bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic attributes of Vibrio cholerae O1 responsible for 2022 massive cholera outbreak in Bangladesh
Authors: Monir Md Mamun , Islam Mohammad Tarequl , Mazumder Razib , Mondal Dinesh , Nahar Kazi Sumaita , Sultana Marzia , Morita Masatomo , Ohnishi Makoto , Huq Anwar , Watanabe Haruo , Qadri Firdausi , Rahman Mustafizur , Thomson Nicholas , Seed Kimberley , Colwell Rita R. , Ahmed Tahmeed , Alam Munirul 
Published: March 2023

AbstractIn 2022, one of its worst cholera outbreaks began in Bangladesh and the icddr,b Dhaka hospital treated more than 1300 patients and ca. 42,000 diarrheal cases from March-1 to April-10, 20221. Here, we present genomic attributes of V. cholerae O1 responsible for the 2022 Dhaka outbreak and 960 7th pandemic El Tor (7PET) strains from 88 countries. Results show strains isolated during the Dhaka outbreak cluster with 7PET wave-3 global clade strains, but comprise subclade BD-1.2, for which the most recent common ancestor appears to be that responsible for recent endemic cholera in India. BD-1.2 strains are present in Bangladesh since 2016, but not establishing dominance over BD-2 lineage strains2 until 2018 and predominantly associated with endemic cholera. In conclusion, the recent shift in lineage and genetic attributes, including serotype switching of BD-1.2 from Ogawa to Inaba, may explain the increasing number of cholera cases in Bangladesh.
Inhibition of ALKBH5 attenuates I/R-induced renal injury in male mice by promoting Ccl28 m6A modification and increasing Treg recruitment
Authors: Chen Juntao , Xu Cuidi , Yang Kun , Gao Rifeng , Cao Yirui , Liang Lifei , Chen Siyue , Xu Shihao , Rong Ruiming , Wang Jina , Zhu Tongyu 
Published: March 2023

AbstractIschemia reperfusion injury (IRI) is a common cause of acute kidney injury (AKI). The role of N6-methyladenosine (m6A) modification in AKI remains unclear. Here, we characterize the role of AlkB homolog 5 (ALKBH5) and m6A modification in an I/R-induced renal injury model in male mice. Alkbh5-knockout mice exhibit milder pathological damage and better renal function than wild-type mice post-IRI, whereas Alkbh5-knockin mice show contrary results. Also conditional knockout of Alkbh5 in the tubular epithelial cells alleviates I/R-induced AKI and fibrosis. CCL28 is identified as a target of ALKBH5. Furthermore, Ccl28 mRNA stability increases with Alkbh5 deficiency, mediating by the binding of insulin-like growth factor 2 binding protein 2. Treg recruitment is upregulated and inflammatory cells are inhibited by the increased CCL28 level in IRI-Alkbh5fl/flKspCre mice. The ALKBH5 inhibitor IOX1 exhibits protective effects against I/R-induced AKI. In summary, inhibition of ALKBH5 promotes the m6A modifications of Ccl28 mRNA, enhancing its stability, and regulating the Treg/inflammatory cell axis. ALKBH5 and this axis is a potential AKI treatment target.
Structural details of a Class B GPCR-arrestin complex revealed by genetically encoded crosslinkers in living cells
Authors: Aydin Yasmin , Böttke Thore , Lam Jordy Homing , Ernicke Stefan , Fortmann Anna , Tretbar Maik , Zarzycka Barbara , Gurevich Vsevolod V. , Katritch Vsevolod , Coin Irene 
Published: March 2023

AbstractUnderstanding the molecular basis of arrestin-mediated regulation of GPCRs is critical for deciphering signaling mechanisms and designing functional selectivity. However, structural studies of GPCR-arrestin complexes are hampered by their highly dynamic nature. Here, we dissect the interaction of arrestin-2 (arr2) with the secretin-like parathyroid hormone 1 receptor PTH1R using genetically encoded crosslinking amino acids in live cells. We identify 136 intermolecular proximity points that guide the construction of energy-optimized molecular models for the PTH1R-arr2 complex. Our data reveal flexible receptor elements missing in existing structures, including intracellular loop 3 and the proximal C-tail, and suggest a functional role of a hitherto overlooked positively charged region at the arrestin N-edge. Unbiased MD simulations highlight the stability and dynamic nature of the complex. Our integrative approach yields structural insights into protein-protein complexes in a biologically relevant live-cell environment and provides information inaccessible to classical structural methods, while also revealing the dynamics of the system.
Circulating tumor DNA reveals complex biological features with clinical relevance in metastatic breast cancer
Authors: Prat Aleix , Brasó-Maristany Fara , Martínez-Sáez Olga , Sanfeliu Esther , Xia Youli , Bellet Meritxell , Galván Patricia , Martínez Débora , Pascual Tomás , Marín-Aguilera Mercedes , Rodríguez Anna , Chic Nuria , Adamo Barbara , Paré Laia , Vidal Maria , Margelí Mireia , Ballana Ester , Gómez-Rey Marina , Oliveira Mafalda , Felip Eudald , Matito Judit , Sánchez-Bayona Rodrigo , Suñol Anna , Saura Cristina , Ciruelos Eva , Tolosa Pablo , Muñoz Montserrat , González-Farré Blanca , Villagrasa Patricia , Parker Joel S. , Perou Charles M. , Vivancos Ana 
Published: March 2023

AbstractLiquid biopsy has proven valuable in identifying individual genetic alterations; however, the ability of plasma ctDNA to capture complex tumor phenotypes with clinical value is unknown. To address this question, we have performed 0.5X shallow whole-genome sequencing in plasma from 459 patients with metastatic breast cancer, including 245 patients treated with endocrine therapy and a CDK4/6 inhibitor (ET + CDK4/6i) from 2 independent cohorts. We demonstrate that machine learning multi-gene signatures, obtained from ctDNA, identify complex biological features, including measures of tumor proliferation and estrogen receptor signaling, similar to what is accomplished using direct tumor tissue DNA or RNA profiling. More importantly, 4 DNA-based subtypes, and a ctDNA-based genomic signature tracking retinoblastoma loss-of-heterozygosity, are significantly associated with poor response and survival outcome following ET + CDK4/6i, independently of plasma tumor fraction. Our approach opens opportunities for the discovery of additional multi-feature genomic predictors coming from ctDNA in breast cancer and other cancer-types.
Transgenic NADH dehydrogenase restores oxygen regulation of breathing in mitochondrial complex I-deficient mice
Authors: Jiménez-Gómez Blanca , Ortega-Sáenz Patricia , Gao Lin , González-Rodríguez Patricia , García-Flores Paula , Chandel Navdeep , López-Barneo José 
Published: March 2023

AbstractThe hypoxic ventilatory response (HVR) is a life-saving reflex, triggered by the activation of chemoreceptor glomus cells in the carotid body (CB) connected with the brainstem respiratory center. The molecular mechanisms underlying glomus cell acute oxygen (O2) sensing are unclear. Genetic disruption of mitochondrial complex I (MCI) selectively abolishes the HVR and glomus cell responsiveness to hypoxia. However, it is unknown what functions of MCI (metabolic, proton transport, or signaling) are essential for O2 sensing. Here we show that transgenic mitochondrial expression of NDI1, a single-molecule yeast NADH/quinone oxidoreductase that does not directly contribute to proton pumping, fully recovers the HVR and glomus cell sensitivity to hypoxia in MCI-deficient mice. Therefore, maintenance of mitochondrial NADH dehydrogenase activity and the electron transport chain are absolutely necessary for O2-dependent regulation of breathing. NDI1 expression also rescues other systemic defects caused by MCI deficiency. These data explain the role of MCI in acute O2 sensing by arterial chemoreceptors and demonstrate the optimal recovery of complex organismal functions by gene therapy.
Heterovalent-doping-enabled atom-displacement fluctuation leads to ultrahigh energy-storage density in AgNbO3-based multilayer capacitors
Authors: Zhu Li-Feng , Deng Shiqing , Zhao Lei , Li Gen , Wang Qi , Li Linhai , Yan Yongke , Qi He , Zhang Bo-Ping , Chen Jun , Li Jing-Feng 
Published: March 2023

AbstractDielectric capacitors with high energy storage performance are highly desired for next-generation advanced high/pulsed power capacitors that demand miniaturization and integration. However, the poor energy-storage density that results from the low breakdown strength, has been the major challenge for practical applications of dielectric capacitors. Herein, we propose a heterovalent-doping-enabled atom-displacement fluctuation strategy for the design of low-atom-displacements regions in the antiferroelectric matrix to achieve the increase in breakdown strength and enhancement of the energy-storage density for AgNbO3-based multilayer capacitors. An ultrahigh breakdown strength ~1450 kV·cm−1 is realized in the Sm0.05Ag0.85Nb0.7Ta0.3O3 multilayer capacitors, especially with an ultrahigh Urec ~14 J·cm−3, excellent η ~ 85% and PD,max ~ 102.84 MW·cm−3, manifesting a breakthrough in the comprehensive energy storage performance for lead-free antiferroelectric capacitors. This work offers a good paradigm for improving the energy storage properties of antiferroelectric multilayer capacitors to meet the demanding requirements of advanced energy storage applications.
Adaptive, problem-tailored variational quantum eigensolver mitigates rough parameter landscapes and barren plateaus
Authors: Grimsley Harper R. , Barron George S. , Barnes Edwin , Economou Sophia E. , Mayhall Nicholas J. 
Published: March 2023

AbstractVariational quantum eigensolvers (VQEs) represent a powerful class of hybrid quantum-classical algorithms for computing molecular energies. Various numerical issues exist for these methods, however, including barren plateaus and large numbers of local minima. In this work, we consider the Adaptive, Problem-Tailored Variational Quantum Eiegensolver (ADAPT-VQE) ansätze, and examine how they are impacted by these local minima. We find that while ADAPT-VQE does not remove local minima, the gradient-informed, one-operator-at-a-time circuit construction accomplishes two things: First, it provides an initialization strategy that can yield solutions with over an order of magnitude smaller error compared to random initialization, and which is applicable in situations where chemical intuition cannot help with initialization, i.e., when Hartree-Fock is a poor approximation to the ground state. Second, even if an ADAPT-VQE iteration converges to a local trap at one step, it can still “burrow” toward the exact solution by adding more operators, which preferentially deepens the occupied trap. This same mechanism helps highlight a surprising feature of ADAPT-VQE: It should not suffer optimization problems due to barren plateaus and random initialization. Even if such barren plateaus appear in the parameter landscape, our analysis suggests that ADAPT-VQE avoids such regions by design.
A 23,000-year-old southern Iberian individual links human groups that lived in Western Europe before and after the Last Glacial Maximum
Authors: Villalba-Mouco Vanessa , van de Loosdrecht Marieke S. , Rohrlach Adam B. , Fewlass Helen , Talamo Sahra , Yu He , Aron Franziska , Lalueza-Fox Carles , Cabello Lidia , Cantalejo Duarte Pedro , Ramos-Muñoz José , Posth Cosimo , Krause Johannes , Weniger Gerd-Christian , Haak Wolfgang 
Published: March 2023

AbstractHuman populations underwent range contractions during the Last Glacial Maximum (LGM) which had lasting and dramatic effects on their genetic variation. The genetic ancestry of individuals associated with the post-LGM Magdalenian technocomplex has been interpreted as being derived from groups associated with the pre-LGM Aurignacian. However, both these ancestries differ from that of central European individuals associated with the chronologically intermediate Gravettian. Thus, the genomic transition from pre- to post-LGM remains unclear also in western Europe, where we lack genomic data associated with the intermediate Solutrean, which spans the height of the LGM. Here we present genome-wide data from sites in Andalusia in southern Spain, including from a Solutrean-associated individual from Cueva del Malalmuerzo, directly dated to ~23,000 cal yr bp. The Malalmuerzo individual carried genetic ancestry that directly connects earlier Aurignacian-associated individuals with post-LGM Magdalenian-associated ancestry in western Europe. This scenario differs from Italy, where individuals associated with the transition from pre- and post-LGM carry different genetic ancestries. This suggests different dynamics in the proposed southern refugia of Ice Age Europe and posits Iberia as a potential refugium for western European pre-LGM ancestry. More, individuals from Cueva Ardales, which were thought to be of Palaeolithic origin, date younger than expected and, together with individuals from the Andalusian sites Caserones and Aguilillas, fall within the genetic variation of the Neolithic, Chalcolithic and Bronze Age individuals from southern Iberia.
Effects of the healthy lifestyle community program (cohort 1) on stress-eating and weight change after 8 weeks: a controlled study
Authors: Anand Corinna , Hengst Karin , Gellner Reinhold , Englert Heike 
Published: March 2023

AbstractStress-eating (eating more or more unhealthily in order to accommodate to stress), contributes to the development and maintenance of obesity. The effect of comprehensive weight loss interventions on changes in stress-eating as well as the contributing role of stress-eating on weight reduction has not been examined. The impact of the 8-week intensive phase of the Healthy Lifestyle Community Programme (HLCP, cohort 1) on emotional, external and restrained eating, as expressions of stress-eating was evaluated in a non-randomized controlled trial. Intervention: 14 seminars (twice per week, including practical units), complemented by stress-regulation and cooking workshops and coaching sessions empowering participants to change their behaviour towards a healthy plant-based diet (ad libitum), stress regulation, regular exercise and to focus on social support. Participants were recruited from the general population. In the intervention group, 91 participants (IG; age: 56 ± 10, 77% female) and in the control group, 52 (CG; age: 62 ± 14, 57% female) were enrolled. At baseline, participants of the IG reported higher levels of stress (9.7 ± 5.4 points [P] vs. 7.6 ± 6.2; p < 0.011), and of emotional eating (27.9 ± 9.4 vs. 20.0 ± 7.1; p < 0.001) and external eating (29.1 ± 4.9 vs. 25.5 ± 5.6; p < 0.001) than participants of the CG. Within 8 weeks, in the IG, scores of emotional eating (− 3.5 ± 5.4 P) and external eating significantly decreased (= − 2.0 ± 3.8 P), while restrained eating increased (2.7 ± 5.0 P; p for all < 0.001). Weight change was negatively correlated with change of external eating (R2 = 0.045; CC = − 0.285; p = 0.014), indicating that a greater weight change was associated with a smaller change of external eating. This is the first study to prospectively investigate the role of stress-eating on the weight reduction effect of comprehensive lifestyle interventions. Our data confirm that overweight is associated with EE and external eating and suggest that the HLCP is capable to reduce both, weight and stress-eating.Trial registration:German Clinical Trials Register (DRKS; reference: DRKS00018821; September 18th 2019; retrospectively registered).
Sortilin knock-down alters the expression and distribution of cathepsin D and prosaposin and up-regulates the cation-dependent mannose-6-phosphate receptor in rat epididymal cells
Authors: Aguilera Andrea Carolina , Leiva Natalia , Alvarez Pablo Ariel , Pulcini Georgina , Pereyra Laura Lucía , Morales Carlos Ramón , Sosa Miguel Ángel , Carvelli Lorena 
Published: March 2023

AbstractThe selective transport to lysosomes can be mediated by either mannose-6-phosphate receptors (CD-MPR and CI-MPR) or sortilin. In mammalian epididymis, some lysosomal proteins are secreted into the lumen through unknown mechanisms. To investigate the underlying mechanisms of lysosomal protein transport in epididymal cells we studied the expression and distribution of cathepsin D (CatD) and prosaposin (PSAP) in a sortilin knocked down RCE-1 epididymal cell line (RCE-1 KD) in comparison with non-transfected RCE-1 cells. In RCE-1 cells, CatD was found in the perinuclear zone and co-localize with sortilin, whereas in RCE-1 KD cells, the expression, distribution and processing of the enzyme were altered. In turn, PSAP accumulated intracellularly upon sortilin knock-down and redistributed from LAMP-1-positive compartment to a perinuclear location, remaining co-localized with CatD. Interestingly, the sortilin knock-down induced CD-MPR overexpression and a redistribution of the receptor from the perinuclear zone to a dispersed cytoplasmic location, accompanied by an increased co-localization with CatD. The increase in CD-MPR could result from a compensatory response for the proper delivery of CatD to lysosomes in epididymal cells. The intracellular pathway taken by lysosomal proteins could be an approach for addressing further studies to understand the mechanism of exocytosis and therefore the role of these proteins in the epididymis.
Microbial community shift on artificial biological reef structures (ABRs) deployed in the South China Sea
Authors: Mohamed Hala F. , Abd-Elgawad Amro , Cai Rongshuo , Luo Zhaohe , Pie Lulu , Xu Changan 
Published: March 2023

AbstractMany Artificial Reefs (ARs) have been used worldwide for marine habitat and coral reef restoration. However, the microbial community structure that colonize the ARs and their progressive development have been seldom investigated. In this study, the successive development of the microbial communities on environmentally friendly Artificial Biological Reef structures (ABRs)R made of special concrete supported with bioactive materials collected from marine algal sources were studied. Three seasons (spring, summer and autumn), three coral reef localities and control models (SCE) without bioactive material and (NCE) made of normal cement were compared. The structure of the microbial pattern exhibited successive shifts from the natural environment to the ABRs supported with bioactive materials (ABAM). Cyanobacteria, Proteobacteria, and Planctomycetota were shown to be the most three dominant phyla. Their relative abundances pointedly increased on ABAM and SCE models compared to the environment. Amplicon Sequence Variant (ASV) Richness and Shannon index were obviously higher on ABAM models and showed significant positive relationship with that of macrobenthos than those on the controls and the natural reef (XR). Our results offer successful establishment of healthy microbial films on the ABR surfaces enhanced the restoration of macrobenthic community in the damaged coral reefs which better understands the ecological role of the ABRs.
Verifying the accuracy of self-reported smoking behavior in female volunteer soldiers
Authors: Chan Wei-Hung , Lai Ching-Huang , Huang Shu-Jia , Huang Chung-Chi , Lai Chung-Yu , Liu Yi-Chun , Jiang Shiang-Huei , Li Shan-Ru , Tzeng Ya-Mei , Kao Senyeong , Chang Yu-Tien , Wu Chia-Chao , Kuo Chao-Yin , Hung Kuang-Chen , Chiu Yu-Lung 
Published: March 2023

AbstractSmoking rates in the military are evaluated through questionnaire surveying. Because the accurate identification of smokers facilitates the provision of smoking cessation services, this study conducted urine cotinine concentration testing to verify the accuracy of self-reported smoking behavior by female volunteer soldiers and analyzed the effects of second-hand smoking on urine cotinine concentrations. This study is a cross-sectional study conducted using purposive sampling on female volunteer soldiers receiving training at the Taichung Recruit Training Center in May 2014. This study simultaneously collected questionnaires and urine samples, and urine samples were analyzed with an enzyme-linked immunosorbent assay. The self-reported smoking rate of female volunteer soldiers was 19.3%, whereas the smoking rate as determined by urine cotinine concentration testing was 26.3%, indicating an overall underestimation of 7.0%. Chi-square (χ2) goodness of fit test results indicated that the distribution of self-reported smoking behaviors and that verified from urine cotinine concentration testing were significantly different. The sensitivity of self-reported smoking behavior was 66.7% with a specificity of 97.6%. There was no significant association between second-hand smoking and urine cotinine concentrations. Questionnaire survey self-reporting methods could underestimate the smoking behavior of female volunteer soldiers and routine testing with biochemical verification is necessary.
Clinical validation of a contactless respiration rate monitor
Authors: Bujan Bartosz , Fischer Tobit , Dietz-Terjung Sarah , Bauerfeind Aribert , Jedrysiak Piotr , Große Sundrup Martina , Hamann Janne , Schöbel Christoph 
Published: March 2023

AbstractRespiratory rate (RR) is an often underestimated and underreported vital sign with tremendous clinical value. As a predictor of cardiopulmonary arrest, chronic obstructive pulmonary disease (COPD) exacerbation or indicator of health state for example in COVID-19 patients, respiratory rate could be especially valuable in remote long-term patient monitoring, which is challenging to implement. Contactless devices for home use aim to overcome these challenges. In this study, the contactless Sleepiz One+ respiration monitor for home use during sleep was validated against the thoracic effort belt. The agreement of instantaneous breathing rate and breathing rate statistics between the Sleepiz One+ device and the thoracic effort belt was initially evaluated during a 20-min sleep window under controlled conditions (no body movement) on a cohort of 19 participants and secondly in a more natural setting (uncontrolled for body movement) during a whole night on a cohort of 139 participants. Excellent agreement was shown for instantaneous breathing rate to be within 3 breaths per minute (Brpm) compared to thoracic effort band with an accuracy of 100% and mean absolute error (MAE) of 0.39 Brpm for the setting controlled for movement, and an accuracy of 99.5% with a MAE of 0.48 Brpm for the whole night measurement, respectively. Excellent agreement was also achieved for the respiratory rate statistics over the whole night with absolute errors of 0.43, 0.39 and 0.67 Brpm for the 10th, 50th and 90th percentiles, respectively. Based on these results we conclude that the Sleepiz One+ can estimate instantaneous respiratory rate and its summary statistics at high accuracy in a clinical setting. Further studies are required to evaluate the performance in the home environment, however, it is expected that the performance is at similar level, as the measurement conditions for the Sleepiz One+ device are better at home than in a clinical setting.