bluuebunny/crossref_metadata_2025_split huggingface dataset:
Light helicity detector based on 2D magnetic semiconductor CrI3
Authors: Cheng Xing , Cheng Zhixuan , Wang Cong , Li Minglai , Gu Pingfan , Yang Shiqi , Li Yanping , Watanabe Kenji , Taniguchi Takashi , Ji Wei , Dai Lun 
Published: November 2021

AbstractTwo-dimensional magnetic semiconductors provide a platform for studying physical phenomena at atomically thin limit, and promise magneto-optoelectronic devices application. Here, we report light helicity detectors based on graphene-CrI3-graphene vdW heterostructures. We investigate the circularly polarized light excited current and reflective magnetic circular dichroism (RMCD) under various magnetic fields in both monolayer and multilayer CrI3 devices. The devices exhibit clear helicity-selective photoresponse behavior determined by the magnetic state of CrI3. We also find abnormal negative photocurrents at higher bias in both monolayer and multilayer CrI3. A possible explanation is proposed for this phenomenon. Our work reveals the interplay between magnetic and optoelectronic properties in CrI3 and paves the way to developing spin-optoelectronic devices.
Reprogramming microbial populations using a programmed lysis system to improve chemical production
Authors: Diao Wenwen , Guo Liang , Ding Qiang , Gao Cong , Hu Guipeng , Chen Xiulai , Li Yang , Zhang Linpei , Chen Wei , Chen Jian , Liu Liming 
Published: November 2021

AbstractMicrobial populations are a promising model for achieving microbial cooperation to produce valuable chemicals. However, regulating the phenotypic structure of microbial populations remains challenging. In this study, a programmed lysis system (PLS) is developed to reprogram microbial cooperation to enhance chemical production. First, a colicin M -based lysis unit is constructed to lyse Escherichia coli. Then, a programmed switch, based on proteases, is designed to regulate the effective lysis unit time. Next, a PLS is constructed for chemical production by combining the lysis unit with a programmed switch. As a result, poly (lactate-co-3-hydroxybutyrate) production is switched from PLH synthesis to PLH release, and the content of free PLH is increased by 283%. Furthermore, butyrate production with E. coli consortia is switched from E. coli BUT003 to E. coli BUT004, thereby increasing butyrate production to 41.61 g/L. These results indicate the applicability of engineered microbial populations for improving the metabolic division of labor to increase the efficiency of microbial cell factories.
Recent changes to Arctic river discharge
Authors: Feng Dongmei , Gleason Colin J. , Lin Peirong , Yang Xiao , Pan Ming , Ishitsuka Yuta 
Published: November 2021

AbstractArctic rivers drain ~15% of the global land surface and significantly influence local communities and economies, freshwater and marine ecosystems, and global climate. However, trusted and public knowledge of pan-Arctic rivers is inadequate, especially for small rivers and across Eurasia, inhibiting understanding of the Arctic response to climate change. Here, we calculate daily streamflow in 486,493 pan-Arctic river reaches from 1984-2018 by assimilating 9.18 million river discharge estimates made from 155,710 satellite images into hydrologic model simulations. We reveal larger and more heterogenous total water export (3-17% greater) and water export acceleration (factor of 1.2-3.3 larger) than previously reported, with substantial differences across basins, ecoregions, stream orders, human regulation, and permafrost regimes. We also find significant changes in the spring freshet and summer stream intermittency. Ultimately, our results represent an updated, publicly available, and more accurate daily understanding of Arctic rivers uniquely enabled by recent advances in hydrologic modeling and remote sensing.
Engineering transient dynamics of artificial cells by stochastic distribution of enzymes
Authors: Song Shidong , Mason Alexander F. , Post Richard A. J. , De Corato Marco , Mestre Rafael , Yewdall N. Amy , Cao Shoupeng , van der Hofstad Remco W. , Sanchez Samuel , Abdelmohsen Loai K. E. A. , van Hest Jan C. M. 
Published: November 2021

AbstractRandom fluctuations are inherent to all complex molecular systems. Although nature has evolved mechanisms to control stochastic events to achieve the desired biological output, reproducing this in synthetic systems represents a significant challenge. Here we present an artificial platform that enables us to exploit stochasticity to direct motile behavior. We found that enzymes, when confined to the fluidic polymer membrane of a core-shell coacervate, were distributed stochastically in time and space. This resulted in a transient, asymmetric configuration of propulsive units, which imparted motility to such coacervates in presence of substrate. This mechanism was confirmed by stochastic modelling and simulations in silico. Furthermore, we showed that a deeper understanding of the mechanism of stochasticity could be utilized to modulate the motion output. Conceptually, this work represents a leap in design philosophy in the construction of synthetic systems with life-like behaviors.
The structural basis for the phospholipid remodeling by lysophosphatidylcholine acyltransferase 3
Authors: Zhang Qing , Yao Deqiang , Rao Bing , Jian Liyan , Chen Yang , Hu Kexin , Xia Ying , Li Shaobai , Shen Yafeng , Qin An , Zhao Jie , Zhou Lu , Lei Ming , Jiang Xian-Cheng , Cao Yu 
Published: November 2021

AbstractAs the major component of cell membranes, phosphatidylcholine (PC) is synthesized de novo in the Kennedy pathway and then undergoes extensive deacylation-reacylation remodeling via Lands’ cycle. The re-acylation is catalyzed by lysophosphatidylcholine acyltransferase (LPCAT) and among the four LPCAT members in human, the LPCAT3 preferentially introduces polyunsaturated acyl onto the sn-2 position of lysophosphatidylcholine, thereby modulating the membrane fluidity and membrane protein functions therein. Combining the x-ray crystallography and the cryo-electron microscopy, we determined the structures of LPCAT3 in apo-, acyl donor-bound, and acyl receptor-bound states. A reaction chamber was revealed in the LPCAT3 structure where the lysophosphatidylcholine and arachidonoyl-CoA were positioned in two tunnels connected near to the catalytic center. A side pocket was found expanding the tunnel for the arachidonoyl CoA and holding the main body of arachidonoyl. The structural and functional analysis provides the basis for the re-acylation of lysophosphatidylcholine and the substrate preference during the reactions.
NogoA-expressing astrocytes limit peripheral macrophage infiltration after ischemic brain injury in primates
Authors: Boghdadi Anthony G. , Spurrier Joshua , Teo Leon , Li Mingfeng , Skarica Mario , Cao Benjamin , Kwan William C. , Merson Tobias D. , Nilsson Susan K. , Sestan Nenad , Strittmatter Stephen M. , Bourne James A. 
Published: November 2021

AbstractAstrocytes play critical roles after brain injury, but their precise function is poorly defined. Utilizing single-nuclei transcriptomics to characterize astrocytes after ischemic stroke in the visual cortex of the marmoset monkey, we observed nearly complete segregation between stroke and control astrocyte clusters. Screening for the top 30 differentially expressed genes that might limit stroke recovery, we discovered that a majority of astrocytes expressed RTN4A/ NogoA, a neurite-outgrowth inhibitory protein previously only associated with oligodendrocytes. NogoA upregulation on reactive astrocytes post-stroke was significant in both the marmoset and human brain, whereas only a marginal change was observed in mice. We determined that NogoA mediated an anti-inflammatory response which likely contributes to limiting the infiltration of peripheral macrophages into the surviving parenchyma.
Real-time ultrafast oscilloscope with a relativistic electron bunch train
Authors: Baek In Hyung , Kim Hyun Woo , Bark Hyeon Sang , Jang Kyu-Ha , Park Sunjeong , Shin Junho , Kim Young Chan , Kim Mihye , Oang Key Young , Lee Kitae , Rotermund Fabian , Vinokurov Nikolay A. , Jeong Young Uk 
Published: November 2021

AbstractThe deflection of charged particles is an intuitive way to visualize an electromagnetic oscillation of coherent light. Here, we present a real-time ultrafast oscilloscope for time-frozen visualization of a terahertz (THz) optical wave by probing light-driven motion of relativistic electrons. We found the unique condition of subwavelength metal slit waveguide for preserving the distortion-free optical waveform during its propagation. Momentary stamping of the wave, transversely travelling inside a metal slit, on an ultrashort wide electron bunch enables the single-shot recording of an ultrafast optical waveform. As a proof-of-concept experiment, we successfully demonstrated to capture the entire field oscillation of a THz pulse with a sampling rate of 75.7 TS/s. Owing to the use of transversely-wide and longitudinally-short electron bunch and transversely travelling wave, the proposed “single-shot oscilloscope” will open up new avenue for developing the real-time petahertz (PHz) metrology.
Assessing population exposure to coastal flooding due to sea level rise
Authors: Hauer Mathew E. , Hardy Dean , Kulp Scott A. , Mueller Valerie , Wrathall David J. , Clark Peter U. 
Published: November 2021

AbstractThe exposure of populations to sea-level rise (SLR) is a leading indicator assessing the impact of future climate change on coastal regions. SLR exposes coastal populations to a spectrum of impacts with broad spatial and temporal heterogeneity, but exposure assessments often narrowly define the spatial zone of flooding. Here we show how choice of zone results in differential exposure estimates across space and time. Further, we apply a spatio-temporal flood-modeling approach that integrates across these spatial zones to assess the annual probability of population exposure. We apply our model to the coastal United States to demonstrate a more robust assessment of population exposure to flooding from SLR in any given year. Our results suggest that more explicit decisions regarding spatial zone (and associated temporal implication) will improve adaptation planning and policies by indicating the relative chance and magnitude of coastal populations to be affected by future SLR.
Dietary essential amino acids restore liver metabolism in ovariectomized mice via hepatic estrogen receptor α
Authors: Della Torre Sara , Benedusi Valeria , Pepe Giovanna , Meda Clara , Rizzi Nicoletta , Uhlenhaut Nina Henriette , Maggi Adriana 
Published: November 2021

AbstractIn female mammals, the cessation of ovarian functions is associated with significant metabolic alterations, weight gain, and increased susceptibility to a number of pathologies associated with ageing. The molecular mechanisms triggering these systemic events are unknown because most tissues are responsive to lowered circulating sex steroids. As it has been demonstrated that isoform alpha of the estrogen receptor (ERα) may be activated by both estrogens and amino acids, we test the metabolic effects of a diet enriched in specific amino acids in ovariectomized (OVX) mice. This diet is able to block the OVX-induced weight gain and fat deposition in the liver. The use of liver-specific ERα KO mice demonstrates that the hepatic ERα, through the control of liver lipid metabolism, has a key role in the systemic response to OVX. The study suggests that the liver ERα might be a valuable target for dietary treatments for the post-menopause.
Analog programing of conducting-polymer dendritic interconnections and control of their morphology
Authors: Janzakova Kamila , Kumar Ankush , Ghazal Mahdi , Susloparova Anna , Coffinier Yannick , Alibart Fabien , Pecqueur Sébastien 
Published: November 2021

AbstractAlthough materials and processes are different from biological cells’, brain mimicries led to tremendous achievements in parallel information processing via neuromorphic engineering. Inexistent in electronics, we emulate dendritic morphogenesis by electropolymerization in water, aiming in operando material modification for hardware learning. Systematic study of applied voltage-pulse parameters details on tuning independently morphological aspects of micrometric dendrites’: fractal number, branching degree, asymmetry, density or length. Growths time-lapse image processing shows spatial features to be dynamically dependent, and expand distinctively before and after conductive bridging with two electro-generated dendrites. Circuit-element analysis and impedance spectroscopy confirms their morphological control in temporal windows where growth kinetics is finely perturbed by the input frequency and duty cycle. By the emulation of one’s most preponderant mechanisms for brain’s long-term memory, its implementation in vicinity of sensing arrays, neural probes or biochips shall greatly optimize computational costs and recognition required to classify high-dimensional patterns from complex environments.
Efficacy and safety of next-generation tick transcriptome-derived direct thrombin inhibitors
Authors: Koh Cho Yeow , Shih Norrapat , Yip Christina Y. C. , Li Aaron Wei Liang , Chen Weiming , Amran Fathiah S. , Leong Esther Jia En , Iyer Janaki Krishnamoorthy , Croft Grace , Mazlan Muhammad Ibrahim Bin , Chee Yen-Lin , Yap Eng-Soo , Monroe Dougald M. , Hoffman Maureane , Becker Richard C. , de Kleijn Dominique P. V. , Verma Vaishali , Gupta Amita , Chaudhary Vijay K. , Richards A. Mark , Kini R. Manjunatha , Chan Mark Y. 
Published: November 2021

AbstractDespite their limitations, unfractionated heparin (UFH) and bivalirudin remain standard-of-care parenteral anticoagulants for percutaneous coronary intervention (PCI). We discovered novel direct thrombin inhibitors (DTIs) from tick salivary transcriptomes and optimised their pharmacologic activity. The most potent, ultravariegin, inhibits thrombin with a Ki of 4.0 pM, 445-fold better than bivalirudin. Unexpectedly, despite their greater antithrombotic effect, variegin/ultravariegin demonstrated less bleeding, achieving a 3-to-7-fold wider therapeutic index in rodent thrombosis and bleeding models. When used in combination with aspirin and ticagrelor in a porcine model, variegin/ultravariegin reduced stent thrombosis compared with antiplatelet therapy alone but achieved a 5-to-7-fold lower bleeding time than UFH/bivalirudin. Moreover, two antibodies screened from a naïve human antibody library effectively reversed the anticoagulant activity of ultravariegin, demonstrating proof-of-principle for antidote reversal. Variegin and ultravariegin are promising translational candidates for next-generation DTIs that may reduce peri-PCI bleeding in the presence of antiplatelet therapy.
AGPAT2 interaction with CDP-diacylglycerol synthases promotes the flux of fatty acids through the CDP-diacylglycerol pathway
Authors: Mak Hoi Yin , Ouyang Qian , Tumanov Sergey , Xu Jiesi , Rong Ping , Dong Feitong , Lam Sin Man , Wang Xiaowei , Lukmantara Ivan , Du Ximing , Gao Mingming , Brown Andrew J. , Gong Xin , Shui Guanghou , Stocker Roland , Huang Xun , Chen Shuai , Yang Hongyuan 
Published: November 2021

AbstractAGPATs (1-acylglycerol-3-phosphate O-acyltransferases) catalyze the acylation of lysophosphatidic acid to form phosphatidic acid (PA), a key step in the glycerol-3-phosphate pathway for the synthesis of phospholipids and triacylglycerols. AGPAT2 is the only AGPAT isoform whose loss-of-function mutations cause a severe form of human congenital generalized lipodystrophy. Paradoxically, AGPAT2 deficiency is known to dramatically increase the level of its product, PA. Here, we find that AGPAT2 deficiency impairs the biogenesis and growth of lipid droplets. We show that AGPAT2 deficiency compromises the stability of CDP-diacylglycerol (DAG) synthases (CDSs) and decreases CDS activity in both cell lines and mouse liver. Moreover, AGPAT2 and CDS1/2 can directly interact and form functional complexes, which promote the metabolism of PA along the CDP-DAG pathway of phospholipid synthesis. Our results provide key insights into the regulation of metabolic flux during lipid synthesis and suggest substrate channelling at a major branch point of the glycerol-3-phosphate pathway.
Giant single-crystal-to-single-crystal transformations associated with chiral interconversion induced by elimination of chelating ligands
Authors: Li Yun , Zhao Bo , Xue Jin-Peng , Xie Jing , Yao Zi-Shuo , Tao Jun 
Published: November 2021

AbstractNumerous single crystals that exhibit single-crystal-to-single-crystal (SCSC) transformations have been reported, and some of them show great promise for application to advanced adsorption materials, magnetic switches, and smart actuators. However, the development of single crystals with super-adaptive crystal lattices capable of huge and reversible structural change remains a great challenge. In this study, we report a ZnII complex that undergoes giant SCSC transformation induced by a two-step thermal elimination of ethylene glycol chelating ligands. Although the structural change is exceptionally large (50% volume shrinkage and 36% weight loss), the single-crystal nature of the complex persists because of the multiple strong hydrogen bonds between the constituent molecules. This allows the reversible zero-dimensional to one-dimension and further to three-dimensional structural changes to be fully characterized by single-crystal X-ray diffraction analyses. The elimination of chelating ligands induces a chiral interconversion in the molecules that manifests as a centric-chiral-polar symmetric variation of the single crystal. The study not only presents a unique material, featuring both a periodic crystal lattice and gel-like super-ductility, but also reveals a possible solid-state reaction method for preparing chiral compounds via the elimination of chelating ligands.
The barley immune receptor Mla recognizes multiple pathogens and contributes to host range dynamics
Authors: Bettgenhaeuser Jan , Hernández-Pinzón Inmaculada , Dawson Andrew M. , Gardiner Matthew , Green Phon , Taylor Jodie , Smoker Matthew , Ferguson John N. , Emmrich Peter , Hubbard Amelia , Bayles Rosemary , Waugh Robbie , Steffenson Brian J. , Wulff Brande B. H. , Dreiseitl Antonín , Ward Eric R. , Moscou Matthew J. 
Published: November 2021

AbstractCrop losses caused by plant pathogens are a primary threat to stable food production. Stripe rust (Puccinia striiformis) is a fungal pathogen of cereal crops that causes significant, persistent yield loss. Stripe rust exhibits host species specificity, with lineages that have adapted to infect wheat and barley. While wheat stripe rust and barley stripe rust are commonly restricted to their corresponding hosts, the genes underlying this host specificity remain unknown. Here, we show that three resistance genes,Rps6,Rps7, andRps8, contribute to immunity in barley to wheat stripe rust.Rps7cosegregates with barley powdery mildew resistance at theMlalocus. Using transgenic complementation of differentMlaalleles, we confirm allele-specific recognition of wheat stripe rust byMla. Our results show that major resistance genes contribute to the host species specificity of wheat stripe rust on barley and that a shared genetic architecture underlies resistance to the adapted pathogen barley powdery mildew and non-adapted pathogen wheat stripe rust.
Engineering a PAM-flexible SpdCas9 variant as a universal gene repressor
Authors: Wang Jian , Teng Yuxi , Zhang Ruihua , Wu Yifei , Lou Lei , Zou Yusong , Li Michelle , Xie Zhong-Ru , Yan Yajun 
Published: November 2021

AbstractThe RNA-guided CRISPR-associated Cas9 proteins have been widely applied in programmable genome recombination, base editing or gene regulation in both prokaryotes and eukaryotes. SpCas9 from Streptococcus pyogenes is the most extensively engineered Cas9 with robust and manifold functionalities. However, one inherent limitation of SpCas9 is its stringent 5′-NGG-3′ PAM requirement that significantly restricts its DNA target range. Here, to repurpose SpCas9 as a universal gene repressor, we generate and screen variants of the deactivated SpCas9 (SpdCas9) with relaxed 5′-CAT-3′ PAM compatibility that can bind to the start codon ATG of almost any gene. Stepwise structure-guided mutations of the PAM-interacting residues and auxiliary PAM-proximal residues of the SpdNG (5′-NG-3′ PAM) create a PAM-flexible variant SpdNG-LWQT that preferentially accommodates 5′-NRN-3′ PAMs. SpdNG-LWQT is demonstrated to be effective in gene repression with the advantage of customizable sgRNA design in both Escherichia coli and Saccharomyces cerevisiae. This work validates the feasibility of purposeful PAM expansion of Cas9 towards signature PAMs and establishes a universal SpdCas9-based gene repressor.
Cholinesterase inhibitors for gait, balance, and fall in Parkinson disease: a meta-analysis
Authors: Chen Jia-Hung , Huang Tsai-Wei , Hong Chien-Tai 
Published: November 2021

AbstractGait disturbance and imbalance are the major symptoms of Parkinson disease (PD), with fall being the most undesirable consequence. However, few effective evidence-based treatments are available for alleviating these symptoms and preventing falls. Cholinesterase inhibitors (ChEIs) are a well-established treatment for PD dementia with possible impacts on gait, balance, and fall reduction. The present study involved a meta-analysis of randomized controlled trials (RCTs) to investigate the effects of ChEIs on gait, balance, and fall in patients with PD. We searched for studies using the PubMed, Embase, and Web of Science databases. The major outcomes were effects on gait parameters, balance, and fall. This study was registered with PROSPERO (CRD42021254733). Five RCTs were included in the present meta-analysis. ChEIs did not significantly increase gait speed in PD patients (mean difference [MD]: 0.03 m/s, 95% confidence interval [CI]: −0.02 to 0.07, p = 0.29). However, ChEI treatment significantly decreased step or stride variability during the single task (standard MD: −0.43, 95% CI = −0.79 to −0.06, p = 0.02). Regarding fall and balance, trending but nonsignificant beneficial effects were observed with ChEI treatment. In conclusion, although ChEI treatment did not significantly improve gait speed and reduce fall, it can significantly reduce step or stride variability. Considering that gait disorder is a challenging issue in patients with PD and that ChEIs are generally tolerable, the present meta-analysis may provide more evidence for the benefit of ChEIs on PD gait disturbance as an alternative treatment consideration.
Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3
Authors: Zeng Wen-Feng , Cao Wei-Qian , Liu Ming-Qi , He Si-Min , Yang Peng-Yuan 
Published: November 2021

AbstractGreat advances have been made in mass spectrometric data interpretation for intact glycopeptide analysis. However, accurate identification of intact glycopeptides and modified saccharide units at the site-specific level and with fast speed remains challenging. Here, we present a glycan-first glycopeptide search engine, pGlyco3, to comprehensively analyze intact N- and O-glycopeptides, including glycopeptides with modified saccharide units. A glycan ion-indexing algorithm developed for glycan-first search makes pGlyco3 5–40 times faster than other glycoproteomic search engines without decreasing accuracy or sensitivity. By combining electron-based dissociation spectra, pGlyco3 integrates a dynamic programming-based algorithm termed pGlycoSite for site-specific glycan localization. Our evaluation shows that the site-specific glycan localization probabilities estimated by pGlycoSite are suitable to localize site-specific glycans. With pGlyco3, we confidently identified N-glycopeptides and O-mannose glycopeptides that were extensively modified by ammonia adducts in yeast samples. The freely available pGlyco3 is an accurate and flexible tool that can be used to identify glycopeptides and modified saccharide units.