bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery of a new class of integrin antibodies for fibrosis
Authors: Zhang Ji , Wang Tao , Saigal Ashmita , Johnson Josephine , Morrisson Jennifer , Tabrizifard Sahba , Hollingsworth Scott A. , Eddins Michael J. , Mao Wenxian , O’Neill Kim , Garcia-Calvo Margarita , Carballo-Jane Ester , Liu DingGang , Ham Taewon , Zhou Qiong , Dong Weifeng , Meng Hsien-Wei , Hicks Jacqueline , Cai Tian-Quan , Akiyama Taro , Pinto Shirly , Cheng Alan C. , Greshock Thomas , Marquis John C. , Ren Zhao , Talukdar Saswata , Shaheen Hussam Hisham , Handa Masahisa 
Published: January 2021

AbstractLung fibrosis, or the scarring of the lung, is a devastating disease with huge unmet medical need. There are limited treatment options and its prognosis is worse than most types of cancer. We previously discovered that MK-0429 is an equipotent pan-inhibitor of αv integrins that reduces proteinuria and kidney fibrosis in a preclinical model. In the present study, we further demonstrated that MK-0429 significantly inhibits fibrosis progression in a bleomycin-induced lung injury model. In search of newer integrin inhibitors for fibrosis, we characterized monoclonal antibodies discovered using Adimab’s yeast display platform. We identified several potent neutralizing integrin antibodies with unique human and mouse cross-reactivity. Among these, Ab-31 blocked the binding of multiple αv integrins to their ligands with IC50s comparable to those of MK-0429. Furthermore, both MK-0429 and Ab-31 suppressed integrin-mediated cell adhesion and latent TGFβ activation. In IPF patient lung fibroblasts, TGFβ treatment induced profound αSMA expression in phenotypic imaging assays and Ab-31 demonstrated potent in vitro activity at inhibiting αSMA expression, suggesting that the integrin antibody is able to modulate TGFβ action though mechanisms beyond the inhibition of latent TGFβ activation. Together, our results highlight the potential to develop newer integrin therapeutics for the treatment of fibrotic lung diseases.
Data science assisted investigation of catalytically active copper hydrate in zeolites for direct oxidation of methane to methanol using H2O2
Authors: Ohyama Junya , Hirayama Airi , Kondou Nahoko , Yoshida Hiroshi , Machida Masato , Nishimura Shun , Hirai Kenji , Miyazato Itsuki , Takahashi Keisuke 
Published: January 2021

AbstractDozens of Cu zeolites with MOR, FAU, BEA, FER, CHA and MFI frameworks are tested for direct oxidation of CH4 to CH3OH using H2O2 as oxidant. To investigate the active structures of the Cu zeolites, 15 structural variables, which describe the features of the zeolite framework and reflect the composition, the surface area and the local structure of the Cu zeolite active site, are collected from the Database of Zeolite Structures of the International Zeolite Association (IZA). Also analytical studies based on inductively coupled plasma-optical emission spectrometry (ICP-OES), X-ray fluorescence (XRF), N2 adsorption specific surface area measurement and X-ray absorption fine structure (XAFS) spectral measurement are performed. The relationships between catalytic activity and the structural variables are subsequently revealed by data science techniques, specifically, classification using unsupervised and supervised machine learning and data visualization using pairwise correlation. Based on the unveiled relationships and a detailed analysis of the XAFS spectra, the local structures of the Cu zeolites with high activity are proposed.
The rostro-caudal gradient in the prefrontal cortex and its modulation by subthalamic deep brain stimulation in Parkinson’s disease
Authors: Schumacher F. Konrad , Schumacher Lena V. , Amtage Florian , Horn Andreas , Egger Karl , Piroth Tobias , Weiller Cornelius , Schelter Björn O. , Coenen Volker A. , Kaller Christoph P. 
Published: January 2021

AbstractDeep brain stimulation of the subthalamic nucleus (STN-DBS) alleviates motor symptoms in Parkinson’s disease (PD) but also affects the prefrontal cortex (PFC), potentially leading to cognitive side effects. The present study tested alterations within the rostro-caudal hierarchy of neural processing in the PFC induced by STN-DBS in PD. Granger-causality analyses of fast functional near-infrared spectroscopy (fNIRS) measurements were used to infer directed functional connectivity from intrinsic PFC activity in 24 PD patients treated with STN-DBS. Functional connectivity was assessed ON stimulation, in steady-state OFF stimulation and immediately after the stimulator was switched ON again. Results revealed that STN-DBS significantly enhanced the rostro-caudal hierarchical organization of the PFC in patients who had undergone implantation early in the course of the disease, whereas it attenuated the rostro-caudal hierarchy in late-implanted patients. Most crucially, this systematic network effect of STN-DBS was reproducible in the second ON stimulation measurement. Supplemental analyses demonstrated the significance of prefrontal networks for cognitive functions in patients and matched healthy controls. These findings show that the modulation of prefrontal functional networks by STN-DBS is dependent on the disease duration before DBS implantation and suggest a neurophysiological mechanism underlying the side effects on prefrontally-guided cognitive functions observed under STN-DBS.
Variability in plant trace element uptake across different crops, soil contamination levels and soil properties in the Xinjiang Uygur Autonomous Region of northwest China
Authors: Liu Weiguo , Yang Xiaodong , Duan Luchun , Naidu Ravi , Yan Kaihong , Liu Yanju , Wang Xiyuan , Gao Yongchao , Chen Yinguang 
Published: January 2021

AbstractThis study investigated contamination status of eight trace elements (As, Cd, Cr, Hg, Pb, Cu, Zn and Ni) in farmland soils and crops at 535 sites across the Xinjiang Uygur Autonomous Region, Northwest China. Land use types of the sampling sites included vegetable patch, grain field and orchard. Our experimental results indicated all farmland soils were considered as trace element contamination based on the Nemerow comprehensive pollution index (NCPI > 1). However, 91.97% of the crop samples were uncontaminated according to the Chinese Risk Control Standard. Soils from the vegetable patch showed higher pollution level comparison with that from grain field and orchard. Health risks for both non-carcinogenic and carcinogenic risks were calculated through crop ingestion exposure pathway. Grain samples showed highest health risks, followed by melon and fruit, and vegetables. The health risks of crops were mainly driven by Cr and Cd. Crop consumption may pose risks for children but not adults. The source of trace element contamination in the different farmland soils varied and may be attributed to the different agricultural activities. Plant type had a greater influence on the trace element accumulation in crops compared with soil trace element contents and physicochemical properties.
Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance
Authors: Yang Yaodong , Bocs Stéphanie , Fan Haikuo , Armero Alix , Baudouin Luc , Xu Pengwei , Xu Junyang , This Dominique , Hamelin Chantal , Iqbal Amjad , Qadri Rashad , Zhou Lixia , Li Jing , Wu Yi , Ma Zilong , Issali Auguste Emmanuel , Rivallan Ronan , Liu Na , Xia Wei , Peng Ming , Xiao Yong 
Published: January 2021

AbstractCoconut (Cocos nucifera) is the emblematic palm of tropical coastal areas all around the globe. It provides vital resources to millions of farmers. In an effort to better understand its evolutionary history and to develop genomic tools for its improvement, a sequence draft was recently released. Here, we present a dense linkage map (8402 SNPs) aiming to assemble the large genome of coconut (2.42 Gbp, 2n = 32) into 16 pseudomolecules. As a result, 47% of the sequences (representing 77% of the genes) were assigned to 16 linkage groups and ordered. We observed segregation distortion in chromosome Cn15, which is a signature of strong selection among pollen grains, favouring the maternal allele. Comparing our results with the genome of the oil palm Elaeis guineensis allowed us to identify major events in the evolutionary history of palms. We find that coconut underwent a massive transposable element invasion in the last million years, which could be related to the fluctuations of sea level during the glaciations at Pleistocene that would have triggered a population bottleneck. Finally, to better understand the facultative halophyte trait of coconut, we conducted an RNA-seq experiment on leaves to identify key players of signaling pathways involved in salt stress response. Altogether, our findings represent a valuable resource for the coconut breeding community.
Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization
Authors: Gauthier Jérémy , Boulain Hélène , van Vugt Joke J. F. A. , Baudry Lyam , Persyn Emma , Aury Jean-Marc , Noel Benjamin , Bretaudeau Anthony , Legeai Fabrice , Warris Sven , Chebbi Mohamed A. , Dubreuil Géraldine , Duvic Bernard , Kremer Natacha , Gayral Philippe , Musset Karine , Josse Thibaut , Bigot Diane , Bressac Christophe , Moreau Sébastien , Periquet Georges , Harry Myriam , Montagné Nicolas , Boulogne Isabelle , Sabeti-Azad Mahnaz , Maïbèche Martine , Chertemps Thomas , Hilliou Frédérique , Siaussat David , Amselem Joëlle , Luyten Isabelle , Capdevielle-Dulac Claire , Labadie Karine , Merlin Bruna Laís , Barbe Valérie , de Boer Jetske G. , Marbouty Martial , Cônsoli Fernando Luis , Dupas Stéphane , Hua-Van Aurélie , Le Goff Gaelle , Bézier Annie , Jacquin-Joly Emmanuelle , Whitfield James B. , Vet Louise E. M. , Smid Hans M. , Kaiser Laure , Koszul Romain , Huguet Elisabeth , Herniou Elisabeth A. , Drezen Jean-Michel 
Published: January 2021

AbstractEndogenous viruses form an important proportion of eukaryote genomes and a source of novel functions. How large DNA viruses integrated into a genome evolve when they confer a benefit to their host, however, remains unknown. Bracoviruses are essential for the parasitism success of parasitoid wasps, into whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome at a chromosomal scale, that bracovirus genes colonized all ten chromosomes ofCotesia congregata. Most form clusters of genes involved in particle production or parasitism success. Genomic comparison with another wasp,Microplitis demolitor, revealed that these clusters were already established ~53 mya and thus belong to remarkably stable genomic structures, the architectures of which are evolutionary constrained. Transcriptomic analyses highlight temporal synchronization of viral gene expression without resulting in immune gene induction, suggesting that no conflicts remain between ancient symbiotic partners when benefits to them converge.
Photolysis of acetonitrile in a water-rich ice as a source of complex organic molecules: CH3CN and H2O:CH3CN ices
Authors: Bulak M. , Paardekooper D. M. , Fedoseev G. , Linnartz H. 
Published: January 2021

Context. Many C-, O-, and H-containing complex organic molecules (COMs) have been observed in the interstellar medium (ISM) and their formation has been investigated in laboratory experiments. An increasing number of recent detections of large N-bearing COMs motivates our experimental investigation of their chemical origin.
Aims. We investigate the potential role of acetonitrile (CH3CN) as a parent molecule to N-bearing COMs, motivated by its omnipresence in the ISM and structural similarity to another well-known precursor species, CH3OH. The aim of the present work is to characterize the chemical complexity that can result from vacuum UV photolysis of a pure CH3CN ice and a more realistic mixture of H2O:CH3CN.
Methods. The CH3CN ice and H2O:CH3CN ice mixtures were UV irradiated at 20 K. Laser desorption post ionization time-of-flight mass spectrometry was used to detect the newly formed COMs in situ. We examined the role of water in the chemistry of interstellar ices through an analysis of two different ratios of H2O:CH3CN (1:1 and 20:1).
Results. We find that CH3CN is an excellent precursor to the formation of larger nitrogen-containing COMs, including CH3CH2CN, NCCN/CNCN, and NCCH2CH2CN. During the UV photolysis of H2O:CH3CN ice, the water derivatives play a key role in the formation of molecules with functional groups of: imines, amines, amides, large nitriles, carboxylic acids, and alcohols. We discuss possible formation pathways for molecules recently detected in the ISM.
Whistler wave occurrence and the interaction with strahl electrons during the first encounter of Parker Solar Probe
Authors: Jagarlamudi V. K. , Dudok de Wit T. , Froment C. , Krasnoselskikh V. , Larosa A. , Bercic L. , Agapitov O. , Halekas J. S. , Kretzschmar M. , Malaspina D. , Moncuquet M. , Bale S. D. , Case A. W. , Kasper J. C. , Korreck K. E. , Larson D. E. , Pulupa M. , Stevens M. L. , Whittlesey P. 
Published: January 2021

Aims.We studied the properties and occurrence of narrowband whistler waves and their interaction with strahl electrons observed between 0.17 and 0.26 au during the first encounter of Parker Solar Probe.Methods.We used Digital Fields Board band-pass filtered (BPF) data from FIELDS to detect the signatures of whistler waves. Additionally parameters derived from the particle distribution functions measured by the Solar Wind Electrons Alphas and Protons (SWEAP) instrument suite were used to investigate the plasma properties, and FIELDS suite measurements were used to investigate the electromagnetic (EM) fields properties corresponding to the observed whistler signatures.Results.We observe that the occurrence of whistler waves is low, nearly ~1.5% and less than 0.5% in the analyzed peak and average BPF data, respectively. Whistlers occur highly intermittently and 80% of the whistlers appear continuously for less than 3 s. The spacecraft frequencies of the analyzed waves are less than 0.2 electron cyclotron frequency (fce). The occurrence rate of whistler waves was found to be anticorrelated with the solar wind bulk velocity. The study of the duration of the whistler intervals revealed an anticorrelation between the duration and the solar wind velocity, as well as between the duration and the normalized amplitude of magnetic field variations. The pitch-angle widths (PAWs) of the field-aligned electron population referred to as the strahl are broader by at least 12 degrees during the presence of large amplitude narrowband whistler waves. This observation points toward an EM wave electron interaction, resulting in pitch-angle scattering. PAWs of strahl electrons corresponding to the short duration whistlers are higher compared to the long duration whistlers, indicating short duration whistlers scatter the strahl electrons better than the long duration ones. Parallel cuts through the strahl electron velocity distribution function (VDF) observed during the whistler intervals appear to depart from the Maxwellian shape typically found in the near-Sun strahl VDFs. The relative decrease in the parallel electron temperature and the increase in PAW for the electrons in the strahl energy range suggests that the interaction with whistler waves results in a transfer of electron momentum from the parallel to the perpendicular direction.
Outcome Prediction in Patients of Traumatic Brain Injury Based on Midline Shift on CT Scan of Brain
Authors: Palekar Shrikant Govindrao , Jaiswal Manish , Patil Mandar , Malpathak Vijay 
Published: January 2021

AbstractBackground Clinicians treating patients with head injury often take decisions based on their assessment of prognosis. Assessment of prognosis could help communication with a patient and the family. One of the most widely used clinical tools for such prediction is the Glasgow coma scale (GCS); however, the tool has a limitation with regard to its use in patients who are under sedation, are intubated, or under the influence of alcohol or psychoactive drugs. CT scan findings such as status of basal cistern, midline shift, associated traumatic subarachnoid hemorrhage (SAH), and intraventricular hemorrhage are useful indicators in predicting outcome and also considered as valid options for prognostication of the patients with traumatic brain injury (TBI), especially in emergency setting.Materials and Methods 108 patients of head injury were assessed at admission with clinical examination, history, and CT scan of brain. CT findings were classified according to type of lesion and midline shift correlated to GCS score at admission. All the subjects in this study were managed with an identical treatment protocol. Outcome of these patients were assessed on GCS score at discharge.Results Among patients with severe GCS, 51% had midline shift. The degree of midline shift in CT head was a statistically significant determinant of outcome (p = 0.023). Seventeen out of 48 patients (35.4%) with midline shift had poor outcome as compared with 8 out of 60 patients (13.3%) with no midline shift.Conclusion In patients with TBI, the degree of midline shift on CT scan was significantly related to the severity of head injury and resulted in poor clinical outcome.
A systematic and interdisciplinary review of mathematical models of language competition
Authors: Boissonneault Michael , Vogt Paul 
Published: January 2021

AbstractDuring the last three decades, scientists in formal and natural sciences have been proposing models of language competition. Such models could prove instrumental in informing efforts made towards preserving the world’s linguistic diversity but have yet to gain significant interest among linguists. This situation could be due to a lack of overlap between the concepts and methods used in those models and those used by linguists. In an effort towards promoting interdisciplinary dialogue on the topic of language competition, this study describes the concepts and methods used in mathematical models of language competition and assesses whether these concepts and methods are becoming more similar over time to those used by linguists. To this end, studies that proposed mathematical models of language competition were systematically retrieved and analysed. Change over time in those models was first assessed concerning the way they are specified, including the parameters they contain. Next, it was checked whether models were increasingly fitted to empirical data. Finally, change in the disciplines covered by the journals where those models were published was evaluated. Results show that overall, models have been including few sociolinguistic parameters, have been relying little on empirical data, and have been mostly published in journals covering the fields of mathematics and physics. However, the last years have seen an important turnaround along each of these three axes. A common language seems to be emerging between fields regarding mathematical models of language competition, which should prove instrumental in informing efforts made towards preserving the world’s linguistic diversity.
On the adhesion–velocity relation and length adaptation of motile cells on stepped fibronectin lanes
Authors: Schreiber Christoph , Amiri Behnam , Heyn Johannes C. J. , Rädler Joachim O. , Falcke Martin 
Published: January 2021

Significance
Cells exert forces on their environment by contracting actin networks, friction of intracellular F-actin flow, and polymerization when they move, e.g., during tumor metastasis or development. In this context, the relation between adhesion and cell velocity is a general cell-type-independent observation, the investigation of which bears the chance of understanding basic mechanisms. Restricting cell motion to one-dimensional lanes simplifies the problem and allows for comparison to mathematical models. Polymerization at the cell’s leading edge drives F-actin network flow and pushes the membrane. The drag of detaching the cell, the membrane, and the cell body resist motion. Since only velocity-controlled forces shape motion, cells can move even across highly adhesive areas without getting stuck.
Conjugative plasmid-encoded toxin–antitoxin system PrpT/PrpA directly controls plasmid copy number
Authors: Ni Songwei , Li Baiyuan , Tang Kaihao , Yao Jianyun , Wood Thomas K. , Wang Pengxia , Wang Xiaoxue 
Published: January 2021

Significance
Since conjugative plasmids are usually large and may carry genes encoding functions that are detrimental to the bacterial host, minimizing plasmid copy number is critical for reducing the host burden. Toxin–antitoxin (TA) systems are one of the conserved modules on conjugative plasmids. Here, we demonstrate the functional significance of a large group of antitoxins on conjugative plasmids: the antitoxin acts as an unexpected player in the negative control of plasmid replication. For the plasmid-encoded PrpT/PrpA TA system, the antitoxin can control toxin production by binding to PrpT and by reducing plasmid copy number. This work shows that the antitoxin can directly regulate plasmid replication, expanding our understanding of the physiological role of TA systems.
The RNA helicase Dhx15 mediates Wnt-induced antimicrobial protein expression in Paneth cells
Authors: Wang Yalong , He Kaixin , Sheng Baifa , Lei Xuqiu , Tao Wanyin , Zhu Xiaoliang , Wei Zheng , Fu Rongjie , Wang Anlei , Bai Shengdan , Zhang Zhao , Hong Na , Ye Chao , Tian Ye , Wang Jun , Li Mingsong , Zhang Kaiguang , Li Lin , Yang Hua , Li Hua-Bing , Flavell Richard A. , Zhu Shu 
Published: January 2021

Significance
RNA helicases play critical roles in multiple biological processes. However, little in vivo data are available because of the lethality of mice completely deficient in RNA helicases. Here, we generate mice with conditional knockout of DEAD-box Helicase 15 (Dhx15) in the intestine, in which we found a specific defect in antimicrobial peptide (AMP) α-defensins in Paneth cells. Additionally, we found that Dhx15-specific depletion in the intestine leads to susceptibility to enteric bacterial infection as well as dextran sulfate sodium-induced colitis in mice. In humans, we also found reduced protein levels of Dhx15 in ulcerative colitis patients.
Genome-wide CRISPR screens reveal multitiered mechanisms through which mTORC1 senses mitochondrial dysfunction
Authors: Condon Kendall J. , Orozco Jose M. , Adelmann Charles H. , Spinelli Jessica B. , van der Helm Pim W. , Roberts Justin M. , Kunchok Tenzin , Sabatini David M. 
Published: January 2021

Significance
The mTORC1 eukaryotic cell growth regulator dynamically responds to changes in environmental nutrient levels. While many upstream regulators are known to modulate mTORC1 activity, the full complement of these is unknown. Here, using a genome-wide FACS-based CRISPR-Cas9 screen, we identify almost all known positive regulators of mTORC1 as well as many others. The results of our screens highlighted the importance of mitochondrial health in the regulation of mTORC1, which led us to investigate how mitochondrial stress impinges on mTORC1 signaling. Ultimately, we found that two kinases, AMPK and HRI, together signal mitochondrial distress to mTORC1. Furthermore, full inhibition of mTORC1 by mitochondrial stress requires the ATF4-dependent up-regulation of two mTORC1 pathway inhibitors, Sestrin2 and Redd1.
An ablative for the Greeks?
Authors: Rooy Raf Van 
Published: January 2021

Summary
In this article, I discuss a grammar dispute that took place between Philipp Nicodemus Frischlin and Martin Crusius in
Tübingen in the winter of 1585/1586. I argue that their diverging views on the ablative case reflect a disagreement on two levels, in
addition to their obvious personal rivalry: (1) the foundations of grammar, which Frischlin based on meaning rather than form, following
J. C. Scaliger, and (2) contrasting attitudes toward the Greek people and heritage. Additionally, I discuss Frischlin’s views on the
article and the optative mood, while also tracing a popular misquote from Scaliger’s work to Frischlin.