bluuebunny/crossref_metadata_2025_split huggingface dataset:
A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm
Authors: Scalabrin Simone , Magris Gabriele , Liva Mario , Vitulo Nicola , Vidotto Michele , Scaglione Davide , Del Terra Lorenzo , Ruosi Manuela Rosanna , Navarini Luciano , Pellegrino Gloria , Berny Mier y Teran Jorge Carlos , Toniutti Lucile , Suggi Liverani Furio , Cerutti Mario , Di Gaspero Gabriele , Morgante Michele 
Published: January 2024

AbstractIn order to better understand the mechanisms generating genetic diversity in the recent allotetraploid speciesCoffea arabica, here we present a chromosome-level assembly obtained with long read technology. Two genomic compartments with different structural and functional properties are identified in the two homoeologous genomes. The resequencing data from a large set of accessions reveals low intraspecific diversity in the center of origin of the species. Across a limited number of genomic regions, diversity increases in some cultivated genotypes to levels similar to those observed within one of the progenitor species,Coffea canephora, presumably as a consequence of introgressions deriving from the so-called Timor hybrid. It also reveals that, in addition to few, early-occurring exchanges between homoeologous chromosomes, there are numerous recent chromosomal aberrations including aneuploidies, deletions, duplications and exchanges. These events are still polymorphic in the germplasm and could represent a fundamental source of genetic variation in such a lowly variable species.
Exosomal secreted SCIMP regulates communication between macrophages and neutrophils in pneumonia
Authors: Pei Xiaolei , Liu Li , Wang Jieru , Guo Changyuan , Li Qingqing , Li Jia , Ren Qian , Ma Runzhi , Zheng Yi , Zhang Yan , Liu Li , Zheng Danfeng , Wang Pingzhang , Jiang Ping , Feng Xiaoming , Jiang Erlie , Wang Ying , Feng Sizhou 
Published: January 2024

AbstractIn pneumonia, the deficient or delayed pathogen clearance can lead to pathogen proliferation and subsequent overactive immune responses, inducing acute lung injury (ALI). While screening human genome coding genes using our peripheral blood cell chemotactic platform, we unexpectedly find SLP adaptor and CSK interacting membrane protein (SCIMP), a protein with neutrophil chemotactic activity secreted during ALI. However, the specific role of SCIMP in ALI remains unclear. In this study, we investigate the secretion of SCIMP in exosomes (SCIMPexo) by macrophages after bacterial stimulation, both in vitro and in vivo. We observe a significant increase in the levels of SCIMPexoin bronchoalveolar lavage fluid and serum of pneumonia patients. We also find that bronchial perfusion with SCIMPexoor SCIMP N-terminal peptides increases the survival rate of the ALI model. This occurs due to the chemoattraction and activation of peripheral neutrophils dependent on formyl peptide receptor 1/2 (FPR1/2). Conversely, exosome suppressors and FPR1/2 antagonists decrease the survival rate in the lethal ALI model.Scimp-deficient andFpr1/2-deficient mice also have lower survival rates and shorter survival times than wild-type mice. However, bronchial perfusion of SCIMP rescuesScimp-deficient mice but notFpr1/2-deficient mice. Collectively, our findings suggest that the macrophage-SCIMP-FPRs-neutrophil axis plays a vital role in the innate immune process underlying ALI.
AKT1 phosphorylation of cytoplasmic ME2 induces a metabolic switch to glycolysis for tumorigenesis
Authors: Chen Taiqi , Xie Siyi , Cheng Jie , Zhao Qiao , Wu Hong , Jiang Peng , Du Wenjing 
Published: January 2024

AbstractMany types of tumors feature aerobic glycolysis for meeting their increased energetic and biosynthetic demands. However, it remains still unclear how this glycolytic phenomenon is achieved and coordinated with other metabolic pathways in tumor cells in response to growth stimuli. Here we report that activation of AKT1 induces a metabolic switch to glycolysis from the mitochondrial metabolism via phosphorylation of cytoplasmic malic enzyme 2 (ME2), named ME2fl (fl means full length), favoring an enhanced glycolytic phenotype. Mechanistically, in the cytoplasm, AKT1 phosphorylates ME2fl at serine 9 in the mitochondrial localization signal peptide at the N-terminus, preventing its mitochondrial translocation. Unlike mitochondrial ME2, which accounts for adjusting the tricarboxylic acid (TCA) cycle, ME2fl functions as a scaffold that brings together the key glycolytic enzymes phosphofructokinase (PFKL), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and pyruvate kinase M2 (PKM2), as well as Lactate dehydrogenase A (LDHA), to promote glycolysis in the cytosol. Thus, through phosphorylation of ME2fl, AKT1 enhances the glycolytic capacity of tumor cells in vitro and in vivo, revealing an unexpected role for subcellular translocation switching of ME2 mediated by AKT1 in the metabolic adaptation of tumor cells to growth stimuli.
Acoustic and language-specific sources for phonemic abstraction from speech
Authors: Mai Anna , Riès Stephanie , Ben-Haim Sharona , Shih Jerry J. , Gentner Timothy Q. 
Published: January 2024

AbstractSpoken language comprehension requires abstraction of linguistic information from speech, but the interaction between auditory and linguistic processing of speech remains poorly understood. Here, we investigate the nature of this abstraction using neural responses recorded intracranially while participants listened to conversational English speech. Capitalizing on multiple, language-specific patterns where phonological and acoustic information diverge, we demonstrate the causal efficacy of the phoneme as a unit of analysis and dissociate the unique contributions of phonemic and spectrographic information to neural responses. Quantitive higher-order response models also reveal that unique contributions of phonological information are carried in the covariance structure of the stimulus-response relationship. This suggests that linguistic abstraction is shaped by neurobiological mechanisms that involve integration across multiple spectro-temporal features and prior phonological information. These results link speech acoustics to phonology and morphosyntax, substantiating predictions about abstractness in linguistic theory and providing evidence for the acoustic features that support that abstraction.
Durvalumab plus pazopanib combination in patients with advanced soft tissue sarcomas: a phase II trial
Authors: Cho Hee Jin , Yun Kum-Hee , Shin Su-Jin , Lee Young Han , Kim Seung Hyun , Baek Wooyeol , Han Yoon Dae , Kim Sang Kyum , Ryu Hyang Joo , Lee Joohee , Cho Iksung , Go Heounjeong , Ko Jiwon , Jung Inkyung , Jeon Min Kyung , Rha Sun Young , Kim Hyo Song 
Published: January 2024

AbstractWe aimed to determine the activity of the anti-VEGF receptor tyrosine-kinase inhibitor, pazopanib, combined with the anti-PD-L1 inhibitor, durvalumab, in metastatic and/or recurrent soft tissue sarcoma (STS). In this single-arm phase 2 trial (NCT03798106), treatment consisted of pazopanib 800 mg orally once a day and durvalumab 1500 mg once every 3 weeks. Primary outcome was overall response rate (ORR) and secondary outcomes included progression-free survival (PFS), overall survival, disease control rate, immune-related response criteria, and safety. The ORR was 30.4% and the trial met the pre-specified endpoint. The median PFS was 7.7 months (95% confidence interval: 5.7–10.4). The common treatment-related adverse events of grades 3–4 included neutropenia (9 [19.1%]), elevated aspartate aminotransferase (7 [14.9%]), alanine aminotransferase (5 [10.6%]), and thrombocytopenia (4 [8.5%]). In a prespecified transcriptomic analysis, the B lineage signature was a significant key determinant of overall response (P = 0.014). In situ analysis also showed that tumours with high CD20+ B cell infiltration and vessel density had a longer PFS (P = 6.5 × 10−4) than those with low B cell infiltration and vessel density, as well as better response (50% vs 12%, P = 0.019). CD20+ B cell infiltration was identified as the only independent predictor of PFS via multivariate analysis. Durvalumab combined with pazopanib demonstrated promising efficacy in an unselected STS cohort, with a manageable toxicity profile.
Dithiine-linked metalphthalocyanine framework with undulated layers for highly efficient and stable H2O2 electroproduction
Authors: Zhi Qianjun , Jiang Rong , Yang Xiya , Jin Yucheng , Qi Dongdong , Wang Kang , Liu Yunpeng , Jiang Jianzhuang 
Published: January 2024

AbstractRealization of stable and industrial-level H2O2 electroproduction still faces great challenge due large partly to the easy decomposition of H2O2. Herein, a two-dimensional dithiine-linked phthalocyaninato cobalt (CoPc)-based covalent organic framework (COF), CoPc-S-COF, was afforded from the reaction of hexadecafluorophthalocyaninato cobalt (II) with 1,2,4,5-benzenetetrathiol. Introduction of the sulfur atoms with large atomic radius and two lone-pairs of electrons in the C-S-C linking unit leads to an undulated layered structure and an increased electron density of the Co center for CoPc-S-COF according to a series of experiments in combination with theoretical calculations. The former structural effect allows the exposition of more Co sites to enhance the COF catalytic performance, while the latter electronic effect activates the 2e− oxygen reduction reaction (2e− ORR) but deactivates the H2O2 decomposition capability of the same Co center, as a total result enabling CoPc-S-COF to display good electrocatalytic H2O2 production performance with a remarkable H2O2 selectivity of >95% and a stable H2O2 production with a concentration of 0.48 wt% under a high current density of 125 mA cm−2 at an applied potential of ca. 0.67 V versus RHE for 20 h in a flow cell, representing the thus far reported best H2O2 synthesis COFs electrocatalysts.
Folding pathway of a discontinuous two-domain protein
Authors: Agam Ganesh , Barth Anders , Lamb Don C. 
Published: January 2024

AbstractIt is estimated that two-thirds of all proteins in higher organisms are composed of multiple domains, many of them containing discontinuous folds. However, to date, most in vitro protein folding studies have focused on small, single-domain proteins. As a model system for a two-domain discontinuous protein, we study the unfolding/refolding of a slow-folding double mutant of the maltose binding protein (DM-MBP) using single-molecule two- and three-color Förster Resonance Energy Transfer experiments. We observe a dynamic folding intermediate population in the N-terminal domain (NTD), C-terminal domain (CTD), and at the domain interface. The dynamic intermediate fluctuates rapidly between unfolded states and compact states, which have a similar FRET efficiency to the folded conformation. Our data reveals that the delayed folding of the NTD in DM-MBP is imposed by an entropic barrier with subsequent folding of the highly dynamic CTD. Notably, accelerated DM-MBP folding is routed through the same dynamic intermediate within the cavity of the GroEL/ES chaperone system, suggesting that the chaperonin limits the conformational space to overcome the entropic folding barrier. Our study highlights the subtle tuning and co-dependency in the folding of a discontinuous multi-domain protein.
Systematic determination of a material’s magnetic ground state from first principles
Authors: Tellez-Mora Andres , He Xu , Bousquet Eric , Wirtz Ludger , Romero Aldo H. 
Published: January 2024

AbstractWe present a self-consistent method based on first-principles calculations to determine the magnetic ground state of materials, regardless of their dimensionality. Our methodology is founded on satisfying the stability conditions derived from the linear spin wave theory (LSWT) by optimizing the magnetic structure iteratively. We demonstrate the effectiveness of our method by successfully predicting the experimental magnetic structures of NiO, FePS3, FeP, MnF2, FeCl2, and CuO. In each case, we compared our results with available experimental data and existing theoretical calculations reported in the literature. Finally, we discuss the validity of the method and the possible extensions.
Electricity and natural gas tariffs at United States wastewater treatment plants
Authors: Chapin Fletcher T. , Bolorinos Jose , Mauter Meagan S. 
Published: January 2024

AbstractWastewater treatment plants (WWTPs) are large electricity and natural gas consumers with untapped potential to recover carbon-neutral biogas and provide energy services for the grid. Techno-economic analysis of emerging energy recovery and management technologies is critical to understanding their commercial viability, but quantifying their energy cost savings potential is stymied by a lack of well curated, nationally representative electricity and natural gas tariff data. We present a dataset of electricity tariffs for the 100 largest WWTPs in the Clean Watershed Needs Survey (CWNS) and natural gas tariffs for the 54 of 100 WWTPs with on-site cogeneration. We manually collected tariffs from each utility’s website and implemented data checks to ensure their validity. The dataset includes facility metadata, electricity tariffs, and natural gas tariffs (where cogeneration is present). Tariffs are current as of November 2021. We provide code for technical validation along with a sample simulation.
A real-world dataset of group emotion experiences based on physiological data
Authors: Bota Patrícia , Brito Joana , Fred Ana , Cesar Pablo , Silva Hugo 
Published: January 2024

AbstractAffective computing has experienced substantial advancements in recognizing emotions through image and facial expression analysis. However, the incorporation of physiological data remains constrained. Emotion recognition with physiological data shows promising results in controlled experiments but lacks generalization to real-world settings. To address this, we present G-REx, a dataset for real-world affective computing. We collected physiological data (photoplethysmography and electrodermal activity) using a wrist-worn device during long-duration movie sessions. Emotion annotations were retrospectively performed on segments with elevated physiological responses. The dataset includes over 31 movie sessions, totaling 380 h+ of data from 190+ subjects. The data were collected in a group setting, which can give further context to emotion recognition systems. Our setup aims to be easily replicable in any real-life scenario, facilitating the collection of large datasets for novel affective computing systems.
Mass spectrometry-based proteomics data from thousands of HeLa control samples
Authors: Webel Henry , Perez-Riverol Yasset , Nielsen Annelaura Bach , Rasmussen Simon 
Published: January 2024

AbstractHere we provide a curated, large scale, label free mass spectrometry-based proteomics data set derived from HeLa cell lines for general purpose machine learning and analysis. Data access and filtering is a tedious task, which takes up considerable amounts of time for researchers. Therefore we provide machine based metadata for easy selection and overview along the 7,444 raw files and MaxQuant search output. For convenience, we provide three filtered and aggregated development datasets on the protein groups, peptides and precursors level. Next to providing easy to access training data, we provide a SDRF file annotating each raw file with instrument settings allowing automated reprocessing. We encourage others to enlarge this data set by instrument runs of further HeLa samples from different machine types by providing our workflows and analysis scripts.
A consolidated and geolocated facility list in Senegal from triangulating secondary data
Authors: Gueye Daouda M. , Ly Alioune Badara , Gueye Babacar , Ndour Papa Ibrahima , Fullman Nancy , Liu Patrick Y. , Mbaye Khadim , Diallo Aliou , Diatta Ibrahima , Diatta Saly Amos , Mane Mouhamadou Moustapha , Ikilezi Gloria , Sarr Moussa 
Published: January 2024

AbstractHaving a geolocated list of all facilities in a country – a “master facility list” (MFL) – can provide critical inputs for health program planning and implementation. To the best of our knowledge, Senegal has never had a centralized MFL, though many data sources currently exist within the broader Senegalese data landscape that could be leveraged and consolidated into a single database – a critical first step toward building a full MFL. We collated 12,965 facility observations from 16 separate datasets and lists in Senegal, and applied matching algorithms, manual checking and revisions as needed, and verification processes to identify unique facilities and triangulate corresponding GPS coordinates. Our resulting consolidated facility list has a total of 4,685 facilities, with 2,423 having at least one set of GPS coordinates. Developing approaches to leverage existing data toward future MFL establishment can help bridge data demands and inform more targeted approaches for completing a full facility census based on areas and facility types with the lowest coverage. Going forward, it is crucial to ensure routine updates of current facility lists, and to strengthen government-led mechanisms around such data collection demands and the need for timely data for health decision-making.
Genome-wide equine preimplantation genetic testing enabled by simultaneous haplotyping and copy number detection
Authors: De Coster T. , Zhao Y. , Tšuiko O. , Demyda-Peyrás S. , Van Soom A. , Vermeesch J. R. , Smits K. 
Published: January 2024

AbstractIn different species, embryonic aneuploidies and genome-wide errors are a major cause of developmental failure. The increasing number of equine embryos being produced worldwide provides the opportunity to characterize and rank or select embryos based on their genetic profile prior to transfer. Here, we explored the possibility of generic, genome-wide preimplantation genetic testing concurrently for aneuploidies (PGT-A) and monogenic (PGT-M) traits and diseases in the horse, meanwhile assessing the incidence and spectrum of chromosomal and genome-wide errors in in vitro-produced equine embryos. To this end, over 70,000 single nucleotide polymorphism (SNP) positions were genotyped in 14 trophectoderm biopsies and corresponding biopsied blastocysts, and in 26 individual blastomeres from six arrested cleavage-stage embryos. Subsequently, concurrent genome-wide copy number detection and haplotyping by haplarithmisis was performed and the presence of aneuploidies and genome-wide errors and the inherited parental haplotypes for four common disease-associated genes with high carrier frequency in different horse breeds (GBE1, PLOD1, B3GALNT2, MUTYH), and for one color coat-associated gene (STX17) were compared in biopsy-blastocyst combinations. The euploid (n = 12) or fully aneuploid (n = 2) state and the inherited parental haplotypes for 42/45 loci of interest of the biopsied blastocysts were predicted by the biopsy samples in all successfully analyzed biopsy-blastocyst combinations (n = 9). Two biopsies showed a loss of maternal chromosome 28 and 31, respectively, which were confirmed in the corresponding blastocysts. In one of those biopsies, additional complex aneuploidies not present in the blastocyst were found. Five out of six arrested embryos contained chromosomal and/or genome-wide errors in most of their blastomeres, demonstrating their contribution to equine embryonic arrest in vitro. The application of the described PGT strategy would allow to select equine embryos devoid of genetic errors and pathogenetic variants, and with the variants of interest, which will improve foaling rate and horse quality. We believe this approach will be a gamechanger in horse breeding.
Reconstruction algorithms for DNA-storage systems
Authors: Sabary Omer , Yucovich Alexander , Shapira Guy , Yaakobi Eitan 
Published: January 2024

AbstractMotivated by DNA storage systems, this work presents theDNA reconstruction problem, in which a length-nstring, is passing through theDNA-storage channel, which introduces deletion, insertion and substitution errors. This channel generates multiple noisy copies of the transmitted string which are calledtraces. ADNA reconstruction algorithmis a mapping which receivesttraces as an input and produces an estimation of the original string. The goal in the DNA reconstruction problem is to minimize the edit distance between the original string and the algorithm’s estimation. In this work, we present several new algorithms for this problem. Our algorithms look globally on the entire sequence of the traces and use dynamic programming algorithms, which are used for theshortest common supersequenceand thelongest common subsequenceproblems, in order to decode the original string. Our algorithms do not require any limitations on the input and the number of traces, and more than that, they perform well even for error probabilities as high as 0.27. The algorithms have been tested on simulated data, on data from previous DNA storage experiments, and on a new synthesized dataset, and are shown to outperform previous algorithms in reconstruction accuracy.
In vivo identification of Drosophila rhodopsin interaction partners by biotin proximity labeling
Authors: Feizy Nilofar , Leuchtenberg Sarah Franziska , Steiner Christine , Würtz Berit , Fliegner Leo , Huber Armin 
Published: January 2024

AbstractProteins exert their function through protein–protein interactions. In Drosophila, G protein-coupled receptors like rhodopsin (Rh1) interact with a G protein to activate visual signal transduction and with arrestins to terminate activation. Also, membrane proteins like Rh1 engage in protein–protein interactions during folding within the endoplasmic reticulum, during their vesicular transport and upon removal from the cell surface and degradation. Here, we expressed a Rh1-TurboID fusion protein (Rh1::TbID) in Drosophila photoreceptors to identify in vivo Rh1 interaction partners by biotin proximity labeling. We show that Rh1::TbID forms a functional rhodopsin that mediates biotinylation of arrestin 2 in conditions where arrestin 2 interacts with rhodopsin. We also observed biotinylation of Rh1::TbID and native Rh1 as well as of most visual signal transduction proteins. These findings indicate that the signaling components in the rhabdomere approach rhodopsin closely, within a range of ca. 10 nm. Furthermore, we have detected proteins engaged in the maturation of rhodopsin and elements responsible for the trafficking of membrane proteins, resembling potential interaction partners of Rh1. Among these are chaperons of the endoplasmic reticulum, proteins involved in Clathrin-mediated endocytosis as well as previously unnoticed contributors to rhodopsin transportation, such as Rab32, Vap33, or PIP82.
Relationship between hemolysis and lipid oxidation in red blood cell-spiked fish muscle; dependance on pH and blood plasma
Authors: Ghirmai Semhar , Krona Annika , Wu Haizhou , Whalin James , Axelsson Michael , Undeland Ingrid 
Published: January 2024

AbstractThe relationship between hemolysis and lipid oxidation was explored in red blood cell (RBCs)-spiked washed cod mince (WCM). At pH 6.8 and 3 ± 1 °C, intact RBCs (71 µM Hb) delayed lipid oxidation by 1 day compared to WCM with partly or fully lysed RBCs which oxidized immediately. Intact RBCs also lowered peak peroxide value (PV) and thiobarbituric acid reactive substances (TBARS) with up to 59.5% and 48.1%, respectively. Adding 3% (v/w) blood plasma to RBC-spiked WCM delayed the lipid oxidation onset from 1 to 3–4 days without delaying hemolysis. At pH 6.4 the oxidation onset in RBC-WCM was the same as for pH 6.8 while at pH 7.2–7.6 lipid oxidation was suppressed for 7 days. Micrographs revealed RBC-lysis from day 2 at pH 6.4 but at pH 7.6, RBC stayed intact for ≥ 7 days. Thus, assuring presence of plasma-derived antioxidants and/or elevating muscle pH to avoid hemolysis can aid valorization of blood rich underutilized fish raw materials.