bluuebunny/crossref_metadata_2025_split huggingface dataset:
circSLC4A7 accelerates stemness and progression of gastric cancer by interacting with HSP90 to activate NOTCH1 signaling pathway
Authors: Hui Yang , Wenguang Yuan , Wei Shang , Haoran Wang , Shanglei Ning , Ju Liu 
Published: July 2023

AbstractGastric cancer stem cells (GCSCs) play critical roles in gastric cancer (GC) initiation and development. Circular RNAs (circRNAs) participate in diverse cancer biological processes and function as tumor suppressors or oncogenes. This study aims to discover the expression profile and functional roles of circRNAs in GCSCs. A spheroid formation assay was conducted to enrich GCSCs. Genome-wide sequencing of circRNAs showed that a novel circRNA, circSLC4A7, was one of the most upregulated circRNAs in GCSCs. CircSLC4A7 was localized to the nucleus, and its level was elevated in GC cells and tissues. Furthermore, circSLC4A7 increased CSC-like properties and drove cell proliferation, migration, and invasion, which were determined by gain- and loss-of-function experiments. Specific circRNA pull-down assays followed by mass spectrometry analysis, RNA immunoprecipitation, and dual RNA-fluorescence in situ hybridization and immunofluorescence assay were conducted and HSP90 was detected to interact with circSLC4A7 and mediate the oncogenic function of circSLC4A7 by activating the Notch1 signaling pathway in GC. This study highlights a novel oncogenic function of circSLC4A7 mediated by its binding with HSP90 and thus activating the Notch1 signaling pathway.
Apoptotic exosome-like vesicles transfer specific and functional mRNAs to endothelial cells by phosphatidylserine-dependent macropinocytosis
Authors: Brodeur Alexandre , Migneault Francis , Lanoie Maude , Beillevaire Déborah , Turgeon Julie , Karakeussian-Rimbaud Annie , Thibodeau Nicolas , Boilard Éric , Dieudé Mélanie , Hébert Marie-Josée 
Published: July 2023

AbstractApoptosis of endothelial cells prompts the release of apoptotic exosome-like vesicles (ApoExos), subtype extracellular vesicles secreted by apoptotic cells after caspase-3 activation. ApoExos are different from both apoptotic bodies and classical exosomes in their protein and nucleic acid contents and functions. In contrast to classical apoptotic bodies, ApoExos induce immunogenic responses that can be maladaptive when not tightly regulated. In the present study, we elucidated the mechanisms by which ApoExos are internalized by endothelial cells, which leads to shared specific and functional mRNAs of importance to endothelial function. Using flow cytometry and confocal microscopy, we revealed that ApoExos were actively internalized by endothelial cells. SiRNA-induced inhibition of classical endocytosis pathways with pharmacological inhibitors showed that ApoExos were internalized via phosphatidylserine-dependent macropinocytosis independently of classical endocytosis pathways. An electron microscopy analysis revealed that ApoExos increased the macropinocytosis rate in endothelial cells, setting in motion a positive feedback loop that increased the amount of internalized ApoExos. Deep sequencing of total RNA revealed that ApoExos possessed a unique protein-coding RNA profile, with PCSK5 being the most abundant mRNA. Internalization of ApoExos by cells led to the transfer of this RNA content from the ApoExos to cells. Specifically, PCSK5 mRNA was transferred to cells that had taken up ApoExos, and these cells subsequently expressed PCSK5. Collectively, our findings suggest that macropinocytosis is an effective entry pathway for the delivery of RNAs carried by ApoExos and that these RNAs are functionally expressed by the endothelial cells that internalize them. As ApoExos express a specific mRNA signature, these results suggest new avenues to understand how ApoExos produced at sites of vascular injury impact vascular function.
The RNA binding proteins TIA1 and TIAL1 promote Mcl1 mRNA translation to protect germinal center responses from apoptosis
Authors: Osma-Garcia Ines C. , Mouysset Mailys , Capitan-Sobrino Dunja , Aubert Yann , Turner Martin , Diaz-Muñoz Manuel D. 
Published: July 2023

AbstractGerminal centers (GCs) are essential for the establishment of long-lasting antibody responses. GC B cells rely on post-transcriptional RNA mechanisms to translate activation-associated transcriptional programs into functional changes in the cell proteome. However, the critical proteins driving these key mechanisms are still unknown. Here, we show that the RNA binding proteins TIA1 and TIAL1 are required for the generation of long-lasting GC responses. TIA1- and TIAL1-deficient GC B cells fail to undergo antigen-mediated positive selection, expansion and differentiation into B-cell clones producing high-affinity antibodies. Mechanistically, TIA1 and TIAL1 control the transcriptional identity of dark- and light-zone GC B cells and enable timely expression of the prosurvival molecule MCL1. Thus, we demonstrate here that TIA1 and TIAL1 are key players in the post-transcriptional program that selects high-affinity antigen-specific GC B cells.
C. elegans ageing is accelerated by a self-destructive reproductive programme
Authors: Kern Carina C. , Srivastava Shivangi , Ezcurra Marina , Hsiung Kuei Ching , Hui Nancy , Townsend StJohn , Maczik Dominik , Zhang Bruce , Tse Victoria , Konstantellos Viktoras , Bähler Jürg , Gems David 
Published: July 2023

AbstractIn post-reproductive C. elegans, destructive somatic biomass repurposing supports production of yolk which, it was recently shown, is vented and can serve as a foodstuff for larval progeny. This is reminiscent of the suicidal reproductive effort (reproductive death) typical of semelparous organisms such as Pacific salmon. To explore the possibility that C. elegans exhibits reproductive death, we have compared sibling species pairs of the genera Caenorhabditis and Pristionchus with hermaphrodites and females. We report that yolk venting and constitutive, early pathology involving major anatomical changes occur only in hermaphrodites, which are also shorter lived. Moreover, only in hermaphrodites does germline removal suppress senescent pathology and markedly increase lifespan. This is consistent with the hypothesis that C. elegans exhibit reproductive death that is suppressed by germline ablation. If correct, this would imply a major difference in the ageing process between C. elegans and most higher organisms, and potentially explain the exceptional plasticity in C. elegans ageing.
Experimental manifestation of redox-conductivity in metal-organic frameworks and its implication for semiconductor/insulator switching
Authors: Li Jingguo , Kumar Amol , Johnson Ben A. , Ott Sascha 
Published: July 2023

AbstractElectric conductivity in metal-organic frameworks (MOFs) follows either a band-like or a redox-hopping charge transport mechanism. While conductivity by the band-like mechanism is theoretically and experimentally well established, the field has struggled to experimentally demonstrate redox conductivity that is promoted by the electron hopping mechanism. Such redox conductivity is predicted to maximize at the mid-point potential of the redox-active units in the MOF, and decline rapidly when deviating from this situation. Herein, we present direct experimental evidence for redox conductivity in fluorine-doped tin oxide surface-grown thin films of Zn(pyrazol-NDI) (pyrazol-NDI = 1,4-bis[(3,5-dimethyl)-pyrazol-4-yl]naphthalenediimide). Following Nernstian behavior, the proportion of reduced and oxidized NDI linkers can be adjusted by the applied potential. Through a series of conductivity measurements, it is demonstrated that the MOF exhibits minimal electric resistance at the mid-point potentials of the NDI linker, and conductivity is enhanced by more than 10000-fold compared to that of either the neutral or completely reduced films. The generality of redox conductivity is demonstrated in MOFs with different linkers and secondary building units, and its implication for applications that require switching between insulating and semiconducting regimes is discussed.
Chemogenetic dissection of a prefrontal-hypothalamic circuit for socially subjective reward valuation in macaques
Authors: Noritake Atsushi , Ninomiya Taihei , Kobayashi Kenta , Isoda Masaki 
Published: July 2023

AbstractThe value of one’s own reward is affected by the reward of others, serving as a source for envy. However, it is not known which neural circuits mediate such socially subjective value modulation. Here, we chemogenetically dissected the circuit from the medial prefrontal cortex (MPFC) to the lateral hypothalamus (LH) while male macaques were presented with visual stimuli that concurrently signaled the prospects of one’s own and others’ rewards. We found that functional disconnection between the MPFC and LH rendered animals significantly less susceptible to others’ but not one’s own reward prospects. In parallel with this behavioral change, inter-areal coordination, as indexed by coherence and Granger causality, decreased primarily in the delta and theta bands. These findings demonstrate that the MPFC-to-LH circuit plays a crucial role in carrying information about upcoming other-rewards for subjective reward valuation in social contexts.
Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics
Authors: White Matthew E. H. , Sinn Ludwig R. , Jones D. Marc , de Folter Joost , Aulakh Simran Kaur , Wang Ziyue , Flynn Helen R. , Krüger Lynn , Tober-Lau Pinkus , Demichev Vadim , Kurth Florian , Mülleder Michael , Blanchard Véronique , Messner Christoph B. , Ralser Markus 
Published: July 2023

AbstractProtein glycosylation, a complex and heterogeneous post-translational modification that is frequently dysregulated in disease, has been difficult to analyse at scale. Here we report a data-independent acquisition technique for the large-scale mass-spectrometric quantification of glycopeptides in plasma samples. The technique, which we named ‘OxoScan-MS’, identifies oxonium ions as glycopeptide fragments and exploits a sliding-quadrupole dimension to generate comprehensive and untargeted oxonium ion maps of precursor masses assigned to fragment ions from non-enriched plasma samples. By applying OxoScan-MS to quantify 1,002 glycopeptide features in the plasma glycoproteomes from patients with COVID-19 and healthy controls, we found that severe COVID-19 induces differential glycosylation in IgA, haptoglobin, transferrin and other disease-relevant plasma glycoproteins. OxoScan-MS may allow for the quantitative mapping of glycoproteomes at the scale of hundreds to thousands of samples.
Realization times of energetic modernization measures for buildings based on interviews with craftworkers
Authors: Richarz Jan , Fuchs Nico , Zurke Jacqueline , Imberg Jan , Datsko Tanja , Hering Dominik , Müller Dirk 
Published: July 2023

AbstractModernizing existing buildings is vital to saving carbon emissions and counteracting global climate change. Many countries face the challenge of modernizing a considerable number of their buildings in the next two decades. Implementing related modernization measures requires a high number of craftworkers. However, current studies indicate that these craftworkers’ current lack will increase. Examining the effects of craftworkers shortage on modernization strategies needs data concerning the realization time of modernization measures. We collected this data based on 90 expert interviews and provide it in this paper. The interview results comprise realization times for insulation measures of the envelope and changes in the heat supply system for typical buildings. This paper describes the data collection and presents the raw data available at a repository at Figshare. The data is internationally applicable in simulation and optimization approaches for building modernization.
Symptoms and quality of life before, during, and after a SARS-CoV-2 PCR positive or negative test: data from Lifelines
Authors: Goërtz Yvonne M. J. , Spruit Martijn A. , Van Herck Maarten , Dukers-Muijrers Nicole ,   Lifelines Corona Research Initiative, Boezen H. Marike , Mierau Jochen O. , Franke H. Lude , Dekens Jackie , Deelen Patrick , Lanting Pauline , Vonk Judith M. , Nolte Ilja , Ori Anil P. S. , Claringbould Annique , Boulogne Floranne , Dijkema Marjolein X. L. , Wiersma Henry H. , Warmerdam Robert , Jankipersadsing Soesma A. , van Blokland Irene , de Bock Geertruida H. , Wijmenga Cisca , van der Kallen Carla J. H. , Burtin Chris , Janssen Daisy J. A. 
Published: July 2023

AbstractThis study evaluates to what extent symptoms are present before, during, and after a positive SARS-CoV-2 polymerase chain reaction (PCR) test, and to evaluate how the symptom burden and quality of Life (QoL) compares to those with a negative PCR test. Participants from the Dutch Lifelines COVID-19 Cohort Study filled-out as of March 2020 weekly, later bi-weekly and monthly, questions about demographics, COVID-19 diagnosis and severity, QoL, and symptoms. The study population included those with one positive or negative PCR test who filled out two questionnaires before and after the test, resulting in 996 SARS-CoV-2 PCR positive and 3978 negative participants. Nearly all symptoms were more often reported after a positive test versus the period before the test (p < 0.05), except fever. A higher symptom prevalence after versus before a test was also found for nearly all symptoms in negatives (p < 0.05). Before the test, symptoms were already partly present and reporting of nearly all symptoms before did not differ between positives and negatives (p > 0.05). QoL decreased around the test for positives and negatives, with a larger deterioration for positives. Not all symptoms after a positive SARS-CoV-2 PCR test might be attributable to the infection and symptoms were also common in negatives.
Fabrication of polyamide thin film composite membranes using aliphatic tetra-amines and terephthaloyl chloride crosslinker for organic solvent nanofiltration
Authors: Waheed Abdul , Baig Umair , Aljundi Isam H. 
Published: July 2023

AbstractGiven the huge significance of organic solvents in several industrial processes, the use of membranes for recovering the solvents has evolved into an industrially viable process. The current work has been focused on studying the effect of minor changes in the chemistry of the reacting monomers on the organic solvent nanofiltration/solvent resistance nanofiltration (OSN/SRNF) performance of the membranes. The two aliphatic amines with varying aliphatic chain lengths between primary and secondary amines were selected for this purpose. Based on the structure of the resultant active layer, the Janus nanofiltration performance of the membrane was evaluated. The two membranes, 4A-TPC@crosslinked PAN and 4A-3P@crosslinked PAN were fabricated by using two different tetra-amines, 4A (N,N′-bis(3-aminopropyl)ethylenediamine) and 4A-3P (N,N′-Bis(2-aminoethyl)-1,3-propanediamine) crosslinked with terephthaloyl chloride (TPC) on a crosslinked polyacryonitrile (PAN) support through interfacial polymerization (IP). The presence of multiple hydrophobic –CH2– groups in the structures of the aliphatic amines 4A and 4A-3P develops hydrophobic sites in the hydrophilic polyamide active layers of the membranes. In addition, 4A has two secondary amino groups separated by ethylene (–CH2–CH2–) groups, whereas in 4A-3P, the two secondary amino groups are separated by propylene (–CH2–CH2–CH2–) leading to variation in the structural features and performance of the two membranes. Both membranes were fully characterized by several membrane characterization techniques and applied for OSN/SRNF using both polar (methanol, ethanol, and isopropanol) and non-polar (n-hexane and toluene) solvents. Different dyes (Congo red, Eriochrome black T, and Methylene blue) were used as model solutes during the filtration experiment. The 4A-3P-TPC@crosslinked PAN showed n-hexane and toluene flux of 109.9 LMH and 95.5 LMH, respectively. The Congo red (CR) showed the highest rejection, reaching 99.1% for the 4A-TPC@Crosslinked PAN membrane and 98.8% for the 4A-3P-TPC@Crosslinked PAN membrane.
Influencing recommendation algorithms to reduce the spread of unreliable news by encouraging humans to fact-check articles, in a field experiment
Authors: Matias J. Nathan 
Published: July 2023

AbstractSociety often relies on social algorithms that adapt to human behavior. Yet scientists struggle to generalize the combined behavior of mutually-adapting humans and algorithms. This scientific challenge is a governance problem when algorithms amplify human responses to falsehoods. Could attempts to influence humans have second-order effects on algorithms? Using a large-scale field experiment, I test if influencing readers to fact-check unreliable sources causes news aggregation algorithms to promote or lessen the visibility of those sources. Interventions encouraged readers to fact-check articles or fact-check and provide votes to the algorithm. Across 1104 discussions, these encouragements increased human fact-checking and reduced vote scores on average. The fact-checking condition also caused the algorithm to reduce the promotion of articles over time by as much as −25 rank positions on average, enough to remove an article from the front page. Overall, this study offers a path for the science of human-algorithm behavior by experimentally demonstrating how influencing collective human behavior can also influence algorithm behavior.
Parental socialization of guilt and shame in early childhood
Authors: Nikolić Milica , Brummelman Eddie , de Castro Bram Orobio , Jorgensen Terrence D. , Colonnesi Cristina 
Published: July 2023

AbstractSelf-conscious emotions emerge early in human development and they help children navigate social relationships. Little is known about the socialization of self-conscious emotions in early childhood. We theorized that parental mental state language use and warmth would be important for young children’s self-conscious emotions and their consequent prosocial behaviors. Ninety-eight children residing in the Netherlands (52% girls) aged 2–5 (M = 48.66 months, SD = 13.50 months) visited the research lab with one parent. First, we observed parental mental state language and warmth. Afterward, children were led to believe that they caused a mishap (i.e., accidentally breaking the experimenter’s favorite toy) to evoke their guilt and shame, which we micro-coded. In subsequent tasks, we observed children’s helping behaviors toward the experimenter. We found that the combination of frequent parental mental state language and high warmth was associated with children’s quicker helping to the previously harmed experimenter across toddlerhood and early childhood. More guilt was related to more helping whereas more shame-like avoidance was related to less helping. Our findings based on the sample of Dutch parents and children suggest that, parental frequent mental state talk, in combination with high warmth, may promote children’s ability to repair social relationships and behave prosocially after mishaps.
Genome-wide analysis reveals distinct global populations of pink bollworm (Pectinophora gossypiella)
Authors: Matheson Paige , Parvizi Elahe , Fabrick Jeffrey A. , Siddiqui Hamid Anees , Tabashnik Bruce E. , Walsh Tom , McGaughran Angela 
Published: July 2023

AbstractThe pink bollworm (Pectinophora gossypiella) is one of the world’s most destructive pests of cotton. This invasive lepidopteran occurs in nearly all cotton-growing countries. Its presence in the Ord Valley of North West Australia poses a potential threat to the expanding cotton industry there. To assess this threat and better understand population structure of pink bollworm, we analysed genomic data from individuals collected in the field from North West Australia, India, and Pakistan, as well as from four laboratory colonies that originated in the United States. We identified single nucleotide polymorphisms (SNPs) using a reduced-representation, genotyping-by-sequencing technique (DArTseq). The final filtered dataset included 6355 SNPs and 88 individual genomes that clustered into five groups: Australia, India-Pakistan, and three groups from the United States. We also analysed sequences from Genbank for mitochondrial DNA (mtDNA) locus cytochrome c oxidase I (COI) for pink bollworm from six countries. We found low genetic diversity within populations and high differentiation between populations from different continents. The high genetic differentiation between Australia and the other populations and colonies sampled in this study reduces concerns about gene flow to North West Australia, particularly from populations in India and Pakistan that have evolved resistance to transgenic insecticidal cotton. We attribute the observed population structure to pink bollworm’s narrow host plant range and limited dispersal between continents.
In-depth metataxonomic investigation reveals low richness, high intervariability, and diverse phylotype candidates of archaea in the human urogenital tract
Authors: Kim Yeon Bee , Whon Tae Woong , Kim Joon Yong , Kim Juseok , Kim Yujin , Lee Se Hee , Park Seong-Eun , Kim Eun-Ju , Son Hong-Seok , Roh Seong Woon 
Published: July 2023

AbstractThe urogenital microbiota is the potential principal factor in the pathophysiology of urinary tract infection and the protection of urinary tract health. Little is known about the urogenital archaeome although several reports have indicated that the archaeomes of various regions of the human body are associated with health. Accordingly, we aimed to determine the presence and diversity of archaeomes in the human urogenital tract. To explore the urogenital archaeome, voided urine specimens from 373 asymptomatic Korean individuals were used. No difference was observed in body mass index, age, or gender, according to presence of archaea. Analysis of archaeal 16S rRNA gene amplicons of archaea positive samples consisted of simple community structures, including diverse archaea, such as the phyla Methanobacteriota, Thermoproteota, and Halobacteriota. Asymptomatic individuals showed high participant-dependent intervariability in their urogenital archaeomes. The mean relative archaeal abundance was estimated to be 0.89%, and fluorescence in situ hybridisation micrographs provided evidence of archaeal cells in the human urogenital tract. In addition, the urogenital archaeome shared partial taxonomic compositional characteristics with those of the other body sites. In this study, Methanobacteriota, Thermoproteota, and Halobacteriota were suggested as inhabitants of the human urogenital tract, and a distinct human urogenital archaeome was characterised. These findings expand our knowledge of archaea-host associations in the human urogenital tract and may lead to novel insights into the role of archaea in urinary tract health.