bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Complement C4 Genetic Diversity in First Episode Psychosis of the OPTiMiSE Cohort
Authors: Mariaselvam Christina M , Wu Ching-Lien , Boukouaci Wahid , Richard Jean-Romain , Barau Caroline , Le Corvoisier Philippe ,   OPTiMiSE Study Group, Dazzan Paola , Egerton Alice , Pollak Thomas A , McGuire Philip , Rujescu Dan , Jamain Stéphane , Leboyer Marion , Tamouza Ryad 
Published: February 2021

AbstractRecent findings implicate the complement C4 gene in gray matter loss in schizophrenia. In a large cohort of patients with first-episode psychosis (FEP), we aimed to (1) characterize the frequency of C4 gene copy number variations (CNVs) and HERV-K Ins/Del events as compared to that in healthy controls (HCs) and (2) evaluate whether C4 gene structural variants influence baseline clinical symptoms and treatment response to amisulpride. A total of 271 FEP subjects and 221 HCs were genotyped for C4 CNV and HERV-Ins/Del (C4A and C4B isoforms; C4-HERV structural forms [C4AL, C4AS, C4BL, C4BS] variations using droplet digital PCR. Overall, the gene frequencies of both C4 isoforms and C4-HERV structural forms did not significantly differ between groups. At the genotype level, we found that the C4 AL-AL-BL-BL genotype (AL-BL haplotype) was significantly more frequent in FEP as compared to HC. Apart from a marginal observation concerning the C4 AL-AL-BL-BL genotype (AL-BL haplotype), possibly reflecting a relationship with schizophrenia, we did not find any correlation between C4 genetic and clinical characteristics or treatment response in FEP.
Control and consent in the connected age: the work of contractors on transnational online education platforms
Authors: Lin Le 
Published: February 2021

Abstract
Drawing on ABCKID, one of the world’s largest online education platforms, and its six competitors, this paper rethinks control and consent of work in the platform economy. Falling into a new category of home-based virtual platforms, ABCKID has mobilized a group of American contractors (e.g. stay-at-home moms) who were previously marginalized in the US labor market. Using interviews, surveys and online data, I found that most ABCKID contractors show high levels of job satisfaction due to their relative gains. Furthermore, although ABCKID imposes strict and direct control over contractors’ work content and schedules, it opens new room for contractors to adapt to control. Contractors’ adaptive practices have also made the platform’s efforts to organize control as games less effective. I argue that consent of work on these platforms is not only a product of relative gains, but also a result of interactions between contractors’ adaptive practices and platforms’ direct controls.
Effects of feeding corn distillers dried grains with solubles diets without or with supplemental enzymes on growth performance of pigs: a meta-analysis
Authors: Jang Jae-Cheol , Zeng Zhikai , Urriola Pedro E , Shurson Gerald C 
Published: February 2021

AbstractA meta-analysis was conducted to determine the effects of the dietary energy system (net energy or metabolizable energy), oil content of corn distillers dried grains with solubles (cDDGS), diet inclusion levels, and pig age on growth performance of pigs fed cDDGS-based diets. Mean differences of average daily gain (ADG), average daily feed intake (ADFI), and gain:feed (G:F) were calculated and expressed as a percentage change relative to feeding corn–soybean meal (SBM)- and cDDGS-based diets to nursery [body weight (BW) &lt; 25 kg] and growing-finishing (BW &gt; 25 kg) pigs, and to compare the effects of supplementing various types of exogenous enzymes without or with phytase on growth performance. A total of 27 studies with 106 growth performance observations were included in the cDDGS dataset, and 34 studies with 84 observations for enzyme responses in cDDGS diets were used in the enzyme dataset. Approximately, 64.7% of the observations showed no change, and 26.7% of observations showed a reduction in ADG, ADFI, and G:F when feeding cDDGS-based diets to the nursery and growing-finishing pigs compared with feeding corn–SBM-based diets. Furthermore, feeding cDDGS diets resulted in decreased (P &lt; 0.01) mean difference of ADG (–4.27%) and G:F (–1.99%) for nursery pigs, and decreased (P &lt; 0.01) mean difference of ADG (–1.68%) and G:F (–1.06%) for growing–finishing pigs. Every percentage unit increase in the inclusion level of cDDGS in growing–finishing pig diet was associated with a decrease (P &lt; 0.01) in ADG (–0.10%) and ADFI (–0.09%). Feeding high oil (≥10% ether extract) cDDGS-based diets to pigs resulted in a 2.96% reduction in ADFI whereas feeding reduced-oil (&lt;10% ether extract) cDDGS-based diets reduced G:F by 1.56% compared with pigs fed corn–SBM-based diets. Supplementation of exogenous enzymes improved (P &lt; 0.05) the mean difference of ADG and G:F by 1.94% and 2.65%, respectively, in corn–SBM-based diets, and by 2.67% and 1.87%, respectively, in cDDGS diets. Supplementation of exogenous protease, enzyme cocktail, or xylanase improved (P &lt; 0.05) ADG by 7.29%, 2.64%, and 2.48% in pigs fed corn–SBM-based diets, respectively. There were no differences between the dietary addition of single enzymes and enzyme combinations for any growth performance parameters in corn–SBM- or cDDGS-based diets. In conclusion, feeding cDDGS-based diets slightly reduces the growth performance of nursery and growing–finishing pigs, but supplementation of xylanase or enzyme cocktail can improve G:F of pigs fed cDDGS-based diets.
SubclonalCHD1deletion is more frequent in African American prostate cancers and associated with rapid disease progression and limited levels of homologous recombination deficiency
Authors: Diossy Miklos , Tisza Viktoria , Li Hua , Zhou Jia , Sztupinszki Zsofia , Young Denise , Nousome Darryl , Kuo Claire , Jiang Jiji , Chen Yongmei , Ebner Reinhard , Sesterhenn Isabell A. , Moncur Joel T. , Chesnut Gregory T. , Petrovics Gyorgy , Klus Gregory T. , Valcz Gabor , Nuzzo Pier Vitale , Ribli Dezso , Schina Aimilia , Börcsök Judit , Prosz Aurel , Krzystanek Marcin , Ried Thomas , Szuts David , Kaochar Salma , Pathania Shailja , D’Andrea Alan D. , Csabai Istvan , Srivastava Shiv , Freedman Matthew L , Dobi Albert , Spisak Sandor , Szallasi Zoltan 
Published: February 2021

AbstractChromodomain helicase DNA-binding protein 1 (CHD1) is frequently deleted in a subset of prostate cancers. We show here that subclonal deletion ofCHD1is nearly three times as frequent in prostate tumors of African American men than in men of European ancestry and it associates with rapid disease progression. We further show thatCHD1deletion is associated with only one type of the homologous recombination deficiency associated mutational signatures in prostate cancer. In prostate cancer cell line modelsCHD1deletion did not induce HRD as detected by RAD51 foci formation assay, which was consistent with the moderate increase of olaparib sensitivity.CHD1deficient prostate cancer cells, however, still showed markedly increased sensitivity to talazoparib, which could be effective for the treatment ofCHD1deficient tumors in the context of hormone therapy resistant prostate cancer.
Attentional Modulations of Alpha Power Are Sensitive to the Task-relevance of Auditory Spatial Information
Authors: Klatt Laura-Isabelle , Getzmann Stephan , Schneider Daniel 
Published: February 2021

AbstractThe topographical distribution of oscillatory power in the alpha band is known to vary depending on the current focus of spatial attention. Here, we investigated to what extend univariate and multivariate measures of post-stimulus alpha power are sensitive to the required spatial specificity of a task. To this end, we varied the perceptual load and the spatial demand in an auditory search paradigm. A centrally presented sound at the beginning of each trial indicated the to-be-localized target sound. This spatially unspecific pre-cue was followed by a sound array, containing either two (low perceptual load) or four (high perceptual load) simultaneously presented lateralized sound stimuli. In separate task blocks, participants were instructed either to report whether the target was located on the left or the right side of the sound array (low spatial demand) or to indicate the exact target location (high spatial demand). Univariate alpha lateralization magnitude was neither affected by perceptual load nor by spatial demand. However, an analysis of onset latencies revealed that alpha lateralization emerged earlier in low (vs. high) perceptual load trials as well as in low (vs. high) spatial demand trials. Finally, we trained a classifier to decode the specific target location based on the multivariate alpha power scalp topography. A comparison of decoding accuracy in the low and high spatial demand conditions suggests that the amount of spatial information present in the scalp distribution of alpha-band power increases as the task demands a higher degree of spatial specificity. Altogether, the results offer new insights into how the dynamic adaption of alpha-band oscillations in response to changing task demands is associated with post-stimulus attentional processing.
Rapid processing and quantitative evaluation of multicontrast EPImix scans for adaptive multimodal imaging
Authors: Váša František , Hobday Harriet , Stanyard Ryan A. , Daws Richard E. , Giampietro Vincent , O’Daly Owen , Lythgoe David J. , Seidlitz Jakob , Skare Stefan , Williams Steven C. R. , Marquand Andre F. , Leech Robert , Cole James H. 
Published: February 2021

AbstractCurrent neuroimaging acquisition and processing approaches tend to be optimised for quality rather than speed. However, rapid acquisition and processing of neuroimaging data can lead to novel neuroimaging paradigms, such as adaptive acquisition, where rapidly processed data is used to inform subsequent image acquisition steps. Here we first evaluate the impact of several processing steps on the processing time and quality of registration of manually labelled T1-weighted MRI scans. Subsequently, we apply the selected rapid processing pipeline both to rapidly acquired multicontrast EPImix scans of 95 participants (which include T1-FLAIR, T2, T2*, T2-FLAIR, DWI & ADC contrasts, acquired in ∼1 minute), as well as to slower, more standard single-contrast T1-weighted scans of a subset of 66 participants. We quantify the correspondence between EPImix and single-contrast T1-weighted scans, using correlations between voxels and regions of interest across participants, measures of within- and between-participant identifiability as well as regional structural covariance networks. Furthermore, we explore the use of EPImix for the rapid construction of morphometric similarity networks. Finally, we quantify the reliability of EPImix-derived data using test-retest scans of 10 participants. Our results demonstrate that quantitative information can be derived from a neuroimaging scan acquired and processed within minutes, which could further be used to implement adaptive multimodal imaging and tailor neuroimaging examinations to individual patients.Abstract FigureGraphical abstract.
Creation of a single cell RNA seq meta-atlas to define human liver immune homeostasis
Authors: Rocque Brittany , Barbetta Arianna , Singh Pranay , Goldbeck Cameron , Helou Doumet Georges , Loh Yong-Hwee Eddie , Ung Nolan , Lee Jerry , Akbari Omid , Emamaullee Juliet 
Published: February 2021

ABSTRACTThe liver is unique in both its ability to maintain immune homeostasis and in its potential for immune tolerance following solid organ transplantation. Single-cell RNA sequencing (scRNA seq) is a powerful approach to generate highly dimensional transcriptome data to understand cellular phenotypes. However, when scRNA data is produced by different groups, with different data models, different standards, and samples processed in different ways, it can be challenging to draw meaningful conclusions from the aggregated data. The goal of this study was to establish a method to combine ‘human liver’ scRNA seq datasets by 1) characterizing the heterogeneity between studies and 2) using the meta-atlas to define the dominant phenotypes across immune cell subpopulations in healthy human liver. Publicly available scRNA seq data generated from liver samples obtained from a combined total of 17 patients and ∼32,000 cells were analyzed. Liver-specific immune cells (CD45+) were extracted from each dataset, and immune cell subpopulations (myeloid cells, NK and T cells, plasma cells, and B cells) were examined using dimensionality reduction (UMAP), differential gene expression, and ingenuity pathway analysis. All datasets co-clustered, but cell proportions differed between studies. Gene expression correlation demonstrated similarity across all studies, and canonical pathways that differed between datasets were related to cell stress and oxidative phosphorylation rather than immune-related function. Next, a meta-atlas was generated via data integration and compared against PBMC data to define gene signatures for each hepatic immune subpopulation. This analysis defined key features of hepatic immune homeostasis, with decreased expression across immunologic pathways and enhancement of pathways involved with cell death. This method for meta-analysis of scRNA seq data provides a novel approach to broadly define the features of human liver immune homeostasis. Specific pathways and cellular phenotypes described in this human liver immune meta-atlas provide a critical reference point for further study of immune mediated disease processes within the liver.
Tree phylogenetic diversity supports nature’s contributions to people, but is at risk from human population growth
Authors: Davies T. Jonathan , Maurin Olivier , Yessoufou Kowiyou , Daru Barnabas H. , Bezeng Bezeng S. , Schaefer Hanno , Thuiller Wilfried , van der Bank Michelle 
Published: February 2021

ABSTRACTThere is growing evidence for a link between biodiversity and ecosystem function, and for a correlation between human population and the species diversity of plants and animals in a region. Here, we suggest these relationships might not be independent. Using a comprehensive phylogeny of southern African trees and structural equation modelling, we show that human population density correlates with tree phylogenetic diversity and show that this relationship is stronger than the correlation with species richness alone. Further, we demonstrate that areas high in phylogenetic diversity support a greater diversity of ecosystem goods and services, indicating that the evolutionary processes responsible for generating variation among living organisms are also key to the provisioning of nature’s contributions to people. Our results raise the intriguing possibility that the history of human settlement in southern Africa may have been shaped, in part, by the evolutionary history of its tree flora. However, the correlation between human population and tree diversity generates a conflict between people and nature. Our study suggests that future human population growth may threaten the contributions to people provided by intact and phylogenetically diverse ecosystems.
Genomic evidence that governmentally producedCannabis sativapoorly represents genetic variation available in state markets
Authors: Vergara Daniela , Huscher Ezra L. , Keepers Kyle G. , Pisupati Rahul , Schwabe Anna L. , McGlaughlin Mitchell E. , Kane Nolan C. 
Published: February 2021

AbstractThe National Institute on Drug Abuse (NIDA) is the sole producer ofCannabisfor research purposes in the United States, including medical investigation. Previous research established that cannabinoid profiles in the NIDA varieties lacked diversity and potency relative to theCannabisproduced commercially. Additionally, microsatellite marker analyses have established that the NIDA varieties are genetically divergent form varieties produced in the private legal market. Here, we analyzed the genome of multipleCannabisvarieties from diverse lineages including two produced by NIDA, and we provide further support that NIDA’s varieties differ from widely available medical, recreational, or industrialCannabis. Furthermore, our results suggest that NIDA’s varieties lack diversity in the single copy portion of the genome, the maternally inherited genomes, the cannabinoid genes, and in the repetitive content of the genome. Therefore, results based on NIDA’s varieties are not generalizable regarding the effects ofCannabisafter consumption. For medical research to be relevant, material that is more widely used would have to be studied. Clearly, having research to date dominated by a single, non-representative source ofCannabishas hindered scientific investigation.
MEMS enabled miniaturized light-sheet microscopy with all optical control
Authors: Bakas Spyridon , Uttamchandani Deepak , Toshiyoshi Hiroshi , Bauer Ralf 
Published: February 2021

AbstractWe have designed and implemented a compact, cost-efficient miniaturised light-sheet microscopy system based on optical Microelectromechanical Systems (MEMS) scanners and tunable lenses. The system occupies a footprint of 20 × 28 × 13 cm3and combines off-the-shelf optics and optomechanics with 3D-printed structural and optical elements, and an economically costed objective lens, excitation laser and camera. All-optical volume scanning enables imaging of 340 × 190 × 60 µm3volumes with 0.25 vps and minimum lateral and axial resolution of 0.9 µm and 2.95 µm respectively. An open-top geometry allows imaging of samples on flat bottomed holders, allowing integration with microfluidic devices, multi-well plates and slide mounted samples, with applications envisaged in biomedical research and pre-clinical settings.
A computational approach to identify possible symbiotic mechanisms betweenKlebsiellaand the Mediterranean fly (Ceratitis capitata)
Authors: Franco L. Augusto , Pariente César Alberto Bravo 
Published: February 2021

AbstractNowadays, scientists develop multiple methods to control pests, like chemical control as the insecticides and biological control as the Sterile Insect Technique (SIT) to release infertile males produced by irradiation. This technique is complemented with research in the medfly’s(Ceratitis capitata)microbiota, this approach is based on the identification of molecular mechanisms from threeKlebsiellastrains using the reconstruction of metabolic pathways technique. We focus on the reconstruction of metabolic pathways involved in nitrogen metabolization because the bacteria are in charge of metabolizing the nitrogen compounds and make available for the medfly. We propose a pipeline to process the genome sequences the bacteria, reconstruct metabolic pathways and identify possible symbiont molecular mechanisms. The result of processing the biological data were ten pathways, six pathways produce L-Glutamate as final product, three pathways with ammonia product and one pathway was discarded because it was an internal pathway and don’t generate a metabolic product. Those pathways corresponding to L-Glutamate and ammonia metabolic products are part of nitrogen metabolism onKlebsiella, which shows that this metabolic process is one of the molecular mechanisms involved in symbiosis process betweenKlebsiellaand the medfly. Finally, by the results of the sequences analysis, in the medfly’s metamorphose the L-Glutamate are used in the synthesis of new proteins and the production of energy. The final consideration suggest that the pipeline propose can be used as first step to identify molecular mechanisms that can improve the production of industrial the medfly.
Structural and thermodynamic analyses of human TMED1 (p24γ1) Golgi dynamics
Authors: Mota Danielly C. A. M. , Mori Renan M. , Batista Mariana R. B. , Basso Luis G. M. , Cardoso Iara A. , Nonato M. Cristina , Costa-Filho Antonio J. , Mendes Luis F. S. 
Published: February 2021

AbstractThe transmembrane emp24 domain-containing proteins (TMED), also called p24 proteins, are members of a family of sorting receptors present in all representatives of the domain Eukarya and abundantly present in all subcompartments of the early secretory pathway, namely the endoplasmic reticulum (ER), the Golgi, and the intermediate compartment. Although essential during the bidirectional transport between the ER and the Golgi, there is still a lack of information regarding the TMEDs structure, oligomerization propensity, and biophysics of their interactions with the transport cargo. Here, we describe the first high-resolution structure of the Golgi dynamics (GOLD) domain of a TMED1 representative and its biophysical characterization in solution. The crystal structure showed a dimer formation that is also present in solution in a salt-dependent manner, suggesting that the GOLD domain can form homodimers even in the absence of the TMED1 coiled-coil region. A molecular dynamics description of the dimer stabilization, with a phylogenetic analysis of the residues important for the oligomerization and a model for the orientation towards the lipid membrane are also presented.
Thiophosphopeptides Instantly Targeting Golgi Apparatus and Selectively Killing Cancer Cells
Authors: Tan Weiyi , Zhang Qiuxin , Wang Jiaqing , Yi Meihui , He Hongjian , Xu Bing 
Published: February 2021

ABSTRACTGolgi apparatus is emerging as a key signaling hub of cells, but there are few approaches for targeting Golgi and selectively killing cancer cells. Here we show an unexpected result that changing an oxygen atom of the phosphoester bond in phospho-peptides by a sulfur atom enables instantly targeting Golgi apparatus (GA) and selectively killing cancer cells by enzymatic self-assembly. Specifically, conjugating cysteamine S-phosphate to the C-terminal of a self-assembling peptide generates a thiophospho-peptide. Being a substrate of alkaline phosphatase (ALP), the thiophosphopeptide undergoes rapid ALP-catalyzed dephosphorylation to form a thiopeptide that self-assembles. The thiophosphopeptide enters cells via caveolin-mediated endocytosis and macropinocytosis and instantly accumulates in GA because of dephosphorylation and formation of disulfide bonds in Golgi. Moreover, the thiophosphopeptide, targeting Golgi, potently and selectively inhibits cancer cells (e.g., HeLa) with the IC50 (about 3 μM), which is an order of magnitude more potent than that of the parent phosphopeptide. This work, as the first report of thiophospho-peptide for targeting Golgi, illustrates a new molecular platform for designing enzyme responsive molecules that target subcellular compartment for functions.