships among macroparasite infection and concentrations of fecal glucocorticoid metabolites (FGMs), an integrated measure of circulating GCs. Our results revealed an association of FGMs with infection by St. robustus, but not with coccidia. Individuals with higher FGMs appear to be responsible for the greatest St. robustus egg shedding within gray squirrel populations, thus possibly acting as superspreaders. However, FGMs were negatively associated with adult St. robustus, suggesting that the abundance of adults of this nematode species does not induce elevation in FGMs, but is only affected by it through immune-mediated effects on its fecundity. Finally, the relationship between St. robustus (both eggs and adult parasites) and FGMs was not linear, suggesting that only high levels of physiological stress influence parasite infection. Our findings highlight that the direction and magnitude of the stress–infection relationship may depend not only on the specific host–parasite system, but also on the different life stages of the same parasite.
Limited time window for retinal gene therapy in a preclinical model of ciliopathy
Authors: Datta Poppy , Ruffcorn Avri , Seo Seongjin 
Published: June 2020

Abstract
Retinal degeneration is a common clinical feature of ciliopathies, a group of genetic diseases linked to ciliary dysfunction, and gene therapy is an attractive treatment option to prevent vision loss. Although the efficacy of retinal gene therapy is well established by multiple proof-of-concept preclinical studies, its long-term effect, particularly when treatments are given at advanced disease stages, is controversial. Incomplete treatment and intrinsic variability of gene delivery methods may contribute to the variable outcomes. Here, we used a genetic rescue approach to ‘optimally’ treat retinal degeneration at various disease stages and examined the long-term efficacy of gene therapy in a mouse model of ciliopathy. We used a Bardet–Biedl syndrome type 17 (BBS17) mouse model, in which the gene-trap that suppresses Bbs17 (also known as Lztfl1) expression can be removed by tamoxifen administration, restoring normal gene expression systemically. Our data indicate that therapeutic effects of retinal gene therapy decrease gradually as treatments are given at later stages. These results suggest the presence of limited time window for successful gene therapy in certain retinal degenerations. Our study also implies that the long-term efficacy of retinal gene therapy may depend on not only the timing of treatment but also other factors such as the function of mutated genes and residual activities of mutant alleles.
Renal pathology in a mouse model of severe Spinal Muscular Atrophy is associated with downregulation of Glial Cell-Line Derived Neurotrophic Factor (GDNF)
Authors: Allardyce Hazel , Kuhn Daniela , Hernandez-Gerez Elena , Hensel Niko , Huang Yu-Ting , Faller Kiterie , Gillingwater Thomas H , Quondamatteo Fabio , Claus Peter , Parson Simon H 
Published: June 2020

AbstractSpinal muscular atrophy (SMA) occurs as a result of cell-ubiquitous depletion of the essential survival motor neuron (SMN) protein. Characteristic disease pathology is driven by a particular vulnerability of the ventral motor neurons of the spinal cord to decreased SMN. Perhaps not surprisingly, many other organ systems are also impacted by SMN depletion. The normal kidney expresses very high levels of SMN protein, equivalent to those found in the nervous system and liver, and levels are dramatically lowered by ~90–95% in mouse models of SMA. Taken together, these data suggest that renal pathology may be present in SMA. We have addressed this using an established mouse model of severe SMA. Nephron number, as assessed by gold standard stereological techniques, was significantly reduced. In addition, morphological assessment showed decreased renal vasculature, particularly of the glomerular capillary knot, dysregulation of nephrin and collagen IV, and ultrastructural changes in the trilaminar filtration layers of the nephron. To explore the molecular drivers underpinning this process, we correlated these findings with quantitative PCR measurements and protein analyses of glial cell-line-derived neurotrophic factor, a crucial factor in ureteric bud branching and subsequent nephron development. Glial cell-line-derived neurotrophic factor levels were significantly reduced at early stages of disease in SMA mice. Collectively, these findings reveal significant renal pathology in a mouse model of severe SMA, further reinforcing the need to develop and administer systemic therapies for this neuromuscular disease.
Learning in foreign and domestic value chains: the role of opportunities and capabilities
Authors: Belderbos René , Grimpe Christoph 
Published: June 2020

AbstractWe suggest that the benefits of learning in international value chains for firms’ innovation performance are heterogeneous and depend on the specific source of learning (customers, suppliers, or competitors), whether these sources are based in countries that are technologically advanced or less advanced (learning opportunities), on technology leadership (learning capabilities) on the part of the focal firm, and on the simultaneous learning that occurs from domestic firms. Using direct survey evidence on learning and innovation by German firms, we confirm that technology leaders benefit from advanced foreign customer and supplier learning, that technology laggards benefit from less advanced foreign customer learning and advanced foreign competitor learning, and that both leaders and laggards benefit from domestic customer learning. The findings suggest a tradeoff between the opportunities to learn from foreign or domestic customers.
Misallocation of scientific credit: the role of hierarchy and preferences. An extension of Lissoniet al.(2013)
Authors: Lissoni Francesco , Montobbio Fabio , Zirulia Lorenzo 
Published: June 2020

AbstractWe extend the results in Lissoni et al. (2013, J. Econ. Behav. Organ., 95, 49–69) on scientific credit misallocation, as measured by misalignment between authorship and inventorship recognition in patent-publication pairs. Extending the analysis to European data, we confirm that, other things being equal, the probability of exclusion of a scientific author from a publication-related patent declines with seniority and increases for women. In addition, we find that the senior scientists’ power to exclude other authors plays a more important role in explaining the patterns of exclusion than differences in authors’ attribution preferences. The unfavorable treatment of young and/or female scientists emerges in particular when patents are owned by companies or individuals, thus providing a warning flag on those institutional arrangements that favor company or individual ownership of academic patents.