bluuebunny/crossref_metadata_2025_split huggingface dataset:
A self-assembled trimeric protein vaccine induces protective immunity against Omicron variant
Authors: He Cai , Yang Jingyun , Hong Weiqi , Chen Zimin , Peng Dandan , Lei Hong , Alu Aqu , He Xuemei , Bi Zhenfei , Jiang Xiaohua , Jia Guowen , Yang Yun , Zhou Yanan , Yu Wenhai , Tang Cong , Huang Qing , Yang Mengli , Li Bai , Li Jingmei , Wang Junbin , Que Haiying , Chen Li , Ren Wenyan , Wan Dandan , Li Jiong , Wang Wei , Shen Guobo , Zhao Zhiwei , Yang Li , Yang Jinliang , Wang Zhenling , Su Zhaoming , Wei Yuquan , Cen Xiaobo , Tanaka Yoshimasa , Song Xiangrong , Lu Shuaiyao , Peng Xiaozhong , Lu Guangwen , Wei Xiawei 
Published: September 2022

AbstractThe recently emerged Omicron (B.1.1.529) variant has rapidly surpassed Delta to become the predominant circulating SARS-CoV-2 variant, given the higher transmissibility rate and immune escape ability, resulting in breakthrough infections in vaccinated individuals. A new generation of SARS-CoV-2 vaccines targeting the Omicron variant are urgently needed. Here, we developed a subunit vaccine named RBD-HR/trimer by directly linking the sequence of RBD derived from the Delta variant (containing L452R and T478K) and HR1 and HR2 in SARS-CoV-2 S2 subunit in a tandem manner, which can self-assemble into a trimer. In multiple animal models, vaccination of RBD-HR/trimer formulated with MF59-like oil-in-water adjuvant elicited sustained humoral immune response with high levels of broad-spectrum neutralizing antibodies against Omicron variants, also inducing a strong T cell immune response in vivo. In addition, our RBD-HR/trimer vaccine showed a strong boosting effect against Omicron variants after two doses of mRNA vaccines, featuring its capacity to be used in a prime-boost regimen. In mice and non-human primates, RBD-HR/trimer vaccination could confer a complete protection against live virus challenge of Omicron and Delta variants. The results qualified RBD-HR/trimer vaccine as a promising next-generation vaccine candidate for prevention of SARS-CoV-2, which deserved further evaluation in clinical trials.
Leakage does not fully offset soy supply-chain efforts to reduce deforestation in Brazil
Authors: Villoria Nelson , Garrett Rachael , Gollnow Florian , Carlson Kimberly 
Published: September 2022

AbstractZero-deforestation supply chain policies that leverage the market power of commodity buyers to change agricultural producer behavior can reduce forest clearing in regions with rapid commodity expansion and weak forest governance. Yet leakage—when deforestation is pushed to other regions—may dilute the global effectiveness of regionally successful policies. Here we show that domestic leakage offsets 43-50% of the avoided deforestation induced by existing and proposed zero-deforestation supply chain policies in Brazil’s soy sector. However, cross-border leakage is insignificant (<3%) because soybean production is displaced to existing U.S. farmland. Eliminating deforestation from the supply chains of all firms exporting Brazilian soy to the EU or China from 2011-2016 could have reduced net global deforestation by 2% and Brazilian deforestation by 9%. Thus, if major tropical commodity importers (e.g., the EU) require traders to eliminate deforestation from their supply chains, it could help bend the curve on global forest loss.
Phylogeographic analysis reveals an ancient East African origin of human herpes simplex virus 2 dispersal out-of-Africa
Authors: Havens Jennifer L. , Calvignac-Spencer Sébastien , Merkel Kevin , Burrel Sonia , Boutolleau David , Wertheim Joel O. 
Published: September 2022

AbstractHuman herpes simplex virus 2 (HSV-2) is a ubiquitous, slowly evolving DNA virus. HSV-2 has two primary lineages, one found in West and Central Africa and the other found worldwide. Competing hypotheses have been proposed to explain how HSV-2 migrated out-of-Africa (i)HSV-2 followed human migration out-of-Africa 50-100 thousand years ago, or (ii)HSV-2 migrated via the trans-Atlantic slave trade 150-500 years ago. Limited geographic sampling and lack of molecular clock signal has precluded robust comparison. Here, we analyze newly sequenced HSV-2 genomes from Africa to resolve geography and timing of divergence events within HSV-2. Phylogeographic analysis consistently places the ancestor of worldwide dispersal in East Africa, though molecular clock is too slow to be detected using available data. Rates 4.2 × 10−8−5.6 × 10−8 substitutions/site/year, consistent with previous age estimates, suggest a worldwide dispersal 22-29 thousand years ago. Thus, HSV-2 likely migrated with humans from East Africa and dispersed after the Last Glacial Maximum.
Mechanism of C-N bonds formation in electrocatalytic urea production revealed by ab initio molecular dynamics simulation
Authors: Liu Xin , Jiao Yan , Zheng Yao , Jaroniec Mietek , Qiao Shi-Zhang 
Published: September 2022

AbstractElectrosynthesis of urea from CO2 and NOX provides an exceptional opportunity for human society, given the increasingly available renewable energy. Urea electrosynthesis is challenging. In order to raise the overall electrosynthesis efficiency, the most critical reaction step for such electrosynthesis, C-N coupling, needs to be significantly improved. The C-N coupling can only happen at a narrow potential window, generally in the low overpotential region, and a fundamental understanding of the C-N coupling is needed for further development of this strategy. In this regard, we perform ab initio Molecular Dynamics simulations to reveal the origin of C-N coupling under a small electrode potential window with both the dynamic nature of water as a solvent, and the electrode potentials considered. We explore the key reaction networks for urea formation on Cu(100) surface in neutral electrolytes. Our work shows excellent agreement with experimentally observed selectivity under different potentials on the Cu electrode. We discover that the *NH and *CO are the key precursors for C-N bonds formation at low overpotential, while at high overpotential the C-N coupling occurs between adsorbed *NH and solvated CO. These insights provide vital information for future spectroscopic measurements and enable us to design new electrochemical systems for more value-added chemicals.
Linking atomic structural defects to mesoscale properties in crystalline solids using graph neural networks
Authors: Yang Zhenze , Buehler Markus J. 
Published: September 2022

AbstractStructural defects are abundant in solids, and vital to the macroscopic materials properties. However, a defect-property linkage typically requires significant efforts from experiments or simulations, and often contains limited information due to the breadth of nanoscopic design space. Here we report a graph neural network (GNN)-based approach to achieve direct translation between mesoscale crystalline structures and atom-level properties, emphasizing the effects of structural defects. Our end-to-end method offers great performance and generality in predicting both atomic stress and potential energy of multiple systems with different defects. Furthermore, the approach also precisely captures derivative properties which strictly observe physical laws and reproduces evolution of properties with varying boundary conditions. By incorporating a genetic algorithm, we then design de novo atomic structures with optimum global properties and target local patterns. The method would significantly enhance the efficiency of evaluating atomic behaviors given structural imperfections and accelerates the design process at the meso-level.
High-throughput screening of room temperature active Peltier cooling materials in Heusler compounds
Authors: Luo Huifang , Li Xin , Wang Yuxiang , Jin Yeqing , Yao Mingjia , Yang Jiong 
Published: September 2022

AbstractActive Peltier cooling enables Peltier heat transfer in addition to the traditional Fourier thermal conductance, which is useful in some special applications, such as the microthermostats. From the material wise, however, the study on the active Peltier cooling materials is rare. We carried out a high-throughput workflow to screen out 5 room-temperature active Peltier cooling materials, GaSbLi2, HgPbCa2, SnTiRu2, GeYbLi2, and GeTiFe2, from 2958 Heusler materials. All the five materials are semimetals or very narrow band gap systems with high electrical conductivity. Some of these materials have relatively large Seebeck coefficients due to the band asymmetry. Their effective thermal conductivity κeffs, which are the summation of active Peltier thermal conductivity and passive thermal conductivity, are all greater than Cu at the room temperature and ΔT = 1 K. The present work gives a possible way to search active cooling Peltier materials for the applications of precise temperature control.
Critical topology and pressure-induced superconductivity in the van der Waals compound AuTe2Br
Authors: Cheng Erjian , Shi Xianbiao , Yan Limin , Huang Tianheng , Liu Fengliang , Ma Wenlong , Wang Zeji , Jia Shuang , Sun Jian , Zhao Weiwei , Yang Wenge , Xu Yang , Li Shiyan 
Published: September 2022

AbstractThe study on quantum spin Hall effect and topological insulators formed the prologue to the surge of research activities in topological materials in the past decade. Compared to intricately engineered quantum wells, three-dimensional weak topological insulators provide a natural route to the quantum spin Hall effect, due to the adiabatic connection between them and a stack of quantum spin Hall insulators, and the convenience in exfoliation of samples associated with their van der Waals-type structure. Despite these advantages, both theoretical prediction and experimental identification of weak topological insulators remain scarce. Here, based on first-principles calculations, we show that AuTe2Br locates at the boundary between a strong and a weak topological semimetal state. We identify the key structural parameter that dictates the traversal of the topological transition, which can be easily realized in experiments. More interestingly, the critical topology of AuTe2Br persists up to an applied pressure of ~15.4 GPa before a structural phase transition accompanied by a change of electronic topology and the onset of superconductivity. Our results establish AuTe2Br as a new candidate for an effective tuning between weak and strong topological phases in a single material, with the potential to realize various other topological phases of matter.
A national-scale land cover reference dataset from local crowdsourcing initiatives in Indonesia
Authors: Hadi  , Yowargana Ping , Zulkarnain Muhammad Thoha , Mohamad Fathir , Goib Bunga K. , Hultera Paul , Sturn Tobias , Karner Mathias , Dürauer Martina , See Linda , Fritz Steffen , Hendriatna Adis , Nursafingi Afi , Melati Dian Nuraini , Prasetya F. V. Astrolabe Sian , Carolita Ita , Kiswanto  , Firdaus Muhammad Iqbal , Rosidi Muhammad , Kraxner Florian 
Published: September 2022

AbstractHere we present a geographically diverse, temporally consistent, and nationally relevant land cover (LC) reference dataset collected by visual interpretation of very high spatial resolution imagery, in a national-scale crowdsourcing campaign (targeting seven generic LC classes) and a series of expert workshops (targeting seventeen detailed LC classes) in Indonesia. The interpreters were citizen scientists (crowd/non-experts) and local LC visual interpretation experts from different regions in the country. We provide the raw LC reference dataset, as well as a quality-filtered dataset, along with the quality assessment indicators. We envisage that the dataset will be relevant for: (1) the LC mapping community (researchers and practitioners), i.e., as reference data for training machine learning algorithms and map accuracy assessment (with appropriate quality-filters applied), and (2) the citizen science community, i.e., as a sizable empirical dataset to investigate the potential and limitations of contributions from the crowd/non-experts, demonstrated for LC mapping in Indonesia for the first time to our knowledge, within the context of complementing traditional data collection by expert interpreters.
Electrical conductivity and thermodynamic studies on Sodium Dimethyldithiocarbamate in non aqueous solvents Dimethylformamide (DMF), at different temperatures
Authors: Hammad W. A. , El-Hammamy N. H. , Morshidy M. H. , Alkamis Kholood , Darweesh M. A. 
Published: September 2022

AbstractThis paper threw some light on the behavior of SodiumN,N-Dimethyldithiocarbamate as an electrolyte. The effect of solvents on the conductance of this salt would be discussed via measurements of Λo, aoand KA, since it can be assumed that the different solvents have a little chance to impose great variations on the solvation processes. The conductance method was chosen as a tool to illustrate the electrolyte-solvent interactions. Fuoss–Onsager equation would be tested using Sodium Dimethyldithiocarbamate in presence of dimethylformamide solvent at different temperatures. The conductance of dilute solutions of SodiumN,N-Dimethyldithiocarbamate is measured in Dimethylformamide, at different temperatures (25, 30, 35 and 40 °C). Accurate values ofΛowere obtained by applying the (Fuoss–Kraus–Shedlovsky) equation. Finally, the (Fuoss–Onsager) equation was solved to give the correct values of the constantsΛo,J, KAand a° (the closest distance of approach) for SodiumN,N-Dimethyldithiocarbamate salt in Dimethylformamide solvent.Λoand a° (solvation) increase with increasing temperatures. Thermodynamic parameters (∆G°, ∆H°, ∆S° and ∆Es) of SodiumN,N-Dimethyldithiocarbamate in Dimethylformamide were calculated from conductance measurements, the activation energy (∆Es), the enthalpy change (heat of association) (∆H°) and the entropy change (∆S°) are positive, however The free energy change (∆G°) values was negative for SodiumN,N-Dimethyl dithiocarbamate in DMF systems studied with increasing the temperature.
Cancer stem cells induced by chronic stimulation with prostaglandin E2 exhibited constitutively activated PI3K axis
Authors: Minematsu Hideki , Afify Said M. , Sugihara Yuki , Hassan Ghmkin , Zahra Maram H. , Seno Akimasa , Adachi Masaki , Seno Masaharu 
Published: September 2022

AbstractPreviously, our group has demonstrated establishment of Cancer Stem Cell (CSC) models from stem cells in the presence of conditioned medium of cancer cell lines. In this study, we tried to identify the factors responsible for the induction of CSCs. Since we found the lipid composition could be traced to arachidonic acid cascade in the CSC model, we assessed prostaglandin E2 (PGE2) as a candidate for the ability to induce CSCs from induced pluripotent stem cells (iPSCs). Mouse iPSCs acquired the characteristics of CSCs in the presence of 10 ng/mL of PGE2 after 4 weeks. Since constitutive Akt activation and pik3cg overexpression were found in the resultant CSCs, of which growth was found independent of PGE2, chronic stimulation of the receptors EP-2/4 by PGE2 was supposed to induce CSCs from iPSCs through epigenetic effect. The bioinformatics analysis of the next generation sequence data of the obtained CSCs proposed not only receptor tyrosine kinase activation by growth factors but also extracellular matrix and focal adhesion enhanced PI3K pathway. Collectively, chronic stimulation of stem cells with PGE2 was implied responsible for cancer initiation enhancing PI3K/Akt axis.
Explainable machine learning analysis reveals sex and gender differences in the phenotypic and neurobiological markers of Cannabis Use Disorder
Authors: Niklason Gregory R. , Rawls Eric , Ma Sisi , Kummerfeld Erich , Maxwell Andrea M. , Brucar Leyla R. , Drossel Gunner , Zilverstand Anna 
Published: September 2022

AbstractCannabis Use Disorder (CUD) has been linked to a complex set of neuro-behavioral risk factors. While many studies have revealed sex and gender differences, the relative importance of these risk factors by sex and gender has not been described. We used an “explainable” machine learning approach that combined decision trees [gradient tree boosting, XGBoost] with factor ranking tools [SHapley’s Additive exPlanations (SHAP)] to investigate sex and gender differences in CUD. We confirmed that previously identified environmental, personality, mental health, neurocognitive, and brain factors highly contributed to the classification of cannabis use levels and diagnostic status. Risk factors with larger effect sizes in men included personality (high openness), mental health (high externalizing, high childhood conduct disorder, high fear somaticism), neurocognitive (impulsive delay discounting, slow working memory performance) and brain (low hippocampal volume) factors. Conversely, risk factors with larger effect sizes in women included environmental (low education level, low instrumental support) factors. In summary, environmental factors contributed more strongly to CUD in women, whereas individual factors had a larger importance in men.
Underestimation in temporal numerosity judgments computationally explained by population coding model
Authors: Kawabe Takahiro , Ujitoko Yusuke , Yokosaka Takumi , Kuroki Scinob 
Published: September 2022

AbstractThe ability to judge numerosity is essential to an animal’s survival. Nevertheless, the number of signals presented in a sequence is often underestimated. We attempted to elucidate the mechanism for the underestimation by means of computational modeling based on population coding. In the model, the population of neurons which were selective to the logarithmic number of signals responded to sequential signals and the population activity was integrated by a temporal window. The total number of signals was decoded by a weighted average of the integrated activity. The model predicted well the general trends in the human data while the prediction was not fully sufficient for the novel aging effect wherein underestimation was significantly greater for the elderly than for the young in specific stimulus conditions. Barring the aging effect, we can conclude that humans judge the number of signals in sequence by temporally integrating the neural representations of numerosity.
Somalian women with female genital mutilation had increased risk of female sexual dysfunction: a cross-sectional observational study
Authors: Mohamed Abdikarim Hussein , Mohamud Rahma Yusuf Haji , Mohamud Hussein Ali , Eraslan Aşır , Gur Metin , Omar Abdikarim Ali , Cimen Sertac 
Published: September 2022

AbstractStudies regarding the impact of female genital mutilation/cutting (FGM/C) on sexual function are scarce. This study is the first to explore the rate of female sexual dysfunction (FSD) among Somalian women who underwent FGM and its association with different FGM types. This study was carried out among women with a history of FGM who visited our clinic for a medical check-up. It relied on data including socio-demographic features, type of FGM determined by an examination, and the Female Sexual Function Index (FSFI) scores. Overall, 255 women were included. While 43.9% (n = 112) of the respondents had a history of Type 3 FGM, 32.2% had Type 2 (n = 82), and 23.9% had Type 1 (n = 61) FGM. Among all patients, 223 had FSD (87.6%). There was a significant association between the FGM type and FSD (p < 0.001). The mean total FSFI score for the patients with Type 1, 2, and 3 FGM was 22.5, 19.7, and 17.3, respectively, all indicating FSD. The FSD is prevalent among mutilated Somalian women. Patients with Type 3 FGM had the lowest mean total FSFI scores indicating that the impact on sexual function was correlated with the extent of tissue damage during FGM.
On the influence of the source of porcine colostrum in the development of early immune ontogeny in piglets
Authors: Maciag Shaiana Salete , Bellaver Franciana Volpato , Bombassaro Gabrielly , Haach Vanessa , Morés Marcos Antônio Zanella , Baron Lana Flávia , Coldebella Arlei , Bastos Ana Paula 
Published: September 2022

AbstractThe effects on the ontogeny of serum cytokines and immune cells caused by feeding suckling piglets with sow/gilt colostrum and milk replacer was assessed in the present study. After farrowing, the piglets born were randomized into six groups: GG and SS (n = 10/group): piglets were kept with their dam; GS (n = 10): piglets were changed from gilts to sows; SG (n = 10): piglets were changed from sows to gilts; GMR (n = 6) and SMR (n = 8): piglets from either gilts or sows were isolated from the dams and were bottle-fed ad libitum with commercial formula milk replacer. The piglets remained in the groups during the first 24 h of life and were later returned to their respective mothers. Serum immunoglobulin concentration and lymphocyte proliferation from the blood, spleen, thymus, and mesenteric lymph node of the piglets were assessed at 24 h and at 28 days of age. Serum cytokine concentrations were measured through a cytokine multiplex assay at 24 h. Overall, piglets suckling on sows (SS and GS) had a higher concentration of serum immunoglobulin at 24 h, which was also associated with a rise in plasma cytokine concentration and greater ability of B and T cells from lymphatic organs and blood mononuclear cells to respond to mitogens. We suggest a bias towards Th1-, Th2-, and Th17-cell polarizing and cytokines during the suckling period, which may be influenced by maternal immunological factors in the colostrum, such as dam parity. All findings suggest sow parity having a possible role, which may contribute to exerting a modulating action on immune response development.
An international working group consensus report for the prioritization of molecular biomarkers for Ewing sarcoma
Authors: Shulman David S. , Whittle Sarah B. , Surdez Didier , Bailey Kelly M. , de Álava Enrique , Yustein Jason T. , Shlien Adam , Hayashi Masanori , Bishop Alexander J. R. , Crompton Brian D. , DuBois Steven G. , Shukla Neerav , Leavey Patrick J. , Lessnick Stephen L. , Kovar Heinrich , Delattre Olivier , Grünewald Thomas G. P. , Antonescu Cristina R. , Roberts Ryan D. , Toretsky Jeffrey A. , Tirode Franck , Gorlick Richard , Janeway Katherine A. , Reed Damon , Lawlor Elizabeth R. , Grohar Patrick J. 
Published: September 2022

AbstractThe advent of dose intensified interval compressed therapy has improved event-free survival for patients with localized Ewing sarcoma (EwS) to 78% at 5 years. However, nearly a quarter of patients with localized tumors and 60–80% of patients with metastatic tumors suffer relapse and die of disease. In addition, those who survive are often left with debilitating late effects. Clinical features aside from stage have proven inadequate to meaningfully classify patients for risk-stratified therapy. Therefore, there is a critical need to develop approaches to risk stratify patients with EwS based on molecular features. Over the past decade, new technology has enabled the study of multiple molecular biomarkers in EwS. Preliminary evidence requiring validation supports copy number changes, and loss of function mutations in tumor suppressor genes as biomarkers of outcome in EwS. Initial studies of circulating tumor DNA demonstrated that diagnostic ctDNA burden and ctDNA clearance during induction are also associated with outcome. In addition, fusion partner should be a pre-requisite for enrollment on EwS clinical trials, and the fusion type and structure require further study to determine prognostic impact. These emerging biomarkers represent a new horizon in our understanding of disease risk and will enable future efforts to develop risk-adapted treatment.