bluuebunny/crossref_metadata_2025_split huggingface dataset:
Marginal speed confinement resolves the conflict between correlation and control in collective behaviour
Authors: Cavagna Andrea , Culla Antonio , Feng Xiao , Giardina Irene , Grigera Tomas S. , Kion-Crosby Willow , Melillo Stefania , Pisegna Giulia , Postiglione Lorena , Villegas Pablo 
Published: May 2022

AbstractSpeed fluctuations of individual birds in natural flocks are moderate, due to the aerodynamic and biomechanical constraints of flight. Yet the spatial correlations of such fluctuations are scale-free, namely they have a range as wide as the entire group, a property linked to the capacity of the system to collectively respond to external perturbations. Scale-free correlations and moderate fluctuations set conflicting constraints on the mechanism controlling the speed of each agent, as the factors boosting correlation amplify fluctuations, and vice versa. Here, using a statistical field theory approach, we suggest that a marginal speed confinement that ignores small deviations from the natural reference value while ferociously suppressing larger speed fluctuations, is able to reconcile scale-free correlations with biologically acceptable group’s speed. We validate our theoretical predictions by comparing them with field experimental data on starling flocks with group sizes spanning an unprecedented interval of over two orders of magnitude.
A randomized controlled trial for response of microbiome network to exercise and diet intervention in patients with nonalcoholic fatty liver disease
Authors: Cheng Runtan , Wang Lu , Le Shenglong , Yang Yifan , Zhao Can , Zhang Xiangqi , Yang Xin , Xu Ting , Xu Leiting , Wiklund Petri , Ge Jun , Lu Dajiang , Zhang Chenhong , Chen Luonan , Cheng Sulin 
Published: May 2022

AbstractExercise and diet are treatments for nonalcoholic fatty liver disease (NAFLD) and prediabetes, however, how exercise and diet interventions impact gut microbiota in patients is incompletely understood. We previously reported a 8.6-month, four-arm (Aerobic exercise, n = 29; Diet, n = 28; Aerobic exercise + Diet, n = 29; No intervention, n = 29) randomized, singe blinded (for researchers), and controlled intervention in patients with NAFLD and prediabetes to assess the effect of interventions on the primary outcomes of liver fat content and glucose metabolism. Here we report the third primary outcome of the trial—gut microbiota composition—in participants who completed the trial (22 in Aerobic exercise, 22 in Diet, 23 in Aerobic exercise + Diet, 18 in No Intervention). We show that combined aerobic exercise and diet intervention are associated with diversified and stabilized keystone taxa, while exercise and diet interventions alone increase network connectivity and robustness between taxa. No adverse effects were observed with the interventions. In addition, in exploratory ad-hoc analyses we find that not all subjects responded to the intervention in a similar manner, when using differentially altered gut microbe amplicon sequence variants abundance to classify the responders and low/non-responders. A personalized gut microbial network at baseline could predict the individual responses in liver fat to exercise intervention. Our findings suggest an avenue for developing personalized intervention strategies for treatment of NAFLD based on host-gut microbiome ecosystem interactions, however, future studies with large sample size are needed to validate these discoveries. The Trial Registration Number is ISRCTN 42622771.
Systematic review and meta-analysis of the effectiveness and perinatal outcomes of COVID-19 vaccination in pregnancy
Authors: Prasad Smriti , Kalafat Erkan , Blakeway Helena , Townsend Rosemary , O’Brien Pat , Morris Edward , Draycott Tim , Thangaratinam Shakila , Le Doare Kirsty , Ladhani Shamez , von Dadelszen Peter , Magee Laura A. , Heath Paul , Khalil Asma 
Published: May 2022

AbstractSafety and effectiveness of COVID-19 vaccines during pregnancy is a particular concern affecting vaccination uptake by this vulnerable group. Here we evaluated evidence from 23 studies including 117,552 COVID-19 vaccinated pregnant people, almost exclusively with mRNA vaccines. We show that the effectiveness of mRNA vaccination against RT-PCR confirmed SARS-CoV-2 infection 7 days after second dose was 89·5% (95% CI 69·0-96·4%, 18,828 vaccinated pregnant people, I2 = 73·9%). The risk of stillbirth was significantly lower in the vaccinated cohort by 15% (pooled OR 0·85; 95% CI 0·73–0·99, 66,067 vaccinated vs. 424,624 unvaccinated, I2 = 93·9%). There was no evidence of a higher risk of adverse outcomes including miscarriage, earlier gestation at birth, placental abruption, pulmonary embolism, postpartum haemorrhage, maternal death, intensive care unit admission, lower birthweight Z-score, or neonatal intensive care unit admission (p > 0.05 for all). COVID-19 mRNA vaccination in pregnancy appears to be safe and is associated with a reduction in stillbirth.
A genome-wide CRISPR-Cas9 knockout screen identifies essential and growth-restricting genes in human trophoblast stem cells
Authors: Dong Chen , Fu Shuhua , Karvas Rowan M. , Chew Brian , Fischer Laura A. , Xing Xiaoyun , Harrison Jessica K. , Popli Pooja , Kommagani Ramakrishna , Wang Ting , Zhang Bo , Theunissen Thorold W. 
Published: May 2022

AbstractThe recent derivation of human trophoblast stem cells (hTSCs) provides a scalable in vitro model system of human placental development, but the molecular regulators of hTSC identity have not been systematically explored thus far. Here, we utilize a genome-wide CRISPR-Cas9 knockout screen to comprehensively identify essential and growth-restricting genes in hTSCs. By cross-referencing our data to those from similar genetic screens performed in other cell types, as well as gene expression data from early human embryos, we define hTSC-specific and -enriched regulators. These include both well-established and previously uncharacterized trophoblast regulators, such as ARID3A, GATA2, and TEAD1 (essential), and GCM1, PTPN14, and TET2 (growth-restricting). Integrated analysis of chromatin accessibility, gene expression, and genome-wide location data reveals that the transcription factor TEAD1 regulates the expression of many trophoblast regulators in hTSCs. In the absence of TEAD1, hTSCs fail to complete faithful differentiation into extravillous trophoblast (EVT) cells and instead show a bias towards syncytiotrophoblast (STB) differentiation, thus indicating that this transcription factor safeguards the bipotent lineage potential of hTSCs. Overall, our study provides a valuable resource for dissecting the molecular regulation of human placental development and diseases.
Environmental cues from neural crest derivatives act as metastatic triggers in an embryonic neuroblastoma model
Authors: Ben Amar Dounia , Thoinet Karine , Villalard Benjamin , Imbaud Olivier , Costechareyre Clélia , Jarrosson Loraine , Reynaud Florie , Novion Ducassou Julia , Couté Yohann , Brunet Jean-François , Combaret Valérie , Corradini Nadège , Delloye-Bourgeois Céline , Castellani Valérie 
Published: May 2022

AbstractEmbryonic malignant transformation is concomitant to organogenesis, often affecting multipotent and migratory progenitors. While lineage relationships between malignant cells and their physiological counterparts are extensively investigated, the contribution of exogenous embryonic signals is not fully known. Neuroblastoma (NB) is a childhood malignancy of the peripheral nervous system arising from the embryonic trunk neural crest (NC) and characterized by heterogeneous and interconvertible tumor cell identities. Here, using experimental models mimicking the embryonic context coupled to proteomic and transcriptomic analyses, we show that signals released by embryonic sympathetic ganglia, including Olfactomedin-1, induce NB cells to shift from a noradrenergic to mesenchymal identity, and to activate a gene program promoting NB metastatic onset and dissemination. From this gene program, we extract a core signature specifically shared by metastatic cancers with NC origin. This reveals non-cell autonomous embryonic contributions regulating the plasticity of NB identities and setting pro-dissemination gene programs common to NC-derived cancers.
Investigating the presence of adsorbed species on Pt steps at low potentials
Authors: Rizo Rubén , Fernández-Vidal Julia , Hardwick Laurence J. , Attard Gary A. , Vidal-Iglesias Francisco J. , Climent Victor , Herrero Enrique , Feliu Juan M. 
Published: May 2022

AbstractThe study of the OH adsorption process on Pt single crystals is of paramount importance since this adsorbed species is considered the main intermediate in many electrochemical reactions of interest, in particular, those oxidation reactions that require a source of oxygen. So far, it is frequently assumed that the OH adsorption on Pt only takes place at potentials higher than 0.55 V (versus the reversible hydrogen electrode), regardless of the Pt surface structure. However, by CO displacement experiments, alternating current voltammetry, and Raman spectroscopy, we demonstrate here that OH is adsorbed at more negative potentials on the low coordinated Pt atoms, the Pt steps. This finding opens a new door in the mechanistic study of many relevant electrochemical reactions, leading to a better understanding that, ultimately, can be essential to reach the final goal of obtaining improved catalysts for electrochemical applications of technological interest.
Multivalent 9-O-Acetylated-sialic acid glycoclusters as potent inhibitors for SARS-CoV-2 infection
Authors: Petitjean Simon J. L. , Chen Wenzhang , Koehler Melanie , Jimmidi Ravikumar , Yang Jinsung , Mohammed Danahe , Juniku Blinera , Stanifer Megan L. , Boulant Steeve , Vincent Stéphane P. , Alsteens David 
Published: May 2022

AbstractThe recent emergence of highly transmissible SARS-CoV-2 variants illustrates the urgent need to better understand the molecular details of the virus binding to its host cell and to develop anti-viral strategies. While many studies focused on the role of the angiotensin-converting enzyme 2 receptor in the infection, others suggest the important role of cell attachment factors such as glycans. Here, we use atomic force microscopy to study these early binding events with the focus on the role of sialic acids (SA). We show that SARS-CoV-2 binds specifically to 9-O-acetylated-SA with a moderate affinity, supporting its role as an attachment factor during virus landing to cell host surfaces. For therapeutic purposes and based on this finding, we have designed novel blocking molecules with various topologies and carrying a controlled number of SA residues, enhancing affinity through a multivalent effect. Inhibition assays show that the AcSA-derived glycoclusters are potent inhibitors of cell binding and infectivity, offering new perspectives in the treatment of SARS-CoV-2 infection.
Twisted oxide lateral homostructures with conjunction tunability
Authors: Wu Ping-Chun , Wei Chia-Chun , Zhong Qilan , Ho Sheng-Zhu , Liou Yi-De , Liu Yu-Chen , Chiu Chun-Chien , Tzeng Wen-Yen , Chang Kuo-En , Chang Yao-Wen , Zheng Junding , Chang Chun-Fu , Tu Chien-Ming , Chen Tse-Ming , Luo Chih-Wei , Huang Rong , Duan Chun-Gang , Chen Yi-Chun , Kuo Chang-Yang , Yang Jan-Chi 
Published: May 2022

AbstractEpitaxial growth is of significant importance over the past decades, given it has been the key process of modern technology for delivering high-quality thin films. For conventional heteroepitaxy, the selection of proper single crystal substrates not only facilitates the integration of different materials but also fulfills interface and strain engineering upon a wide spectrum of functionalities. Nevertheless, the lattice structure, regularity and crystalline orientation are determined once a specific substrate is chosen. Here, we reveal the growth of twisted oxide lateral homostructure with controllable in-plane conjunctions. The twisted lateral homostructures with atomically sharp interfaces can be composed of epitaxial “blocks” with different crystalline orientations, ferroic orders and phases. We further demonstrate that this approach is universal for fabricating various complex systems, in which the unconventional physical properties can be artificially manipulated. Our results establish an efficient pathway towards twisted lateral homostructures, adding additional degrees of freedom to design epitaxial films.
Deterministic control of ferroelectric polarization by ultrafast laser pulses
Authors: Chen Peng , Paillard Charles , Zhao Hong Jian , Íñiguez Jorge , Bellaiche Laurent 
Published: May 2022

AbstractUltrafast light-matter interactions present a promising route to control ferroelectric polarization at room temperature, which is an exciting idea for designing novel ferroelectric-based devices. One emergent light-induced technique for controlling polarization consists in anharmonically driving a high-frequency phonon mode through its coupling to the polarization. A step towards such control has been recently accomplished, but the polarization has been reported to be only partially reversed and for a short lapse of time. Such transient partial reversal is not currently understood, and it is presently unclear if full control of polarization, by, e.g., fully reversing it or even making it adopt different directions (thus inducing structural phase transitions), can be achieved by activating the high-frequency phonon mode via terahertz pulse stimuli. Here, by means of realistic simulations of a prototypical ferroelectric, we reveal and explain (1) why a transient partial reversal has been observed, and (2) how to deterministically control the ferroelectric polarization thanks to these stimuli. Such results can provide guidance for realizing original ultrafast optoferroic devices.
Photovoltage memory effect in a portable Faradaic junction solar rechargeable device
Authors: Wang Pin , Xue Mengfan , Jiang Dongjian , Yang Yanliang , Zhang Junzhe , Dong Hongzheng , Sun Gengzhi , Yao Yingfang , Luo Wenjun , Zou Zhigang 
Published: May 2022

AbstractTwo-electrode solar rechargeable device is one of the promising technologies to address the problem of solar energy storage in large scale. However, the mechanism of dark output voltage remains unclear and the low volumetric energy density also limits its practical applications. Herein, we report that a Si/CoOx/KBi(aq)/MnOx Faradaic junction device exhibits a photovoltage memory effect, that is, the dark output voltage can precisely record the value of the photovoltage in the device. To investigate the mechanism of the effect, we develop an open circuit potential method to real-time monitor the photo charge and dark discharge processes in the Faradaic junction device. This effect leads to minimized interface energy loss in the Faradaic junction device, which achieves much higher performances than the devices without the effect. Moreover, we realize a portable device with a record value of the dark volumetric energy density (∼1.89 mJ cm−3) among all reported two-electrode solar rechargeable devices. These results offer guidance to improve the performance of a solar rechargeable device and design other photoelectric devices for new applications.
Identification of biomarkers of response to preoperative talazoparib monotherapy in treatment naïve gBRCA+ breast cancers
Authors: Liu Xuan , Ge Zhongqi , Yang Fei , Contreras Alejandro , Lee Sanghoon , White Jason B. , Lu Yiling , Labrie Marilyne , Arun Banu K. , Moulder Stacy L. , Mills Gordon B. , Piwnica-Worms Helen , Litton Jennifer K. , Chang Jeffrey T. 
Published: May 2022

AbstractGermline mutations inBRCA1orBRCA2exist in ~2–7% of breast cancer patients, which has led to the approval of PARP inhibitors in the advanced setting. We have previously reported a phase II neoadjuvant trial of single agent talazoparib for patients with germlineBRCApathogenic variants with a pathologic complete response (pCR) rate of 53%. As nearly half of the patients treated did not have pCR, better strategies are needed to overcome treatment resistance. To this end, we conducted multi-omic analysis of 13 treatment naïve breast cancer tumors from patients that went on to receive single-agent neoadjuvant talazoparib. We looked for biomarkers that were predictive of response (assessed by residual cancer burden) after 6 months of therapy. We found that all resistant tumors exhibited either the loss of SHLD2, expression of a hypoxia signature, or expression of a stem cell signature. These results indicate that the deep analysis of pre-treatment tumors can identify biomarkers that are predictive of response to talazoparib and potentially other PARP inhibitors, and provides a framework that will allow for better selection of patients for treatment, as well as a roadmap for the development of novel combination therapies to prevent emergence of resistance.
Impact of the valley orbit coupling on exchange gate for spin qubits in silicon
Authors: Tariq Bilal , Hu Xuedong 
Published: May 2022

AbstractThe mixing of conduction band valleys plays a critical role in determining electronic spectrum and dynamics in a silicon nanostructure. Here, we investigate theoretically how valley–orbit coupling affects the exchange interaction in a silicon double quantum dot. We find that exchange splitting can be strongly suppressed at finite valley phase differences between the dots because of the valley-phase-dependent dressing of the ground states and Coulomb exchange integrals, and a small valley splitting can render the exchange Hamiltonian incomplete in describing low-energy dynamics due to nearby excited valley states. The higher orbital states are also vital in calculating the exchange splitting, which is crucial for applications such as exchange gates for spin qubits.
Dissecting schizophrenia phenotypic variation: the contribution of genetic variation, environmental exposures, and gene–environment interactions
Authors: Zhang Hanxin , Khan Atif , Kushner Steven A. , Rzhetsky Andrey 
Published: May 2022

AbstractSchizophrenia is among the leading causes of disability worldwide. Prior studies have conclusively demonstrated that the etiology of schizophrenia contains a strong genetic component. However, the understanding of environmental contributions and gene–environment interactions have remained less well understood. Here, we estimated the genetic and environmental contributions to schizophrenia risk using a unique combination of data sources and mathematical models. We used the administrative health records of 481,657 U.S. individuals organized into 128,989 families. In addition, we employed rich geographically specific measures of air, water, and land quality across the United States. Using models of progressively increasing complexity, we examined both linear and non-linear contributions of genetic variation and environmental exposures to schizophrenia risk. Our results demonstrate that heritability estimates differ significantly when gene–environment interactions are included in the models, dropping from 79% for the simplest model, to 46% in the best-fit model which included the full set of linear and non-linear parameters. Taken together, these findings suggest that environmental factors are an important source of explanatory variance underlying schizophrenia risk. Future studies are warranted to further explore linear and non-linear environmental contributions to schizophrenia risk and investigate the causality of these associations.
Comprehensive 16S rRNA and metagenomic data from the gut microbiome of aging and rejuvenation mouse models
Authors: Shin Jongoh , Noh Jung-Ran , Choe Donghui , Lee Namil , Song Yoseb , Cho Suhyung , Kang Eun-Jung , Go Min-Jeong , Ha Seok Kyun , Kim Jae-Hoon , Kim Yong-Hoon , Kim Kyoung-Shim , Kim Byoung-Chan , Lee Chul-Ho , Cho Byung-Kwan 
Published: May 2022

AbstractThe gut microbiota is associated with the health and longevity of the host. A few methods, such as fecal microbiota transplantation and oral administration of probiotics, have been applied to alter the gut microbiome and promote healthy aging. The changes in host microbiomes still remain poorly understood. Here, we characterized both the changes in gut microbial communities and their functional potential derived from colon samples in mouse models during aging. We achieved this through four procedures including co-housing, serum injection, parabiosis, and oral administration of Akkermansia muciniphila as probiotics using bacterial 16 S rRNA sequencing and shotgun metagenomic sequencing. The dataset comprised 16 S rRNA sequencing (36,249,200 paired-end reads, 107 sequencing data) and metagenomic sequencing data (307,194,369 paired-end reads, 109 sequencing data), characterizing the taxonomy of bacterial communities and their functional potential during aging and rejuvenation. The generated data expand the resources of the gut microbiome related to aging and rejuvenation and provide a useful dataset for research on developing therapeutic strategies to achieve healthy active aging.
Global forest management data for 2015 at a 100 m resolution
Authors: Lesiv Myroslava , Schepaschenko Dmitry , Buchhorn Marcel , See Linda , Dürauer Martina , Georgieva Ivelina , Jung Martin , Hofhansl Florian , Schulze Katharina , Bilous Andrii , Blyshchyk Volodymyr , Mukhortova Liudmila , Brenes Carlos Luis Muñoz , Krivobokov Leonid , Ntie Stephan , Tsogt Khongor , Pietsch Stephan Alexander , Tikhonova Elena , Kim Moonil , Di Fulvio Fulvio , Su Yuan-Fong , Zadorozhniuk Roma , Sirbu Flavius Sorin , Panging Kripal , Bilous Svitlana , Kovalevskii Sergii B. , Kraxner Florian , Rabia Ahmed Harb , Vasylyshyn Roman , Ahmed Rekib , Diachuk Petro , Kovalevskyi Serhii S. , Bungnamei Khangsembou , Bordoloi Kusumbor , Churilov Andrii , Vasylyshyn Olesia , Sahariah Dhrubajyoti , Tertyshnyi Anatolii P. , Saikia Anup , Malek Žiga , Singha Kuleswar , Feshchenko Roman , Prestele Reinhard , Akhtar Ibrar ul Hassan , Sharma Kiran , Domashovets Galyna , Spawn-Lee Seth A. , Blyshchyk Oleksii , Slyva Oleksandr , Ilkiv Mariia , Melnyk Oleksandr , Sliusarchuk Vitalii , Karpuk Anatolii , Terentiev Andrii , Bilous Valentin , Blyshchyk Kateryna , Bilous Maxim , Bogovyk Nataliia , Blyshchyk Ivan , Bartalev Sergey , Yatskov Mikhail , Smets Bruno , Visconti Piero , Mccallum Ian , Obersteiner Michael , Fritz Steffen 
Published: May 2022

AbstractSpatially explicit information on forest management at a global scale is critical for understanding the status of forests, for planning sustainable forest management and restoration, and conservation activities. Here, we produce the first reference data set and a prototype of a globally consistent forest management map with high spatial detail on the most prevalent forest management classes such as intact forests, managed forests with natural regeneration, planted forests, plantation forest (rotation up to 15 years), oil palm plantations, and agroforestry. We developed the reference dataset of 226 K unique locations through a series of expert and crowdsourcing campaigns using Geo-Wiki (https://www.geo-wiki.org/). We then combined the reference samples with time series from PROBA-V satellite imagery to create a global wall-to-wall map of forest management at a 100 m resolution for the year 2015, with forest management class accuracies ranging from 58% to 80%. The reference data set and the map present the status of forest ecosystems and can be used for investigating the value of forests for species, ecosystems and their services.