bluuebunny/crossref_metadata_2025_split huggingface dataset:
A stochastic-programming approach for scheduling catch-up rounds in round-robin sport leagues
Authors: Yi Xiajie , Goossens Dries 
Published: October 2020

AbstractIn most sport leagues, a schedule is announced before the start of the season. However, due to unexpected events (e.g. bad weather conditions), some games cannot be played on the announced date. To handle this, before the start of the season, empty so-called catch-up rounds are positioned in the schedule as a buffer. During the season, games can then be rescheduled to these catch-up rounds. We develop a two-stage stochastic programming approach to determine where to position the catch-up rounds in order to maintain the quality of the realized schedule. While our method is generally applicable, we demonstrate its use with soccer. Scenarios and their probabilities are deduced from historical data from 10 major European soccer leagues. We study the impact of the number of catch-up rounds and costs on the positions of catch-up rounds and compare our method with other proactive strategies from the literature. We conclude with a case study based on the English Premier League. In particular when many games cannot be played as planned and few catch-up rounds are available, our stochastic programming approach outperforms existing methods with respect to maintaining a fair ranking and avoiding cancelled games.
Longitudinal Serological Analysis and Neutralizing Antibody Levels in Coronavirus Disease 2019 Convalescent Patients
Authors: Muecksch Frauke , Wise Helen , Batchelor Becky , Squires Maria , Semple Elizabeth , Richardson Claire , McGuire Jacqueline , Clearly Sarah , Furrie Elizabeth , Greig Neil , Hay Gordon , Templeton Kate , Lorenzi Julio C C , Hatziioannou Theodora , Jenks Sara , Bieniasz Paul D 
Published: October 2020

Abstract

Background
Understanding the longitudinal trajectory of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies is crucial for diagnosis of prior infection and predicting future immunity.

Methods
We conducted a longitudinal analysis of coronavirus disease 2019 convalescent patients, with neutralizing antibody assays and SARS-CoV-2 serological assay platforms using SARS-CoV-2 spike (S) or nucleocapsid (N) antigens.

Results
Sensitivities of serological assays in diagnosing prior SARS-CoV-2 infection changed with time. One widely used commercial platform that had an initial sensitivity of &gt;95% declined to 71% at 81–100 days after diagnosis. The trajectories of median binding antibody titers measured over approximately 3–4 months were not dependent on the use of SARS-CoV-2 N or S proteins as antigen. The median neutralization titer decreased by approximately 45% per month. Each serological assay gave quantitative antibody titers that were correlated with SARS-CoV-2 neutralization titers, but S-based serological assay measurements better predicted neutralization potency. Correlation between S-binding and neutralization titers deteriorated with time, and decreases in neutralization titers were not predicted by changes in S-binding antibody titers.

Conclusions
Different SARS-CoV-2 serological assays are more or less well suited for surveillance versus prediction of serum neutralization potency. Extended follow-up should facilitate the establishment of appropriate serological correlates of protection against SARS-CoV-2 reinfection.
The success of particular Acinetobacter baumannii clones: accumulating resistance and virulence inside a sugary shield
Authors: Silva Liliana , Grosso Filipa , Rodrigues Carla , Ksiezarek Magdalena , Ramos Helena , Peixe Luísa 
Published: October 2020

Abstract

Background
In Portugal, carbapenem-resistant Acinetobacter baumannii (CRAB) has been associated with ST98, ST103 and ST208 (Oxford Scheme, Oxf) and a clone has usually been associated with a particular period of time. These clonal shifts were primarily explained by an increased antimicrobial resistance profile. Here we explore genomic and biochemical differences among these and more recent clones, which could further explain the diversity and evolution of this species.

Methods
A total of 116 CRAB isolates (2010–15), together with representatives of a previously described CRAB collection (4 isolates, 2001–06) were characterized by attenuated total reflection Fourier transform infrared spectroscopy (FTIR-ATR) and MLST. Representatives of different FTIR-ATR/MLST clusters were selected for WGS (n = 13), which allowed the in silico extraction of resistance and virulence genes, capsule locus and SNP analysis.

Results
A. baumannii clonal shifts of OXA-58-producing ST103Oxf (2001–04), OXA-40-producing ST98Oxf (2002–06), OXA-23-producing ST208Oxf (2006–10) and OXA-23-producing ST218Oxf (2010–15) were accompanied by an increase in AMR genes and virulence factors. FTIR-ATR clustering was congruent with sugar composition predicted from the capsular locus: a fucosamine cluster comprising ST98Oxf, ST103Oxf and a single ST218Oxf isolate; a pseudaminic acid cluster of ST208Oxf and ST1557Oxf isolates; and legionaminic acid, resembling the sialic acid from mammalian cells, in a cluster comprising ST218Oxf isolates. The whole-genome phylogenetic tree was congruent with MLST, with isolates presenting 5–28 938 SNPs. ST208Oxf and ST218Oxf presented ∼1900 SNPs while ST103Oxf and ST1557Oxf showed a greater number of SNPs (∼28 000).

Conclusions
Clonal shifts of CRAB were promoted, in our country, by consecutive virulence and AMR gene pool enlargement, together with features increasing pathogen–host adaptation. Worldwide dominance of ST218Oxf is supported by the combination of high AMR and virulence levels.
Incorporation of Methoxyphenamine into Hair in Early Stage after Intake
Authors: Nitta Atsushi , Shima Noriaki , Kamata Tooru , Sasaki Keiko , Matsuta Shuntaro , Ishikawa Akari , Asai Ryutaro , Wada Misato , Kakehashi Hidenao , Fujii Shihoko , Kamata Hiroe , Nishioka Hiroshi , Sato Takako , Tsuchihashi Hitoshi , Miki Akihiro , Katagi Munehiro 
Published: October 2020

Abstract
In order to investigate the incorporation behavior of drugs into hair in early stage (within 24 h) after intake, time-course changes in drug distribution in black hair were carefully analyzed after a single oral administration of methoxyphenamine (MOP), a non-regulated analog of methamphetamine. Single-hair specimens collected by plucking with the roots intact at appropriate intervals post-intake were each divided into 1-mm segments from the proximal end, and MOP in each segment was determined by a validated liquid chromatography–tandem mass spectrometry procedure. At 10 min after intake, MOP was not detected in any of the segments. MOP became detectable 30 min after intake in the hair bulb (0–1-mm segment from the proximal end) and 1 h after intake in the upper dermis zone (1–2-mm to 4–5-mm segments). The amount of MOP in the hair bulb increased rapidly over 3 h after intake and reached a maximum concentration of ∼100–900 pg/1-mm single hair (11–95 ng/mg) around 3–10 h after intake, whereas that in the upper dermis zone increased at a more gradual pace over 24 h and reached a plateau at ∼30–100 pg/1-mm hair (3–11 ng/mg). These differences can be attributed to the different incorporation mechanisms of the drug. Results from this study can further elucidate the drug incorporation mechanism, which is crucial for accurately interpreting results in hair analyses. Our findings also suggest that hair drug analysis with special attention to the hair root can serve as a useful complementary approach to urine- and blood-based testing in the field of forensic toxicology.
State of Exception
Authors: Imseis Ardi 
Published: October 2020

Abstract
In December 2019, the Prosecutor of the International Criminal Court concluded her preliminary examination into the situation in Palestine, determining there is a reasonable basis to initiate an investigation into the situation. Instead of doing so, she first decided to seek a ruling from the Pre-Trial Chamber on the scope of the Court’s territorial jurisdiction, specifically aimed at confirming her view that the ‘territory’ over which the Court may exercise its jurisdiction comprises the Occupied Palestinian Territory (OPT). This article focuses on the amici curiae observations and other communications made by eight states parties in the proceedings — Australia, Austria, Brazil, Canada, Czech Republic, Germany, Hungary and Uganda. A critical examination of these observations and communications reveals that they did not answer the question posed by the OTP, but rather advanced a number of strained arguments aimed, inter alia, at impugning the very notion that the Court has any jurisdiction at all on the basis that Palestine is not a state. When juxtaposed against the ostensible commitment of these states parties to the object and purpose of the Statute, their observations and other communications reveal a conspicuous hypocrisy. If accepted by the Court, these observations and communications would operate to not only affirm the continued contingency of the state of Palestine on the international plane, but, even worse, to shield persons known to have committed or be committing crimes of the gravest concern to the international community with impunity.
Local effects of global climate on a small rodentNecromys lasiurus
Authors: Magnusson William , Rosa Clarissa , Layme Viviane Maria Guedes , Ghizoni Ivo Rohling , Lima Albertina Pimentel 
Published: October 2020

AbstractGlobal climate drivers often have strong effects on the carrying capacity of animal populations, but little is known about how effects differ between regional and local scales. In this paper we evaluated how climate variables were correlated with regional and local fluctuations of a small rodent, Necromys lasiurus, in an Amazonian savanna. Between 2000 and 2019, we evaluated the temporal variation in abundance of N. lasiurus in eight 4.0-ha plots separated by 0.8 – 10.6 km. Using generalized linear mixed models, we found that, at a regional scale, the abundance of rodents captured was positively associated with the abundance in the prior year, but had little relationship with the Southern Oscillation Index (SOI), which had been shown to affect rats in a single plot in a previous study. However, variation in densities among years was coordinated among some plots, leading to patchiness in population dynamics. Based on the patterns of density fluctuations, the plots formed three clusters. Analyses based on these clusters indicated that only one was strongly affected by SOI, as in the previous study. The differences in the effects of global climate drivers on populations of a single species in relatively homogeneous habitat indicate that predictions about the effects of climate change should be based on simultaneous studies in a variety of sites or they may lead to spurious relationships.
Pattern of Neuronal and Axonal Damage, Glial Response, and Synaptic Changes in Rat Cerebellum within the First Week following Traumatic Brain Injury
Authors: Dolenec Petra , Pilipović Kristina , Janković Tamara , Župan Gordana 
Published: October 2020

Abstract
We examined damage and repair processes in the rat cerebellum within the first week following moderate traumatic brain injury (TBI) induced by lateral fluid percussion injury (LFPI) over the left parietal cortex. Rats were killed 1, 3, or 7 days after the injury or sham procedure. Fluoro-Jade B staining revealed 2 phases of neurodegenerative changes in the cell bodies and fibers: first, more focal, 1 day after the LFPI, and second, widespread, starting on post-injury day 3. Purkinje cell loss was detected in posterior lobule IX 1 day following LFPI. Apoptosis was observed in the cerebellar cortex, on days 1 and 7 following LFPI, and was not caspase- or apoptosis-inducing factor (AIF)-mediated. AIF immunostaining indicated axonal damage in the cerebellar white matter tracts 3- and 7-days post-injury. Significant astrocytosis and microgliosis were noticed on day 7 following LFPI at the sites of neuronal damage and loss. Immunohistochemical labeling with the presynaptic markers synaptophysin and growth-associated protein-43 revealed synaptic perturbations already on day 1 that were more pronounced at later time points following LFPI. These results provide new insights into pathophysiological alterations in the cerebellum and their mechanisms following cerebral TBI.
How Are Residents Trained in Neuropathology? A Survey of Neurology Program Directors in the United States
Authors: Rayi Appaji , Rajneesh Kiran , Punia Vineet , Start Amanda R 
Published: October 2020

Abstract
To understand the current state of neurology residents training in neuropathology, we electronically distributed a 16-item survey to 150 adult and 70 child neurology program directors (PDs). The survey inquired about their program characteristics, neuropathology curriculum and assessment methods, trainee performance, and attitudes. Descriptive analysis was used to summarize categorical variables as frequencies and percentages and continuous as means and standard deviations. We conducted a series of Mann-Whitney U and Fisher’s exact tests to evaluate differences between various program characteristics. Sixty-four (29%) PDs responded to the survey, including 45 (30%) adult and 19 (27%) child neurology PDs. Thirty-one programs required a dedicated neuropathology rotation. The majority (92%) used the Residency In-Service Training Examination (RITE) to assess trainee’s knowledge. Approximately 86% of the PDs agreed that neuropathology is essential and a defined curriculum is necessary during residency training. There was no difference in the RITE scores between programs. We conclude that a neuropathology rotation was felt to be essential even though the RITE scores did not differ between programs with and without a dedicated rotation. Alternative evaluation and training methods may need consideration. A future survey of all the stakeholders may be required to thoroughly understand and disseminate the neuropathology education well.
Morphometry as a probe of the evolution of jellyfish galaxies: evidence of broadening in the surface brightness profiles of ram-pressure stripping candidates in the multicluster system A901/A902
Authors: Roman-Oliveira Fernanda , Chies-Santos Ana L , Ferrari Fabricio , Lucatelli Geferson , Rodríguez Del Pino Bruno 
Published: October 2020

ABSTRACT
We explore the morphometric properties of a group of 73 ram-pressure stripping candidates in the A901/A902 multicluster system, at z∼ 0.165, to characterize the morphologies and structural evolution of jellyfish galaxies. By employing a quantitative measurement of morphometric indicators with the algorithm morfometryka on Hubble Space Telescope (F606W) images of the galaxies, we present a novel morphology-based method for determining trail vectors. We study the surface brightness profiles and curvature of the candidates and compare the results obtained with two analysis packages, morfometryka and iraf/ellipse on retrieving information of the irregular structures present in the galaxies. Our morphometric analysis shows that the ram-pressure stripping candidates have peculiar concave regions in their surface brightness profiles. Therefore, these profiles are less concentrated (lower Sérsic indices) than other star-forming galaxies that do not show morphological features of ram-pressure stripping. In combination with morphometric trail vectors, this feature could both help identify galaxies undergoing ram-pressure stripping and reveal spatial variations in the star formation rate.
Implications of Einstein–Maxwell dilaton–axion gravity from the black hole continuum spectrum
Authors: Banerjee Indrani , Mandal Bhaswati , SenGupta Soumitra 
Published: October 2020

ABSTRACT
String inspired models can serve as potential candidates to replace general relativity (GR) in the high-energy/high-curvature regime where quantum gravity is expected to play a vital role. Such models not only subsume the ultraviolet nature of gravity but also exhibit promising prospects in resolving issues like dark matter and dark energy, which cannot be adequately addressed within the framework of GR. The Einstein–Maxwell dilaton–axion (EMDA) theory that is central to this work is one such string inspired model arising in the low energy effective action of the heterotic string theory with interesting implications in inflationary cosmology and in the late-time acceleration of the Universe. It is therefore important to survey the role of such a theory in explaining astrophysical observations, e.g. the continuum spectrum of black holes which is expected to hold a wealth of information regarding the background metric. The Kerr–Sen space–time corresponds to the exact, stationary, and axisymmetric black hole solution in EMDA gravity, possessing dilatonic charge and angular momentum originating from the axionic field. In this work, we compute the theoretical spectrum from the accretion disc around quasars in the Kerr–Sen background assuming the thin accretion disc model due to Novikov and Thorne. This is then used to evaluate the theoretical estimates of optical luminosity for a sample of eighty Palomar Green quasars which are subsequently compared with the available observations. Our results based on χ2 analysis indicate that the dilaton parameter r2 ∼ 0.2 is favoured by optical observations of quasars which is further corroborated by other error estimators e.g. the Nash–Sutcliffe efficiency, the index of agreement and their modified versions. We further report that strong dilaton charges (r2 &gt; 1.6) are disfavoured by quasar optical data and the spins associated with the quasars are also estimated.
Neutron star crust in Voigt approximation: general symmetry of the stress–strain tensor and an universal estimate for the effective shear modulus
Authors: Chugunov Andrey I 
Published: October 2020

ABSTRACT
I discuss elastic properties of neutron star crust in the framework of static Coulomb solid model when atomic nuclei are treated as non-vibrating point charges; electron screening is neglected. The results are also applicable for solidified white dwarf cores and other materials, which can be modelled as Coulomb solids (dusty plasma, trapped ions, etc.). I demonstrate that the Coulomb part of the stress–strain tensor has additional symmetry: contraction Bijil = 0. It does not depend on the structure (crystalline or amorphous) and composition. I show as a result of this symmetry the effective (Voigt averaged) shear modulus of the polycrystalline or amorphous matter to be equal to −2/15 of the Coulomb (Madelung) energy density at undeformed state. This result is general and exact within the model applied. Since the linear mixing rule and the ion sphere model are used, I can suggest a simple universal estimate for the effective shear modulus: $\sum _Z 0.12\, n_Z Z^{5/3}e^2 /a_\mathrm{e}$. Here summation is taken over ion species, nZ is number density of ions with charge Ze. Finally, ae = (4πne/3)−1/3 is electron sphere radius. Quasi-neutrality condition ne = ∑ZZnZ is assumed.
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more
Authors: Altenhoff Adrian M , Train Clément-Marie , Gilbert Kimberly J , Mediratta Ishita , Mendes de Farias Tarcisio , Moi David , Nevers Yannis , Radoykova Hale-Seda , Rossier Victor , Warwick Vesztrocy Alex , Glover Natasha M , Dessimoz Christophe 
Published: October 2020

Abstract
OMA is an established resource to elucidate evolutionary relationships among genes from currently 2326 genomes covering all domains of life. OMA provides pairwise and groupwise orthologs, functional annotations, local and global gene order conservation (synteny) information, among many other functions. This update paper describes the reorganisation of the database into gene-, group- and genome-centric pages. Other new and improved features are detailed, such as reporting of the evolutionarily best conserved isoforms of alternatively spliced genes, the inferred local order of ancestral genes, phylogenetic profiling, better cross-references, fast genome mapping, semantic data sharing via RDF, as well as a special coronavirus OMA with 119 viruses from the Nidovirales order, including SARS-CoV-2, the agent of the COVID-19 pandemic. We conclude with improvements to the documentation of the resource through primers, tutorials and short videos. OMA is accessible at https://omabrowser.org.
Impact of dialysis modality on major adverse cardiovascular events and all-cause mortality: a national population-based study
Authors: Hu Ping-Jen , Chen Yu-Wei , Chen Tzu-Ting , Sung Li-Chin , Wu Mei-Yi , Wu Mai-Szu 
Published: October 2020

AbstractBackgroundOnly few studies with inconsistent results comparing the relative risk of cardiac mortality between peritoneal dialysis (PD) and hemodialysis (HD). Switches between renal replacement therapy (RRT) modalities render objective assessment of survival benefits a greater challenge.MethodsData were retrieved from Taiwan’s National Health Insurance Database from 1 January 2006 to 31 December 2015. We included 13 662 and 41 047 long-term dialysis patients in a propensity score matching study design and a time-varying study design, respectively, to compare major adverse cardiovascular events (MACEs) between patients receiving PD and HD. We also included 109 256 dialysis patients to compare the all-cause mortality among different RRT modalities.ResultsFor MACE, the hazard ratio (HR) for PD patients compared to HD patients was 0.95 [95% confidence interval (CI) 0.89–1.02] in the propensity score study design and 1.06 (95% CI 1.01–1.12) in the time-varying study design. For all-cause mortality, the HR for PD patients compared to HD patients was 1.09 (95% CI 1.05–1.13) in the propensity score study design and 1.13 (95% CI 1.09–1.17) in the time-varying study design. The HR for death was higher at a level of statistical significance for females (1.21, 95% CI 1.15–1.28), patients ≥65 years old (1.30, 95% CI 1.24–1.36) and diabetes mellitus (DM; 1.28, 95% CI 1.22–1.34).ConclusionsThe HR for MACE is significantly higher among PD patients in time-varying design analysis. In addition, all-cause mortality was higher in PD patients compared to patients with HD, especially in those who were aged ≥65 years, female or DM.