bluuebunny/crossref_metadata_2025_split huggingface dataset:
Practical rationality as a determinant of formality in communicative situations: toward a procedure for causal interpretation in qualitative communication research
Authors: Shavit Nimrod 
Published: July 2022

AbstractThis article develops an updated version of formality as an analytical framework in the comparative study of communicative situations, and especially of meetings. The discussion remakes Judith Irvine’s formality framework by adding to it the explanatory principle of practical rationality as used within Weber’s Interpretive Sociology. This conceptual move provides an efficient and accurate means by which to infer the final causes, reasons, or ends of communicative situations. To illustrate this analytical approach and how it can contribute to qualitative theorization in general, the article conducts an in-depth ethnographic and comparative examination of civic software production meetings in Israel and the United States. The overall argument of the article is that practical rationality can provide a valuable means for deepening explanations of cultural difference in qualitative communication research.
Dynamics of the most common pathogenic mtDNA variant m.3243A &gt; G demonstrate frequency-dependency in blood and positive selection in the germline
Authors: Franco Melissa , Pickett Sarah J , Fleischmann Zoe , Khrapko Mark , Cote-L’Heureux Auden , Aidlen Dylan , Stein David , Markuzon Natasha , Popadin Konstantin , Braverman Maxim , Woods Dori C , Tilly Jonathan L , Turnbull Doug M , Khrapko Konstantin 
Published: July 2022

Abstract
The A-to-G point mutation at position 3243 in the human mitochondrial genome (m.3243A &gt; G) is the most common pathogenic mtDNA variant responsible for disease in humans. It is widely accepted that m.3243A &gt; G levels decrease in blood with age, and an age correction representing ~ 2% annual decline is often applied to account for this change in mutation level. Here we report that recent data indicate that the dynamics of m.3243A &gt; G are more complex and depend on the mutation level in blood in a bi-phasic way. Consequently, the traditional 2% correction, which is adequate ‘on average’, creates opposite predictive biases at high and low mutation levels. Unbiased age correction is needed to circumvent these drawbacks of the standard model. We propose to eliminate both biases by using an approach where age correction depends on mutation level in a biphasic way to account for the dynamics of m.3243A &gt; G in blood. The utility of this approach was further tested in estimating germline selection of m.3243A &gt; G. The biphasic approach permitted us to uncover patterns consistent with the possibility of positive selection for m.3243A &gt; G. Germline selection of m.3243A &gt; G shows an ‘arching’ profile by which selection is positive at intermediate mutant fractions and declines at high and low mutant fractions. We conclude that use of this biphasic approach will greatly improve the accuracy of modelling changes in mtDNA mutation frequencies in the germline and in somatic cells during aging.
Limit Shape of Perfect Matchings on Rail-Yard Graphs
Authors: Li Zhongyang 
Published: July 2022

AbstractWe obtain limit shape of perfect matchings on a large class of rail-yard graphs with right boundary condition given by the empty partition and left boundary condition given by either by a staircase partition with constant density or a piecewise partition with densities either 1 or 0. We prove the parametric equations for the frozen boundary and find conditions under which the frozen boundary is a cloud curve, or a union of disjoint cloud curves.
Consecutive Real Quadratic Fields with Large Class Numbers
Authors: Cherubini Giacomo , Fazzari Alessandro , Granville Andrew , Kala Vítězslav , Yatsyna Pavlo 
Published: July 2022

Abstract
For a given positive integer $k$, we prove that there are at least $x^{1/2-o(1)}$ integers $d\leq x$ such that the real quadratic fields ${\mathbb {Q}}(\sqrt {d+1}),\dots ,{\mathbb {Q}}(\sqrt {d+k})$ have class numbers essentially as large as possible.
Natural History of Malaria Infections During Early Childhood in Twins
Authors: Gonçalves Bronner P , Pérez-Caballero Raúl , Barry Amadou , Gaoussou Santara , Lewin Alexandra , Issiaka Djibrilla , Keita Sekouba , Diarra Bacary S , Mahamar Almahamoudou , Attaher Oumar , Narum David L , Kurtis Jonathan D , Dicko Alassane , Duffy Patrick E , Fried Michal 
Published: July 2022

Abstract

Background
The frequency and clinical presentation of malaria infections show marked heterogeneity in epidemiological studies. However, deeper understanding of this variability is hampered by the difficulty in quantifying all relevant factors. Here, we report the history of malaria infections in twins, who are exposed to the same in utero milieu, share genetic factors, and are similarly exposed to vectors.

Methods
Data were obtained from a Malian longitudinal birth cohort. Samples from 25 twin pairs were examined for malaria infection and antibody responses. Bayesian models were developed for the number of infections during follow-up.

Results
In 16 of 25 pairs, both children were infected and often developed symptoms. In 8 of 25 pairs, only 1 twin was infected, but usually only once or twice. Statistical models suggest that this pattern is not inconsistent with twin siblings having the same underlying infection rate. In a pair with discordant hemoglobin genotype, parasite densities were consistently lower in the child with hemoglobin AS, but antibody levels were similar.

Conclusions
By using a novel design, we describe residual variation in malaria phenotypes in naturally matched children and confirm the important role of environmental factors, as suggested by the between-twin pair heterogeneity in malaria history.
Mechanisms of high-level fosfomycin resistance in Staphylococcus aureus epidemic lineage ST5
Authors: Chen Tianchi , Zhao Lin , Liu Yao , Wang Ya’nan , Jian Ying , Zhao Na , Yang Ziyu , Wang Xi , Liu Qian , Li Min 
Published: July 2022

Abstract

Objectives
Fosfomycin resistance has become a clinical concern. In this study, we analysed the dynamic change of fosfomycin MIC in the epidemic Staphylococcus aureus lineages in a teaching hospital in Shanghai for 12 years and sought to elucidate the major underlying mechanisms.

Methods
MLST was conducted for 4580 S. aureus isolates recovered from 2008 to 2019. Fosfomycin MIC was determined by the agar dilution method. The genome data of 230 S. aureus epidemic lineage isolates were acquired from a next-generation sequencing (NGS) platform. Gene deletion and corresponding complementation mutants were constructed to confirm the mechanism of fosfomycin resistance.

Results
The predominant S. aureus lineages during the past 12 years were ST5 and ST239 (45.6%; 2090/4580). However, ST5 has been spreading clinically, while ST239 has gradually disappeared recently. Consistent with epidemic trends, fosfomycin-resistant ST5 increased from 19.5% to 67.3%. Most fosfomycin-resistant ST5 isolates (92.7%; 647/698) possessed high-level resistance (MIC &gt; 1024 mg/L) with combined mutations mainly in glpT and uhpT. In contrast, fosfomycin-resistant ST239 isolates (76.8%; 149/194) mainly acquired low-level resistance (MIC = 64–128 mg/L) with mutation primarily in hptA. Deletion of a single resistant gene merely resulted in low-level fosfomycin resistance, while double-gene mutants ΔglpTΔuhpT, ΔglpTΔhptA and ΔglpTΔhptR acquired high-level fosfomycin resistance.

Conclusions
The high-level fosfomycin resistance of S. aureus epidemic lineage ST5 is mainly due to the accumulation of mutations in the resistant genes related to membrane transporter systems, and partly contributes to its persistent prevalence under clinical antibiotic pressure.
Identification and validation of a metabolism-related gene signature for the prognosis of colorectal cancer: a multicenter cohort study
Authors: Han Ping , Yang Xiudeng , Li Lina , Bao Jie , Zhang Wenqiong , Zai Shubei , Zhu Zhaoqin , Wu Minle 
Published: July 2022

AbstractObjectiveCell metabolism plays a vital role in the proliferation, metastasis and sensitivity to chemotherapy drugs of colorectal cancer. The purpose of this multicenter cohort study is to investigate the potential genes indicating clinical outcomes in colorectal cancer patients.MethodsWe analyzed gene expression profiles of colorectal cancer to identify differentially expressed genes then used these differentially expressed genes to construct prognostic signature based on the least absolute shrink-age and selection operator Cox regression model. In addition, the multi-gene signature was validated in independent datasets including our multicenter cohort. Finally, nomograms were set up to evaluate the prognosis of colorectal cancer patients.ResultsSeventeen metabolism-related genes were determined in the least absolute shrink-age and selection operator model to construct signature, with area under receiver operating characteristic curve for relapse-free survival, 0.741, 0.755 and 0.732 at 1, 3 and 5 year, respectively. External validation datasets, GSE14333, GSE37892, GSE17538 and the Cancer Genome Atlas cohorts, were analyzed and stratified, indicating that the metabolism-related signature was reliable in discriminating high- and low-risk colorectal cancer patients. Area under receiver operating characteristic curves for relapse-free survival in our multicenter validation cohort were 0.801, 0.819 and 0.857 at 1, 3 and 5 year, respectively. Nomograms incorporating the genetic biomarkers and clinical pathological features were set up, which yielded good discrimination and calibration in the prediction of prognosis for colorectal cancer patients.ConclusionAn original metabolism-related signature was developed as a predictive model for the prognosis of colorectal cancer patients. A nomogram based on the signature was advantageous to facilitate personalized counselling and treatment of colorectal cancer patients.
Associates from infancy influence postweaning juvenile associations for common bottlenose dolphins (Tursiops truncatus) in Florida
Authors: Greenfield Michelle R , Durden Wendy N , Jablonski Teresa A , Moreland Lydia D , Fabry Agatha C , Gemma Lisa Y , Clifford Heidy H 
Published: July 2022

AbstractIn many long-lived mammalian species, association patterns between individuals have been found to influence sociality, behavioral traits, survival, and longevity. In common bottlenose dolphins (Tursiops truncatus), the early stages of development are of particular importance as associations experienced as dependent calves may influence future association patterns. While behavioral characteristics associated with the transition from a dependent calf state to an independent juvenile state have been documented, there are limited studies that examine associations between these time periods. This study aims to document association longevity for bottlenose dolphins as they transition from calves to juveniles and determine the extent to which kinship plays a role in the development of these associations. Using social network analysis, a generalized linear mixed model (GLMM), and a tiered association scale, we found 53.7% of associations were retained from the calf to the juvenile phase. GLMM results indicated that preferred associates (half-weight index [HWI] &gt; 0.178) from the calf state were 3.6 times more likely to associate in the juvenile state (0.178 &gt; HWI &gt; 0) and 5.67 times more likely to be preferred associates in the juvenile state compared to nonpreferred calf associates. The majority of juveniles, 76.92%, maintained a low–moderate to moderate level association (0.089–0.54) with their mother, and a few retained their mother as their top associate. Kin were preferred associates in 46.15% of cases and found to be the top juvenile associate in 26.92% of cases. Identifying continuity in associations, particularly from the calving state to the juvenile state, is imperative as mammalian association patterns may influence community structure, disease transmission, reproductive success, and predict survival.
Risk and Protective Factors for Physical Activity Engagement Among Adolescents With Comorbid Asthma and Obesity
Authors: Yourell Jacqlyn , Koskela-Staples Natalie , Doty Jennifer , Fedele David A 
Published: July 2022

AbstractObjectiveThe current study identifies levels of physical activity (PA) engagement among adolescents with neither asthma nor overweight/obesity (OW/OB), one, or both conditions. Risk and protective factors are examined across groups.MethodsData from 8th, 9th, and 11th graders were obtained from the 2019 Minnesota Student Survey (N = 125,164). One-way analysis of variance was used to assess PA levels across risk groups. Linear regressions were used to examine patterns of risk and protective factors for adolescent PA engagement across four groups (neither asthma nor OW/OB, asthma only, OW/OB only, and comorbid asthma + OW/OB). Results were stratified by race/ethnicity.ResultsAdolescents with OW/OB only or asthma + OW/OB had significantly lower PA levels than youth with asthma only or neither condition (M = 3.65–3.67 days/week, SD = 2.20 vs M = 4.15–4.19 days/week, SD = 2.16–2.17, p &lt; .001). The following variables were associated with adolescent PA (p &lt; .001): Adult community care across all risk groups (β ranges = .13–.16), depressive symptoms among those with neither and both asthma + OW/OB (β’s = –.10), and extracurriculars among those with asthma + OW/OB (β = .10). Extracurriculars and parent connectedness were protective for Hispanic adolescents.ConclusionsAdolescents with OW/OB had significantly lower levels of PA compared to those without, regardless of asthma status. Individual and relational factors influenced adolescent PA. Future research investigating factors influencing adolescent PA should consider depressive symptoms, connectedness to adults in the community, non-sport-related extracurricular activity involvement, and address disparities among minoritized youth.
Effects on Pediatric Cancer Survivors: The FAMily-Oriented Support (FAMOS) Randomized Controlled Trial
Authors: Bidstrup Pernille E , Salem Hanin , Andersen Elisabeth Wreford , Schmiegelow Kjeld , Rosthøj Steen , Wehner Peder Skov , Hasle Henrik , Dalton Susanne O , Johansen Christoffer , Kazak Anne E 
Published: July 2022

Abstract

Objective
To examine as secondary analyses the effect the FAMily-Oriented Support (FAMOS) family therapy program on reducing parent-reported medical traumatic stress in the sub-sample of pediatric cancer survivors, age 2–5 years.

Methods
The FAMOS study was a national multicenter randomized controlled trial with all four pediatric oncology departments in Denmark (Clinicaltrials.gov [NCT02200731]). Families were randomized in parallel design (1:1) to intervention or usual care. The FAMOS program includes seven home-based psychotherapeutic sessions and is based on family systems therapy to address the individuals in the family system using cognitive behavioral, problem-solving and goal-setting techniques. Questionnaires were completed by parents at baseline, 6, and 12 months. In linear mixed-effects models, the effect of FAMOS on reducing children’s trauma-related behavior after 6 and 12 months was examined in 62 children (31 in the intervention and 29 in the control group, respectively). It was also examined if a trauma-related behavior effect was mediated through reduced symptoms of depression in mothers and fathers, respectively.

Results
On average, children in the intervention group experienced significantly larger decreases in trauma-related behaviors at 6 and 12 months than the control group (predicted mean difference –3.89, p = .02 and –6.24, p = .003, respectively). The effect on trauma-related behavior was partly mediated through reduced symptoms of depression in mothers, but not fathers.

Conclusions
Adding to previously reported positive effects of the FAMOS intervention on parents’ symptoms of post-traumatic stress and depression, significant improvements were found in young children’s trauma related-behavior. Further research is needed to develop therapy for children with cancer.
The small subunit of Rubisco and its potential as an engineering target
Authors: Mao Yuwei , Catherall Ella , Díaz-Ramos Aranzazú , Greiff George R L , Azinas Stavros , Gunn Laura , McCormick Alistair J 
Published: July 2022

AbstractRubisco catalyses the first rate-limiting step in CO2 fixation and is responsible for the vast majority of organic carbon present in the biosphere. The function and regulation of Rubisco remain an important research topic and a longstanding engineering target to enhance the efficiency of photosynthesis for agriculture and green biotechnology. The most abundant form of Rubisco (Form I) consists of eight large and eight small subunits, and is found in all plants, algae, cyanobacteria, and most phototrophic and chemolithoautotrophic proteobacteria. Although the active sites of Rubisco are located on the large subunits, expression of the small subunit regulates the size of the Rubisco pool in plants and can influence the overall catalytic efficiency of the Rubisco complex. The small subunit is now receiving increasing attention as a potential engineering target to improve the performance of Rubisco. Here we review our current understanding of the role of the small subunit and our growing capacity to explore its potential to modulate Rubisco catalysis using engineering biology approaches.
The Custodial History of the Sadler Partbooks (Oxford, Bodleian Library MSS Mus. e. 1–5)
Authors: Burke James 
Published: July 2022

ABSTRACT
The Sadler partbooks (Oxford, Bodleian Library, MSS Mus. e. 1–5), one of the most important English polyphonic sources to survive from the sixteenth century, reflect the interventions of several generations of later owners. Today the volumes bear a number of marks that were clearly not coeval with their copying in the sixteenth century; they have also been subjected to at least one rebinding, and some leaves are in a disrupted position, hitherto unobserved (and still misplaced). This article seeks to account for the custodial history of the Sadler partbooks, and to chart the bearing that their later owners have had on the partbooks’ present state. Apart from showing that the books travelled widely—they can be traced in Norwich, London, Bath, Bristol, Manchester, and eventually Oxford—it also shows that the partbooks came to the brink of destruction in the hands of one former owner, surviving fire, flood, and theft.
The very knotty lenser: Exploring the role of regularization in source and potential reconstructions using Gaussian process regression
Authors: Vernardos G , Koopmans L V E 
Published: July 2022

ABSTRACTReconstructing lens potentials and lensed sources can easily become an underconstrained problem, even when the degrees of freedom are low, due to degeneracies, particularly when potential perturbations superimposed on a smooth lens are included. Regularization has traditionally been used to constrain the solutions where the data failed to do so, e.g. in unlensed parts of the source. In this exploratory work, we go beyond the usual choices of regularization and adopt observationally motivated priors for the source brightness. We also perform a similar comparison when reconstructing lens potential perturbations, which are assumed to be stationary, i.e. permeate the entire field of view. We find that physically motivated priors lead to lower residuals, avoid overfitting, and are decisively preferred within a Bayesian quantitative framework in all the examples considered. For the perturbations, choosing the wrong regularization can have a detrimental effect that even high-quality data cannot correct for, while using a purely smooth lens model can absorb them to a very high degree and lead to biased solutions. Finally, our new implementation of the semi-linear inversion technique provides the first quantitative framework for measuring degeneracies between the source and the potential perturbations.
Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer–promoter interactions
Authors: Wang Kaiyuan , Escobar Mario , Li Jing , Mahata Barun , Goell Jacob , Shah Spencer , Cluck Madeleine , Hilton Isaac B 
Published: July 2022

Abstract
Nuclease-inactivated CRISPR/Cas-based (dCas-based) systems have emerged as powerful technologies to synthetically reshape the human epigenome and gene expression. Despite the increasing adoption of these platforms, their relative potencies and mechanistic differences are incompletely characterized, particularly at human enhancer–promoter pairs. Here, we systematically compared the most widely adopted dCas9-based transcriptional activators, as well as an activator consisting of dCas9 fused to the catalytic core of the human CBP protein, at human enhancer–promoter pairs. We find that these platforms display variable relative expression levels in different human cell types and that their transactivation efficacies vary based upon the effector domain, effector recruitment architecture, targeted locus and cell type. We also show that each dCas9-based activator can induce the production of enhancer RNAs (eRNAs) and that this eRNA induction is positively correlated with downstream mRNA expression from a cognate promoter. Additionally, we use dCas9-based activators to demonstrate that an intrinsic transcriptional and epigenetic reciprocity can exist between human enhancers and promoters and that enhancer-mediated tracking and engagement of a downstream promoter can be synthetically driven by targeting dCas9-based transcriptional activators to an enhancer. Collectively, our study provides new insights into the enhancer-mediated control of human gene expression and the use of dCas9-based activators.
Elucidation of structure–function relationships in Methanocaldococcus jannaschii RNase P, a multi-subunit catalytic ribonucleoprotein
Authors: Phan Hong-Duc , Norris Andrew S , Du Chen , Stachowski Kye , Khairunisa Bela H , Sidharthan Vaishnavi , Mukhopadhyay Biswarup , Foster Mark P , Wysocki Vicki H , Gopalan Venkat 
Published: July 2022

Abstract
RNase P is a ribonucleoprotein (RNP) that catalyzes removal of the 5′ leader from precursor tRNAs in all domains of life. A recent cryo-EM study of Methanocaldococcus jannaschii (Mja) RNase P produced a model at 4.6-Å resolution in a dimeric configuration, with each holoenzyme monomer containing one RNase P RNA (RPR) and one copy each of five RNase P proteins (RPPs; POP5, RPP30, RPP21, RPP29, L7Ae). Here, we used native mass spectrometry (MS), mass photometry (MP), and biochemical experiments that (i) validate the oligomeric state of the Mja RNase P holoenzyme in vitro, (ii) find a different stoichiometry for each holoenzyme monomer with up to two copies of L7Ae, and (iii) assess whether both L7Ae copies are necessary for optimal cleavage activity. By mutating all kink-turns in the RPR, we made the discovery that abolishing the canonical L7Ae–RPR interactions was not detrimental for RNase P assembly and function due to the redundancy provided by protein–protein interactions between L7Ae and other RPPs. Our results provide new insights into the architecture and evolution of RNase P, and highlight the utility of native MS and MP in integrated structural biology approaches that seek to augment the information obtained from low/medium-resolution cryo-EM models.