bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beta vulgaris ssp. vulgaris chromosome 8 shows significant association with geosmin concentration in table beet
Authors: Hanson Solveig J , Dawson Julie C , Goldman Irwin L 
Published: September 2021

Abstract
Geosmin, a degraded sesquiterpene molecule with earthy and musty odor, imbues table beet with its characteristic aroma. Geosmin is heritable and endogenously produced in table beet; its earthy aroma is sought by some consumers but deters others. Geosmin biosynthesis is catalyzed by a bifunctional geosmin synthase enzyme in diverse bacteria and fungi, but a mechanism for geosmin biosynthesis in plants has not been reported. This work employed association analysis and selective genotyping of a segregating F2:3 mapping population to seek QTL associated with geosmin concentration in table beet. GBS reads were aligned to sugar beet reference genome EL10.2, and association analysis revealed two QTL for geosmin concentration on Beta vulgaris ssp. vulgaris chromosome 8. QTL at EL10.2 positions 28,017,624 and 38,488,687 each show effect size 8.7 μg·kg-1 geosmin and explain 8.5% and 6.4% of total variation in geosmin concentration, respectively. Resolution was low due to large recombination bin size and imperfect alignment between the reference genome and mapping population, but population size and selection proportion were sufficient to detect moderate to large effect QTL. This study, the first molecular genetic mapping experiment in table beet, succeeded in finding QTL for geosmin concentration in table beet, and it provides the basis for fine mapping or candidate gene investigation of functional loci for this distinctive sensory trait.
SCIGA: Software for large-scale, single-cell immunoglobulin repertoire analysis
Authors: Ye Haocheng , Cheng Lin , Ju Bin , Xu Gang , Liu Yang , Zhang Shuye , Wang Lifei , Zhang Zheng 
Published: September 2021

Abstract

Background
B-cell immunoglobulin repertoires with paired heavy and light chain can be determined by means of 10X single-cell V(D)J sequencing. Precise and quick analysis of 10X single-cell immunoglobulin repertoires remains a challenge owing to the high diversity of immunoglobulin repertoires and a lack of specialized software that can analyze such diverse data.

Findings
In this study, specialized software for 10X single-cell immunoglobulin repertoire analysis was developed. SCIGA (Single-Cell Immunoglobulin Repertoire Analysis) is an easy-to-use pipeline that performs read trimming, immunoglobulin sequence assembly and annotation, heavy and light chain pairing, statistical analysis, visualization, and multiple sample integration analysis, which is all achieved by using a 1-line command. Then SCIGA was used to profile the single-cell immunoglobulin repertoires of 9 patients with coronavirus disease 2019 (COVID-19). Four neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified from these repertoires.

Conclusions
SCIGA provides a complete and quick analysis for 10X single-cell V(D)J sequencing datasets. It can help researchers to interpret B-cell immunoglobulin repertoires with paired heavy and light chain.
The potential for mitigation of methane emissions in ruminants through the application of metagenomics, metabolomics, and other -OMICS technologies
Authors: Asselstine Victoria , Lam Stephanie , Miglior Filippo , Brito Luiz F , Sweett Hannah , Guan Leluo , Waters Sinead M , Plastow Graham , Cánovas Angela 
Published: September 2021

Abstract
Ruminant supply chains contribute 5.7 gigatons of CO2-eq per annum, which represents approximately 80% of the livestock sector emissions. One of the largest sources of emission in the ruminant sector is methane (CH4), accounting for approximately 40% of the sectors total emissions. With climate change being a growing concern, emphasis is being put on reducing greenhouse gas emissions, including those from ruminant production. Various genetic and environmental factors influence cattle CH4 production, such as breed, genetic makeup, diet, management practices, and physiological status of the host. The influence of genetic variability on CH4 yield in ruminants indicates that genomic selection for reduced CH4 emissions is possible. Although the microbiology of CH4 production has been studied, further research is needed to identify key differences in the host and microbiome genomes and how they interact with one another. The advancement of “-omics” technologies, such as metabolomics and metagenomics, may provide valuable information in this regard. Improved understanding of genetic mechanisms associated with CH4 production and the interaction between the microbiome profile and host genetics will increase the rate of genetic progress for reduced CH4 emissions. Through a systems biology approach, various “-omics” technologies can be combined to unravel genomic regions and genetic markers associated with CH4 production, which can then be used in selective breeding programs. This comprehensive review discusses current challenges in applying genomic selection for reduced CH4 emissions, and the potential for “-omics” technologies, especially metabolomics and metagenomics, to minimize such challenges. The integration and evaluation of different levels of biological information using a systems biology approach is also discussed, which can assist in understanding the underlying genetic mechanisms and biology of CH4 production traits in ruminants and aid in reducing agriculture’s overall environmental footprint.
Structure of the Acinetobacter baumannii PmrA receiver domain and insights into clinical mutants affecting DNA binding and promoting colistin resistance
Authors: Palethorpe Samantha , Milton Morgan E , Pesci Everett C , Cavanagh John 
Published: September 2021

Abstract
Acinetobacter baumannii is an insidious emerging nosocomial pathogen that has developed resistance to all available antimicrobials, including the last resort antibiotic, colistin. Colistin resistance often occurs due to mutations in the PmrAB two-component regulatory system. To better understand the regulatory mechanisms contributing to colistin resistance, we have biochemically characterized the A. baumannii PmrA response regulator. Initial DNA-binding analysis shows that A. baumannii PmrA bound to the Klebsiella pneumoniae PmrA box motif. This prompted analysis of the putative A. baumannii PmrAB regulon that indicated that the A. baumannii PmrA consensus box is 5′-HTTAAD N5 HTTAAD. Additionally, we provide the first structural information for the A. baumannii PmrA N-terminal domain through X-ray crystallography and we present a full-length model using molecular modelling. From these studies, we were able to infer the effects of two critical PmrA mutations, PmrA::I13M and PmrA::P102R, both of which confer increased colistin resistance. Based on these data, we suggest structural and dynamic reasons for how these mutations can affect PmrA function and hence encourage resistive traits. Understanding these mechanisms will aid in the development of new targeted antimicrobial therapies.
Late Eocene Two-Pyroxene Trachydacites from the Southern Qiangtang Terrane, Central Tibetan Plateau: High-Temperature Melting of Overthickened and Dehydrated Lower Crust
Authors: Zeng Yun-Chuan , Xu Ji-Feng , Li Ming-Jian , Chen Jian-Lin , Wang Bao-Di , Huang Feng , Ren Shu-Hui 
Published: September 2021

AbstractOrthopyroxene-bearing granitic rock (e.g. charnockite) is relatively rare but provides an excellent opportunity to probe the thermal and tectonic evolution of deep orogenic crust because of its distinct mineral assemblage. Here we present petrological, mineralogical, elemental, and Sr–Nd–Hf–O isotopic data for late Eocene (ca. 36 Ma; zircon U–Pb ages) volcanic rocks exposed in the Ejiu region in the southern Qiangtang Terrane to investigate how the central Tibetan crust evolved to its modern thickness and thermal state. The Ejiu volcanic rocks (EVRs) are trachydacites with anhydrous mineral assemblages (i.e. two pyroxenes, sanidine, plagioclase, and ilmenite, without amphibole and biotite) and geochemical characteristics (e.g. high P2O5 and TiO2) that resemble those of charnockite-type magmatic rocks. Mineral and whole-rock thermometry and hygrometry suggests that the parent magma crystallized under hot (~1000°C) and dry (H2O &lt; 2 wt.%) condition. Besides, the EVRs display adakitic affinities according to their high SiO2 and Al2O3 contents, high Sr/Y, La/Yb, and Gd/Yb ratios, and low Y and Yb contents, without marked negative Eu anomalies. The calculated melts in equilibrium with pyroxenes also display adakitic compositions (e.g. high Sr/Y and La/Yb ratios), indicating that the adakitic compositions of the EVRs did not result from late-stage magmatic evolution. In addition, the melts of the EVRs were saturated in TiO2, as inferred from the high TiO2 contents of these rocks and the presence of ilmenite. An integrated analysis of the geochemical, petrological, and mineralogical data suggests that the EVRs were neither evolutional products nor partial melts of hydrous mafic materials at normal crustal pressures, but were formed by fusion of an eclogitized mafic protolith with residue containing garnet and rutile but lacking amphibole and plagioclase. The whole-rock Sr–Nd and zircon Hf isotope compositions of the EVRs [(87Sr/86Sr)i = 0.7053 to 0.7066; εNd(t) = −1.40 to −0.99; zircon εHf(t) = +1.08 to +5.31] indicate that the parental protolith was relatively juvenile in nature, but also contained some supracrustal materials given the high zircon δ18O values [zircon δ18O = +8.21‰ to +11.00‰]. The above arguments lead us to propose that of partial melting of a previously dehydrated—but chemically undepleted—mafic lower continental crust at high pressure (&gt;1.5 GPa) and high temperature (&gt;1000°C) generated the EVRs. Based on a synthesis of independent geological and geophysical data, we further suggest that the southern Qiangtang Terrane crust of the central Tibetan Plateau was thick, dry, and elevated during the Late Cretaceous to early Eocene time, and that it became abnormally hot owing to the ascending asthenosphere after lithospheric foundering during the middle Eocene.
Existence of core excited 8Be* =α+α* cluster structure inα+αscattering
Authors: Hirabayashi Yoshiharu , Ohkubo Shigeo 
Published: September 2021

AbstractWe show the existence of the $\alpha+\alpha^*$ cluster structure at the highly excited energy around $E_x=20$ MeV in $^{8}$Be for the first time in the coupled-channel calculations. An extended double-folding model derived using a realistic precise cluster wave function with a well-developed $N+3N$ cluster structure for the first excited state of $^4$He was employed. The calculation reproduces the experimental phase shifts in $\alpha + \alpha$ scattering up to $E_{\rm c.m.}=21$ MeV well. The result shows that the well-developed core-excited $\alpha+\alpha^*$ structure appears as resonances for $L=0$ and $2$ near the $\alpha+\alpha^*$ threshold which correspond to the experimental states at $E_x=20.20$ MeV and $E_x=22.24$ MeV in $^8$Be.
Excluding beneficiaries: a decision not to be taken lightly
Authors: Goldstein Claire , McKenzie André 
Published: September 2021

Abstract
The power to exclude beneficiaries is a little different from other powers given to trustees which must all be exercised in the best interests of the beneficiaries. In the case of exclusion, however, it will not in general, for obvious reasons, be in the interests of the person being excluded (except where there is a fiscal advantage to that person in the exclusion). Instead it may be exercised in the interests of the remaining beneficiaries, will be distinctly averse to the interests of the beneficiary being excluded and once the beneficiary has been excluded he can take no further interest under the settlement (although, of course, the precise scope of the exclusion will depend upon the terms of the power). The trustee is therefore under an obligation to properly consider the position of the person being excluded and as with all powers conveyed on a trustee, the power must be exercised carefully and not capriciously or in bad faith.
Production of Agrocinopine A by Ipomoea batatas Agrocinopine Synthase in Transgenic Tobacco and Its Effect on the Rhizosphere Microbial Community
Authors: Tanaka Aiko , Ryder Maarten H. , Suzuki Takamasa , Uesaka Kazuma , Yamaguchi Nobuo , Amimoto Tomoko , Otani Motoyasu , Nakayachi Osamu , Arakawa Kenji , Tanaka Nobukazu , Takemoto Daigo 
Published: September 2021

Agrobacterium tumefaciens is a bacterial pathogen that causes crown gall disease on a wide range of eudicot plants by genetic transformation. Besides T-DNA integrated by natural transformation of plant vegetative tissues by pathogenic Agrobacterium spp., previous reports have indicated that T-DNA sequences originating from an ancestral Agrobacterium sp. are present in the genomes of all cultivated sweet potato (Ipomoea batatas) varieties analyzed. Expression of an Agrobacterium-derived agrocinopine synthase (ACS) gene was detected in leaf and root tissues of sweet potato, suggesting that the plant can produce agrocinopine, a sugar-phosphodiester opine considered to be utilized by some strains of Agrobacterium spp. in crown gall. To validate the product synthesized by Ipomoea batatas ACS (IbACS), we introduced IbACS into tobacco under a constitutive promoter. High-voltage paper electrophoresis followed by alkaline silver nitrate staining detected the production of an agrocinopine-like substance in IbACS1-expressing tobacco, and further mass spectrometry and nuclear magnetic resonance analyses of the product confirmed that IbACS can produce agrocinopine A from natural plant substrates. The partially purified compound was biologically active in an agrocinopine A bioassay. A 16S ribosomal RNA amplicon sequencing and meta-transcriptome analysis revealed that the rhizosphere microbial community of tobacco was affected by the expression of IbACS. A new species of Leifsonia (actinobacteria) was isolated as an enriched bacterium in the rhizosphere of IbACS1-expressing tobacco. This Leifsonia sp. can catabolize agrocinopine A produced in tobacco, indicating that the production of agrocinopine A attracts rhizosphere bacteria that can utilize this sugar-phosphodiester. These results suggest a potential role of IbACS conserved among sweet potato cultivars in manipulating their microbial community. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Validation of the Short-Form Reproductive Coercion Scale With Appalachian Women
Authors: Swan Laura E. T. , Hales Travis , Ely Gretchen E. , Auerbach Samantha L. , Agbemenu Kafuli 
Published: September 2021

(Abstracted from Contraception 2021;104:265–270)
Reproductive coercion is a collection of behaviors intended to maintain power and control in a relationship, typically perpetuated by an intimate partner by interfering with autonomous reproductive decision making. Pregnancy coercion is a form of reproductive coercion wherein threats and pressuring behaviors are exhibited to promote pregnancy.
Maternal Oxygen Supplementation Compared With Room Air for Intrauterine Resuscitation: A Systematic Review and Meta-analysis
Authors: Raghuraman Nandini , Temming Lorene A. , Doering Michelle M. , Stoll Carolyn R. , Palanisamy Arvind , Stout Molly J. , Colditz Graham A. , Cahill Alison G. , Tuuli Methodius G. 
Published: September 2021

(Abstracted from JAMA Pediatr 2021;175:368–376)
In the United States, 2 of 3 pregnant women receive oxygen supplementation at some point during labor. It is provided to increase placental oxygen transfer and prevent neonatal acidemia when fetal heart rate (FHR) tracings suggest fetal hypoxia.
Ursodeoxycholic Acid in Intrahepatic Cholestasis of Pregnancy: A Systematic Review and Individual Participant Data Meta-analysis
Authors: Ovadia Caroline , Sajous Jenna , Seed Paul T. , Patel Kajol , Williamson Nicholas J. , Attilakos George , Azzaroli Francesco , Bacq Yannick , Batsry Linoy , Broom Kelsey , Brun-Furrer Romana , Bull Laura , Chambers Jenny , Cui Yue , Ding Min , Dixon Peter H. , Estiú Maria C. , Gardiner Fergus W. , Geenes Victoria , Grymowicz Monika , Günaydin Berrin , Hague William M. , Haslinger Christian , Hu Yayi , Indraccolo Ugo , Juusela Alexander , Kane Stefan C. , Kebapcilar Ayse , Kebapcilar Levent , Kohari Katherine , Kondrackienė Jūratė , Koster Maria P. H. , Lee Richard H. , Liu Xiaohua , Locatelli Anna , Macias Rocio I. R. , Madazli Riza , Majewska Agata , Maksym Kasia , Marathe Jessica A. , Morton Adam , Oudijk Martijn A. , Öztekin Deniz , Peek Michael J. , Shennan Andrew H. , Tribe Rachel M. , Tripodi Valeria , Özterlemez Naciye Türk , Vasavan Tharni , Wong L. F. Audris , Yinon Yoav , Zhang Qianwen , Zloto Keren , Marschall Hanns-Ulrich , Thornton Jim , Chappell Lucy C. , Williamson Catherine 
Published: September 2021

(Abstracted from Lancet Gastroenterol Hepatol 2021;6:547–558)
Ursodeoxycholic acid (UA) is a common treatment for intrahepatic cholestasis of pregnancy (ICP), and its use is supported by the Society for Maternal-Fetal Medicine. However, evidence of the benefit of UA to fetal and neonatal outcomes in this patient population is unclear.
Tranexamic Acid for the Prevention of Blood Loss After Cesarean Delivery
Authors: Sentilhes Loic , Sénat Marie V. , Le Lous Maela , Winer Norbert , Rozenberg Patrick , Kayem Gilles , Verspyck Eric , Fuchs Florent , Azria Elie , Gallot Denis , Korb Diane , Desbrière Raoul , Le Ray Camille , Chauleur Celine , de Marcillac Fanny , Perrotin Franck , Parant Olivier , Salomon Laurent J. , Gauchotte Emilie , Bretelle Florence , Sananès Nicolas , Bohec Caroline , Mottet Nicolas , Legendre Guillaume , Letouzey Vincent , Haddad Bassam , Vardon Delphine , Madar Hugo , Mattuizzi Aurelien , Daniel Valerie , Regueme Sophie , Roussillon Caroline , Benard Antoine , Georget Aurore , Darsonval Astrid , Deneux-Tharaux Catherine ,   for the Groupe de Recherche en Obstétrique et Gynécologie
Published: September 2021

(Abstracted from N Engl J Med 2021;384:1623–1634)
Uterotonic agents are recommended to prevent postpartum hemorrhage (PPH). Tranexamic acid (TXA) has emerged as another medical approach to prevent blood loss after delivery.
Ovarian Cancer Population Screening and Mortality After Long-Term Follow-up in the UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS): A Randomised Controlled Trial
Authors: Menon Usha , Gentry-Maharaj Aleksandra , Burnell Matthew , Singh Naveena , Ryan Andy , Karpinskyj Chloe , Carlino Giulia , Taylor Julie , Massingham Susan K. , Raikou Maria , Kalsi Jatinderpal K. , Woolas Robert , Manchanda Ranjit , Arora Rupali , Casey Laura , Dawnay Anne , Dobbs Stephen , Leeson Simon , Mould Tim , Seif Mourad W. , Sharma Aarti , Williamson Karin , Liu Yiling , Fallowfield Lesley , McGuire Alistair J. , Campbell Stuart , Skates Steven J. , Jacobs Ian J. , Parmar Mahesh 
Published: September 2021

(Abstracted from Lancet 2021;397:2182–2193)
Ovarian cancer is most commonly diagnosed at an advanced stage (3 or 4) and remains the deadliest gynecologic malignancy. When diagnosed at stage 1, a survival rate of greater than 90% has been demonstrated, compared with a 5-year survival rate of 27% and 13% for stage 3 and stage 4 disease, respectively.
Protocol for a pilot feasibility, safety and efficacy study of artificially introducing an air-pleura interface for detection of pleural nodules by computed tomography: the AIR study
Authors: Sidhu Calvin , Fysh Edward T. , Roy Bapti , Kuok Yi Jin , Muruganandan Sanjeevan , Lan Norris S.H. , Mevavala Bhaumik V. , Read Catherine , Tan Ai Ling , Thomas Rajesh , Lee Y. C. Gary 
Published: September 2021

Abstract

Background:
Pleural effusions are common and can arise from many causes including primary or metastatic malignancies. Computed tomography (CT) is part of the routine workup for pleural effusions especially if pleural fluid analysis fails to show an underlying cause. CT can help detect pleural abnormalities such as thickening or nodules and allow imaging guided percutaneous biopsies. Otherwise surgical procedures are often required to obtain histological specimens but have inherent risks. The presence of air in the pleural cavity (eg with trapped lung) has been shown in a case series to enhance CT detection of pleural abnormalities.
The AIR study is a prospective, pilot, proof-of-concept study to assess the feasibility and safety of instilling air intrapleurally to create an air-pleura interface during CT imaging, and the efficacy of this artificial pneumothorax in aiding CT detection of pleural abnormalities.

Methods:
This study will recruit 40 patients with suspected or proven malignant pleural effusions that have a chest tube (including indwelling pleural catheter) in-situ and no pre-existing radiological evidence of advanced pleural abnormalities. A standard CT scan with pleural phase contrast enhancement will be performed. Air will be instilled via the chest tube to introduce an artificial air-pleura interface and a second (non-contrast) CT chest scan will be performed in the prone position. The air will be immediately aspirated after the procedure. The aims of this study are to determine 1) the feasibility and safety of introducing an air-pleura interface using a pre-defined protocol and 2) its effectiveness in detecting additional pleural abnormalities.

Discussion:
The AIR study is the first study to evaluate the feasibility, safety and efficacy of creating an artificial air-pleura interface to enhance detection of pleural abnormalities by CT. Improvements in detection may inform imaging-guided tissue sampling, avoid more invasive tissue acquisition procedures, and add to the assessment of pleural disease burden.
Effects of angiotensin-receptor neprilysin inhibitor on exercise capacity, quality of life, and cardiac function in heart failure with preserved ejection fraction
Authors: Fukuta Hidekatsu , Hagiwara Hiromi , Kamiya Takeshi 
Published: September 2021

Abstract

Background:
Nearly half of patients with heart failure have preserved ejection fraction (EF) and the mortality and morbidity of patients with heart failure with preserved EF (HFpEF) are high. Patients with HFpEF are often elderly and their primary chronic symptom is severe exercise intolerance that results in a reduced quality of life (QOL). Thus, improvement of exercise capacity presents another important clinical outcome in HFpEF patients. Left ventricular diastolic dysfunction is associated with the pathophysiology of HFpEF and it contributes importantly to exercise intolerance in HFpEF patients. The angiotensin-receptor neprilysin inhibitor (ARNI) sacubitril/valsartan was shown to be associated with better survival in HFpEF patients. However, there is insufficient evidence as to the effects of ARNI on exercise capacity and cardiac function in these patients. Accordingly, the purpose of this meta-analysis is to evaluate the effects of ARNI on exercise capacity and QOL as well as cardiac function in HFpEF patients.

Methods:
This meta-analysis will include randomized controlled trials examining the effects of ARNI on exercise capacity, health-related QOL, or cardiac function in HFpEF patients. Information of studies will be collected from PubMed, Web of Science, Cochrane Library, and ClinicalTrials.gov. The primary outcome will be exercise capacity (6-minute walking distance). The secondary outcomes will be health-related QOL and left ventricular structure and function.

Discussion:
This meta-analysis will evaluate the effects of ARNI on exercise capacity, QOL, and cardiac function in HFpEF patients, providing evidence regarding the clinical use of ARNI in these patients.

Systematic review registration:
INPLASY202170076