bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental study on the control of a suspended cable-driven parallel robot for object tracking purpose
Authors: Zare Soroush , Yazdi Mohammad Reza Hairi , Masouleh Mehdi Tale , Zhang Dan , Ajami Sahand , Afkhami Ardekani Amirhossein 
Published: May 2022

AbstractIn this paper, control of a suspended cable-driven parallel robot has been experimentally investigated based on the dynamic model of the robot for object tracking purpose. In order to improve the tracking ability of the robot, three control approaches, namely kinematic PID, dynamic PD, and a kinematic sliding mode control (SMC), have been implemented, both on the Simscape and on the robot constructed at the Human and Robot Interaction Laboratory. Neural network controller and dynamic SMC have been implemented on the Simscape model. Afterward, the effectiveness of each approach has been investigated by employing the root mean square error (RMSE) index. Simulation and experimental results reveal the ability of each controller for precise and smooth control. For precise and real-time object tracking, YOLOv5-s and YOLOv4-tiny model are trained. By comparing the obtained index values, the kinematic PID demonstrates the best performance with the maximum RMSE value of 0.018 compared to other methods.
Contour: A semi-automated segmentation and quantitation tool for cryo-soft-X-ray tomography
Authors: Nahas Kamal L. , Fernandes João Ferreira , Vyas Nina , Crump Colin , Graham Stephen , Harkiolaki Maria 
Published: May 2022

Abstract
Cryo-soft-X-ray tomography is being increasingly used in biological research to study the morphology of cellular compartments and how they change in response to different stimuli, such as viral infections. Segmentation of these compartments is limited by time-consuming manual tools or machine learning algorithms that require extensive time and effort to train. Here we describe Contour, a new, easy-to-use, highly automated segmentation tool that enables accelerated segmentation of tomograms to delineate distinct cellular compartments. Using Contour, cellular structures can be segmented based on their projection intensity and geometrical width by applying a threshold range to the image and excluding noise smaller in width than the cellular compartments of interest. This method is less laborious and less prone to errors from human judgement than current tools that require features to be manually traced, and it does not require training datasets as would machine-learning driven segmentation. We show that high-contrast compartments such as mitochondria, lipid droplets, and features at the cell surface can be easily segmented with this technique in the context of investigating herpes simplex virus 1 infection. Contour can extract geometric measurements from 3D segmented volumes, providing a new method to quantitate cryo-soft-X-ray tomography data. Contour can be freely downloaded at github.com/kamallouisnahas/Contour.
Summertime High Abundances of Succinic, Citric, and Glyoxylic Acids in Antarctic Aerosols: Implications to Secondary Organic Aerosol Formation
Authors: Boreddy Suresh K. R. , Hegde Prashant , Aswini A. R. 
Published: May 2022

AbstractObservations of organic compounds associated with natural sources are scarce in Antarctica, which limits our understanding of their sources and formation processes over the pristine region. Summertime Antarctic PM10 samples collected from Bharati station were studied for a homologous series of dicarboxylic acids (C2‐C12), ω‐oxoacids (C2‐C9), α‐dicarbonyls (C2‐C3) as well as citric and pyruvic acids by employing a water‐extraction followed by dibutyl ester derivatization technique and analyzed using capillary gas chromatography (GC). Results show that succinic (C4) and citric acids are the foremost abundant among the measured organic acids followed by glyoxylic (ωC2), azelaic (C9), and adipic (C6) acids. Such a typical molecular distribution of organic acids suggests the dominance of natural sources over the Antarctic. Two distinct air masses arrived from different altitudes, high and low altitude‐troposphere (HTAs and LTAs), showed a significant difference in mass concentrations of organic acids with higher values in LTAs. Total diacids‐C accounted for ∼9% of total carbon in HTAs, which is linked to chemical aging during long‐range transport. The higher abundance of C4 and citric acids are likely produced through secondary photooxidation of marine‐derived organic precursors, such as unsaturated fatty acids, phenolic, and biogenic isoprene compounds enriched in sea‐surface microlayer, via sea‐to‐air emission as confirmed by the significant (p < 0.05) correlations among the organic tracer compounds. Minor concentrations of oxalic and malonic (C2 and C3) acids were attributed to photo iron‐complex reactions in the aqueous‐phase atmosphere. These findings may help in reducing model uncertainties and present new insights into the secondary formation of organic aerosols in the polar environment.
Impacts of Lake Surface Temperature on the Summer Climate Over the Great Lakes Region
Authors: Wang Jiali , Xue Pengfei , Pringle William , Yang Zhao , Qian Yun 
Published: May 2022

AbstractThe surface of the Great Lakes interacts with the atmosphere, influencing the weather and climate over the Great Lakes Region (GLR). However, most climate models were not designed with sufficient emphasis on lake–atmosphere interactions, which could potentially cause model biases over the GLR. To understand how lake surface temperature (LST) affects the regional summer climate over the GLR, we conducted twin experiments using the Weather Research and Forecasting model at a spatial resolution of 4 km using two different LST data sets as the bottom boundary condition over the Great Lakes. Our simulations include 10 ensemble members for the summer of 2018 and a single multiyear run for the summers of 2014–2020. Results show that variations in LST influence atmospheric temperature and moisture at a local scale—while affecting the convective environment and precipitation processes over a much larger spatial scale. In particular, an LST that is only 1°C–3°C warmer (depending on the lake) increases near‐surface air temperature by 1.93°C and 0.97°C over Lake Superior and Lake Erie, respectively, and increases evaporation over the lakes by 0.23 and 1.1 mm day−1. The warmer LST reduces mesoscale convective precipitation upstream of the GLR; however, it increases isolated deep convective precipitation and nonconvective precipitation downstream of GLR due to increased local instability and enhancement of moisture transport. Our analyses confirm the robustness of these impacts, which is at least 2 times larger than the model internal variability and is seen across all simulated summer seasons.
Recruitment of monocytes primed to express heme oxygenase-1 ameliorates pathological lung inflammation in cystic fibrosis
Authors: Di Pietro Caterina , Öz Hasan H. , Zhang Ping-xia , Cheng Ee-chun , Martis Valentino , Bonfield Tracey L. , Kelley Thomas J. , Jubin Ronald , Abuchowski Abraham , Krause Diane S. , Egan Marie E. , Murray Thomas S. , Bruscia Emanuela M. 
Published: May 2022

AbstractOverwhelming neutrophilic inflammation is a leading cause of lung damage in many pulmonary diseases, including cystic fibrosis (CF). The heme oxygenase-1 (HO-1)/carbon monoxide (CO) pathway mediates the resolution of inflammation and is defective in CF-affected macrophages (MΦs). Here, we provide evidence that systemic administration of PP-007, a CO releasing/O2 transfer agent, induces the expression of HO-1 in a myeloid differentiation factor 88 (MyD88) and phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT)-dependent manner. It also rescues the reduced HO-1 levels in CF-affected cells induced in response to lipopolysaccharides (LPS) or Pseudomonas aeruginosa (PA). Treatment of CF and muco-obstructive lung disease mouse models with a single clinically relevant dose of PP-007 leads to effective resolution of lung neutrophilia and to decreased levels of proinflammatory cytokines in response to LPS. Using HO-1 conditional knockout mice, we show that the beneficial effect of PP-007 is due to the priming of circulating monocytes trafficking to the lungs in response to infection to express high levels of HO-1. Finally, we show that PP-007 does not compromise the clearance of PA in the setting of chronic airway infection. Overall, we reveal the mechanism of action of PP-007 responsible for the immunomodulatory function observed in clinical trials for a wide range of diseases and demonstrate the potential use of PP-007 in controlling neutrophilic pulmonary inflammation by promoting the expression of HO-1 in monocytes/macrophages.
Direct demonstration of triplet excimer in purely organic room temperature phosphorescence through rational molecular design
Authors: Liu Zhenjiang , Tian Yu , Yang Jie , Li Aisen , Wang Yunsheng , Ren Jia , Fang Manman , Tang Ben Zhong , Li Zhen 
Published: May 2022

AbstractOrganic luminogens with room temperature phosphorescence (RTP) have been paid great attention and developed rapidly for their wide application values. Until now, the internal mechanism and source of phosphorescence are still obscure, especially for the relationship between molecular dimer and RTP emission. Hence, we designed and synthesized eight phenothiazine 5,5-dioxide derivatives to directly reveal how the monomer and dimer in packing affect the RTP behavior. Dimers with strong π-π stacking (θ < 20.66°; d < 3.86 Å) lead to pure triplet excimer emission, while those with weak π-π stacking (27.02°< θ < 40.64°; 3.84 Å < d < 4.41 Å) contribute to dual RTP emissions of both monomer and triplet excimer. The valuable information of this work would promote the further development of this research field, as well as others in aggregate.
Gestational immune activation disrupts hypothalamic neurocircuits of maternal care behavior
Authors: Zambon Alice , Rico Laura Cuenca , Herman Mathieu , Gundacker Anna , Telalovic Amina , Hartenberger Lisa-Marie , Kuehn Rebekka , Romanov Roman A. , Hussaini S. Abid , Harkany Tibor , Pollak Daniela D. 
Published: May 2022

AbstractImmune activation is one of the most common complications during pregnancy, predominantly evoked by viral infections. Nevertheless, how immune activation affects mother–offspring relationships postpartum remains unknown. Here, by using the polyinosinic-polycytidylic acid (Poly I:C) model of gestational infection we show that viral-like immune activation at mid-gestation persistently changes hypothalamic neurocircuit parameters in mouse dams and, consequently, is adverse to parenting behavior. Poly I:C-exposed dams favor non-pup-directed exploratory behavior at the expense of pup retrieval. These behavioral deficits are underlain by dendrite pruning and lesser immediate early gene activation in Galanin (Gal)+ neurons with dam-specific transcriptional signatures that reside in the medial preoptic area (mPOA). Reduced activation of an exclusively inhibitory contingent of these distal-projecting Gal+ neurons allows for increased feed-forward inhibition onto putative dopaminergic neurons in the ventral tegmental area (VTA) in Poly I:C-exposed dams. Notably, destabilized VTA output specifically accompanies post-pup retrieval epochs. We suggest that gestational immunogenic insults bias both threat processing and reward perception, manifesting as disfavored infant caregiving.
Immune response in COVID-19: what is next?
Authors: Li Qing , Wang Ying , Sun Qiang , Knopf Jasmin , Herrmann Martin , Lin Liangyu , Jiang Jingting , Shao Changshun , Li Peishan , He Xiaozhou , Hua Fei , Niu Zubiao , Ma Chaobing , Zhu Yichao , Ippolito Giuseppe , Piacentini Mauro , Estaquier Jerome , Melino Sonia , Weiss Felix Daniel , Andreano Emanuele , Latz Eicke , Schultze Joachim L. , Rappuoli Rino , Mantovani Alberto , Mak Tak Wah , Melino Gerry , Shi Yufang 
Published: May 2022

AbstractThe coronavirus disease 2019 (COVID-19) has been a global pandemic for more than 2 years and it still impacts our daily lifestyle and quality in unprecedented ways. A better understanding of immunity and its regulation in response to SARS-CoV-2 infection is urgently needed. Based on the current literature, we review here the various virus mutations and the evolving disease manifestations along with the alterations of immune responses with specific focuses on the innate immune response, neutrophil extracellular traps, humoral immunity, and cellular immunity. Different types of vaccines were compared and analyzed based on their unique properties to elicit specific immunity. Various therapeutic strategies such as antibody, anti-viral medications and inflammation control were discussed. We predict that with the available and continuously emerging new technologies, more powerful vaccines and administration schedules, more effective medications and better public health measures, the COVID-19 pandemic will be under control in the near future.
Dynamics of sex-biased gene expression during development in the stick insect Timema californicum
Authors: Djordjevic Jelisaveta , Dumas Zoé , Robinson-Rechavi Marc , Schwander Tanja , Parker Darren James 
Published: May 2022

AbstractSexually dimorphic phenotypes are thought to arise primarily from sex-biased gene expression during development. Major changes in developmental strategies, such as the shift from hemimetabolous to holometabolous development, are therefore expected to have profound consequences for the dynamics of sex-biased gene expression. However, no studies have previously examined sex-biased gene expression during development in hemimetabolous insects, precluding comparisons between developmental strategies. Here we characterized sex-biased gene expression at three developmental stages in a hemimetabolous stick insect (Timema californicum): hatchlings, juveniles, and adults. As expected, the proportion of sex-biased genes gradually increased during development, mirroring the gradual increase of phenotypic sexual dimorphism. Sex-biased genes identified at early developmental stages were generally consistently male- or female-biased at later stages, suggesting their importance in sexual differentiation. Additionally, we compared the dynamics of sex-biased gene expression during development inT. californicumto those of the holometabolous flyDrosophila melanogasterby reanalyzing publicly available RNA-seq data from third instar larval, pupal and adult stages. InD. melanogaster, 84% of genes were sex-biased at the adult stage (compared to only 20% inT. californicum), and sex-biased gene expression increased abruptly at the adult stage when morphological sexual dimorphism is manifested. Our findings are consistent with the prediction that the dynamics of sex-biased gene expression during development differ extensively between holometabolous and hemimetabolous insect species.
A rare homozygous missense mutation of COL7A1 in a Vietnamese family
Authors: Duong Nguyen Thuy , Anh Luong Thi Lan , Sau Nguyen Huu , Anh Nguyen Bao , Miyake Noriko , Van Hai Nong , Matsumoto Naomichi 
Published: May 2022

AbstractWe present a homozygous missense mutation in the COL7A1 gene (NM_000094.4: c.6262G>A, p.G2088R) in a case of inversa recessive dystrophic epidermolysis bullosa (RDEB-I) from a nonconsanguineous Vietnamese family. Although a heterozygous form of this mutation in combination with a premature termination codon allele has been shown to cause RDEB-I, this is the first report of homozygosity of this mutation as the etiology. Here, we investigated the molecular basis of the patient’s disease for prenatal diagnosis after genetic counseling of the parents.
Novel COL2A1 variants in Japanese patients with spondyloepiphyseal dysplasia congenita
Authors: Akahira-Azuma Moe , Enomoto Yumi , Nakamura Naoyuki , Yokoi Takayuki , Minatogawa Mari , Harada Noriaki , Tsurusaki Yoshinori , Kurosawa Kenji 
Published: May 2022

AbstractSpondyloepiphyseal dysplasia congenita (SEDC) is a multisystemic skeletal disorder caused by pathogenic variants inCOL2A1. Here, we report the genotype-phenotype correlations in five Japanese patients with SEDC based on their clinical and radiological findings. All five patients had novel missense variants resulting in glycine substitutions (G474V, G543E, G567S, G594R, and G1170R). Genetic testing is important for early intervention for the extraskeletal complications of SEDC. Spondyloepiphyseal dysplasia congenita (SEDC) (OMIM#183900) is an autosomal dominant chondrodysplasia characterized by disproportionate short stature, abnormal epiphyses, flattened vertebral bodies (skeletal abnormalities), and extraskeletal features, including myopia, retinal degeneration with retinal detachment, and cleft palate. SEDC is caused by a heterozygous variant in the collagen II alpha 1 (COL2A1) gene.
Clinical course of a Japanese patient with developmental delay linked to a small 6q16.1 deletion
Authors: Okazaki Tetsuya , Kawaguchi Tatsuya , Saiki Yusuke , Aoki Chisako , Kasagi Noriko , Adachi Kaori , Saida Ken , Matsumoto Naomichi , Nanba Eiji , Maegaki Yoshihiro 
Published: May 2022

AbstractThere is only one report of patients with developmental delay due to a 6q16.1 deletion that does not contain the SIM1 gene. A 3-year-old female showed strabismus, cleft soft palate, hypotonia at birth, and global developmental delay. Exome sequencing detected a de novo 6q16.1 deletion (chr6: 99282717–100062596) (hg19). The following genes were included in this region: POU3F2, FBXL4, FAXC, COQ3, PNISR, USP45, TSTD3, CCNC, and PRDM13.
Mutational landscape of normal epithelial cells in Lynch Syndrome patients
Authors: Lee Bernard C. H. , Robinson Philip S. , Coorens Tim H. H. , Yan Helen H. N. , Olafsson Sigurgeir , Lee-Six Henry , Sanders Mathijs A. , Siu Hoi Cheong , Hewinson James , Yue Sarah S. K. , Tsui Wai Yin , Chan Annie S. Y. , Chan Anthony K. W. , Ho Siu Lun , Campbell Peter J. , Martincorena Inigo , Buczacki Simon J. A. , Yuen Siu Tsan , Leung Suet Yi , Stratton Michael R. 
Published: May 2022

AbstractLynch Syndrome (LS) is an autosomal dominant disease conferring a high risk of colorectal cancer due to germline heterozygous mutations in a DNA mismatch repair (MMR) gene. Although cancers in LS patients show elevated somatic mutation burdens, information on mutation rates in normal tissues and understanding of the trajectory from normal to cancer cell is limited. Here we whole genome sequence 152 crypts from normal and neoplastic epithelial tissues from 10 LS patients. In normal tissues the repertoire of mutational processes and mutation rates is similar to that found in wild type individuals. A morphologically normal colonic crypt with an increased mutation burden and MMR deficiency-associated mutational signatures is identified, which may represent a very early stage of LS pathogenesis. Phylogenetic trees of tumour crypts indicate that the most recent ancestor cell of each tumour is already MMR deficient and has experienced multiple cycles of clonal evolution. This study demonstrates the genomic stability of epithelial cells with heterozygous germline MMR gene mutations and highlights important differences in the pathogenesis of LS from other colorectal cancer predisposition syndromes.
A Middle Pleistocene Denisovan molar from the Annamite Chain of northern Laos
Authors: Demeter Fabrice , Zanolli Clément , Westaway Kira E. , Joannes-Boyau Renaud , Duringer Philippe , Morley Mike W. , Welker Frido , Rüther Patrick L. , Skinner Matthew M. , McColl Hugh , Gaunitz Charleen , Vinner Lasse , Dunn Tyler E. , Olsen Jesper V. , Sikora Martin , Ponche Jean-Luc , Suzzoni Eric , Frangeul Sébastien , Boesch Quentin , Antoine Pierre-Olivier , Pan Lei , Xing Song , Zhao Jian-Xin , Bailey Richard M. , Boualaphane Souliphane , Sichanthongtip Phonephanh , Sihanam Daovee , Patole-Edoumba Elise , Aubaile Françoise , Crozier Françoise , Bourgon Nicolas , Zachwieja Alexandra , Luangkhoth Thonglith , Souksavatdy Viengkeo , Sayavongkhamdy Thongsa , Cappellini Enrico , Bacon Anne-Marie , Hublin Jean-Jacques , Willerslev Eske , Shackelford Laura 
Published: May 2022

AbstractThe Pleistocene presence of the genusHomoin continental Southeast Asia is primarily evidenced by a sparse stone tool record and rare human remains. Here we report a Middle Pleistocene hominin specimen from Laos, with the discovery of a molar from the Tam Ngu Hao 2 (Cobra Cave) limestone cave in the Annamite Mountains. The age of the fossil-bearing breccia ranges between 164–131 kyr, based on the Bayesian modelling of luminescence dating of the sedimentary matrix from which it was recovered, U-series dating of an overlying flowstone, and U-series–ESR dating of associated faunal teeth. Analyses of the internal structure of the molar in tandem with palaeoproteomic analyses of the enamel indicate that the tooth derives from a young, likely female,Homoindividual. The close morphological affinities with the Xiahe specimen from China indicate that they belong to the same taxon and that Tam Ngu Hao 2 most likely represents a Denisovan.
Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes
Authors: Knörlein Anna , Sarnowski Chris P. , de Vries Tebbe , Stoltz Moritz , Götze Michael , Aebersold Ruedi , Allain Frédéric H.-T. , Leitner Alexander , Hall Jonathan 
Published: May 2022

AbstractPhoto-induced cross-linking is a mainstay technique to characterize RNA-protein interactions. However, UV-induced cross-linking between RNA and proteins at “zero-distance” is poorly understood. Here, we investigate cross-linking of the RBFOX alternative splicing factor with its hepta-ribonucleotide binding element as a model system. We examine the influence of nucleobase, nucleotide position and amino acid composition using CLIR-MS technology (crosslinking-of-isotope-labelled-RNA-and-tandem-mass-spectrometry), that locates cross-links on RNA and protein with site-specific resolution. Surprisingly, cross-linking occurs only at nucleotides that are π-stacked to phenylalanines. Notably, this π-stacking interaction is also necessary for the amino-acids flanking phenylalanines to partake in UV-cross-linking. We confirmed these observations in several published datasets where cross-linking sites could be mapped to a high resolution structure. We hypothesize that π-stacking to aromatic amino acids activates cross-linking in RNA-protein complexes, whereafter nucleotide and peptide radicals recombine. These findings will facilitate interpretation of cross-linking data from structural studies and from genome-wide datasets generated using CLIP (cross-linking-and-immunoprecipitation) methods.
Drought assessment has been outpaced by climate change: empirical arguments for a paradigm shift
Authors: Hoylman Zachary H. , Bocinsky R. Kyle , Jencso Kelsey G. 
Published: May 2022

AbstractDespite the acceleration of climate change, erroneous assumptions of climate stationarity are still inculcated in the management of water resources in the United States (US). The US system for drought detection, which triggers billions of dollars in emergency resources, adheres to this assumption with preference towards 60-year (or longer) record lengths for drought characterization. Using observed data from 1,934 Global Historical Climate Network (GHCN) sites across the US, we show that conclusions based on long climate records can substantially bias assessment of drought severity. Bias emerges by assuming that conditions from the early and mid 20th century are as likely to occur in today’s climate. Numerical simulations reveal that drought assessment error is relatively low with limited climatology lengths (~30 year) and that error increases with longer record lengths where climate is changing rapidly. We assert that non-stationarity in climate must be accounted for in contemporary assessments to more accurately portray present drought risk.