bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosome-level genome assembly of Plazaster borealis sheds light on the morphogenesis of multiarmed starfish and its regenerative capacity
Authors: Lee Yujung , Kim Bongsang , Jung Jaehoon , Koh Bomin , Jhang So Yun , Ban Chaeyoung , Chi Won-Jae , Kim Soonok , Yu Jaewoong 
Published: July 2022

Abstract

Background
Plazaster borealis has a unique morphology, displaying multiple arms with a clear distinction between disk and arms, rather than displaying pentaradial symmetry, a remarkable characteristic of echinoderms. Herein we report the first chromosome-level reference genome of P. borealis and an essential tool to further investigate the basis of the divergent morphology.

Findings
In total, 57.76 Gb of a long read and 70.83 Gb of short-read data were generated to assemble a de novo 561-Mb reference genome of P. borealis, and Hi-C sequencing data (57.47 Gb) were used for scaffolding into 22 chromosomal scaffolds comprising 92.38% of the genome. The genome completeness estimated by BUSCO was 98.0% using the metazoan set, indicating a high-quality assembly. Through the comparative genome analysis, we identified evolutionary accelerated genes known to be involved in morphogenesis and regeneration, suggesting their potential role in shaping body pattern and capacity of regeneration.

Conclusion
This first chromosome-level genome assembly of P. borealis provides fundamental insights into echinoderm biology, as well as the genomic mechanism underlying its unique morphology and regeneration.
Chromosome-level assembly and annotation of the blue catfishIctalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies
Authors: Wang Haolong , Su Baofeng , Butts Ian A E , Dunham Rex A , Wang Xu 
Published: July 2022

AbstractBackgroundThe blue catfish is of great value in aquaculture and recreational fisheries. The F1 hybrids of female channel catfish (Ictalurus punctatus) × male blue catfish (Ictalurusfurcatus) have been the primary driver of US catfish production in recent years because of superior growth, survival, and carcass yield. The channel–blue hybrid also provides an excellent model to investigate molecular mechanisms of environment-dependent heterosis. However, transcriptome and methylome studies suffered from low alignment rates to the channel catfish genome due to divergence, and the genome resources for blue catfish are not publicly available.ResultsThe blue catfish genome assembly is 841.86 Mbp in length with excellent continuity (8.6 Mbp contig N50, 28.2 Mbp scaffold N50) and completeness (98.6% Eukaryota and 97.0% Actinopterygii BUSCO). A total of 30,971 protein-coding genes were predicted, of which 21,781 were supported by RNA sequencing evidence. Phylogenomic analyses revealed that it diverged from channel catfish approximately 9 million years ago with 15.7 million fixed nucleotide differences. The within-species single-nucleotide polymorphism (SNP) density is 0.32% between the most aquaculturally important blue catfish strains (D&B and Rio Grande). Gene family analysis discovered significant expansion of immune-related families in the blue catfish lineage, which may contribute to disease resistance in blue catfish.ConclusionsWe reported the first high-quality, chromosome-level assembly of the blue catfish genome, which provides the necessary genomic tool kit for transcriptome and methylome analysis, SNP discovery and marker-assisted selection, gene editing and genome engineering, and reproductive enhancement of the blue catfish and hybrid catfish.
Messianism Refigured: Tadeusz Zygfryd Kassern’s Musical Monument to the Warsaw Ghetto Uprising
Authors: Pierce J Mackenzie 
Published: July 2022

Abstract
This essay explores the commemorative stance of Tadeusz Zygfryd Kassern’s opera The Anointed (1951) toward the Warsaw Ghetto Uprising and situates the work within an early and volatile period of cultural responses to the Holocaust in Poland and the United States. Through a close examination of the opera’s literary sources and musical setting, as well as the archival materials related to its creation, the essay shows how the opera treats Polish Romantic messianism as a symbolic language with which to grapple with Jewish resistance to the Holocaust, even as similar messianic tropes were being used to consolidate Polish ethnonationalist memory of  World War II.
Medicine recovery and reuse in a hospital setting: a lesson from Italy
Authors: Gianino Maria Michela , Cotugno Valentina , Scattaglia Marco , Colasanto Irene , Scaldaferri Matilde , Cattel Francesco 
Published: July 2022

Abstract

Objectives
In 2017, a new programme was created for recovering and reusing (i) unexpired Class A medicines (i.e. dispensed either by community pharmacies or by hospitals) in hospital settings and (ii) medicines for hospital use only (Class H). The aim of this study was to describe a three-year reuse programme and assess its impact on medicines cost savings.

Methods
The setting was AOU Città della salute e della Scienza—in Turin (Italy). All the collected data referred to packages of medicines collected by/assigned to AOU for reuse over the 1 December 2017/1 December 2020 period. Retail prices were used to calculate the financial value of the medication. Costs for the time required for the reuse programme (a working group comprising a pharmacist, an administrative and a warehouse worker) were estimated.

Key findings
A total of 10 450 boxes were recovered for reuse (corresponding to 52% of donated boxes). The total value was €1 300 000. Class H accounted for 73% (€952 000) of the total value of the recovered medicines, while they represented only 9% of the packages collected by/assigned to AOU. Estimated cost for the reuse programme was €75 806.

Conclusions
Medicine recycling programmes with appropriate checks can be implemented to facilitate reuse of medications in hospital settings. This study provides evidence that a reuse programme reduced drug expenditures, especially regarding the Class H medications. These results contribute to the debate regarding opportunity for recycling and sustainability in medicines management.
Building Walls at Sea: An Assessment of the Legality of the Greek Floating Barrier
Authors: Georgoula Danae F 
Published: July 2022

Abstract
In January 2020, against the backdrop of the Mediterranean refugee crisis, Greece announced its intention to install a floating barrier in the maritime passage between Turkey and Lesvos as a measure to deter the flow of asylum seekers arriving by sea. This article analyses the implications and assesses the legality of installing a floating barrier in light of the law of the sea, human rights law, and refugee law.
Grazing bifurcations and transitions between periodic states of the PP04 model for the glacial cycle
Authors: Budd Chris , Morupisi Kgomotso S 
Published: July 2022

Abstract
We look at the periodic behaviour of the Earth’s glacial cycles and the transitions between different periodic states when either external parameters (such as $\omega $) or internal parameters (such as $d$) are varied. We model this using the PP04 model of climate change. This is a forced discontinuous Filippov (non-smooth) dynamical system. When periodically forced this has coexisting periodic orbits. We find that the transitions in this system are mainly due to grazing events, leading to grazing bifurcations. An analysis of the grazing bifurcations is given and the impact of these on the domains of attraction and regions of existence of the periodic orbits is determined under various changes in the parameters of the system. Grazing transitions arise for general variations in the parameters (both internal and external) of the PP04 model. We find that the grazing transitions between the period orbits resemble those of the Mid-Pleistocene-Transition.
Medical visits and health-care expenditures of patients attending orthopedic clinics during the COVID-19 pandemic in Japan: LIFE Study
Authors: Tani Naomichi , Fukuda Haruhisa 
Published: July 2022

Abstract

Background
The first state of emergency for coronavirus disease 2019 (COVID-19) in Japan was imposed from April to May 2020. During that period, people were urged to avoid non-essential outings, which may have reduced their access to health care.

Methods
Using health-care claims data from a city in Fukuoka prefecture, Japan, we conducted a retrospective cohort study of the state of emergency’s impact on patients’ medical visits to orthopedic clinics and their associated health-care expenditures. These measures were compared between 2019 and 2020 using a year-over-year analysis and unpaired t-tests.

Results
The analysis showed that medical visits in 2020 significantly decreased by 23.7% in April (P &lt; 0.01) and 17.6% in May (P &lt; 0.01) when compared with the previous year. Similarly, monthly outpatient health-care expenditure significantly decreased by 2.4% (P &lt; 0.01) in April 2020 when compared with April 2019. In contrast, the health-care expenditure per capita per visit significantly increased by 1.5% (P &lt; 0.01) in June 2020 (after the state of emergency was lifted) when compared with June 2019.

Conclusion
As orthopedic clinics in Japan are reimbursed using a fee-for-service system, the increases in per capita expenditures after the state of emergency may be indicative of physician-induced demand. However, we posit that it is more likely that a post-emergency increase in anti-inflammatory and analgesic treatments for spondylopathies, low back pain and sciatica induced a temporary rise in these expenditures.
Can Critical Religion Play by Its Own Rules? Why There Must Be More Ways to Be “Critical” in the Study of Religion
Authors: Watts Galen , Mosurinjohn Sharday 
Published: July 2022

AbstractAccording to some of the most vocal proponents of Critical Religion (CR), taking CR seriously entails accepting that religion as an analytic category leads to reification and naturalization and is unduly normative, thus critical scholars of religion should abandon it and restrict ourselves to studying discursive battles over the uses of religion. In this article, we build on the case for alternative critical proposals by offering an immanent critique of the work of proponents of CR. In doing so, we identify and outline CR’s major analytical flaws, which we name as follows: inconsistent historicization, crypto-normativity, and arbitrary abandonment. We conclude that CR scholarship cannot but fail to live up to its own ideals, and moreover that much would be lost were we to limit the critical study of religion to CR.
An ordinal severity scale for COVID-19 retrospective studies using Electronic Health Record data
Authors: Khodaverdi Maryam , Price Bradley S , Porterfield J Zachary , Bunnell H Timothy , Vest Michael T , Anzalone Alfred Jerrod , Harper Jeremy , Kimble Wes D , Moradi Hamidreza , Hendricks Brian , Santangelo Susan L , Hodder Sally L ,   N3C Consortium Collaborators, Chute Christopher G , Haendel Melissa A , Walden Anita 
Published: July 2022

Abstract

Objectives
Although the World Health Organization (WHO) Clinical Progression Scale for COVID-19 is useful in prospective clinical trials, it cannot be effectively used with retrospective Electronic Health Record (EHR) datasets. Modifying the existing WHO Clinical Progression Scale, we developed an ordinal severity scale (OS) and assessed its usefulness in the analyses of COVID-19 patient outcomes using retrospective EHR data.

Materials and Methods
An OS was developed to assign COVID-19 disease severity using the Observational Medical Outcomes Partnership common data model within the National COVID Cohort Collaborative (N3C) data enclave. We then evaluated usefulness of the developed OS using heterogenous EHR data from January 2020 to October 2021 submitted to N3C by 63 healthcare organizations across the United States. Principal component analysis (PCA) was employed to characterize changes in disease severity among patients during the 28-day period following COVID-19 diagnosis.

Results
The data set used in this analysis consists of 2 880 456 patients. PCA of the day-to-day variation in OS levels over the totality of the 28-day period revealed contrasting patterns of variation in disease severity within the first and second 14 days and illustrated the importance of evaluation over the full 28-day period.

Discussion
An OS with well-defined, robust features, based on discrete EHR data elements, is useful for assessments of COVID-19 patient outcomes, providing insights on the progression of COVID-19 disease severity over time.

Conclusions
The OS provides a framework that can facilitate better understanding of the course of acute COVID-19, informing clinical decision-making and resource allocation.
The Potential of Arterial Pulse Wave Analysis in Burn Resuscitation: A Pilot In Vivo Study
Authors: ArabiDarrehDor Ghazal , Kao Yi-Ming , Oliver Mary A , Parajuli Babita , Carney Bonnie C , Keyloun John W , Moffatt Lauren T , Shupp Jeffrey W , Hahn Jin-Oh , Burmeister David M 
Published: July 2022

Abstract
While urinary output (UOP) remains the primary endpoint for titration of intravenous fluid resuscitation, it is an insufficient indicator of fluid responsiveness. Although advanced hemodynamic monitoring (including arterial pulse wave analysis [PWA]) is of recent interest, the validity of PWA-derived indices in burn resuscitation extremes has not been established. The goal of this paper is to test the hypothesis that PWA-derived cardiac output (CO) and stroke volume (SV) indices as well as pulse pressure variation (PPV) and systolic pressure variation (SPV) can play a complementary role to UOP in burn resuscitation. Swine were instrumented with a Swan-Ganz catheter for reference CO and underwent a 40% TBSA burns with varying resuscitation paradigms, and were monitored for 24 hours in an ICU setting under mechanical ventilation. The longitudinal changes in PWA-derived indices were investigated, and resuscitation adequacy was compared as determined by UOP vs PWA indices. The results indicated that PWA-derived indices exhibited trends consistent with reference CO and SV measurements: CO and SV indices were proportional to reference CO and SV, respectively (CO: postcalibration limits of agreement [LoA] = ±24.7 [ml/min/kg], SV: postcalibration LoA = ±0.30 [ml/kg]) while PPV and SPV were inversely proportional to reference SV (PPV: postcalibration LoA = ±0.32 [ml/kg], SPV: postcalibration LoA = ±0.31 [ml/kg]). The results also indicated that PWA-derived indices exhibited notable discrepancies from UOP in determining adequate burn resuscitation. Hence, it was concluded that the PWA-derived indices may have complementary value to UOP in assessing and guiding burn resuscitation.
Reference Genome of the Black Surfperch,Embiotoca jacksoni(Embiotocidae, Perciformes), a California Kelp Forest Fish That Lacks a Pelagic Larval Stage
Authors: Bernardi Giacomo , Toy Jason A , Escalona Merly , Marimuthu Mohan P A , Sahasrabudhe Ruta , Nguyen Oanh , Sacco Samuel , Beraut Eric , Toffelmier Erin , Miller Courtney , Shaffer H Bradley 
Published: July 2022

AbstractSurfperches (Family Embiotocidae) are viviparous temperate reef fishes that brood their young. This life history trait translates into limited dispersal, strong population structure, and an unusually strong potential for local adaptation in a marine fish. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Black Surfperch, Embiotoca jacksoni, to establish a genomic model for understanding phylogeographic patterns of marine organisms in California. These patterns, in turn, may inform the design of marine protected areas using dispersal models based on genomic data. The genome of E. jacksoni is typical of marine fishes at less than 1Gb (genome size = 635 Mb), and our assembly is near-chromosome level (contig N50 = 6.5Mb, scaffold N50 = 15.5 Mb, BUSCO = 98.1%). Within the context of the CCGP, the genome will be used as a reference for future whole genome resequencing projects aimed at enhancing our knowledge of the population structure of the species, and efficacy of Marine Protected Areas across the state.
Estimating a Non-parametric Memory Kernel for Mutually Exciting Point Processes
Authors: Clements A E , Hurn A S , Lindsay K A , Volkov V V 
Published: July 2022

AbstractSelf- and cross-excitation in point processes are commonly captured in the financial econometrics literature using a multivariate exponential memory kernel. In this article, the exponential assumption is relaxed and the resultant non-parametric memory kernel is estimated by a method based on second-order cumulants. The estimator is shown to be consistent and asymptotically normally distributed and performs well under simulation. An empirical application based on 10 international stock indices is presented. Two different indices of contagion between markets are constructed from the point process models in order to examine interconnection over time. A conclusion which emerges from these results is the assumption that a parametric kernel may be too restrictive as the application reveals interesting features, and in some cases substantial differences, between the exponential and non-parametric kernels.
Estimating Unobserved Soft Adjustment in Credit Rating Models: Before and after the Dodd–Frank Act
Authors: Gu Zhutong , Jiang Yixiao , Yang Shuyang 
Published: July 2022

Abstract
Credit Rating Agencies (CRAs) adjust preliminary bond ratings with knowledge beyond publicly available information. These unobserved “soft adjustments” may reflect material nonpublic information and rating biases due to conflicts of interest, making certain bond characteristics endogenous. We model and quantify soft adjustments as bond-specific thresholds in a semiparametric ordered-response model and exploit ownership structures of bond-issuers to control for endogeneity. Relying on the shift restrictions, we develop a location estimator for models of ordered choices with correlated heterogenous thresholds. Using Moody’s initial ratings from 2000 to 2016, we find a significant reduction of soft adjustment after the Dodd–Frank reform.
Characterization of the Blood-Feeding Patterns of Culex quinquefasciatus (Diptera: Culicidae) in San Bernardino County, California
Authors: Guinn Aelish , Su Tianyun , Thieme Jennifer , Cheng Min-Lee , Brown Michelle Q , Thiemann Tara 
Published: July 2022

Abstract
West Nile virus (WNV) is a zoonotic disease that is endemic in North America and is known to cause a range of symptoms from mild to life threatening in humans. Culex quinquefasciatus is one of the most prominent vectors of WNV in Southern California. The goal of this study was to identify which animal species are most fed upon by these mosquitoes in various habitats in the West Valley area of San Bernardino County, California, and determine the relationship between blood-feeding patterns and WNV activity in the region. Culex quinquefasciatus specimens were collected by West Valley Mosquito and Vector Control District during 2011 from 32 different sites. The bloodmeals of 683 individuals (92.4% of those tested) were identified using the mitochondrial gene cytochrome c oxidase 1 (COI). These bloodmeals comprised 29 vertebrate species across four different habitats. Species richness (ranging from 10 to 17) was not significantly different between habitats when rarified to account for sample size. Across habitats, the highest percentage of avian bloodmeals were taken from house sparrows (18.8–39.1%) and house finches (2.6–31.5%). Bloodmeals were identified from five mammalian species, accounting for 5.1–59.2% of bloodmeals by habitat, including humans (0–4.1%). A seasonal shift towards increased mammalian bloodmeal prevalence, specifically for domestic dog and human bloodmeals, was observed in urban habitats. The WNV activity during 2011 in San Bernardino County occurred mostly in urban and suburban areas as indicated by minimum infection rate (MIR) in Culex quinquefasciatus, notable as all human bloodmeals were identified from these two habitats.
Management of Chronic Pain and PTSD in Veterans With tDCS+Prolonged Exposure: A Pilot Study
Authors: Hernandez-Tejada Melba A , Cherry Kathryn E , Rauch Sheila A M , Acierno Ron , Fries Gabriel R , Muzzy Wendy , Teng Ellen J , Wangelin Bethany , Ahn Hyochol 
Published: July 2022

ABSTRACT

Introduction
Chronic pain and posttraumatic stress disorder (PTSD) are prevalent comorbid conditions, particularly in Veterans; however, there are few integrated treatments for chronic pain and PTSD. Instead, interventions are typically implemented separately and may involve addictive opioids. Although there are highly effective, non-pharmacological treatments for PTSD, they are plagued by high dropout, which may be exacerbated by comorbid pain, as these PTSD treatments typically require increased activity. Importantly, a noninvasive pain treatment, tDCS (transcranial direct current stimulation) shows indications of effectiveness and may be integrated with psychological treatments, even when delivered via telehealth. This study examines the feasibility and initial efficacy of integrating home telehealth tDCS with prolonged exposure (PE), an evidence-based PTSD treatment.

Materials and Methods
Thirty-nine Veterans were contacted, 31 consented to evaluation, 21 were enrolled, and 16 completed treatment and provided pre- and post-treatment data at one of two Veterans Affairs Medical Centers. Transcranial direct current stimulation sessions corresponded with PE exposure assignments, as there is theoretical reason to believe that tDCS may potentiate extinction learning featured in PE.

Results
Patients evinced significant improvement in both pain interference and PTSD symptoms and a trend toward improvement in depression symptoms. However, a significant change in pain intensity was not observed, likely because of the small sample size.

Discussion
The findings provide initial support for the feasibility of an entirely home-based, integrated treatment for comorbid PTSD and pain.
Population synthesis of AX J1745.6−2901 X-ray nova-type binaries with rapidly decreasing orbital periods
Authors: Bogomazov A I , Cherepashchuk A M , Khruzina T S , Tutukov A V 
Published: July 2022

ABSTRACT
The neutron star low-mass X-ray binary (LMXB) AX J1745.6−2901 was detected with an anomalously fast decrease of its orbital period. The decreasing rate of the orbital period exceeds the contribution of all processes extracting angular momentum from the binary star in the standard model. Using the scenario machine code, we conducted a population synthesis study of X-ray novae with neutron stars to investigate a possible formation and evolution of such binaries. Such close LMXBs should experience a preceding common envelope stage, in which the magnetic fields of the low-mass main-sequence donor stars can be dramatically amplified. Our calculations show that the magnetic stellar wind of the optical companion can efficiently extract angular momentum from the binary systems, and produce the observed orbital-period derivatives of AX J1745.6−2901 and black hole LMXBs. The estimated values of the required magnetic field induction are the following: Bd ≈ 400 G (AX J1745.6−2901), Bd ≈ 1500 G (KV UMa), Bd ≈ 400 G (A0620−00) and Bd ≈ 1800 G (Nova Muscae). We successfully reproduced the current observational abundance of such anomalous neutron star X-ray novae, and computed the appropriate value of the parameter of magnetic braking λMSW (0.8−0.6 for Roche lobe filling stars and 0.4−0.15 for binaries with partial Roche lobe filling).