bluuebunny/crossref_metadata_2025_split huggingface dataset:
Galaxy velocity bias in cosmological simulations: towards per cent-level calibration
Authors: Anbajagane Dhayaa , Aung Han , Evrard August E , Farahi Arya , Nagai Daisuke , Barnes David J , Cui Weiguang , Dolag Klaus , McCarthy Ian G , Rasia Elena , Yepes Gustavo 
Published: December 2021

ABSTRACT
Galaxy cluster masses, rich with cosmological information, can be estimated from internal dark matter (DM) velocity dispersions, which in turn can be observationally inferred from satellite galaxy velocities. However, galaxies are biased tracers of the DM, and the bias can vary over host halo and galaxy properties as well as time. We precisely calibrate the velocity bias, bv – defined as the ratio of galaxy and DM velocity dispersions – as a function of redshift, host halo mass, and galaxy stellar mass threshold ($M_{\rm \star , sat}$), for massive haloes ($M_{\rm 200c}\gt 10^{13.5} \, {\rm M}_\odot$) from five cosmological simulations: IllustrisTNG, Magneticum, Bahamas + Macsis, The Three Hundred Project, and MultiDark Planck-2. We first compare scaling relations for galaxy and DM velocity dispersion across simulations; the former is estimated using a new ensemble velocity likelihood method that is unbiased for low galaxy counts per halo, while the latter uses a local linear regression. The simulations show consistent trends of bv increasing with M200c and decreasing with redshift and $M_{\rm \star , sat}$. The ensemble-estimated theoretical uncertainty in bv is 2–3 per cent, but becomes percent-level when considering only the three highest resolution simulations. We update the mass–richness normalization for an SDSS redMaPPer cluster sample, and find our improved bv estimates reduce the normalization uncertainty from 22 to 8 per cent, demonstrating that dynamical mass estimation is competitive with weak lensing mass estimation. We discuss necessary steps for further improving this precision. Our estimates for $b_v(M_{\rm 200c}, M_{\rm \star , sat}, z)$ are made publicly available.
Statistical similarity between soft gamma repeaters and repeating fast radio bursts
Authors: Sang Yu , Lin Hai-Nan 
Published: December 2021

ABSTRACT
We study the statistical properties of the soft gamma repeater SGR 1935+2154. We find that the cumulative distributions of duration, waiting time, fluence, and flux can be well fitted by bent power law. In addition, the probability density functions of fluctuations of duration, waiting time, fluence, and flux well follow the Tsallis q-Gaussian distribution. The q values keep steady for different temporal scale intervals, indicating a scale-invariant structure of the bursts. Those features are very similar to the property of the repeating fast radio burst FRB 121102, indicating the underlying association between the origins of soft gamma repeaters and repeating fast radio bursts.
Grouped star formation: converting sink particles to stars in hydrodynamical simulations
Authors: Liow Kong You , Rieder Steven , Dobbs Clare L , Jaffa Sarah E 
Published: December 2021

ABSTRACT
Modelling star formation and resolving individual stars in numerical simulations of molecular clouds and galaxies is highly challenging. Simulations on very small scales can be sufficiently well resolved to consistently follow the formation of individual stars, whilst on larger scales sinks that have masses sufficient to fully sample the IMF can be converted into realistic stellar populations. However, as yet, these methods do not work for intermediate scale resolutions whereby sinks are more massive compared to individual stars but do not fully sample the IMF. In this paper, we introduce the grouped star formation prescription, whereby sinks are first grouped according to their positions, velocities, and ages, then stars are formed by sampling the IMF using the mass of the groups. We test our grouped star formation method in simulations of various physical scales, from sub-parsec to kilo-parsec, and from static isolated clouds to colliding clouds. With suitable grouping parameters, this star formation prescription can form stars that follow the IMF and approximately mimic the original stellar distribution and velocity dispersion. Each group has properties that are consistent with a star-forming region. We show that our grouped star formation prescription is robust and can be adapted in simulations with varying physical scales and resolution. Such methods are likely to become more important as galactic or even cosmological scale simulations begin to probe sub-parsec scales.
The dark matter haloes of HI selected galaxies
Authors: Dutta Saili , Khandai Nishikanta , Rana Sandeep 
Published: December 2021

ABSTRACT
We present the neutral hydrogen mass (MHI) function (HIMF) and velocity width (w50) function (HIWF) based on a sample of 7857 galaxies from the 40 per cent data release of the ALFALFA survey (α.40). The low mass (velocity width) end of the HIMF (HIWF) is dominated by the blue population of galaxies whereas the red population dominates the HIMF (HIWF) at the high mass (velocity width) end. We use a deconvolution method to estimate the HI rotational velocity (Vrot) functions (HIVF) from the HIWF for the total, red, and blue samples. The HIWF and HIVF for the red and blue samples are well separated at the knee of the function compared to their HIMFs. We then use recent stacking results from the ALFALFA survey to constrain the halo mass (Mh) function of HI-selected galaxies. This allows us to obtain various scaling relations between MHI−w50−Vrot−Mh, which we present. The MHI−Mh relation has a steep slope ∼2.10 at small masses and flattens to ∼0.34 at masses larger than a transition halo mass, $\log _{10}(M_{\rm{ht}}h_{70}^2/M_{\odot })=10.62$. Our scaling relation is robust and consistent with a volume-limited sample of α.40. The MHI−Mh relation is qualitatively similar to the Mstar−Mh relation but the transition halo mass is smaller by ∼1.4 dex compared to that of the Mstar−Mh relation. Our results suggest that baryonic processes like heating and feedback in larger mass haloes suppress HI gas on a shorter time-scale compared to star formation.
Adaptation and Cryptic Pseudogenization in Penguin Toll-Like Receptors
Authors: Fiddaman Steven R , Vinkler Michal , Spiro Simon G , Levy Hila , Emerling Christopher A , Boyd Amy C , Dimopoulos Evangelos A , Vianna Juliana A , Cole Theresa L , Pan Hailin , Fang Miaoquan , Zhang Guojie , Hart Tom , Frantz Laurent A F , Smith Adrian L 
Published: December 2021

AbstractPenguins (Sphenisciformes) are an iconic order of flightless, diving seabirds distributed across a large latitudinal range in the Southern Hemisphere. The extensive area over which penguins are endemic is likely to have fostered variation in pathogen pressure, which in turn will have imposed differential selective pressures on the penguin immune system. At the front line of pathogen detection and response, the Toll-like receptors (TLRs) provide insight into host evolution in the face of microbial challenge. TLRs respond to conserved pathogen-associated molecular patterns and are frequently found to be under positive selection, despite retaining specificity for defined agonist classes. We undertook a comparative immunogenetics analysis of TLRs for all penguin species and found evidence of adaptive evolution that was largely restricted to the cell surface-expressed TLRs, with evidence of positive selection at, or near, key agonist-binding sites in TLR1B, TLR4, and TLR5. Intriguingly, TLR15, which is activated by fungal products, appeared to have been pseudogenized multiple times in the Eudyptes spp., but a full-length form was present as a rare haplotype at the population level. However, in vitro analysis revealed that even the full-length form of Eudyptes TLR15 was nonfunctional, indicating an ancestral cryptic pseudogenization prior to its eventual disruption multiple times in the Eudyptes lineage. This unusual pseudogenization event could provide an insight into immune adaptation to fungal pathogens such as Aspergillus, which is responsible for significant mortality in wild and captive bird populations.
Covariation of viral recombination with single nucleotide variants during virus evolution revealed by CoVaMa
Authors: Wang Shiyi , Sotcheff Stephanea L , Gallardo Christian M , Jaworski Elizabeth , Torbett Bruce E , Routh Andrew L 
Published: December 2021

AbstractAdaptation of viruses to their environments occurs through the acquisition of both novel single-nucleotide variants (SNV) and recombination events including insertions, deletions, and duplications. The co-occurrence of SNVs in individual viral genomes during their evolution has been well-described. However, unlike covariation of SNVs, studying the correlation between recombination events with each other or with SNVs has been hampered by their inherent genetic complexity and a lack of bioinformatic tools. Here, we expanded our previously reported CoVaMa pipeline (v0.1) to measure linkage disequilibrium between recombination events and SNVs within both short-read and long-read sequencing datasets. We demonstrate this approach using long-read nanopore sequencing data acquired from Flock House virus (FHV) serially passaged in vitro. We found SNVs that were either correlated or anti-correlated with large genomic deletions generated by nonhomologous recombination that give rise to Defective-RNAs. We also analyzed NGS data from longitudinal HIV samples derived from a patient undergoing antiretroviral therapy who proceeded to virological failure. We found correlations between insertions in the p6Gag and mutations in Gag cleavage sites. This report confirms previous findings and provides insights on novel associations between SNVs and specific recombination events within the viral genome and their role in viral evolution.
Determinants of the temperature adaptation of mRNA degradation
Authors: Jaquet Vincent , Wallerich Sandrine , Voegeli Sylvia , Túrós Demeter , Viloria Eduardo C , Becskei Attila 
Published: December 2021

Abstract
The rate of chemical reactions increases proportionally with temperature, but the interplay of biochemical reactions permits deviations from this relation and adaptation. The degradation of individual mRNAs in yeast increased to varying degrees with temperature. We examined how these variations are influenced by the translation and codon composition of mRNAs. We developed a method that revealed the existence of a neutral half-life above which mRNAs are stabilized by translation but below which they are destabilized. The proportion of these two mRNA subpopulations remained relatively constant under different conditions, even with slow cell growth due to nutrient limitation, but heat shock reduced the proportion of translationally stabilized mRNAs. At the same time, the degradation of these mRNAs was partially temperature-compensated through Upf1, the mediator of nonsense-mediated decay. Compensation was also promoted by some asparagine and serine codons, whereas tyrosine codons promote temperature sensitization. These codons play an important role in the degradation of mRNAs encoding key cell membrane and cell wall proteins, which promote cell integrity.
Variegated Accountability: Devolved Public Accounts Committees in the UK
Authors: Foster Helen , Knox Colin 
Published: December 2021

Abstract
Devolution in the UK has now been in place for over 20 years. A key support mechanism for the devolved administrations in Scotland, Wales and Northern Ireland is the Public Account Committees (PACs). Aside from their formal role in ensuring financial regularity and probity, they aim to strengthen accountability at the regional level. This study examines the effectiveness of the PACs measured through the perception of key stakeholders (PAC members, witnesses, auditors and officials). Using Q methodology, it identifies four clusters of participants: Team Players, Peace Makers, Bureaucrats and Attention Seekers, and captures their perceptions of what makes the devolved PACs most effective.
Discursive Activists or Patriarchal Bargainers? Religion, Gender, and Neoliberal Governance in the “New” Turkey
Authors: Özdemir Şeyma 
Published: December 2021

AbstractThis article aims first to contribute to discussions on both the agency of religious women and feminist transversal politics, and second, to emphasize the need to build solidarity coalitions to resist interlocking oppressive structures. It examines the intellectual mobilization of religious women in Turkey (2010–2016), drawing on an ethnographic study of an Istanbul women’s organization. It explores the way religious women contextualized Turkey’s socio-political transformation and analyzed earlier initiatives, and analyses their struggle to challenge the perceptions of them as outsiders vis-a-vis the secularist Republican state patriarchy and Islamist neoliberal patriarchal state. The study concludes that national socio-political transformations curtailed their discursive activism and that broader solidarity networks, transversal politics, and feminist coalitions are necessary to resist such oppressive structures.
Original Research: Nurses' Experiences of Caring for Patients and Families During the COVID-19 Pandemic: Communication Challenges
Authors: Pariseault Christine A. , Copel Linda Carman , McKay Michelle A. 
Published: December 2021

ABSTRACT

Objective:
The purpose of this study was to gain a better understanding of the perceptions and experiences of nurses caring for patients and families under the COVID-19 pandemic's socially restrictive practices and policies.

Background:
The COVID-19 global pandemic has affected the delivery of health care to patients and their families, with many aspects altered because of the need for social distancing, social isolation, and visitation restriction policies. These policies have created communication challenges for interdisciplinary health care teams, patients, and families. As frontline caregivers, nurses have felt strongly the impact of these challenges.

Methods:
A qualitative descriptive study was conducted among 17 RNs who were caring for patients during the COVID-19 pandemic and were recruited via social media posts on Facebook, Twitter, and LinkedIn. Watson's theory of human caring served as the conceptual framework for the study.

Results:
Several themes emerged regarding nurses' experiences of communication with patients and families. These include communication challenges and barriers, prioritization, integration of group communication, nurse self-reflection, and acceptance of gratitude.

Conclusions:
The study findings underscore the importance of nurses' communication with patients and families under the pandemic's restricted conditions. They demonstrate the value of nurses' ability to innovate in fostering all parties' participation in the plan of care, and highlight the comfort nurses provide to patients who are isolated from loved ones. Strategies that fostered communication were identified, as were areas for further research.
Genomic evolution during locoregional recurrence in colorectal cancer determined by whole-exome sequencing: a retrospective observational study
Authors: Lan Xiaoliang , Wu Xiaoxiao , Zhang Chao , Wei Genxia , Li Bingbing , Qiu Weihao , Li Danyi , Wu Huanwen , Ding Yanqing , Yuan Jie , Tai Zaixian , Yang Zuoquan , Liang Zhiyong , Su Dan , Liang Li 
Published: December 2021

Objective:
The genomic landscapes of metastatic colorectal cancer (mCRC) have been extensively studied; however, the genetic mechanisms underlying the locoregional recurrence (LR) of CRC remain unclear. The objective of our study was to investigate genomic evolution during LR in CRC using high-throughput sequencing.

Methods:
Twenty-three CRC patients with matched primary and LR tissues were recruited from Nanfang Hospital and Zhejiang Cancer Hospital between January 2011 and December 2018. The last date of follow-up was March 2020. Tissue samples were analyzed by whole-exome sequencing and the genomic profiles were depicted by single nucleotide variation, mutational signature, copy number variation, clonal architecture, and other features. The evolutionary process was speculated with comparison of the genetic variations between primary and LR lesions. The disseminating clusters from primary to LR lesions were identified by variant allele frequency dynamics. Furthermore, the early-recurrent biomarker was explored by comparing the indel signature between early- and late-recurrent patients. The study was approved by the Institutional Review Board of Nanfang Hospital of Southern Medical University (approval No. 2020010) on September 11, 2020.

Results:

The results highlighted distinct origins of LR between patients with high microsatellite instability and microsatellite stability. LR lesions evolved independently in patients with high microsatellite instability, while LR lesions were highly clonally related to the primary lesions in patients with microsatellite stability. Late-acquired variations in LR lesions encompassed a wide range of driver genes involved in histone methylation, DNA replication, T cell activation,
PDCD1
gain, and
LMNA
loss. Furthermore, clonal analysis of the disseminating cells identified a dominant polyclonal seeding pattern during LR. The indel signature ID4 was associated with significantly shorter disease-free survival in patients with relapsed CRC according to a public dataset.

Conclusion:
These findings pose a challenge for the development of new approaches targeting the interactions of multiple clones in the establishment of LR and in terms of optimizing the clinical management of susceptible patients.
A Survey of Entry-Level Physical Therapy Education Content for Vestibular Rehabilitation
Authors: Galgon Anne K. , Roberts Holly J. , Littmann Andrew E. , Heusel-Gillig Lisa L. , Dransfield Lisa , Plishka Charles M. , Wrisley Diane M. 
Published: December 2021

Introduction.
Vestibular rehabilitation (VR) represents an evolving area of physical therapy practice and is therefore pertinent to entry-level education. Currently, there is no consensus regarding the extent of content that should be covered in entry-level Doctor of Physical Therapy (DPT) programs. The first step in establishing standards of education in VR is to determine what content is currently taught and what is perceived to be important. The purpose of this study was to survey entry-level DPT programs as to what VR content is included in their curriculum and their perceptions of importance of VR examination and intervention techniques.

Methods.
Directors of 229 accredited physical therapy education programs in the United States were contacted to complete the survey. A task force of 3 clinicians and 4 faculty used a modified Delphi process to select survey items to examine content exposure, student assessment, and a rating for overall expected expertise. Modifications were made to the final survey for clarity and time requirements based on pilot survey data. Descriptive and correlational statistics were applied to the data.

Results.
Ninety-nine programs (43.23%) responded to the survey. More than 90% rated 7 vestibular conditions (unilateral vestibular hypofunction, posterior semicircular canal canalithiasis and cupulolithiasis, vestibular neuritis, labyrinthitis, bilateral vestibular hypofunction, and horizontal semicircular canal canalithiasis) as essential for entry-level practice. More than 90% of respondents rated all elements of clinical application and decision-making as essential for entry-level education except for billing/diagnosis codes. Most respondents expected students to perform at the intermediate or advanced beginner level in vestibular assessment and rehabilitation on graduation.

Discussion and Conclusion.
Disparities in VR content, expected level of performance, and the amount of time dedicated to VR exist. Vestibular rehabilitation education may not match current clinical practice. Future research should determine the level of education clinicians expect of entry-level DPT graduates.
Perfectionism, Stress, and the Entry-Level Doctor of Physical Therapy Student: A Cross-Sectional, Observational Study
Authors: Richardson Michael V. , Miller Haylie , Papa Evan , Santurri Laura 
Published: December 2021

Introduction.
Perfectionism consists of high standards and hypercritical self-evaluation. Some doctor of physical therapy (DPT) students experience increased stress levels due to rigorous academic expectations. There is limited understanding of how successful these students are at managing increased stress, especially among perfectionists. The purpose was to examine perfectionism among entry-level DPT students and its relationship to perceived stress.

Review of Literature.
Researchers have studied perfectionism and stress in health professions programs, but not DPT programs. Being a Maladaptive Perfectionist (MP) was positively and strongly associated with stress among health professions students.

Subjects.
Convenience sample of first-year, second-year, and third-year DPT students (n = 163).

Methods.
This was a nonexperimental, single-site, cross-sectional study. Investigators used 3-way analysis of variance to compare student characteristics and binomial logistic regressions to determine whether characteristic and/or perceived stress was predictive of perfectionism subtype. They completed bivariate correlations to determine associations between perfectionism and stress.

Results.
Sample results demonstrated 41.10% Adaptive Perfectionists and 25.15% MPs. There was a moderate, direct association between perceived stress and the perfectionism discrepancy measure (r

s
= .51, P < .01). The perceived stress and perfectionism subtype logistic regression model was statistically significant, χ2(1) = 18.73, P < .01. Participants with increased perceived stress had 1.17 times higher odds of being categorized as an MP than those with lower stress levels.

Discussion and Conclusion.

Maladaptive Perfectionist students may be at greater risk for stress-related issues. Perfectionism and stress measures may assist educators in identifying at-risk students, monitor student response to stress management interventions, and consider curricular changes to lower stress. Students who effectively manage stress may ultimately have overall greater well-being.