bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resistance in smallflower umbrella sedge (Cyperus difformis) to an acetolactate synthase–inhibiting herbicide in rice: first case in India
Authors: Choudhary Vijay K. , Reddy Seshadri S. , Mishra Subhash K. , Kumar Bhumesh , Gharde Yogita , Kumar Sunil , Yadav Mayank , Barik Suhrid , Singh P. K. 
Published: September 2021

AbstractSmallflower umbrella sedge is one of the most problematic weeds in direct-seeded rice in India. Bispyribac-sodium (acetolactate synthase [ALS]-inhibiting herbicide) is commonly used in rice, but growers have recently reported lack of smallflower umbrella sedge control with this herbicide. An extensive survey was carried out in two rice-growing states, Chhattisgarh and Kerala, where 53 putative bispyribac-sodium-resistant (BR) biotypes were collected. Studies were conducted to confirm resistance to bispyribac-sodium and to test the efficacy of the newly developed synthetic auxin herbicide florpyrauxifen-benzyl on putative BR biotypes. A whole-plant bioassay revealed that bispyribac-sodium is no longer effective. Of 53 putative BR biotypes, 17 biotypes survived the recommended label rate of 25 g ai ha−1. The effective bispyribac-sodium rate required to control 50% of the plants in most of the BR biotypes (ED50) ranged from 19 to 96 g ha−1, whereas it was 10 g ha−1in a susceptible biotype. In two highly resistant biotypes, the ED50was beyond the maximum tested rate, 200 g ha−1. This suggests 2- to >20-fold resistance in BR biotypes. An ALS enzyme activity assay suggests an altered target site as mechanism of resistance to bispyribac-sodium. This study confirms the first case of evolved resistance to bispyribac-sodium in smallflower umbrella sedge in India. However, the newly developed synthetic auxin florpyrauxifen-benzyl effectively controlled all BR biotypes at the field use rate of 31.25 g ai ha−1.
The role of meningeal populations of type II innate lymphoid cells in modulating neuroinflammation in neurodegenerative diseases
Authors: Yeung Sherry Sin-Hang , Ho Yuen-Shan , Chang Raymond Chuen-Chung 
Published: September 2021

AbstractRecent research into meningeal lymphatics has revealed a never-before appreciated role of type II innate lymphoid cells (ILC2s) in modulating neuroinflammation in the central nervous system (CNS). To date, the role of ILC2-mediated inflammation in the periphery has been well studied. However, the exact distribution of ILC2s in the CNS and therefore their putative role in modulating neuroinflammation in neurodegenerative diseases such as Alzheimer’s disease (AD), multiple sclerosis (MS), Parkinson’s disease (PD), and major depressive disorder (MDD) remain highly elusive. Here, we review the current evidence of ILC2-mediated modulation of neuroinflammatory cues (i.e., IL-33, IL-25, IL-5, IL-13, IL-10, TNFα, and CXCL16-CXCR6) within the CNS, highlight the distribution of ILC2s in both the periphery and CNS, and discuss some challenges associated with cell type-specific targeting that are important for therapeutics. A comprehensive understanding of the roles of ILC2s in mediating and responding to inflammatory cues may provide valuable insight into potential therapeutic strategies for many dementia-related disorders.
Predictive performance and metabolite dynamics of proton MR spectroscopy in neonatal hypoxic–ischemic encephalopathy
Authors: Barta Hajnalka , Jermendy Agnes , Kovacs Livia , Schiever Noemie , Rudas Gabor , Szabo Miklos 
Published: September 2021

Abstract
Background
Prognostic value of proton MR spectroscopy (H-MRS) in hypoxic–ischemic encephalopathy (HIE) is acknowledged; however, effects of gestational age (GA) and postnatal age (PA) on prediction and metabolite levels are unknown.

Methods
One hundred and sixty-nine newborns with moderate-to-severe HIE were studied, having ≥1 H-MRS scan during postnatal days 0–14 and known neurodevelopmental outcome (Bayley-II score/cerebral palsy/death). Initial scans were categorized by PA (day 1–3/4–6/≥7), and metabolite ratios were compared by predictive value. Metabolite dynamics were assessed in a total of 214 scans performed in the study population, using regression modeling, with predictors GA, PA, and outcome.

Results
N-acetyl-aspartate (NAA)/creatine (Cr) and myo-inositol (mI)/NAA height ratios were consistently associated with outcome throughout the first 14 days, with the highest predictive value in the late (≥7 days) period (AUC = 0.963 and 0.816, respectively). Neither GA nor PA had an overall effect on these metabolite ratios, which showed strongest association with outcome (p < 0.001). Assessed separately in patients with good outcome, GA became a significant covariate for metabolite ratios (p = 0.0058 and 0.0002, respectively). However, this association disappeared in the poor outcome group.

Conclusions
In HIE, NAA/Cr and mI/NAA give most accurate outcome prediction throughout postnatal days 0–14. GA only affected metabolite levels in the good outcome group.

Impact

Proton MR spectroscopy metabolite ratios N-acetyl-aspartate/creatine and myo-inositol/N-acetyl-aspartate have persistently high predictive value throughout postnatal days 0–14 in newborns with hypoxic–ischemic encephalopathy, with the highest predictive power between postnatal days 7 and 14.

Overall, neither metabolite ratio was affected by gestational age nor by postnatal age, while they showed the strongest association with neurological outcome.

However, in newborns facing good outcome, metabolite ratios were associated with gestational age, whereas in cases facing poor outcome, this association disappeared.

Proton MR spectroscopy provides valuable prognostic information in neonatal hypoxic–ischemic encephalopathy throughout the first 2 weeks of life, irrespective of the timing of MR scan.
Learning interpretable cellular and gene signature embeddings from single-cell transcriptomic data
Authors: Zhao Yifan , Cai Huiyu , Zhang Zuobai , Tang Jian , Li Yue 
Published: September 2021

AbstractThe advent of single-cell RNA sequencing (scRNA-seq) technologies has revolutionized transcriptomic studies. However, large-scale integrative analysis of scRNA-seq data remains a challenge largely due to unwanted batch effects and the limited transferabilty, interpretability, and scalability of the existing computational methods. We present single-cell Embedded Topic Model (scETM). Our key contribution is the utilization of a transferable neural-network-based encoder while having an interpretable linear decoder via a matrix tri-factorization. In particular, scETM simultaneously learns an encoder network to infer cell type mixture and a set of highly interpretable gene embeddings, topic embeddings, and batch-effect linear intercepts from multiple scRNA-seq datasets. scETM is scalable to over 106 cells and confers remarkable cross-tissue and cross-species zero-shot transfer-learning performance. Using gene set enrichment analysis, we find that scETM-learned topics are enriched in biologically meaningful and disease-related pathways. Lastly, scETM enables the incorporation of known gene sets into the gene embeddings, thereby directly learning the associations between pathways and topics via the topic embeddings.
Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails
Authors: Peng Yunhui , Li Shuxiang , Onufriev Alexey , Landsman David , Panchenko Anna R. 
Published: September 2021

AbstractLittle is known about the roles of histone tails in modulating nucleosomal DNA accessibility and its recognition by other macromolecules. Here we generate extensive atomic level conformational ensembles of histone tails in the context of the full nucleosome, totaling 65 microseconds of molecular dynamics simulations. We observe rapid conformational transitions between tail bound and unbound states, and characterize kinetic and thermodynamic properties of histone tail-DNA interactions. Different histone types exhibit distinct binding modes to specific DNA regions. Using a comprehensive set of experimental nucleosome complexes, we find that the majority of them target mutually exclusive regions with histone tails on nucleosomal/linker DNA around the super-helical locations ± 1, ± 2, and ± 7, and histone tails H3 and H4 contribute most to this process. These findings are explained within competitive binding and tail displacement models. Finally, we demonstrate the crosstalk between different histone tail post-translational modifications and mutations; those which change charge, suppress tail-DNA interactions and enhance histone tail dynamics and DNA accessibility.
Structure of the native pyruvate dehydrogenase complex reveals the mechanism of substrate insertion
Authors: Škerlová Jana , Berndtsson Jens , Nolte Hendrik , Ott Martin , Stenmark Pål 
Published: September 2021

AbstractThe pyruvate dehydrogenase complex (PDHc) links glycolysis to the citric acid cycle by converting pyruvate into acetyl-coenzyme A. PDHc encompasses three enzymatically active subunits, namely pyruvate dehydrogenase, dihydrolipoyl transacetylase, and dihydrolipoyl dehydrogenase. Dihydrolipoyl transacetylase is a multidomain protein comprising a varying number of lipoyl domains, a peripheral subunit-binding domain, and a catalytic domain. It forms the structural core of the complex, provides binding sites for the other enzymes, and shuffles reaction intermediates between the active sites through covalently bound lipoyl domains. The molecular mechanism by which this shuttling occurs has remained elusive. Here, we report a cryo-EM reconstruction of the native E. coli dihydrolipoyl transacetylase core in a resting state. This structure provides molecular details of the assembly of the core and reveals how the lipoyl domains interact with the core at the active site.
Direct measurement of ferroelectric polarization in a tunable semimetal
Authors: de la Barrera Sergio C. , Cao Qingrui , Gao Yang , Gao Yuan , Bheemarasetty Vineetha S. , Yan Jiaqiang , Mandrus David G. , Zhu Wenguang , Xiao Di , Hunt Benjamin M. 
Published: September 2021

AbstractFerroelectricity, the electrostatic counterpart to ferromagnetism, has long been thought to be incompatible with metallicity due to screening of electric dipoles and external electric fields by itinerant charges. Recent measurements, however, demonstrated signatures of ferroelectric switching in the electrical conductance of bilayers and trilayers of WTe2, a semimetallic transition metal dichalcogenide with broken inversion symmetry. An especially promising aspect of this system is that the density of electrons and holes can be continuously tuned by an external gate voltage. This degree of freedom enables measurement of the spontaneous polarization as free carriers are added to the system. Here we employ capacitive sensing in dual-gated mesoscopic devices of bilayer WTe2 to directly measure the spontaneous polarization in the metallic state and quantify the effect of free carriers on the polarization in the conduction and valence bands, separately. We compare our results to a low-energy model for the electronic bands and identify the layer-polarized states that contribute to transport and polarization simultaneously. Bilayer WTe2 is thus shown to be a fully tunable ferroelectric metal and an ideal platform for exploring polar ordering, ferroelectric transitions, and applications in the presence of free carriers.
Capillary-associated microglia regulate vascular structure and function through PANX1-P2RY12 coupling in mice
Authors: Bisht Kanchan , Okojie Kenneth A. , Sharma Kaushik , Lentferink Dennis H. , Sun Yu-Yo , Chen Hong-Ru , Uweru Joseph O. , Amancherla Saipranusha , Calcuttawala Zainab , Campos-Salazar Antony Brayan , Corliss Bruce , Jabbour Lara , Benderoth Jordan , Friestad Bria , Mills William A. , Isakson Brant E. , Tremblay Marie-Ève , Kuan Chia-Yi , Eyo Ukpong B. 
Published: September 2021

AbstractMicroglia are brain-resident immune cells with a repertoire of functions in the brain. However, the extent of their interactions with the vasculature and potential regulation of vascular physiology has been insufficiently explored. Here, we document interactions between ramified CX3CR1 + myeloid cell somata and brain capillaries. We confirm that these cells are bona fide microglia by molecular, morphological and ultrastructural approaches. Then, we give a detailed spatio-temporal characterization of these capillary-associated microglia (CAMs) comparing them with parenchymal microglia (PCMs) in their morphological activities including during microglial depletion and repopulation. Molecularly, we identify P2RY12 receptors as a regulator of CAM interactions under the control of released purines from pannexin 1 (PANX1) channels. Furthermore, microglial elimination triggered capillary dilation, blood flow increase, and impaired vasodilation that were recapitulated in P2RY12−/− and PANX1−/− mice suggesting purines released through PANX1 channels play important roles in activating microglial P2RY12 receptors to regulate neurovascular structure and function.
Structural proof of a [C–F–C]+ fluoronium cation
Authors: Hoffmann Kurt F. , Wiesner Anja , Müller Carsten , Steinhauer Simon , Beckers Helmut , Kazim Muhammad , Pitts Cody Ross , Lectka Thomas , Riedel Sebastian 
Published: September 2021

AbstractOrganic fluoronium ions can be described as positively charged molecules in which the most electronegative and least polarizable element fluorine engages in two partially covalent bonding interactions to two carbon centers. While recent solvolysis experiments and NMR spectroscopic studies on a metastable [C–F–C]+fluoronium ion strongly support the divalent fluoronium structure over the alternative rapidly equilibrating classical carbocation, the model system has, to date, eluded crystallographic analysis to confirm this phenomenon in the solid state. Herein, we report the single crystal structure of a symmetrical [C–F–C]+fluoronium cation. Besides its synthesis and crystallographic characterization as the [Sb2F11]−salt, vibrational spectra are discussed and a detailed analysis concerning the nature of the bonding situation in this fluoronium ion and its heavier halonium homologues is performed, which provides detailed insights on this molecular structure.
Regulation of functional groups on graphene quantum dots directs selective CO2 to CH4 conversion
Authors: Zhang Tianyu , Li Weitao , Huang Kai , Guo Huazhang , Li Zhengyuan , Fang Yanbo , Yadav Ram Manohar , Shanov Vesselin , Ajayan Pulickel M. , Wang Liang , Lian Cheng , Wu Jingjie 
Published: September 2021

AbstractA catalyst system with dedicated selectivity toward a single hydrocarbon or oxygenate product is essential to enable the industrial application of electrochemical conversion of CO2 to high-value chemicals. Cu is the only known metal catalyst that can convert CO2 to high-order hydrocarbons and oxygenates. However, the Cu-based catalysts suffer from diverse selectivity. Here, we report that the functionalized graphene quantum dots can direct CO2 to CH4 conversion with simultaneous high selectivity and production rate. The electron-donating groups facilitate the yield of CH4 from CO2 electro-reduction while electron-withdrawing groups suppress CO2 electro-reduction. The yield of CH4 on electron-donating group functionalized graphene quantum dots is positively correlated to the electron-donating ability and content of electron-donating group. The graphene quantum dots functionalized by either –OH or –NH2 functional group could achieve Faradaic efficiency of 70.0% for CH4 at −200 mA cm−2 partial current density of CH4. The superior yield of CH4 on electron-donating group- over the electron-withdrawing group-functionalized graphene quantum dots possibly originates from the maintenance of higher charge density of potential active sites (neighboring C or N) and the interaction between the electron-donating group and key intermediates. This work provides insight into the design of active carbon catalysts at the molecular scale for the CO2 electro-reduction.
Nrf1 promotes heart regeneration and repair by regulating proteostasis and redox balance
Authors: Cui Miao , Atmanli Ayhan , Morales Maria Gabriela , Tan Wei , Chen Kenian , Xiao Xue , Xu Lin , Liu Ning , Bassel-Duby Rhonda , Olson Eric N. 
Published: September 2021

AbstractFollowing injury, cells in regenerative tissues have the ability to regrow. The mechanisms whereby regenerating cells adapt to injury-induced stress conditions and activate the regenerative program remain to be defined. Here, using the mammalian neonatal heart regeneration model, we show that Nrf1, a stress-responsive transcription factor encoded by the Nuclear Factor Erythroid 2 Like 1 (Nfe2l1) gene, is activated in regenerating cardiomyocytes. Genetic deletion of Nrf1 prevented regenerating cardiomyocytes from activating a transcriptional program required for heart regeneration. Conversely, Nrf1 overexpression protected the adult mouse heart from ischemia/reperfusion (I/R) injury. Nrf1 also protected human induced pluripotent stem cell-derived cardiomyocytes from doxorubicin-induced cardiotoxicity and other cardiotoxins. The protective function of Nrf1 is mediated by a dual stress response mechanism involving activation of the proteasome and redox balance. Our findings reveal that the adaptive stress response mechanism mediated by Nrf1 is required for neonatal heart regeneration and confers cardioprotection in the adult heart.
Endothelium-specific depletion of LRP1 improves glucose homeostasis through inducing osteocalcin
Authors: Mao Hua , Li Luge , Fan Qiying , Angelini Aude , Saha Pradip K. , Coarfa Cristian , Rajapakshe Kimal , Perera Dimuthu , Cheng Jizhong , Wu Huaizhu , Ballantyne Christie M. , Sun Zheng , Xie Liang , Pi Xinchun 
Published: September 2021

AbstractThe vascular endothelium is present within metabolic organs and actively regulates energy metabolism. Here we show osteocalcin, recognized as a bone-secreted metabolic hormone, is expressed in mouse primary endothelial cells isolated from heart, lung and liver. In human osteocalcin promoter-driven green fluorescent protein transgenic mice, green fluorescent protein signals are enriched in endothelial cells lining aorta, small vessels and capillaries and abundant in aorta, skeletal muscle and eye of adult mice. The depletion of lipoprotein receptor-related protein 1 induces osteocalcin through a Forkhead box O -dependent pathway in endothelial cells. Whereas depletion of osteocalcin abolishes the glucose-lowering effect of low-density lipoprotein receptor-related protein 1 depletion, osteocalcin treatment normalizes hyperglycemia in multiple mouse models. Mechanistically, osteocalcin receptor-G protein-coupled receptor family C group 6 member A and insulin-like-growth-factor-1 receptor are in the same complex with osteocalcin and required for osteocalcin-promoted insulin signaling pathway. Therefore, our results reveal an endocrine/paracrine role of endothelial cells in regulating insulin sensitivity, which may have therapeutic implications in treating diabetes and insulin resistance through manipulating vascular endothelium.
Structural basis of RNA processing by human mitochondrial RNase P
Authors: Bhatta Arjun , Dienemann Christian , Cramer Patrick , Hillen Hauke S. 
Published: September 2021

AbstractHuman mitochondrial transcripts contain messenger and ribosomal RNAs flanked by transfer RNAs (tRNAs), which are excised by mitochondrial RNase (mtRNase) P and Z to liberate all RNA species. In contrast to nuclear or bacterial RNase P, mtRNase P is not a ribozyme but comprises three protein subunits that carry out RNA cleavage and methylation by unknown mechanisms. Here, we present the cryo-EM structure of human mtRNase P bound to precursor tRNA, which reveals a unique mechanism of substrate recognition and processing. Subunits TRMT10C and SDR5C1 form a subcomplex that binds conserved mitochondrial tRNA elements, including the anticodon loop, and positions the tRNA for methylation. The endonuclease PRORP is recruited and activated through interactions with its PPR and nuclease domains to ensure precise pre-tRNA cleavage. The structure provides the molecular basis for the first step of RNA processing in human mitochondria.
Intra-group decision-making in agent-based models
Authors: Beal Cohen Allegra A. , Muneepeerakul Rachata , Kiker Gregory 
Published: September 2021

AbstractMany agent-based models (ABMs) try to explain large-scale phenomena by reducing them to behaviors at lower scales. At these scales in social systems are functional groups such as households, religious congregations, coops and local governments. The intra-group dynamics of functional groups often generate inefficient or unexpected behavior that cannot be predicted by modeling groups as basic units. We introduce a framework for modeling intra-group decision-making and its interaction with social norms, using the household as our focus. We select phenomena related to women’s empowerment in agriculture as examples influenced by both intra-household dynamics and gender norms. Our framework proves more capable of replicating these phenomena than two common types of ABMs. We conclude that it is not enough to build multi-scale models; explaining social behaviors entails modeling intra-scale dynamics.
Dectin-2 mediates phagocytosis of Lactobacillus paracasei KW3110 and IL-10 production by macrophages
Authors: Yoshikawa Mia , Yamada Sayuri , Sugamata Miho , Kanauchi Osamu , Morita Yuji 
Published: September 2021

AbstractLactic acid bacteria (LAB) are most generally used as probiotics and some strains of LAB are known to have anti-inflammatory effects. A specific strain of lactic acid bacteria, Lactobacillus paracasei KW3110 (KW3110), activates macrophages to produce interleukin-10 (IL-10), an anti-inflammatory cytokine; however, the biological mechanism remains unclear. In this study, we showed that the amount of incorporated KW3110 into a macrophage cell line, RAW 264.7, was higher than other genetically related strains using fluorescence microscopy. RNA-seq analysis indicated that treatment of macrophages with KW3110 induced Dectin-2 gene expression, which is a pattern recognition receptor, recognizing α-mannose. In addition, antibody treatment and knock down of Dectin-2, or factors downstream in the signaling pathway, decreased the amount of incorporated KW3110 and IL-10 production. Substantial lectin array analysis also revealed that KW3110 had higher binding affinities to lectins, which recognize the carbohydrate chains comprised of α-mannose, than two other LAB. In conclusion, KW3110 is readily incorporated into macrophages, leading to IL-10 production. Dectin-2 mediated the phagocytosis of KW3110 into macrophages and this may be involved with the characteristic carbohydrate chains of KW3110.