bluuebunny/crossref_metadata_2025_split huggingface dataset:
Persistent spin texture enforced by symmetry
Authors: Tao L. L. , Tsymbal Evgeny Y. 
Published: July 2018

AbstractPersistent spin texture (PST) is the property of some materials to maintain a uniform spin configuration in the momentum space. This property has been predicted to support an extraordinarily long spin lifetime of carriers promising for spintronics applications. Here, we predict that there exists a class of noncentrosymmetric bulk materials, where the PST is enforced by the nonsymmorphic space group symmetry of the crystal. Around certain high symmetry points in the Brillouin zone, the sublattice degrees of freedom impose a constraint on the effective spin–orbit field, which orientation remains independent of the momentum and thus maintains the PST. We illustrate this behavior using density-functional theory calculations for a handful of promising candidates accessible experimentally. Among them is the ferroelectric oxide BiInO3—a wide band gap semiconductor which sustains a PST around the conduction band minimum. Our results broaden the range of materials that can be employed in spintronics.
Cold deep subduction recorded by remnants of a Paleoproterozoic carbonated slab
Authors: Xu Cheng , Kynický Jindřich , Song Wenlei , Tao Renbiao , Lü Zeng , Li Yunxiu , Yang Yueheng , Pohanka Miroslav , Galiova Michaela V. , Zhang Lifei , Fei Yingwei 
Published: July 2018

AbstractThe absence of low-thermal gradients in old metamorphic rocks (<350 °C GPa−1) has been used to argue for a fundamental change in the style of plate tectonics during the Neoproterozoic Era. Here, we report data from an eclogite xenolith in Paleoproterozoic carbonatite in the North China craton that argues for cold subduction as early as 1.8 Ga. The carbonatite has a sediment-derived C isotope signature and enriched initial Sr–Nd isotope composition, indicative of ocean-crust components in the source. The eclogite records peak metamorphic pressures of 2.5–2.8 GPa at 650–670 °C, indicating a cold thermal gradient, 250(±15) °C GPa−1. Our data, combined with old low-temperature events in the West African and North American cratons, reveal a global pattern that modern-style subduction may have been established during the Paleoproterozoic Era. Paleoproterozoic carbonatites are closely associated with granulites and eclogites in orogens worldwide, playing a critical role in the Columbia supercontinent amalgamation and deep carbon cycle through time.
Exchange-biasing topological charges by antiferromagnetism
Authors: He Qing Lin , Yin Gen , Grutter Alexander J. , Pan Lei , Che Xiaoyu , Yu Guoqiang , Gilbert Dustin A. , Disseler Steven M. , Liu Yizhou , Shafer Padraic , Zhang Bin , Wu Yingying , Kirby Brian J. , Arenholz Elke , Lake Roger K. , Han Xiaodong , Wang Kang L. 
Published: July 2018

AbstractGeometric Hall effect is induced by the emergent gauge field experienced by the carriers adiabatically passing through certain real-space topological spin textures, which is a probe to non-trivial spin textures, such as magnetic skyrmions. We report experimental indications of spin-texture topological charges induced in heterostructures of a topological insulator (Bi,Sb)2Te3 coupled to an antiferromagnet MnTe. Through a seeding effect, the pinned spins at the interface leads to a tunable modification of the averaged real-space topological charge. This effect experimentally manifests as a modification of the field-dependent geometric Hall effect when the system is field-cooled along different directions. This heterostructure represents a platform for manipulating magnetic topological transitions using antiferromagnetic order.
A TRAF3-NIK module differentially regulates DNA vs RNA pathways in innate immune signaling
Authors: Parvatiyar Kislay , Pindado Jose , Dev Anurupa , Aliyari Saba Roghiyh , Zaver Shivam A. , Gerami Hoda , Chapon Maxime , Ghaffari Amir A. , Dhingra Anant , Cheng Genhong 
Published: July 2018

AbstractDetection of viral genomes by the innate immune system elicits an antiviral gene program mediated by type I interferons (IFNs). While viral RNA and DNA species induce IFN via separate pathways, the mechanisms by which these pathways are differentially modulated are unknown. Here we show that the positive regulator of IFN in the RNA pathway, TRAF3, has an inhibitory function in the DNA pathway. Loss of TRAF3 coincides with increased expression of the alternative NF-κB-inducing molecule, NIK, which interacts with the DNA pathway adaptor, STING, to enhance IFN induction. Cells lacking NIK display defective IFN activation in the DNA pathway due to impaired STING signaling, and NIK-deficient mice are more susceptible to DNA virus infection. Mechanistically, NIK operates independently from alternative NF-κB signaling components and instead requires autophosphorylation and oligomerization to activate STING. Thus a previously undescribed pathway for NIK exists in activating IFN in the DNA pathway.
Insightful classification of crystal structures using deep learning
Authors: Ziletti Angelo , Kumar Devinder , Scheffler Matthias , Ghiringhelli Luca M. 
Published: July 2018

AbstractComputational methods that automatically extract knowledge from data are critical for enabling data-driven materials science. A reliable identification of lattice symmetry is a crucial first step for materials characterization and analytics. Current methods require a user-specified threshold, and are unable to detect average symmetries for defective structures. Here, we propose a machine learning-based approach to automatically classify structures by crystal symmetry. First, we represent crystals by calculating a diffraction image, then construct a deep learning neural network model for classification. Our approach is able to correctly classify a dataset comprising more than 100,000 simulated crystal structures, including heavily defective ones. The internal operations of the neural network are unraveled through attentive response maps, demonstrating that it uses the same landmarks a materials scientist would use, although never explicitly instructed to do so. Our study paves the way for crystal structure recognition of—possibly noisy and incomplete—three-dimensional structural data in big-data materials science.
The replication initiation determinant protein (RepID) modulates replication by recruiting CUL4 to chromatin
Authors: Jang Sang-Min , Zhang Ya , Utani Koichi , Fu Haiqing , Redon Christophe E. , Marks Anna B. , Smith Owen K. , Redmond Catherine J. , Baris Adrian M. , Tulchinsky Danielle A. , Aladjem Mirit I. 
Published: July 2018

AbstractCell cycle progression in mammals is modulated by two ubiquitin ligase complexes, CRL4 and SCF, which facilitate degradation of chromatin substrates involved in the regulation of DNA replication. One member of the CRL4 complex, the WD-40 containing protein RepID (DCAF14/PHIP), selectively binds and activates a group of replication origins. Here we show that RepID recruits the CRL4 complex to chromatin prior to DNA synthesis, thus playing a crucial architectural role in the proper licensing of chromosomes for replication. In the absence of RepID, cells rely on the alternative ubiquitin ligase, SKP2-containing SCF, to progress through the cell cycle. RepID depletion markedly increases cellular sensitivity to SKP2 inhibitors, which triggered massive genome re-replication. Both RepID and SKP2 interact with distinct, non-overlapping groups of replication origins, suggesting that selective interactions of replication origins with specific CRL components execute the DNA replication program and maintain genomic stability by preventing re-initiation of DNA replication.
Highly active enzymes by automated combinatorial backbone assembly and sequence design
Authors: Lapidoth Gideon , Khersonsky Olga , Lipsh Rosalie , Dym Orly , Albeck Shira , Rogotner Shelly , Fleishman Sarel J. 
Published: July 2018

AbstractAutomated design of enzymes with wild-type-like catalytic properties has been a long-standing but elusive goal. Here, we present a general, automated method for enzyme design through combinatorial backbone assembly. Starting from a set of homologous yet structurally diverse enzyme structures, the method assembles new backbone combinations and uses Rosetta to optimize the amino acid sequence, while conserving key catalytic residues. We apply this method to two unrelated enzyme families with TIM-barrel folds, glycoside hydrolase 10 (GH10) xylanases and phosphotriesterase-like lactonases (PLLs), designing 43 and 34 proteins, respectively. Twenty-one GH10 and seven PLL designs are active, including designs derived from templates with <25% sequence identity. Moreover, four designs are as active as natural enzymes in these families. Atomic accuracy in a high-activity GH10 design is further confirmed by crystallographic analysis. Thus, combinatorial-backbone assembly and design may be used to generate stable, active, and structurally diverse enzymes with altered selectivity or activity.
Direct observation of DNA target searching and cleavage by CRISPR-Cas12a
Authors: Jeon Yongmoon , Choi You Hee , Jang Yunsu , Yu Jihyeon , Goo Jiyoung , Lee Gyejun , Jeong You Kyeong , Lee Seung Hwan , Kim In-San , Kim Jin-Soo , Jeong Cherlhyun , Lee Sanghwa , Bae Sangsu 
Published: July 2018

AbstractCas12a (also called Cpf1) is a representative type V-A CRISPR effector RNA-guided DNA endonuclease, which provides an alternative to type II CRISPR–Cas9 for genome editing. Previous studies have revealed that Cas12a has unique features distinct from Cas9, but the detailed mechanisms of target searching and DNA cleavage by Cas12a are still unclear. Here, we directly observe this entire process by using single-molecule fluorescence assays to study Cas12a from Acidaminococcus sp. (AsCas12a). We determine that AsCas12a ribonucleoproteins search for their on-target site by a one-dimensional diffusion along elongated DNA molecules and induce cleavage in the two DNA strands in a well-defined order, beginning with the non-target strand. Furthermore, the protospacer-adjacent motif (PAM) for AsCas12a makes only a limited contribution of DNA unwinding during R-loop formation and shows a negligible role in the process of DNA cleavage, in contrast to the Cas9 PAM.
MiR-221/222 promote epithelial-mesenchymal transition by targeting Notch3 in breast cancer cell lines
Authors: Liang Yuan-Ke , Lin Hao-Yu , Dou Xiao-Wei , Chen Min , Wei Xiao-Long , Zhang Yong-Qu , Wu Yang , Chen Chun-Fa , Bai Jing-Wen , Xiao Ying-Sheng , Qi Yu-Zhu , Kruyt Frank A. E. , Zhang Guo-Jun 
Published: July 2018

AbstractBasal-like breast cancer (BLBC) is an aggressive subtype with a strong tendency to metastasize. Due to the lack of effective chemotherapy, BLBC has a poor prognosis compared with luminal subtype breast cancer. MicroRNA-221 and -222 (miR-221/222) are overexpressed in BLBC and associate with metastasis as well as poor prognosis; however, the mechanisms by which miR-221/222 function as oncomiRs remain unknown. Here, we report that miR-221/222 expression is inversely correlated with Notch3 expression in breast cancer cell lines. Notch3 is known to be overexpressed in luminal breast cancer cells and inhibits epithelial to mesenchymal transition (EMT). We demonstrate that miR-221/222 target Notch3 by binding to its 3′ untranslated region and suppressing protein translation. Ectopic expression of miR-221/222 significantly promotes EMT, whereas overexpression of Notch3 intracellular domain attenuates the oncogenic function of miR-221/222, suggesting that miR-221/222 exerts its oncogenic role by negatively regulating Notch3. Taken together, our results elucidated that miR-221/222 promote EMT via targeting Notch3 in breast cancer cell lines suggesting that miR-221/222 can serve as a potential therapeutic target in BLBC.
Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome
Authors: Sork Helena , Corso Giulia , Krjutskov Kaarel , Johansson Henrik J. , Nordin Joel Z. , Wiklander Oscar P. B. , Lee Yi Xin Fiona , Westholm Jakub Orzechowski , Lehtiö Janne , Wood Matthew J. A. , Mäger Imre , EL Andaloussi Samir 
Published: July 2018

AbstractExtracellular vesicles (EVs) mediate cell-to-cell communication by delivering or displaying macromolecules to their recipient cells. While certain broad-spectrum EV effects reflect their protein cargo composition, others have been attributed to individual EV-loaded molecules such as specific miRNAs. In this work, we have investigated the contents of vesicular cargo using small RNA sequencing of cells and EVs from HEK293T, RD4, C2C12, Neuro2a and C17.2. The majority of RNA content in EVs (49–96%) corresponded to rRNA-, coding- and tRNA fragments, corroborating with our proteomic analysis of HEK293T and C2C12 EVs which showed an enrichment of ribosome and translation-related proteins. On the other hand, the overall proportion of vesicular small RNA was relatively low and variable (2-39%) and mostly comprised of miRNAs and sequences mapping to piRNA loci. Importantly, this is one of the few studies, which systematically links vesicular RNA and protein cargo of vesicles. Our data is particularly useful for future work in unravelling the biological mechanisms underlying vesicular RNA and protein sorting and serves as an important guide in developing EVs as carriers for RNA therapeutics.
A Universal Live Cell Barcoding-Platform for Multiplexed Human Single Cell Analysis
Authors: Hartmann Felix J. , Simonds Erin F. , Bendall Sean C. 
Published: July 2018

AbstractSingle-cell barcoding enables the combined processing and acquisition of multiple individual samples as one. This maximizes assay efficiency and eliminates technical variability in both sample preparation and analysis. Remaining challenges are the barcoding of live, unprocessed cells to increase downstream assay performance combined with the flexibility of the approach towards a broad range of cell types. To that end, we developed a novel antibody-based platform that allows the robust barcoding of live human cells for mass cytometry (CyTOF). By targeting both the MHC class I complex (beta-2-microglobulin) and a broadly expressed sodium-potassium ATPase-subunit (CD298) with platinum-conjugated antibodies, human immune cells, stem cells as well as tumor cells could be multiplexed in the same single-cell assay. In addition, we present a novel palladium-based covalent viability reagent compatible with this barcoding strategy. Altogether, this platform enables mass cytometry-based, live-cell barcoding across a multitude of human sample types and provides a scheme for multiplexed barcoding of human single-cell assays in general.
Strontium isotope analysis on cremated human remains from Stonehenge support links with west Wales
Authors: Snoeck Christophe , Pouncett John , Claeys Philippe , Goderis Steven , Mattielli Nadine , Parker Pearson Mike , Willis Christie , Zazzo Antoine , Lee-Thorp Julia A. , Schulting Rick J. 
Published: July 2018

AbstractCremated human remains from Stonehenge provide direct evidence on the life of those few select individuals buried at this iconic Neolithic monument. The practice of cremation has, however, precluded the application of strontium isotope analysis of tooth enamel as the standard chemical approach to study their origin. New developments in strontium isotopic analysis of cremated bone reveal that at least 10 of the 25 cremated individuals analysed did not spend their lives on the Wessex chalk on which the monument is found. Combined with the archaeological evidence, we suggest that their most plausible origin lies in west Wales, the source of the bluestones erected in the early stage of the monument’s construction. These results emphasise the importance of inter-regional connections involving the movement of both materials and people in the construction and use of Stonehenge.
The associations between maternal lifestyles and antenatal stress and anxiety in Chinese pregnant women: A cross-sectional study
Authors: Hou Qingzhi , Li Shanshan , Jiang Chao , Huang Yaling , Huang Lulu , Ye Juan , Pan Zhijian , Teng Tao , Wang Qiuyan , Jiang Yonghua , Zhang Haiying , Liu Chaoqun , Li Mujun , Mo Zengnan , Yang Xiaobo 
Published: July 2018

AbstractThe study aimed to investigate the associations between maternal lifestyles and antenatal stress and anxiety. 1491 pregnant women were drawn from the Guangxi birth cohort study (GBCS). A base line questionnaire was used to collect demographic information and maternal lifestyles. The Pregnancy Stress Rating Scale (PSRS) and Self-Rating Anxiety Scale (SAS) were used to assess prenatal stress and anxiety, respectively. Regression analyses identified the relationship between maternal lifestyles and prenatal stress and anxiety: (1) Hours of phone use per day was positively correlated to prenatal stress and anxiety and increased with stress and anxiety levels (all P trend < 0.05). In addition, not having baby at home was positively correlated to prenatal stress. (2) Self-reported sleep quality was negative with prenatal stress and anxiety, and decreased with stress and anxiety levels (all P trend < 0.01). Moreover, not frequent cooking was negatively correlated to prenatal stress and having pets was negatively correlated to prenatal anxiety (P < 0.05). However, having pets was not correlated to prenatal stress (P > 0.05). Our results showed that adverse lifestyles increase the risk of antenatal stress and anxiety, a regular routine and a variety of enjoyable activities decreases the risk of prenatal stress and anxiety.
Socioeconomic determinants of sarcopenic obesity and frail obesity in community-dwelling older adults: The Seniors-ENRICA Study
Authors: Moreno-Franco Belén , Pérez-Tasigchana Raúl F. , Lopez-Garcia Esther , Laclaustra Martin , Gutierrez-Fisac Juan L. , Rodríguez-Artalejo Fernando , Guallar-Castillón Pilar 
Published: July 2018

AbstractInformation on the association between socioeconomic status (SES) throughout life and sarcopenic obesity is scarce, whereas no study has been focused on the association between SES and frail obesity. This analysis estimated the prevalence of sarcopenic obesity and frail obesity, and their associations with SES in older adults. Data were collected in 2012 from 1,765 non-institutionalized individuals aged ≥65 participating in the Seniors-ENRICA study in Spain, by using standardized techniques and equipment. SES throughout life was evaluated with the father’s occupation, participant’s educational level, former own occupation, and current poor housing condition. Overall, 17.2% of participants had sarcopenic obesity, and 4.0% frail obesity. No association was found between SES and sarcopenic obesity. In contrast, the prevalence of frail obesity was higher in those with lower education, having worked in manual job, and currently having poor housing condition. Having ≥1 social disadvantages throughout life was associated with higher prevalence of frail obesity. The prevalence of this disorder increased by 1.49 (95% CI: 1.21–1.85) times for each social disadvantage added. The OR (95% CI) of frail obesity was 3.13 (1.71–5.7) for those having 3 or 4 vs. 0 or 1 social disadvantages, implying a more complex process beginning early in life.
Development of nsP2 protease based cell free high throughput screening assay for evaluation of inhibitors against emerging Chikungunya virus
Authors: Saha Amrita , Acharya Badri Narayan , Priya Raj , Tripathi Nagesh K. , Shrivastava Ambuj , Rao M. Kameswara , Kesari Pooja , Narwal Manju , Tomar Shailly , Bhagyawant Sameer S. , Parida Manmohan , Dash Paban Kumar 
Published: July 2018

AbstractChikungunya virus has emerged as one of the most important global arboviral threats over the last decade. Inspite of large scale morbidity, with long lasting polyarthralgia, so far no licensed vaccine or antiviral is available. CHIKV nsP2 protease is crucial for processing of viral nonstructural polypeptide precursor to release enzymes required for viral replication, thus making it a promising drug target. In this study, high cell density cultivation (HCDC) ofEscherichia coliin batch process was carried out to produce rCHIKV nsP2pro in a cost-effective manner. The purified nsP2pro and fluorogenic peptide substrate have been adapted for fluorescence resonance energy transfer (FRET) based high throughput screening (HTS) assay with Z’ value and CV of 0.67 ± 0.054 and <10% respectively. We used this cell free HTS system to screen panel of metal ions and its conjugate which revealed zinc acetate as a potential candidate, which was further found to inhibit CHIKV in Vero cells. Scale-up process has not been previously reported for any of the arboviral nonstructural enzymes. The successful scale-up method for viral protease together with a HTS assay could lead to the development of industrial level large-scale screening platform for identification of protease inhibitors against emerging and re-emerging viruses.
Impact of Edible Cricket Consumption on Gut Microbiota in Healthy Adults, a Double-blind, Randomized Crossover Trial
Authors: Stull Valerie J. , Finer Elijah , Bergmans Rachel S. , Febvre Hallie P. , Longhurst Colin , Manter Daniel K. , Patz Jonathan A. , Weir Tiffany L. 
Published: July 2018

AbstractEdible insects are often considered a nutritious, protein-rich, environmentally sustainable alternative to traditional livestock with growing popularity among North American consumers. While the nutrient composition of several insects is characterized, all potential health impacts have not been evaluated. In addition to high protein levels, crickets contain chitin and other fibers that may influence gut health. In this study, we evaluated the effects of consuming 25 grams/day whole cricket powder on gut microbiota composition, while assessing safety and tolerability. Twenty healthy adults participated in this six-week, double-blind, crossover dietary intervention. Participants were randomized into two study arms and consumed either cricket-containing or control breakfast foods for 14 days, followed by a washout period and assignment to the opposite treatment. Blood and stool samples were collected at baseline and after each treatment period to assess liver function and microbiota changes. Results demonstrate cricket consumption is tolerable and non-toxic at the studied dose. Cricket powder supported growth of the probiotic bacterium, Bifidobacterium animalis, which increased 5.7-fold. Cricket consumption was also associated with reduced plasma TNF-α. These data suggest that eating crickets may improve gut health and reduce systemic inflammation; however, more research is needed to understand these effects and underlying mechanisms.
Buparlisib is a brain penetrable pan-PI3K inhibitor
Authors: de Gooijer Mark C. , Zhang Ping , Buil Levi C. M. , Çitirikkaya Ceren H. , Thota Nishita , Beijnen Jos H. , van Tellingen Olaf 
Published: July 2018

AbstractCharacterization of the genomic landscapes of intracranial tumours has revealed a clear role for the PI3K-AKT-mTOR pathway in tumorigenesis and tumour maintenance of these malignancies, making phosphatidylinositol 3-kinase (PI3K) inhibition a promising therapeutic strategy for these tumours. Buparlisib is a novel pan-PI3K inhibitor that is currently in clinical development for various cancers, including primary and secondary brain tumours. Importantly however, earlier studies have revealed that sufficient brain penetration is a prerequisite for antitumor efficacy against intracranial tumours. We therefore investigated the brain penetration of buparlisib using a comprehensive set of in vitro and in vivo mouse models. We demonstrate that buparlisib has an excellent brain penetration that is unaffected by efflux transporters at the blood-brain barrier, complete oral bioavailability and efficient intracranial target inhibition at clinically achievable plasma concentrations. Together, these characteristics make buparlisib the ideal candidate for intracranially-targeted therapeutic strategies that involve PI3K inhibition.