bluuebunny/crossref_metadata_2025_split huggingface dataset:
The hyperthermophilic archaeon Thermococcus kodakarensis is resistant to pervasive negative supercoiling activity of DNA gyrase
Authors: Villain Paul , da Cunha Violette , Villain Etienne , Forterre Patrick , Oberto Jacques , Catchpole Ryan , Basta Tamara 
Published: November 2021

Abstract
In all cells, DNA topoisomerases dynamically regulate DNA supercoiling allowing essential DNA processes such as transcription and replication to occur. How this complex system emerged in the course of evolution is poorly understood. Intriguingly, a single horizontal gene transfer event led to the successful establishment of bacterial gyrase in Archaea, but its emergent function remains a mystery. To better understand the challenges associated with the establishment of pervasive negative supercoiling activity, we expressed the gyrase of the bacterium Thermotoga maritima in a naïve archaeon Thermococcus kodakarensis which naturally has positively supercoiled DNA. We found that the gyrase was catalytically active in T. kodakarensis leading to strong negative supercoiling of plasmid DNA which was stably maintained over at least eighty generations. An increased sensitivity of gyrase-expressing T. kodakarensis to ciprofloxacin suggested that gyrase also modulated chromosomal topology. Accordingly, global transcriptome analyses revealed large scale gene expression deregulation and identified a subset of genes responding to the negative supercoiling activity of gyrase. Surprisingly, the artificially introduced dominant negative supercoiling activity did not have a measurable effect on T. kodakarensis growth rate. Our data suggest that gyrase can become established in Thermococcales archaea without critically interfering with DNA transaction processes.
Reevaluating surgery and re-irradiation for locally recurrent pediatric ependymoma—a multi-institutional study
Authors: Mak David Y , Laperriere Normand , Ramaswamy Vijay , Bouffet Eric , Murray Jeffrey C , McNall-Knapp Rene Y , Bielamowicz Kevin , Paulino Arnold C , Zaky Wafik , McGovern Susan L , Okcu M Fatih , Tabori Uri , Atwi Doaa , Dirks Peter B , Taylor Michael D , Tsang Derek S , Bavle Abhishek 
Published: November 2021

Abstract

Background
The goal of this study was to evaluate extent of surgical resection, and timing and volume of re-irradiation, on survival for children with locally recurrent ependymoma.

Methods
Children with locally recurrent ependymoma treated with a second course of fractionated radiotherapy (RT2) from 6 North American cancer centers were reviewed. The index time was from the start of RT2 unless otherwise stated.

Results
Thirty-five patients were included in the study. The median doses for first radiation (RT1) and RT2 were 55.8 and 54 Gy, respectively. Median follow-up time was 5.6 years. Median overall survival (OS) for all patients from RT2 was 65 months. Gross total resection (GTR) was performed in 46% and 66% of patients prior to RT1 and RT2, respectively. GTR prior to RT2 was independently associated with improved progression-free survival (PFS) for all patients (HR 0.41, P = 0.04), with an OS benefit (HR 0.26, P = 0.03) for infratentorial tumors. Median PFS was superior with craniospinal irradiation (CSI) RT2 (not reached) compared to focal RT2 (56.9 months; log-rank P = 0.03). All distant failures (except one) occurred after focal RT2. Local failures after focal RT2 were predominantly in patients with less than GTR pre-RT2.

Conclusions
Patients with locally recurrent pediatric ependymoma should be considered for re-treatment with repeat maximal safe resection (ideally GTR) and CSI re-irradiation, with careful discussion of the potential side effects of these treatments.
What Helps and What Hinders the Creation of a Smoke-free Home: A Qualitative Study of Fathers in Scotland
Authors: O’Donnell Rachel , McCulloch Peter , Greaves Lorraine , Semple Sean , Amos Amanda 
Published: November 2021

Abstract

Introduction
Few studies have explored fathers’ views and experiences of creating a smoke-free home, with interventions largely targeting mothers. This study aimed to identify barriers and facilitators to fathers creating a smoke-free home, to inform future intervention development.

Methods
Eighteen fathers who were smokers and lived in Scotland were recruited from Dads’ community groups, Early Years Centres and through social media advertising. Semi-structured interviews explored their views and experiences of creating a smoke-free home. A theory-informed thematic analysis using the COM-B model highlighted ways in which capability, opportunity, and motivations shaped fathers’ home smoking behaviors.

Results
Several fathers understood the health risks of second-hand smoke exposure through public health messaging associated with recent smoke-free legislation prohibiting smoking in cars carrying children. Limited understanding of effective exposure reduction strategies and personal mental health challenges reduced some fathers’ ability to create a smoke-free home. Fathers were keen to maintain their smoke-free home rules, and their motivations for this largely centered on their perceived role as protector of their children, and their desire to be a good role model.

Conclusions
Fathers’ abilities to create a smoke-free home are shaped by a range of capabilities, opportunities, and motivations, some of which relate to their role as a father. Establishing a fuller understanding of the contextual and gender-specific factors that shape fathers’ views on smoking in the home will facilitate the development of interventions and initiatives that fathers can identify and engage with, for the broader benefit of families and to improve gender equity and health.

Implications
Our findings can inform future development of father-centered and household-level smoke-free home interventions. They identify fathers’ views and experiences and help reframe smoking in the home as a gendered family-wide issue, which is important in building consensus on how best to support parents to create a smoke-free home. Our findings highlight the need for additional research to develop understanding of the ways in which gender-related aspects of family structures, heterosexual relationships, and child living arrangements influence home smoking rules and how to tailor interventions accordingly.
Age-Related Interactions on Key Theoretical Determinants of Smoking Cessation: Findings from the ITC Four Country Smoking and Vaping Surveys (2016–2020)
Authors: Le Grande Michael , Borland Ron , Yong Hua-Hie , McNeill Ann , Fong Geoffrey , Cummings K Michael 
Published: November 2021

AbstractBackgroundThis paper explores whether plans to quit, wanting to quit, and quit efficacy add predictive value over measures of habit strength and dependence in making quit attempts and/or attaining smoking abstinence.Aims and MethodsWe used three waves of the International Tobacco Control (ITC) Four Country Smoking and Vaping Survey conducted in 2016, 2018, and 2020. Baseline daily smokers (N = 6710) who provided data for at least one wave-to-wave transition (W1 to W2, N = 3511 or W2 to W3, N = 3199) and provided outcome data at the next wave (follow-up) formed the analytic sample. Generalized estimating equations (GEE) logistic regression analyses examined predictors of quit attempts and abstinence at follow-up (1- and 6-month sustained abstinence).ResultsWanting and planning to quit were significantly positively associated with making quit attempts, but negatively associated with smoking abstinence. A significant interaction between the Heaviness of Smoking Index and age warranted an age-stratified analysis for both abstinence outcomes. Lower HSI predicted abstinence in only the younger smokers Motivation and plans to quit were positively associated with abstinence in younger smokers, but surprisingly were negatively associated with abstinence in older smokers. Quit efficacy was associated with abstinence in the older, but not the younger smokers.ConclusionsModels of smoking abstinence are significantly improved by including motivational predictors of smoking. Age was an important moderator of the association between abstinence for both dependence and motivational variables.ImplicationsThe findings from this large cohort study indicate there are age-related differences in predictors of smoking abstinence but not quit attempts. These associations may reflect differential experiences of older and younger cohorts of smokers, which may have implications for interventions to motivate and assist smokers in quitting.
A Measure of Illness Awareness in Individuals With Nicotine Dependence—Nicotine Use Awareness and Insight Scale
Authors: Kim Julia , Kambari Yasaman , Taggar Anmol , Quilty Lena C , Selby Peter , Caravaggio Fernando , Ueno Fumihiko , Song Jianmeng , Pollock Bruce G , Graff-Guerrero Ariel , Gerretsen Philip 
Published: November 2021

Abstract

Introduction
Impaired illness awareness or the inability to recognize that one has a dependence on nicotine may be a major barrier to seeking cessation treatment. To better understand the role of impaired illness awareness on treatment-seeking behavior and clinical outcomes, we developed and examined the psychometric properties of a novel scale measuring illness awareness in individuals with dependence on nicotine.

Aims and Methods
We developed the Nicotine Use Awareness and Insight Scale (NAS), a 7-item self-report measure to assess the theoretical construct of illness awareness in individuals with dependence on nicotine (www.illnessawarenessscales.com). Data from participants 18 years of age or older were collected via a web-based survey company, Dynata. Participants with moderate dependence on nicotine were included, defined by a score of four or more on the Fagerström Test for Cigarette Dependence (FTCD) or the FTCD adapted for electronic cigarettes (eFTCD).

Results
A total of 100 participants (mean [SD] age = 49.1 [16.1] years, 52% women) that met the inclusion criteria for either FTCD (n = 50) or eFTCD (n = 50) were included. The NAS demonstrated good convergent (r = .74, p &lt; .001) and discriminant validity (r = .03, p = .786). It also demonstrated good internal consistency (Cronbach’s alpha = 0.78) and one-month test-retest reliability (intra-class correlation = 0.86). An exploratory factor analysis yielded the retention of two components.

Conclusions
The NAS is a novel scale to asses illness awareness in individuals with dependence on nicotine. This study provides initial support for the psychometric validity and reliability of NAS.

Implications
The NAS may be used in research and clinical practice to evaluate the impact of impaired illness awareness on treatment-seeking behavior and clinical outcomes.
CFM6 is an Essential CRM Protein Required for the Splicing ofnad5Transcript in Arabidopsis Mitochondria
Authors: Lin Wei-Chih , Chen Ya-Huei , Gu Shin-Yuan , Shen Hwei-Ling , Huang Kai-Chau , Lin Wen-Dar , Chang Men-Chi , Chang Ing-Feng , Hong Chwan-Yang , Cheng Wan-Hsing 
Published: November 2021

AbstractPlant chloroplast RNA splicing and ribosome maturation (CRM)-domain-containing proteins are capable of binding RNA to facilitate the splicing of group I or II introns in chloroplasts, but their functions in mitochondria are less clear. In the present study, Arabidopsis thaliana CFM6, a protein with a single CRM domain, was expressed in most plant tissues, particularly in flower tissues, and restricted to mitochondria. Mutation of CFM6 causes severe growth defects, including stunted growth, curled leaves, delayed embryogenesis and pollen development. CFM6 functions specifically in the splicing of group II intron 4 of nad5, which encodes a subunit of mitochondrial complex I, as evidenced by the loss of nad5 intron 4 splicing and high accumulation of its pretranscripts in cfm6 mutants. The phenotypic and splicing defects of cfm6 were rescued in transgenic plants overexpressing 35S::CFM6-YFP. Splicing failure in cfm6 also led to the loss of complex I activity and to its improper assembly. Moreover, dysfunction of complex I induced the expression of proteins or genes involved in alternative respiratory pathways in cfm6. Collectively, CFM6, a previously uncharacterized CRM domain-containing protein, is specifically involved in the cis-splicing of nad5 intron 4 and plays a pivotal role in mitochondrial complex I biogenesis and normal plant growth.
Early Paleogene Magmatism in the Pinaleño Mountains, Arizona: Evidence for Crustal Melting of Diverse Basement Assemblages during the Laramide Orogeny
Authors: Scoggin Shane H , Chapman James B , Shields Jessie E , Trzinski Adam E , Ducea Mihai N 
Published: November 2021

AbstractGranitic rocks, interpreted to be related to crustal melting, were emplaced into regions of thickened crust in southern Arizona during the Laramide orogeny (80–40 Ma). Laramide-age anatectic rocks are exposed as plutons, sills, and dike networks that are commonly found in the exhumed footwalls of metamorphic core complexes. This study investigates newly discovered exposures of granodioritic–leucogranitic rocks from three intrusive phases in the footwall of the Pinaleño–Jackson Mountain metamorphic core complex of southeastern Arizona, called the Relleno suite. Zircon U–Pb geochronology indicates that the suite was emplaced from 58 to 52 Ma. Zircon Lu/Hf isotope geochemistry, whole-rock Sr and Nd isotope geochemistry, and mineral O isotope geochemistry were used to investigate the source of these rocks and evaluate whether they are related to crustal anatexis. Average zircon εHf(t) values of the suite range from −4.7 to −7.9, whole-rock εNd(i) and 87Sr/86Sr(i) values range from −9.4 to −11.8 and 0.7064 to 0.7094 respectively, and quartz δ18OVSMOW values range from 6.8 to 9.4 ‰. Isotopic and geochemical data of these rocks are consistent with derivation from and assimilation of intermediate–mafic (meta)igneous rocks, at deep crustal levels, and are supported by thermodynamic melt models of Proterozoic igneous rocks equivalent to those exposed in the Pinaleño Mountains. In comparison with other Laramide-age anatectic granites in SE Arizona, those exposed in the Pinaleño Mountains are temporally similar but present compositional and isotopic differences that reflect melting and assimilation of different lithologies, producing distinct mineralogical and isotopic characteristics. The results suggest that crustal melting during this interval was not limited to metasedimentary protoliths and may have affected large portions of the deep crust. The early Paleogene Relleno suite in the Pinaleño Mountains strengthens the relationship between crustal melting and regions of thickened crust associated with the Sevier and Laramide orogenies.
Use of Complementary and Integrative Health Therapies Before Intensive Functional Restoration in Active Duty Service Members with Chronic Pain
Authors: Flynn Diane M , McQuinn Honor , Burke Larisa , Steffen Alana , Fairchok Alexandra , Snow Tyler , Doorenbos Ardith Z 
Published: November 2021

Abstract

Objective
Psychosocial factors are known to predict chronic pain, and the use of complementary and integrative health (CIH) therapies to address pain is emerging among the military population. However, conflicting results on pain outcomes warrant additional research. This study aimed to 1) evaluate the benefit of adding a CIH pain management program to standard rehabilitative care (SRC), as compared with SRC alone, as a precursor to an intensive functional restoration (FR) program; 2) identify factors that predict improvement in pain outcomes after treatment; and 3) determine the proportion of participants who experience a clinically meaningful response.

Design
Pragmatic randomized controlled clinical trial. Participants were randomized to a 3-week course of either SRC alone or SRC+CIH (stage 1), followed by a 3- to 6-week course of FR (stage 2).

Subjects
Active duty service members with chronic pain.

Methods
Participants completed either SRC alone or SRC+CIH (stage 1), followed by a course of FR (stage 2). Patient-reported and provider-determined outcomes were collected at baseline, after stage 1, and after stage 2. A covariance pattern model with an unstructured residual covariance matrix was used to compare treatment arms while accounting for dependency due to repeated measurements.

Results
A total of 210 service members participated. Most were in the Army (82%) and were male (84%). Participants randomized to the SRC+CIH intervention had greater improvement in the pain impact score than did those in the SRC-alone group. Predictors of outcomes were baseline impact score, anger, depression, and educational status.

Conclusions
This study found that military service members with the highest pain impact benefit the most from interdisciplinary pain care.
mTOR activation in CD8+ cells contributes to disease activity of rheumatoid arthritis and increases therapeutic response to TNF inhibitors
Authors: Zhang Mingzeng , Iwata Shigeru , Sonomoto Koshiro , Ueno Masanobu , Fujita Yuya , Anan Junpei , Miyazaki Yusuke , Ohkubo Naoaki , Sumikawa Maiko Hajime , Todoroki Yasuyuki , Miyata Hiroko , Nagayasu Atsushi , Kanda Ryuichiro , Hao He , Trimova Gulzhan , Lee Seunghyun , Nakayamada Shingo , Sakata Kei , Tanaka Yoshiya 
Published: November 2021

AbstractObjectiveThis study aimed to understand the role of mammalian target of rapamycin (mTOR) in CD8+ cells in the pathogenicity of RA and the changes after treatment with biologic drugs.MethodsPeripheral blood mononuclear cells (PBMCs) were isolated from 17 healthy controls and 86 patients with RA. Phosphorylation of mTOR (p-mTOR) and its clinical relevance were evaluated. The role of mTOR in CD8+ cells was also examined in vitro.ResultsPatients with RA who had a moderate or high disease activity, were biologic-naïve, and were refractory to MTX were enrolled in this study. The p-mTOR levels in CD8+ cells were higher in patients with RA than in healthy controls, and they positively correlated with the disease activity in such patients. However, after one year of treatment with TNF inhibitors, the p-mTOR levels in CD8+ cells were suppressed and showed a positive correlation with the treatment response, which was not observed in the abatacept-treatment group. In vitro stimulation of CD8+ cells with anti-CD3 and anti-CD28 antibodies induced mTOR phosphorylation and increased the production of granzyme B, granulysin, TNF-α and IFN-γ but decreased the production of granzyme K. However, on treatment with TNF inhibitors, p-mTOR levels in CD8+ cells and granzyme B production decreased, while granzyme K production increased. The production of granulysin and IFN-γ was not affected by the TNF inhibitors.ConclusionThese results suggested that mTOR activation in CD8+ cells may be a novel evaluation marker for RA disease activity and a predictive marker of therapeutic response to TNF inhibitors.
Taking the pulse of science diplomacy and developing practices of valuation
Authors: Flink Tim 
Published: November 2021

AbstractScience diplomacy has caught remarkable attention in public policy and academic research over the last fifteen years. However, the concept is plagued by a huge talk–action discrepancy: its public discourse has reached a problematic state of dazzling self-adulation, while it is unclear if and how the actual policies and associated organizations live up to these expectations. The article reconstructs three structural causes to explain the recent hype about science diplomacy. It further encourages actors to organize evaluations that ask whether and how actions of science diplomacy can be valuable. In this regard, a first set of fundamental principles is proposed for setting up an evaluative framework. In conclusion, the article advises science diplomacy actors from democratic states and institutions, from both academic research and public policy, to stop dreaming about soft power influence on authoritarian states and regimes but rather face new geopolitical realities.
GoldBricks: an improved cloning strategy that combines features of Golden Gate and BioBricks for better efficiency and usability
Authors: Chaudhari Vishalsingh R , Hanson Maureen R 
Published: November 2021

Abstract
With increasing complexity of expression studies and the repertoire of characterized sequences, combinatorial cloning has become a common necessity. Techniques like BioBricks and Golden Gate aim to standardize and speed up the process of cloning large constructs while enabling sharing of resources. The BioBricks format provides a simplified and flexible approach to endless assembly with a compact library and useful intermediates but is a slow process, joining only two parts in a cycle. Golden Gate improves upon the speed with use of Type IIS enzymes and joins several parts in a cycle but requires a larger library of parts and logistical inefficiencies scale up significantly in the multigene format. We present here a method that provides improvement over these techniques by combining their features. By using Type IIS enzymes in a format like BioBricks, we have enabled a faster and efficient assembly with reduced scarring, which performs at a similarly fast pace as Golden Gate, but significantly reduces library size and user input. Additionally, this method enables faster assembly of operon-style constructs, a feature requiring extensive workaround in Golden Gate. Our format allows such inclusions resulting in faster and more efficient assembly.
Hidden Phylogenomic Signal Helps Elucidate Arsenurine Silkmoth Phylogeny and the Evolution of Body Size and Wing Shape Trade-Offs
Authors: Hamilton Chris A , Winiger Nathalie , Rubin Juliette J , Breinholt Jesse , Rougerie Rodolphe , Kitching Ian J , Barber Jesse R , Kawahara Akito Y 
Published: November 2021

Abstract
One of the key objectives in biological research is understanding how evolutionary processes have produced Earth’s diversity. A critical step toward revealing these processes is an investigation of evolutionary tradeoffs—that is, the opposing pressures of multiple selective forces. For millennia, nocturnal moths have had to balance successful flight, as they search for mates or host plants, with evading bat predators. However, the potential for evolutionary trade-offs between wing shape and body size are poorly understood. In this study, we used phylogenomics and geometric morphometrics to examine the evolution of wing shape in the wild silkmoth subfamily Arsenurinae (Saturniidae) and evaluate potential evolutionary relationships between body size and wing shape. The phylogeny was inferred based on 782 loci from target capture data of 42 arsenurine species representing all 10 recognized genera. After detecting in our data one of the most vexing problems in phylogenetic inference—a region of a tree that possesses short branches and no “support” for relationships (i.e., a polytomy), we looked for hidden phylogenomic signal (i.e., inspecting differing phylogenetic inferences, alternative support values, quartets, and phylogenetic networks) to better illuminate the most probable generic relationships within the subfamily. We found there are putative evolutionary trade-offs between wing shape, body size, and the interaction of fore- and hindwing (HW) shape. Namely, body size tends to decrease with increasing HW length but increases as forewing (FW) shape becomes more complex. Additionally, the type of HW (i.e., tail or no tail) a lineage possesses has a significant effect on the complexity of FW shape. We outline possible selective forces driving the complex HW shapes that make Arsenurinae, and silkmoths as a whole, so charismatic. [Anchored hybrid enrichment; Arsenurinae; geometric morphometrics; Lepidoptera; phylogenomics; Saturniidae.]