bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seven‐plus hours of daily sedentary time and the subsequent risk of breast cancer: Japan Multi‐Institutional Collaborative Cohort Study
Authors: Tomida Satomi , Koyama Teruhide , Ozaki Etsuko , Takashima Naoyuki , Morita Midori , Sakaguchi Koichi , Naoi Yasuto , Nishida Yuichiro , Hara Megumi , Hishida Asahi , Tamura Takashi , Okada Rieko , Kubo Yoko , Otonari Jun , Ikezaki Hiroaki , Nakamura Yohko , Kusakabe Miho , Tanoue Shiroh , Koriyama Chihaya , Koyanagi Yuriko N. , Ito Hidemi , Suzuki Sadao , Otani Takahiro , Miyagawa Naoko , Okami Yukiko , Arisawa Kokichi , Watanabe Takeshi , Kuriki Kiyonori , Wakai Kenji , Matsuo Keitaro 
Published: December 2023

AbstractThis study aimed to investigate the association between daily sedentary time and the risk of breast cancer (BC) in a large Japanese population. The participants were 36,023 women aged 35–69 years from the Japan Multi‐Institutional Collaborative Cohort Study. Cox proportional hazards analysis was used to estimate adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) for BC incidence in relation to time spent sedentarily (categorical variables: <7 and ≥7 hours/day [h/d]). Additionally, the associations of BC incidence to the joint effect of sedentary time with each component of physical activity, such as leisure‐time metabolic equivalents (METs), frequency of leisure‐time physical activity, and daily walking time, were examined. During 315,189 person‐years of follow‐up, 554 incident cases of BC were identified. When compared to participants who spent <7 h/d sedentary, those who spent ≥7 h/d sedentary have a significantly higher risk of BC (HR, 1.36; 95% CI, 1.07–1.71). The corresponding HRs among participants who spent ≥7 h/d sedentary with more physical activity, such as ≥1 h/d for leisure‐time METs, ≥3 days/week of leisure‐time physical activity, and ≥1 h/d of daily walking were 1.58 (95% CI, 1.11–2.25), 1.77 (95% CI, 1.20–2.61), and 1.42 (95% CI, 1.10–1.83), respectively, compared with those who spent <7 h/d sedentary. This study found that spending ≥7 h/d of sedentary time is associated with the risk of BC. Neither leisure‐time physical activity nor walking had a BC‐preventive effect in those with ≥7 h/d of sedentary time.
BRCA1/2 reversion mutations in a pan‐cancer cohort
Authors: Nakamura Kohei , Hayashi Hideyuki , Kawano Ryutaro , Ishikawa Marin , Aimono Eriko , Mizuno Takaaki , Kuroda Hajime , Kojima Yasuyuki , Niikura Naoki , Kawanishi Aya , Takeshita Kei , Suzuki Shinsuke , Ueno Shinichi , Okuwaki Kosuke , Sasaki Jiichiro , Yamaguchi Masatoshi , Masuda Kenta , Chiyoda Tatsuyuki , Yamagami Wataru , Okada Chihiro , Nohara Sachio , Tanishima Shigeki , Nishihara Hiroshi 
Published: December 2023

AbstractTumor sensitivity to platinum (Pt)‐based chemotherapy and poly(adenosine diphosphate ribose) polymerase (PARP) inhibitors is increased by homologous recombination deficiency‐causing mutations; in particular, reversion mutations cause drug resistance by restoring protein function. Treatment response is predicted by breast cancer susceptibility gene 1/2 (BRCA1/2) mutations; however, BRCA1/2 reversion mutations have not been comprehensively studied in pan‐cancer cohorts. We aimed to characterize BRCA1/2 reversion mutations in a large pan‐cancer cohort of Japanese patients by retrospectively analyzing sequencing data for BRCA1/2 pathogenic/likely pathogenic mutations in 3738 patients with 32 cancer types. We identified somatic mutations in tumors or circulating cell‐free DNA that could restore the ORF of adverse alleles, including reversion mutations. We identified 12 (0.32%) patients with somatic BRCA1 (n = 3) and BRCA2 (n = 9) reversion mutations in breast (n = 4), ovarian/fallopian tube/peritoneal (n = 4), pancreatic (n = 2), prostate (n = 1), and gallbladder (n = 1) cancers. We identified 21 reversion events—BRCA1 (n = 3), BRCA2 (n = 18)—including eight pure deletions, one single‐nucleotide variant, six multinucleotide variants, and six deletion–insertions. Seven (33.3%) reversion deletions showed a microhomology length greater than 1 bp, suggesting microhomology‐mediated end‐join repair. Disease course data were obtained for all patients with reversion events: four patients acquired mutations after PARP‐inhibitor treatment failure, two showed somatic reversion mutations after disease progression, following Pt‐based treatment, five showed mutations after both treatments, one patient with pancreatic cancer and BRCA1 reversion mutations had no history of either treatment. Although reversion mutations commonly occur in BRCA‐associated cancers, our findings suggest that reversion mutations due to Pt‐chemotherapy might be correlated with BRCA1/2‐mediated tumorigenesis even in non‐BRCA‐associated histologies.
Younger, not older, children trust an inaccurate human informant more than an inaccurate robot informant
Authors: Li Xiaoqian , Yow W. Quin 
Published: December 2023

AbstractThis study examined preschoolers' trust toward accurate and inaccurate robot informants versus human informants. Singaporean children aged 3–5 years (N = 120, 57 girls, mostly Asian; data collected from 2017 to 2018) viewed either a robot or a human adult label familiar objects either accurately or inaccurately. Children's trust was assessed by examining their subsequent willingness to accept novel object labels provided by the same informant. Regardless of age, children trusted accurate robots to a similar extent as accurate humans. However, while older children (dis)trusted inaccurate robots and humans comparably, younger children trusted inaccurate robots less than inaccurate humans. The results indicate a developmental change in children's reliance on informants' characteristics to decide whom to trust.
Characterization of D4Z4 alleles and assessment of de novo cases in Facioscapulohumeral dystrophy (FSHD) in a cohort of Italian families
Authors: Strafella Claudia , Colantoni Luca , Megalizzi Domenica , Trastulli Giulia , Piorgo Emma Proietti , Primiano Guido , Sancricca Cristina , Ricci Giulia , Siciliano Gabriele , Caltagirone Carlo , Filosto Massimiliano , Tasca Giorgio , Ricci Enzo , Cascella Raffaella , Giardina Emiliano 
Published: December 2023

AbstractFacioscapulohumeral dystrophy (FSHD) is an autosomal dominant disease, although 10%–30% of cases are sporadic. However, this percentage may include truly de novo patients (carrying a reduced D4Z4 allele that is not present in either of the parents) and patients with apparently sporadic disease resulting from mosaicism, non‐penetrance, or complex genetic situations in either patients or parents. In this study, we characterized the D4Z4 Reduced Alleles (DRA) and evaluated the frequency of truly de novo cases in FSHD1 in a cohort of DNA samples received consecutively for FSHD‐diagnostic from 100 Italian families. The D4Z4 testing revealed that 60 families reported a DRA compatible with FSHD1 (1–10 RU). The DRA co‐segregated with the disease in most cases. Five families with truly de novo cases were identified, suggesting that this condition may be slightly lower (8%) than previously reported. In addition, D4Z4 characterization in the investigated families showed 4% of mosaic cases and 2% with translocations. This study further highlighted the importance of performing family studies for clarifying apparently sporadic FSHD cases, with significant implications for genetic counseling, diagnosis, clinical management, and procreative choices for patients and families.
ONTbarcoder 2.0: rapid species discovery and identification with real‐time barcoding facilitated by Oxford Nanopore R10.4
Authors: Srivathsan Amrita , Feng Vivian , Suárez Daniel , Emerson Brent , Meier Rudolf 
Published: December 2023

AbstractMost arthropod species are undescribed and hidden in specimen‐rich samples that are difficult to sort to species using morphological characters. For such samples, sorting to putative species with DNA barcodes is an attractive alternative, but needs cost‐effective techniques that are suitable for use in many laboratories around the world. Barcoding using the portable and inexpensive MinION sequencer produced by Oxford Nanopore Technologies (ONT) could be useful for presorting specimen‐rich samples with DNA barcodes because it requires little space and is inexpensive. However, similarly important is user‐friendly and reliable software for analysis of the ONT data. It is here provided in the form of ONTbarcoder 2.0 that is suitable for all commonly used operating systems and includes a Graphical User Interface (GUI). Compared with an earlier version, ONTbarcoder 2.0 has three key improvements related to the higher read quality obtained with ONT's latest flow cells (R10.4), chemistry (V14 kits) and basecalling model (super‐accuracy model). First, the improved read quality of ONT's latest flow cells (R10.4) allows for the use of primers with shorter indices than those previously needed (9 bp vs. 12–13 bp). This decreases the primer cost and can potentially improve PCR success rates. Second, ONTbarcoder now delivers real‐time barcoding to complement ONT's real‐time sequencing. This means that the first barcodes are obtained within minutes of starting a sequencing run; i.e. flow cell use can be optimized by terminating sequencing runs when most barcodes have already been obtained. The only input needed by ONTbarcoder 2.0 is a demultiplexing sheet and sequencing data (raw or basecalled) generated by either a Mk1B or a Mk1C. Thirdly, we demonstrate that the availability of R10.4 chemistry for the low‐cost Flongle flow cell is an attractive option for users who require only 200–250 barcodes at a time.
Additional Cover
Authors: Lyu Chunzi , Ni Tianxiang , Guo Yaqiu , Zhou Tingting , Chen Zi‐Jiang , Yan Junhao , Li Yan 
Published: December 2023

The cover image is based on the Original Article Insufficient GDF15 expression predisposes women to unexplained recurrent pregnancy loss by impairing extravillous trophoblast invasion by Chunzi Lyu et al., https://doi.org/10.1111/cpr.13514.
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Administrative coding of frailty: Its association with clinical outcomes and resource use in kidney transplantation
Authors: Mallick Saad , Sakowitz Sara , Bakhtiyar Syed Shahyan , Chervu Nikhil , Valenzuela Alberto , Kim Shineui , Benharash Peyman 
Published: December 2023

AbstractIntroductionAlthough not formalized into current risk assessment models, frailty has been associated with negative postoperative outcomes in many specialties. However, national analyses of the association between frailty and post‐transplant outcomes following kidney transplantation (KT) are lacking.MethodsThis was a retrospective cohort study of adults undergoing KT from 2016 to 2020 in the Nationwide Readmissions Databases. Frailty was defined using the Johns Hopkins Adjusted Clinical Groups frailty indicator.ResultsOf an estimated 95 765 patients undergoing KT during the study period, 4918 (5.1%) were frail. After risk adjustment, frail patients were associated with significantly higher odds of in‐hospital mortality (AOR 2.17, 95% CI: 1.33–3.57) compared to their non‐frail counterparts. Our findings indicate that frail patients had an average increase in postoperative hospital stay of 1.44 days, a $2300 increase in hospitalization costs, as well as higher odds of developing a major perioperative complication as compared to their non‐frail counterparts. Frailty was also associated with greater adjusted risk of non‐home discharge.ConclusionsFrailty, as identified by administrative coding, is independently associated with worse surgical outcomes, including increased mortality and resource use, in adults undergoing KT. Given the already limited donor organ pool, novel efforts are needed to ensure adequate optimization and timely post‐transplantation care of the growing frail cohort undergoing KT.
Day 100 Natural Killer Cell/CD14+HLA‐DRDIMratio and survival in lymphoma post‐autologous peripheral blood hematopoietic stem cell transplantation
Authors: Porrata Luis F. , Ansell Stephen M. , Micallef Ivana N. , Johnston Patrick B. , Villasboas Jose C. , Paludo Jonas , Durani Urshila , Markovic Svetomir N. 
Published: December 2023

AbstractIntroductionThe infusion of autograft Natural Killer Cells (NKC)/CD14+HLA‐DRDIMratio is a predictor of survival in lymphoma patients undergoing autologous peripheral blood hematopoietic stem cell transplantation (APBHSCT). This study evaluated if the Day 100 NKC/CD14+HLA‐DRDIMratio still functions as a prognostic immune‐biomarker.MethodsThis was a retrospective, single‐institution, cohort analysis including 107 patients in this study that had clinical assessment at Day 100 post‐APBHSCT from our prior phase III trial. We evaluated the prognostic ability of the Day 100 NKC/CD14+HLA‐DRDIMratio to predict overall survival (OS) and progression‐free survival (PFS) using Cox regression model for outcome analysis and survival by Kaplan–Meier method.ResultsThe median follow‐up from day 100 was 94.7 months (range 4.83–158.1 months) for the entire cohort. Patients with a Day 100 NKC/CD14+HLA‐DRDIMratio ≥1.67 experienced better OS and PFS versus those with a Day 100 NKC/CD14+HLA‐DRDIMratio <1.67: median OS was not reached versus 49.7 months, the 5‐year OS rates were 91% (95% CI, 81%–96%) versus 40% (95% CI, 27%–55%),p < .0001, respectively; and median PFS was not reached versus 23.5 months, the 5‐year PFS rates were 66% (95% CI, 55%–81%) versus 21% (95% CI, 15%–40%),p < .0001, respectively. Day 100 NKC/CD14+HLA‐DRDIMratio was an independent predictor for OS and PFS in the multivariate analysis.ConclusionsDay 100 NKC/CD14+HLA‐DRDIMratio is a prognostic immune‐biomarker in lymphoma patients post‐ APBHSCT.
Utilizing geometric morphometrics to investigate gene function during organ growth: Insights through the study of beetle horn shape allometry
Authors: Rohner Patrick T. , Hu Yonggang , Moczek Armin P. 
Published: December 2023

AbstractStatic allometry is a major component of morphological variation. Much of the literature on the development of allometry investigates how functional perturbations of diverse pathways affect the relationship between trait size and body size. Often, this is done with the explicit objective to identify developmental mechanisms that enable the sensing of organ size and the regulation of relative growth. However, changes in relative trait size can also be brought about by a range of other distinctly different developmental processes, such as changes in patterning or tissue folding, yet standard univariate biometric approaches are usually unable to distinguish among alternative explanations. Here, we utilize geometric morphometrics to investigate the degree to which functional genetic manipulations known to affect the size of dung beetle horns also recapitulate the effect of horn shape allometry. We reasoned that the knockdown phenotypes of pathways governing relative growth should closely resemble shape variation induced by natural allometric variation. In contrast, we predicted that if genes primarily affect alternative developmental processes, knockdown effects should align poorly with shape allometry. We find that the knockdown effects of several genes (e.g., doublesex, Foxo) indeed closely aligned with shape allometry, indicating that their corresponding pathways may indeed function primarily in the regulation of relative trait growth. In contrast, other knockdown effects (e.g., Distal‐less, dachs) failed to align with allometry, implicating these pathways in potentially scaling‐independent processes. Our findings moderate the interpretation of studies focusing on trait length and highlight the usefulness of multivariate approaches to study allometry and phenotypic plasticity.
‘The same contract that is suitable for your Excellency’: Immigration and emulation in the adoption of sharecropping‐cum‐debt arrangements in Brazil (1835‒80)
Authors: Witzel de Souza Bruno Gabriel 
Published: December 2023

AbstractThis paper studies the history of contractual choice in coffee plantations of São Paulo, Brazil. It focuses on the consolidation of non‐captive labour markets in the early phases of the transition from slavery in the country, particularly in the 1840s–50s. Vis‐à‐vis the alternatives of fixed rents and fixed payments per time worked or piece rates, the paper examines the rationale for the adoption of sharecropping arrangements with European bonded labourers. New archival evidence suggests that sharecropping had no obvious productivity advantage over alternative labour–rental arrangements in this period, and that the adoption of sharecropping arrangements resulted from the positional advantage of its first proposers, who influenced later choices of contractual design. A credit‐labour tie‐up long outlived the original sharecropping arrangements, in turn allowing for the immigration of poor and credit‐constrained Europeans, paving the way to insert Brazil into the circuits of mass migration without promoting institutional reforms to attract non‐bonded immigrants.
Pharmacokinetics of d‐ and l‐norfenfluramine following their administration as individual enantiomers in rats
Authors: Erenburg Natalia , Hamed Roa'a , Shaul Chanan , Barasch Dinorah , Perucca Emilio , Bialer Meir 
Published: December 2023

AbstractThe effect of fenfluramine and norfenfluramine enantiomers in rodent seizure models and their correlation with the pharmacokinetics of d‐ and l‐fenfluramine in rats have been reported recently. To complement these findings, we investigated the pharmacokinetics of d‐ and l‐ norfenfluramine in rat plasma and brain. Sprague‐Dawley rats were injected intraperitoneally with 20 mg/kg and 1 mg/kg l‐ norfenfluramine. A 1 mg/kg dose of d‐norfenfluramine was used because higher doses caused severe toxicity. The concentration of each enantiomer in plasma and brain was determined at different time points by liquid chromatography/mass spectrometry. Pharmacokinetic parameters were compared between norfenfluramine enantiomers, and with those reported previously for fenfluramine enantiomers after a 20 mg/kg, i.p., dose. All enantiomers were absorbed rapidly and eliminated, with half‐lives ranging from 0.9 h (l‐fenfluramine) to 6.1 h (l‐ norfenfluramine, 20 mg/kg) in plasma, and from 3.6 h (d‐fenfluramine) to 8.0 h (l‐fenfluramine) in brain. Brain‐to‐plasma concentration ratios ranged from 15.4 (d‐fenfluramine) to 27.6 (d‐norfenfluramine), indicating extensive brain penetration. The fraction of d‐ and l‐fenfluramine metabolized to norfenfluramine was estimated to be close to unity. This work is part of ongoing investigations to determine the potential value of developing enantiomerically pure l‐fenfluramine or l‐norfenfluramine as follow‐up compounds to the marketed racemic fenfluramine.
Effect of Bacille‐Calmette‐Guerin vaccine against rotenone‐induced Parkinson's disease: Role of neuroinflammation and neurotransmitters
Authors: Yedke Narhari Gangaram , Soni Divya , Kumar Puneet 
Published: December 2023

AbstractBackgroundParkinson's disease (PD) is an extrapyramidal movement disorder associated with a hypokinetic condition generated by impairment in dopaminergic neuronal viability in the nigrostriatal region of the brain. Current medications can only provide symptomatic management; to date, no permanent cure is available. To compensate for this lacuna, researchers are gaining interest in antigen‐based therapy, and Bacille‐Calmette‐Guerin (BCG) is one of the vaccines with a high safety margin that acts by stimulating immunoreactive T‐cells in the CNS and reducing expression of pro‐inflammatory cytokines including interleukin (IL)‐1β and tumor necrotic factor (TNF‐α) to produce neuroprotection. A previous study reported that BCG exerts a neuroprotective effect against several neurodegenerative disorders, such as Alzheimer's disease.ObjectiveThe objective of this study is to explore the neuroprotective effect of the BCG vaccine against the rotenone model of PD.MethodsRotenone (1.5 mg/kg, s.c) for 28 days, and BCG vaccine (2 × 107 cfu, i.p) single dose was injected to rats, and behavioral assessments were performed on the 21st and 28th day. On the 29th day, rats were sacrificed, and brains were isolated for biochemical and neurochemical estimation.ResultsBCG vaccine significantly restored rotenone‐induced motor deficits (open field test, narrow beam walk, and rotarod), biochemical levels (GSH, SOD, catalase, MDA, and nitrite), neurotransmitters (dopamine, 5‐hydroxy tryptamine, norepinephrine, 3,4‐dihydroxyphenylacetic acid, hemovanillic acid, and 5‐hydroxy indoleacetic acid), and levels of inflammatory cytokines (IL‐1β and TNF‐α) in the striatum. It also prevents histopathological changes by reducing eosinophilic lesions in the striatum.ConclusionFrom the results, we conclude that BCG vaccine showed neuroprotection through antioxidant and anti‐inflammatory effect. Thus, in the future, it can be used as a neuroprotective agent for other neurological disorders, including PD.
Community size‐spectra applied to recreational freshwater fisheries in Puerto Rican reservoirs
Authors: Murry Brent A. , Olmeda María de Lourdes , Lilyestrom Craig , Adams Daniel S. , Adase Katherine , García‐Bermudez Miguel 
Published: December 2023

AbstractWe developed a management framework based on community size‐spectra (CSS) to establish targets to maximize desirable gamefish. We evaluated the influence of relative abundance of fish functional groups and watershed characteristics on the slope of the CSS or ecological efficiency. Both ecological efficiency and capacity were strongly influenced by relative abundance of fish functional groups and the degree of water level variation. Steeper slopes indicated overfished gamefish populations, whereas flatter slopes indicated systems dominated by undesirable invasive large‐bodied low trophic position fish. We hypothesize that a desirable fishery would have a target range of CSS slopes that provides a deterministic community‐based framework of predictable responses to environmental and food web changes that can be used to evaluate outcomes of management actions and a means to assess annual progress toward desirable conditions.
How much organic carbon could the soil store? The carbon sequestration potential of Australian soil
Authors: Viscarra Rossel R. A. , Webster R. , Zhang M. , Shen Z. , Dixon K. , Wang Y.‐P. , Walden L. 
Published: December 2023

AbstractSoil is a huge carbon (C) reservoir, but where and how much extra C can be stored is unknown. Current methods to estimate the maximum amount of mineral‐associated organic carbon (MAOC) stabilized in the fine fraction (clay + silt, ) fit through the MAOC versus clay + silt relationship, not their maxima, making their estimates more uncertain and unreliable. We need a function that ‘envelopes’ that relationship. Here, using 5089 observations, we estimated that the uppermost 30 cm of Australian soil holds 13 Gt (10–18 Gt) of MAOC. We then fitted frontier lines, by soil type, to the relationship between MAOC and the percentage of clay + silt to estimate the maximum amounts of MAOC that Australian soils could store in their current environments, and calculated the MAOC deficit, or C sequestration potential. We propagated the uncertainties from the frontier line fitting and mapped the estimates of these values over Australia using machine learning and kriging with external drift. The maps show regions where the soil is more in MAOC deficit and has greater sequestration potential. The modelling shows that the variation over the whole continent is determined mainly by climate, linked to vegetation and soil mineralogy. We find that the MAOC deficit in Australian soil is 40 Gt (25–60 Gt). The deficit in the vast rangelands is 20.84 Gt (13.97–29.70 Gt) and the deficit in cropping soil is 1.63 Gt (1.12–2.32 Gt). Management could increase C sequestration in these regions if the climate allowed it. Our findings provide new information on the C sequestration potential of Australian soils and highlight priority regions for soil management. Australia could benefit environmentally, socially and economically by unlocking even a tiny portion of its soil's C sequestration potential.