bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early biological markers of post-acute sequelae of SARS-CoV-2 infection
Authors: Lu Scott , Peluso Michael J. , Glidden David V. , Davidson Michelle C. , Lugtu Kara , Pineda-Ramirez Jesus , Tassetto Michel , Garcia-Knight Miguel , Zhang Amethyst , Goldberg Sarah A. , Chen Jessica Y. , Fortes-Cobby Maya , Park Sara , Martinez Ana , So Matthew , Donovan Aidan , Viswanathan Badri , Hoh Rebecca , Donohue Kevin , McIlwain David R. , Gaudiliere Brice , Anglin Khamal , Yee Brandon C. , Chenna Ahmed , Winslow John W. , Petropoulos Christos J. , Deeks Steven G. , Briggs-Hagen Melissa , Andino Raul , Midgley Claire M. , Martin Jeffrey N. , Saydah Sharon , Kelly J. Daniel 
Published: August 2024

AbstractTo understand the roles of acute-phase viral dynamics and host immune responses in post-acute sequelae of SARS-CoV-2 infection (PASC), we enrolled 136 participants within 5 days of their first positive SARS-CoV-2 real-time PCR test. Participants self-collected up to 21 nasal specimens within the first 28 days post-symptom onset; interviewer-administered questionnaires and blood samples were collected at enrollment, days 9, 14, 21, 28, and month 4 and 8 post-symptom onset. Defining PASC as the presence of any COVID-associated symptom at their 4-month visit, we compared viral markers (quantity and duration of nasal viral RNA load, infectious viral load, and plasma N-antigen level) and host immune markers (IL-6, IL-10, TNF-α, IFN-α, IFN-γ, MCP, IP-10, and Spike IgG) over the acute period. Compared to those who fully recovered, those reporting PASC demonstrated significantly higher maximum levels of SARS-CoV-2 RNA and N-antigen, burden of RNA and infectious viral shedding, and lower Spike-specific IgG levels within 9 days post-illness onset. No significant differences were identified among a panel of host immune markers. Our results suggest early viral dynamics and the associated host immune responses play a role in the pathogenesis of PASC, highlighting the importance of understanding early biological markers in the natural history of PASC.
An intronic copy number variation in Syntaxin 17 determines speed of greying and melanoma incidence in Grey horses
Authors: Rubin Carl-Johan , Hodge McKaela , Naboulsi Rakan , Beckman Madeleine , Bellone Rebecca R. , Kallenberg Angelica , J’Usrey Stephanie , Ohmura Hajime , Seki Kazuhiro , Furukawa Risako , Ohnuma Aoi , Davis Brian W. , Tozaki Teruaki , Lindgren Gabriella , Andersson Leif 
Published: August 2024

AbstractThe Greying with age phenotype in horses involves loss of hair pigmentation whereas skin pigmentation is not reduced, and a predisposition to melanoma. The causal mutation was initially reported as a duplication of a 4.6 kb intronic sequence in Syntaxin 17. The speed of greying varies considerably among Grey horses. Here we demonstrate the presence of two different Grey alleles, G2 carrying two tandem copies of the duplicated sequence and G3 carrying three. The latter is by far the most common allele, probably due to strong selection for the striking white phenotype. Our results reveal a remarkable dosage effect where the G3 allele is associated with fast greying and high incidence of melanoma whereas G2 is associated with slow greying and low incidence of melanoma. The copy number expansion transforms a weak enhancer to a strong melanocyte-specific enhancer that underlies hair greying (G2 and G3) and a drastically elevated risk of melanoma (G3 only). Our direct pedigree-based observation of the origin of a G2 allele from a G3 allele by copy number contraction demonstrates the dynamic evolution of this locus and provides the ultimate evidence for causality of the copy number variation of the 4.6 kb intronic sequence.
Orbital modulation of subtropical versus subantarctic moisture sources in the southeast Pacific mid-latitudes
Authors: Kaiser Jérôme , Schefuß Enno , Collins James , Garreaud René , Stuut Jan-Berend W. , Ruggieri Nicoletta , De Pol-Holz Ricardo , Lamy Frank 
Published: August 2024

AbstractReconstructing rainfall variability and moisture sources is a critical aspect to understand past and future hydroclimate dynamics. Here, we use changes in the deuterium content of land-plant leaf waxes from two marine sediment cores located off Chile to reconstruct changes in rainfall amount and variation in moisture sources over the last ~50 ka. The records indicate increased moisture in central Chile during precession maxima, but an obliquity modulation is evident in southern Chile. While the southern westerly winds are the dominant factor of precipitation in southern Chile by bringing moisture and perturbations from the extratropics, the subtropics represent an additional moisture source during precession maxima due to a stronger subtropical jet increasing moisture transport from the tropics to the mid-latitudes. These findings imply that a combination of orbital modulation of moisture sources and rainfall amount explains the last glacial moisture maximum and early Holocene moisture minimum in south-central Chile.
Solid Earth forcing of Mesozoic oceanic anoxic events
Authors: Gernon T. M. , Mills B. J. W. , Hincks T. K. , Merdith A. S. , Alcott L. J. , Rohling E. J. , Palmer M. R. 
Published: August 2024

AbstractOceanic anoxic events are geologically abrupt phases of extreme oxygen depletion in the oceans that disrupted marine ecosystems and brought about evolutionary turnover. Typically lasting ~1.5 million years, these events occurred frequently during the Mesozoic era, from about 183 to 85 million years ago, an interval associated with continental breakup and widespread large igneous province volcanism. One hypothesis suggests that anoxic events resulted from enhanced chemical weathering of Earth’s surface in a greenhouse world shaped by high volcanic carbon outgassing. Here we test this hypothesis using a combination of plate reconstructions, tectonic–geochemical analysis and global biogeochemical modelling. We show that enhanced weathering of mafic lithologies during continental breakup and nascent seafloor spreading can plausibly drive a succession of anoxic events. Weathering pulses collectively gave rise to substantial releases of the nutrient phosphorus to the oceans, stimulating biological primary production. This, in turn, enhanced organic carbon burial and caused widespread ocean deoxygenation on a scale sufficient to drive recurrent anoxia. This model complements volcanic outgassing-centred hypotheses for triggering these events by demonstrating well-quantified basaltic sources of phosphorus release during periods of intense weathering related to climate warmth. Our study highlights a close coupling between the solid Earth and biosphere during continental reorganization.
Characteristics of blood–brain barrier heterogeneity between brain regions revealed by profiling vascular and perivascular cells
Authors: Pfau Sarah J. , Langen Urs H. , Fisher Theodore M. , Prakash Indumathi , Nagpurwala Faheem , Lozoya Ricardo A. , Lee Wei-Chung Allen , Wu Zhuhao , Gu Chenghua 
Published: August 2024

AbstractThe blood–brain barrier (BBB) protects the brain and maintains neuronal homeostasis. BBB properties can vary between brain regions to support regional functions, yet how BBB heterogeneity occurs is poorly understood. Here, we used single-cell and spatial transcriptomics to compare the mouse median eminence, one of the circumventricular organs that has naturally leaky blood vessels, with the cortex. We identified hundreds of molecular differences in endothelial cells (ECs) and perivascular cells, including astrocytes, pericytes and fibroblasts. Using electron microscopy and an aqueous-based tissue-clearing method, we revealed distinct anatomical specializations and interaction patterns of ECs and perivascular cells in these regions. Finally, we identified candidate regionally enriched EC–perivascular cell ligand–receptor pairs. Our results indicate that both molecular specializations in ECs and unique EC–perivascular cell interactions contribute to BBB functional heterogeneity. This platform can be used to investigate BBB heterogeneity in other regions and may facilitate the development of central nervous system region-specific therapeutics.
Developing an image-based grading scale for peripheral drusen to investigate associations of peripheral drusen type with age-related macular degeneration
Authors: Sharma Paripoorna , Kalaw Fritz Gerald P. , Lin Andrew , Walker Evan H. , Borooah Shyamanga 
Published: August 2024

AbstractAge-related macular degeneration (AMD) is a leading cause of blindness. It is associated with peripheral drusen which has not been categorized. We investigated peripheral drusen to validate an image grading system and to understand possible associations between peripheral drusen and AMD. We collated clinical data, ultra-widefield (UWF) pseudocolor fundus images and Spectral-Domain Optical Coherence Tomography (SD-OCT) scans from consecutive retinal patients. SD-OCT scans were used to determine AMD stage. A masked retinal specialist recorded the types of peripheral drusen observed in UWF images. Eyes whose UWF images did not pass quality screening and those without AMD and peripheral drusen were excluded from the study. Statistical tests were utilized to determine the validity of our grading system and associations of peripheral drusen with AMD. A total of 481 eyes (283 subjects) were included in the study (mean age 73.1 ± 1.2years, 64.3% female). Interobserver and test–retest statistical analyses to evaluate the UWF image grading system resulted in Cohen’s Kappa 0.649 (p < 0.001) and 0.922 (p < 0.001) respectively. A total of 284 (59.0%), 28 (5.8%), 15 (3.1%), 22 (4.6%), 4 (0.8%), 39 (8.1%), and 32 (6.7%) eyes had hard, soft, reticular, cuticular, atrophic, mixed drusen, and mixed drusen and atrophy respectively in at least one peripheral retinal quadrant. Hard peripheral drusen was significantly associated with the presence of AMD (p = 0.010). Peripheral drusen types were variably seen in retinal patients with and without AMD. We validated a peripheral drusen grading system and provided an image library to assist in the identification of peripheral drusen. Our study found an association between peripheral hard drusen and an AMD diagnosis but did not find a link between peripheral drusen and severity of AMD.
Sex-specific differences in the growth and population characteristics of Sand crab Ovalipes punctatus (De Haan, 1833) in coastal waters of Korea
Authors: Lee Hyeon Gyu , Jeong Jae Mook , Choi Youn Hee 
Published: August 2024

AbstractThe sex-specific differences in the growth and population characteristics of the high-commercial-value sand crab Ovalipes punctatus were investigated in Korea. The estimated allometric growth between the sexes showed significant differences in all morphometric measurements. In the classification of growth types, carapace width-chela length exhibited positive and negative allometric growth in males and females, respectively. Carapace width-abdominal width showed positive relative growth in both sexes, and orbital spine width exhibited negative relative growth in both sexes. Consequently, sexual dimorphism was evident in all measured traits. Growth parameters estimated using the ELEFAN function of the FiSAT II program indicated higher values in males compared to females. Asymptotic length (CW∞) for males was estimated at 139.2 mm, whereas for females it was 116.6 mm. Additionally, the growth coefficient (K) was higher in males (0.65) than in females (0.54), suggesting faster growth in males. The winter point (WP) was 1 for males and 0.7 for females, indicating slower growth in males during the colder December and slower growth in females during the spawning period in August. The modified von Bertalanffy growth curves indicated asymptotic growth in all sexes, and the growth performance index (φ') showed higher values in males (4.10) compared to females (3.87), reflecting differences in growth curves. The steady increase in recruitment rates from July to September was associated with the appearance of larvae and their subsequent growth into juveniles, leading to their recruitment into the population during this period. Therefore, O. punctatus exhibited sex-specific differences in growth parameters, suggesting distinct growth strategies between the sexes.
Neutrophil-specific interactome of ARHGAP25 reveals novel partners and regulatory insights
Authors: Sasvári Péter , Pettkó-Szandtner Aladár , Wisniewski Éva , Csépányi-Kömi Roland 
Published: August 2024

AbstractARHGAP25, a crucial molecule in immunological processes, serves as a Rac-specific GTPase-activating protein. Its role in cell migration and phagocyte functions, affecting the outcome of complex immunological diseases such as rheumatoid arthritis, renders it a promising target for drug research. Despite its importance, our knowledge of its intracellular interactions is still limited. This study employed proteomic analysis of glutathione S-transferase (GST)-tag pulldowns and co-immunoprecipitation from neutrophilic granulocyte cell lysate, revealing 76 candidates for potential physical interactions that complement ARHGAP25’s known profile. Notably, four small GTPases (RAC2, RHOG, ARF4, and RAB27A) exhibited high affinity for ARHGAP25. The ARHGAP25–RAC2 and ARHGAP25–RHOG interactions appeared to be affected by the activation state of the small GTPases, suggesting a GTP–GDP cycle-dependent interaction. In silico dimer prediction pinpointed ARHGAP25’s GAP domain as a credible binding interface, suggesting its suitability for GTP hydrolysis. Additionally, a list of Fc receptor-related kinases, phosphatases, and three of the 14-3-3 members were identified as potential partners, with in silico predictions highlighting eight binding sites, presenting novel insight on a potential regulatory mechanism for ARHGAP25.
Enhanced forest fire evacuation planning using real-time sensor and GPS algorithm
Authors: Sharma Vishal , Nagpal Deepali , Monga Suhasini , Almogren Ahmad , Srivastava Durgesh , Altameem Ayman , Choi Jaeyoung 
Published: August 2024

AbstractForest fires are the source of countless fatalities and extreme economic repercussions. The safe evacuation of residents of an area affected by forest fires is the highest priority of local authorities, and finding the most optimal course of action has been a primary research focus for years. Previous studies over several decades have attempted to find an optimal solution using the applications of bug navigation systems, road network reconfiguration, graph traversals, swarm optimization, etc. The author, with the motivation to prevent human casualties at the time of such calamity, presents a novel study which solves the problem in nearly linear time computation, surpassing the performance standards of previous research, and accommodates the unpredictability of the spread of forest fires. This includes a proposal of an algorithm which builds upon the application of Spielman and Teng’s Electrical Circuit Approach to solve for maximum flow in a network and implements this with real-time sensor and Global Positioning System input.
Validity and reliability of a finger training tool for assessing metacarpal phalangeal joint ranges of motion in asymptomatic participants
Authors: Kuvijitsuwan P. , Klaphajone J. , Singjai P. , Kumpika T. , Thawinchai N. , Angkurawaranon C. , Aramrat C. , Utarachon K. 
Published: August 2024

AbstractThis pilot study aims to evaluate concurrent validity using the goniometer as a reference tool and test–retest reliability of flexion of metacarpal phalangeal joint (MCP) measurements taken from a finger training device (air-guitar system) in healthy participants. There were ten self -reported asymptomatic participants recruited to test the devices. The measurements of all metacarpophangeal joints of the dominant hands were conducted using a finger goniometer and the air-guitar system. Two measuring sessions were conducted on the same day. The concurrent validity of the air-guitar indicated by strong concordance correlation coefficient (0.62–0.90) with the goniometer and mean difference (approximately 1°) between the two instruments are well below the limit of 5°. The test–retest reliability of MCP measurements from the air-guitar glove (0.82–0.99) was acceptable as a clinically meaningful measurement tool as the intraclass correlation coefficients were higher than 0.7. The standard error of measurement and minimal detectable change of the air-guitar are similar to those of the goniometer. The air-guitar tracking features, when used as a home-based therapy tool, may assist in monitoring change of MCP flexion over a time course with good reliability and strongly associated with the measurements from the goniometer.
Tropical Pacific trends explain the discrepancy between observed and modelled rainfall change over the Americas
Authors: Qiu Weiteng , Collins Matthew , Scaife Adam A. , Santoso Agus 
Published: August 2024

AbstractUnderstanding the causes for discrepancies between modelled and observed regional climate trends is important for improving present-day climate simulation and reducing uncertainties in future climate projections. Here, we analyse the performance of coupled climate models in reproducing regional precipitation trends during the satellite era. We find statistically significant observed drying in southwestern North America and wetting in the Amazon during the period 1979–2014. Historical climate model simulations do not capture these observed precipitation trends. We trace this discrepancy to the inability of coupled simulations to capture the observed Pacific trade wind intensification over this period. A linear adjustment of free running historical simulations, based on the observed strengthening of the Pacific trade winds and modeled ENSO teleconnections, explains the discrepancy in precipitation trends. Furthermore, both the Pacific trade wind trends and regional precipitation trends are reproduced in climate simulations with prescribed observed sea surface temperatures (SST), underscoring the role of the tropical Pacific SST patterns.
Quantum-classical separations in shallow-circuit-based learning with and without noises
Authors: Zhang Zhihan , Gong Weiyuan , Li Weikang , Deng Dong-Ling 
Published: August 2024

AbstractAn essential problem in quantum machine learning is to find quantum-classical separations between learning models. However, rigorous and unconditional separations are lacking for supervised learning. Here we construct a classification problem defined by a noiseless constant depth (i.e., shallow) quantum circuit and rigorously prove that any classical neural network with bounded connectivity requires logarithmic depth to output correctly with a larger-than-exponentially-small probability. This unconditional near-optimal quantum-classical representation power separation originates from the quantum nonlocality property that distinguishes quantum circuits from their classical counterparts. We further characterize the noise regimes for demonstrating such a separation on near-term quantum devices under the depolarization noise model. In addition, for quantum devices with constant noise strength, we prove that no super-polynomial classical-quantum separation exists for any classification task defined by Clifford circuits, independent of the structures of the circuits that specify the learning models.
Global 13C tracing and metabolic flux analysis of intact human liver tissue ex vivo
Authors: Grankvist Nina , Jönsson Cecilia , Hedin Karin , Sundqvist Nicolas , Sandström Per , Björnsson Bergthor , Begzati Arjana , Mickols Evgeniya , Artursson Per , Jain Mohit , Cedersund Gunnar , Nilsson Roland 
Published: August 2024

AbstractLiver metabolism is central to human physiology and influences the pathogenesis of common metabolic diseases. Yet, our understanding of human liver metabolism remains incomplete, with much of current knowledge based on animal or cell culture models that do not fully recapitulate human physiology. Here, we perform in-depth measurement of metabolism in intact human liver tissue ex vivo using global 13C tracing, non-targeted mass spectrometry and model-based metabolic flux analysis. Isotope tracing allowed qualitative assessment of a wide range of metabolic pathways within a single experiment, confirming well-known features of liver metabolism but also revealing unexpected metabolic activities such as de novo creatine synthesis and branched-chain amino acid transamination, where human liver appears to differ from rodent models. Glucose production ex vivo correlated with donor plasma glucose, suggesting that cultured liver tissue retains individual metabolic phenotypes, and could be suppressed by postprandial levels of nutrients and insulin, and also by pharmacological inhibition of glycogen utilization. Isotope tracing ex vivo allows measuring human liver metabolism with great depth and resolution in an experimentally tractable system.
Ribosomal S6 kinase 1 regulates inflammaging via the senescence secretome
Authors: Gallage Suchira , Irvine Elaine E. , Barragan Avila Jose Efren , Reen Virinder , Pedroni Silvia M. A. , Duran Imanol , Ranvir Vikas , Khadayate Sanjay , Pombo Joaquim , Brookes Sharon , Heide Danijela , Dharmalingham Gopuraja , Choudhury Agharul I. , Singh Indrabahadur , Herranz Nicolás , Vernia Santiago , Heikenwalder Mathias , Gil Jesús , Withers Dominic J. 
Published: August 2024

AbstractInhibition of S6 kinase 1 (S6K1) extends lifespan and improves healthspan in mice, but the underlying mechanisms are unclear. Cellular senescence is a stable growth arrest accompanied by an inflammatory senescence-associated secretory phenotype (SASP). Cellular senescence and SASP-mediated chronic inflammation contribute to age-related pathology, but the specific role of S6K1 has not been determined. Here we show that S6K1 deletion does not reduce senescence but ameliorates inflammation in aged mouse livers. Using human and mouse models of senescence, we demonstrate that reduced inflammation is a liver-intrinsic effect associated with S6K deletion. Specifically, we show that S6K1 deletion results in reduced IRF3 activation; impaired production of cytokines, such as IL1β; and reduced immune infiltration. Using either liver-specific or myeloid-specific S6K knockout mice, we also demonstrate that reduced immune infiltration and clearance of senescent cells is a hepatocyte-intrinsic phenomenon. Overall, deletion of S6K reduces inflammation in the liver, suggesting that suppression of the inflammatory SASP by loss of S6K could underlie the beneficial effects of inhibiting this pathway on healthspan and lifespan.
A survey-based, quasi-experimental study assessing a high-cannabidiol suppository for menstrual-related pain and discomfort
Authors: Dahlgren M. Kathryn , Smith Rosemary T. , Kosereisoglu Deniz , Sagar Kelly A. , Lambros Ashley M. , El-Abboud Celine , Gruber Staci A. 
Published: August 2024

AbstractThe endocannabinoid system is involved in gynecological functions, with cannabidiol (CBD) demonstrating promise for alleviating menstrual-related symptoms. This survey-based, quasi-experimental study assessedpro re nata(PRN) use of a commercially-available, hemp-derived, broad-spectrum, high-CBD (100 mg) vaginal suppository (Foria®) for menstrual-related pain and discomfort compared to a treatment-as-usual (TAU) group (CBDn = 77, TAUn = 230), with survey assessments collected at baseline and two monthly follow-ups (~2 menstrual cycles). The CBD group demonstrated significantly reduced frequency and severity of menstrual-related symptoms, impact of symptoms on daily functioning, need for analgesics, and number of analgesics used relative to the TAU group (ps ≤ 0.032). Correlation analyses indicated a potential dose-dependent response, with increased suppository use associated with greater reduction of symptoms (ps ≤ 0.025). Most CBD participants reported at least moderate improvement of symptoms (follow-up 1 = 72.9%, follow-up 2 = 81.1%). Future studies (including replication in randomized clinical trials) assessing pharmacokinetics/pharmacodynamics, mechanism(s) of action, efficacy for other gynecological indications, and potential adverse events (e.g., drug-drug interactions) are indicated.