bluuebunny/crossref_metadata_2025_split huggingface dataset:
Natural variation of DROT1 confers drought adaptation in upland rice
Authors: Sun Xingming , Xiong Haiyan , Jiang Conghui , Zhang Dongmei , Yang Zengling , Huang Yuanping , Zhu Wanbin , Ma Shuaishuai , Duan Junzhi , Wang Xin , Liu Wei , Guo Haifeng , Li Gangling , Qi Jiawei , Liang Chaobo , Zhang Zhanying , Li Jinjie , Zhang Hongliang , Han Lujia , Zhou Yihua , Peng Youliang , Li Zichao 
Published: July 2022

AbstractUpland rice is a distinct ecotype that grows in aerobic environments and tolerates drought stress. However, the genetic basis of its drought resistance is unclear. Here, using an integrative approach combining a genome-wide association study with analyses of introgression lines and transcriptomic profiles, we identify a gene, DROUGHT1 (DROT1), encoding a COBRA-like protein that confers drought resistance in rice. DROT1 is specifically expressed in vascular bundles and is directly repressed by ERF3 and activated by ERF71, both drought-responsive transcription factors. DROT1 improves drought resistance by adjusting cell wall structure by increasing cellulose content and maintaining cellulose crystallinity. A C-to-T single-nucleotide variation in the promoter increases DROT1 expression and drought resistance in upland rice. The potential elite haplotype of DROT1 in upland rice could originate in wild rice (O. rufipogon) and may be beneficial for breeding upland rice varieties.
Discovering the drivers of clonal hematopoiesis
Authors: Pich Oriol , Reyes-Salazar Iker , Gonzalez-Perez Abel , Lopez-Bigas Nuria 
Published: July 2022

AbstractMutations in genes that confer a selective advantage to hematopoietic stem cells (HSCs) drive clonal hematopoiesis (CH). While some CH drivers have been identified, the compendium of all genes able to drive CH upon mutations in HSCs remains incomplete. Exploiting signals of positive selection in blood somatic mutations may be an effective way to identify CH driver genes, analogously to cancer. Using the tumor sample in blood/tumor pairs as reference, we identify blood somatic mutations across more than 12,000 donors from two large cancer genomics cohorts. The application of IntOGen, a driver discovery pipeline, to both cohorts, and more than 24,000 targeted sequenced samples yields a list of close to 70 genes with signals of positive selection in CH, available at http://www.intogen.org/ch. This approach recovers known CH genes, and discovers other candidates.
Postmitotic differentiation of human monocytes requires cohesin-structured chromatin
Authors: Minderjahn Julia , Fischer Alexander , Maier Konstantin , Mendes Karina , Nuetzel Margit , Raithel Johanna , Stanewsky Hanna , Ackermann Ute , Månsson Robert , Gebhard Claudia , Rehli Michael 
Published: July 2022

AbstractCohesin is a major structural component of mammalian genomes and is required to maintain loop structures. While acute depletion in short-term culture models suggests a limited importance of cohesin for steady-state transcriptional circuits, long-term studies are hampered by essential functions of cohesin during replication. Here, we study genome architecture in a postmitotic differentiation setting, the differentiation of human blood monocytes (MO). We profile and compare epigenetic, transcriptome and 3D conformation landscapes during MO differentiation (either into dendritic cells or macrophages) across the genome and detect numerous architectural changes, ranging from higher level compartments down to chromatin loops. Changes in loop structures correlate with cohesin-binding, as well as epigenetic and transcriptional changes during differentiation. Functional studies show that the siRNA-mediated depletion of cohesin (and to a lesser extent also CTCF) markedly disturbs loop structures and dysregulates genes and enhancers that are primarily regulated during normal MO differentiation. In addition, gene activation programs in cohesin-depleted MO-derived macrophages are disturbed. Our findings implicate an essential function of cohesin in controlling long-term, differentiation- and activation-associated gene expression programs.
Development of a nanoparticle-based immunotherapy targeting PD-L1 and PLK1 for lung cancer treatment
Authors: Reda Moataz , Ngamcherdtrakul Worapol , Nelson Molly A. , Siriwon Natnaree , Wang Ruijie , Zaidan Husam Y. , Bejan Daniel S. , Reda Sherif , Hoang Ngoc Ha , Crumrine Noah A. , Rehwaldt Justin P. C. , Bindal Akash , Mills Gordon B. , Gray Joe W. , Yantasee Wassana 
Published: July 2022

AbstractImmune checkpoint inhibitors (ICIs) targeting PD-L1 and PD-1 have improved survival in a subset of patients with advanced non-small cell lung cancer (NSCLC). However, only a minority of NSCLC patients respond to ICIs, highlighting the need for superior immunotherapy. Herein, we report on a nanoparticle-based immunotherapy termed ARAC (Antigen Release Agent and Checkpoint Inhibitor) designed to enhance the efficacy of PD-L1 inhibitor. ARAC is a nanoparticle co-delivering PLK1 inhibitor (volasertib) and PD-L1 antibody. PLK1 is a key mitotic kinase that is overexpressed in various cancers including NSCLC and drives cancer growth. Inhibition of PLK1 selectively kills cancer cells and upregulates PD-L1 expression in surviving cancer cells thereby providing opportunity for ARAC targeted delivery in a feedforward manner. ARAC reduces effective doses of volasertib and PD-L1 antibody by 5-fold in a metastatic lung tumor model (LLC-JSP) and the effect is mainly mediated by CD8+ T cells. ARAC also shows efficacy in another lung tumor model (KLN-205), which does not respond to CTLA-4 and PD-1 inhibitor combination. This study highlights a rational combination strategy to augment existing therapies by utilizing our nanoparticle platform that can load multiple cargo types at once.
Supercurrent diode effect and magnetochiral anisotropy in few-layer NbSe2
Authors: Bauriedl Lorenz , Bäuml Christian , Fuchs Lorenz , Baumgartner Christian , Paulik Nicolas , Bauer Jonas M. , Lin Kai-Qiang , Lupton John M. , Taniguchi Takashi , Watanabe Kenji , Strunk Christoph , Paradiso Nicola 
Published: July 2022

AbstractNonreciprocal transport refers to charge transfer processes that are sensitive to the bias polarity. Until recently, nonreciprocal transport was studied only in dissipative systems, where the nonreciprocal quantity is the resistance. Recent experiments have, however, demonstrated nonreciprocal supercurrent leading to the observation of a supercurrent diode effect in Rashba superconductors. Here we report on a supercurrent diode effect in NbSe2 constrictions obtained by patterning NbSe2 flakes with both even and odd layer number. The observed rectification is a consequence of the valley-Zeeman spin-orbit interaction. We demonstrate a rectification efficiency as large as 60%, considerably larger than the efficiency of devices based on Rashba superconductors. In agreement with recent theory for superconducting transition metal dichalcogenides, we show that the effect is driven by the out-of-plane component of the magnetic field. Remarkably, we find that the effect becomes field-asymmetric in the presence of an additional in-plane field component transverse to the current direction. Supercurrent diodes offer a further degree of freedom in designing superconducting quantum electronics with the high degree of integrability offered by van der Waals materials.
A phylogenetically-restricted essential cell cycle progression factor in the human pathogen Candida albicans
Authors: Jaitly Priya , Legrand Mélanie , Das Abhijit , Patel Tejas , Chauvel Murielle , Maufrais Corinne , d’Enfert Christophe , Sanyal Kaustuv 
Published: July 2022

AbstractChromosomal instability caused by cell division errors is associated with antifungal drug resistance in fungal pathogens. Here, we identify potential mechanisms underlying such instability by conducting an overexpression screen monitoring chromosomal stability in the human fungal pathogen Candida albicans. Analysis of ~1000 genes uncovers six chromosomal stability (CSA) genes, five of which are related to cell division genes of other organisms. The sixth gene, CSA6, appears to be present only in species belonging to the CUG-Ser clade, which includes C. albicans and other human fungal pathogens. The protein encoded by CSA6 localizes to the spindle pole bodies, is required for exit from mitosis, and induces a checkpoint-dependent metaphase arrest upon overexpression. Thus, Csa6 is an essential cell cycle progression factor that is restricted to the CUG-Ser fungal clade, and could therefore be explored as a potential antifungal target.
Phenylalanine impairs insulin signaling and inhibits glucose uptake through modification of IRβ
Authors: Zhou Qian , Sun Wan-Wan , Chen Jia-Cong , Zhang Hui-Lu , Liu Jie , Lin Yan , Lin Peng-Cheng , Wu Bai-Xing , An Yan-Peng , Huang Lin , Sun Wen-Xing , Zhou Xin-Wen , Li Yi-Ming , Yuan Yi-Yuan , Zhao Jian-Yuan , Xu Wei , Zhao Shi-Min 
Published: July 2022

AbstractWhether amino acids act on cellular insulin signaling remains unclear, given that increased circulating amino acid levels are associated with the onset of type 2 diabetes (T2D). Here, we report that phenylalanine modifies insulin receptor beta (IRβ) and inactivates insulin signaling and glucose uptake. Mice fed phenylalanine-rich chow or phenylalanine-producing aspartame or overexpressing human phenylalanyl-tRNA synthetase (hFARS) develop insulin resistance and T2D symptoms. Mechanistically, FARS phenylalanylate lysine 1057/1079 of IRβ (F-K1057/1079), inactivating IRβ and preventing insulin from promoting glucose uptake by cells. SIRT1 reverse F-K1057/1079 and counteract the insulin-inactivating effects of hFARS and phenylalanine. F-K1057/1079 and SIRT1 levels in white blood cells from T2D patients are positively and negatively correlated with T2D onset, respectively. Blocking F-K1057/1079 with phenylalaninol sensitizes insulin signaling and relieves T2D symptoms in hFARS-transgenic and db/db mice. These findings shed light on the activation of insulin signaling and T2D progression through inhibition of phenylalanylation.
K-point longitudinal acoustic phonons are responsible for ultrafast intervalley scattering in monolayer MoSe2
Authors: Bae Soungmin , Matsumoto Kana , Raebiger Hannes , Shudo Ken-ichi , Kim Yong-Hoon , Handegård Ørjan Sele , Nagao Tadaaki , Kitajima Masahiro , Sakai Yuji , Zhang Xiang , Vajtai Robert , Ajayan Pulickel , Kono Junichiro , Takeda Jun , Katayama Ikufumi 
Published: July 2022

AbstractIn transition metal dichalcogenides, valley depolarization through intervalley carrier scattering by zone-edge phonons is often unavoidable. Although valley depolarization processes related to various acoustic phonons have been suggested, their optical verification is still vague due to nearly degenerate phonon frequencies on acoustic phonon branches at zone-edge momentums. Here we report an unambiguous phonon momentum determination of the longitudinal acoustic (LA) phonons at the K point, which are responsible for the ultrafast valley depolarization in monolayer MoSe2. Using sub-10-fs-resolution pump-probe spectroscopy, we observed coherent phonons signals at both even and odd-orders of zone-edge LA mode involved in intervalley carrier scattering process. Our phonon-symmetry analysis and first-principles calculations reveal that only the LA phonon at the K point, as opposed to the M point, can produce experimental odd-order LA phonon signals from its nonlinear optical modulation. This work will provide momentum-resolved descriptions of phonon-carrier intervalley scattering processes in valleytronic materials.
Tailoring thermal insulation architectures from additive manufacturing
Authors: An Lu , Guo Zipeng , Li Zheng , Fu Yu , Hu Yong , Huang Yulong , Yao Fei , Zhou Chi , Ren Shenqiang 
Published: July 2022

AbstractTailoring thermal transport by structural parameters could result in mechanically fragile and brittle networks. An indispensable goal is to design hierarchical architecture materials that combine thermal and mechanical properties in a continuous and cohesive network. A promising strategy to create such a hierarchical network targets additive manufacturing of hybrid porous voxels at nanoscale. Here we describe the convergence of agile additive manufacturing of porous hybrid voxels to tailor hierarchically and mechanically tunable objects. In one strategy, the uniformly distributed porous silica voxels, which form the basis for the control of thermal transport, are non-covalently interfaced with polymeric networks, yielding hierarchic super-elastic architectures with thermal insulation properties. Another additive strategy for achieving mechanical strength involves the versatile orthogonal surface hybridization of porous silica voxels retains its low thermal conductivity of 19.1 mW m−1 K−1, flexible compressive recovery strain (85%), and tailored mechanical strength from 71.6 kPa to 1.5 MPa. The printed lightweight high-fidelity objects promise thermal aging mitigation for lithium-ion batteries, providing a thermal management pathway using 3D printed silica objects.
A single immunization with a modified vaccinia Ankara vectored vaccine producing Sudan virus-like particles protects from lethal infection
Authors: Malherbe Delphine C. , Domi Arban , Hauser Mary J. , Atyeo Caroline , Fischinger Stephanie , Hyde Matthew A. , Williams Julie M. , Alter Galit , Guirakhoo Farshad , Bukreyev Alexander 
Published: July 2022

AbstractA new vectored vaccine MVA-VLP-SUDV was generated against Sudan ebolavirus (SUDV) combining the advantages of the immunogenicity of a live attenuated vaccine vector (Modified Vaccinia Ankara, MVA) with the authentic conformation of virus-like particles (VLPs). The vaccine expresses minimal components to generate self-assembling VLPs in the vaccinee: the envelope glycoprotein GP and the matrix protein VP40. Guinea pigs vaccinated with one dose of MVA-VLP-SUDV generated SUDV-specific binding and neutralizing antibody responses as well as Fc-mediated protective effects. These responses were boosted by a second vaccine dose. All vaccinated animals which received either one or two vaccine doses were protected from death and disease symptoms following challenge with a lethal dose of SUDV. These data demonstrate single dose protection and potency of the MVA-VLP platform for use in emergency situations to contain outbreaks.
Global Soil Hydraulic Properties dataset based on legacy site observations and robust parameterization
Authors: Gupta Surya , Papritz Andreas , Lehmann Peter , Hengl Tomislav , Bonetti Sara , Or Dani 
Published: July 2022

AbstractThe representation of land surface processes in hydrological and climatic models critically depends on the soil water characteristics curve (SWCC) that defines the plant availability and water storage in the vadose zone. Despite the availability of SWCC datasets in the literature, significant efforts are required to harmonize reported data before SWCC parameters can be determined and implemented in modeling applications. In this work, a total of 15,259 SWCCs from 2,702 sites were assembled from published literature, harmonized, and quality-checked. The assembled SWCC data provide a global soil hydraulic properties (GSHP) database. Parameters of the van Genuchten (vG) SWCC model were estimated from the data using the R package ‘soilhypfit’. In many cases, information on the wet- or dry-end of the SWCC measurements were missing, and we used pedotransfer functions (PTFs) to estimate saturated and residual water contents. The new database quantifies the differences of SWCCs across climatic regions and can be used to create global maps of soil hydraulic properties.
Observing the Central Arctic Atmosphere and Surface with University of Colorado uncrewed aircraft systems
Authors: de Boer Gijs , Calmer Radiance , Jozef Gina , Cassano John J. , Hamilton Jonathan , Lawrence Dale , Borenstein Steven , Doddi Abhiram , Cox Christopher , Schmale Julia , Preußer Andreas , Argrow Brian 
Published: July 2022

AbstractOver a five-month time window between March and July 2020, scientists deployed two small uncrewed aircraft systems (sUAS) to the central Arctic Ocean as part of legs three and four of the MOSAiC expedition. These sUAS were flown to measure the thermodynamic and kinematic state of the lower atmosphere, including collecting information on temperature, pressure, humidity and winds between the surface and 1 km, as well as to document ice properties, including albedo, melt pond fraction, and open water amounts. The atmospheric state flights were primarily conducted by the DataHawk2 sUAS, which was operated primarily in a profiling manner, while the surface property flights were conducted using the HELiX sUAS, which flew grid patterns, profiles, and hover flights. In total, over 120 flights were conducted and over 48 flight hours of data were collected, sampling conditions that included temperatures as low as −35 °C and as warm as 15 °C, spanning the summer melt season.
SARS-ANI: a global open access dataset of reported SARS-CoV-2 events in animals
Authors: Nerpel Afra , Yang Liuhuaying , Sorger Johannes , Käsbohrer Annemarie , Walzer Chris , Desvars-Larrive Amélie 
Published: July 2022

AbstractThe zoonotic origin of SARS-CoV-2, the etiological agent of COVID-19, is not yet fully resolved. Although natural infections in animals are reported in a wide range of species, large knowledge and data gaps remain regarding SARS-CoV-2 in animal hosts. We used two major health databases to extract unstructured data and generated a global dataset of SARS-CoV-2 events in animals. The dataset presents harmonized host names, integrates relevant epidemiological and clinical data on each event, and is readily usable for analytical purposes. We also share the code for technical and visual validation of the data and created a user-friendly dashboard for data exploration. Data on SARS-CoV-2 occurrence in animals is critical to adapting monitoring strategies, preventing the formation of animal reservoirs, and tailoring future human and animal vaccination programs. The FAIRness and analytical flexibility of the data will support research efforts on SARS-CoV-2 at the human-animal-environment interface. We intend to update this dataset weekly for at least one year and, through collaborations, to develop it further and expand its use.
Expert tumor annotations and radiomics for locally advanced breast cancer in DCE-MRI for ACRIN 6657/I-SPY1
Authors: Chitalia Rhea , Pati Sarthak , Bhalerao Megh , Thakur Siddhesh Pravin , Jahani Nariman , Belenky Vivian , McDonald Elizabeth S. , Gibbs Jessica , Newitt David C. , Hylton Nola M. , Kontos Despina , Bakas Spyridon 
Published: July 2022

AbstractBreast cancer is one of the most pervasive forms of cancer and its inherent intra- and inter-tumor heterogeneity contributes towards its poor prognosis. Multiple studies have reported results from either private institutional data or publicly available datasets. However, current public datasets are limited in terms of having consistency in: a) data quality, b) quality of expert annotation of pathology, and c) availability of baseline results from computational algorithms. To address these limitations, here we propose the enhancement of the I-SPY1 data collection, with uniformly curated data, tumor annotations, and quantitative imaging features. Specifically, the proposed dataset includes a) uniformly processed scans that are harmonized to match intensity and spatial characteristics, facilitating immediate use in computational studies, b) computationally-generated and manually-revised expert annotations of tumor regions, as well as c) a comprehensive set of quantitative imaging (also known as radiomic) features corresponding to the tumor regions. This collection describes our contribution towards repeatable, reproducible, and comparative quantitative studies leading to new predictive, prognostic, and diagnostic assessments.
Dataset on social and psychological effects of COVID-19 pandemic in Turkey
Authors: Sari Emre , Kağan Gamze , Karakuş Buse Şencan , Özdemir Özgür 
Published: July 2022

AbstractThis data was gathered to investigate how individuals’ levels of intolerance to distress and instant anxiety are related to some of the behaviors that people can change in response to the COVID-19 pandemic. We present a dataset based on a four-wave survey of the social and psychological effects of the COVID-19 pandemic in Turkey (N = 2,817). Turkey was heavily impacted by the first waves of infections in 2020, and citizens were forced to adapt to governmental measures. So, the dataset provides unique opportunities to investigate the COVID-19 pandemic’s role in shaping people’s intolerance to distress and instant anxiety. The survey considered personal cleaning behavior, bank/credit card usage, online spending habits, individual security perception, and stockpile behavior. Furthermore, in this data, whether an individual or a household member was officially diagnosed with COVID-19 and socio-demographic indicators were determined. Hence, the resulting dataset can enable various analyses on social, psychological, perceived security, and self-rated health, influencing how individuals’ levels of intolerance to distress and instant anxiety.
Zero standby power crop water-stress detector leading to the optimization of water usage and yield
Authors: Risso Antea , Rajaram Vageeswar , Kang Sungho , Calisgan Sila Deniz , Pavese Matilde Maria , Qian Zhenyun , Rinaldi Matteo 
Published: July 2022

AbstractAgricultural sensors are powerful tools to optimize crop productivity while conserving natural resources. Here we report a crop water-stress detector based on a plasmonically-enhanced micromechanical photoswitch capable of detecting water content in leaves that is lower than a predetermined threshold without consuming electrical power when the leaf is healthy. The detection mechanism exploits the energy in a specific narrow-spectral band of solar radiation reflected off leaves that is strongly correlated to the water content in plants. This biosensor relies on a spectrally selective infrared plasmonic absorber and a thermally sensitive micro-cantilever to harvest the reflected solar energy and further produce a digitized wakeup-bit only when the monitored leaf is water-stressed. In particular, we demonstrate that the detector activates a commercial water pump when a soybean plant is water-stressed. The 10-year battery lifetime of the proposed detector pave the way for the development of high-granularity, maintenance-free sensor networks for large-scale smart-farms.