bluuebunny/crossref_metadata_2025_split huggingface dataset:
A dominance of Mu class glutathione transferases within the equine tapeworm Anoplocephala perfoliata
Authors: Northcote Holly M. , Wititkornkul Boontarikaan , Cutress David J. , Allen Nathan D. , Brophy Peter M. , Wonfor Ruth E. , Morphew Russell M. 
Published: January 2024

AbstractThe most common equine tapeworm, Anoplocephala perfoliata, has often been neglected amongst molecular investigations and has been faced with limited treatment options. However, the recent release of a transcriptome dataset has now provided opportunities for in-depth analysis of A. perfoliata protein expression. Here, global, and sub-proteomic approaches were utilized to provide a comprehensive characterization of the A. perfoliata soluble glutathione transferases (GST) (ApGST). Utilizing both bioinformatics and gel-based proteomics, GeLC and 2D-SDS PAGE, the A. perfoliata ‘GST-ome’ was observed to be dominated with Mu class GST representatives. In addition, both Sigma and Omega class GSTs were identified, albeit to a lesser extent and absent from affinity chromatography approaches. Moreover, 51 ApGSTs were localized across somatic (47 GSTs), extracellular vesicles (EVs) (Whole: 1 GST, Surface: 2 GSTs) and EV depleted excretory secretory product (ESP) (9 GSTs) proteomes. In related helminths, GSTs have shown promise as novel anthelmintic or vaccine targets for improved helminth control. Thus, provides potential targets for understanding A. perfoliata novel infection mechanisms, host–parasite relationships and anthelmintic treatments.
Reward anticipation-related neural activation following cued reinforcement in adults with psychotic psychopathology and biological relatives
Authors: Demro Caroline , Lahud Elijah , Burton Philip C. , Purcell John R. , Simon Joe J. , Sponheim Scott R. 
Published: January 2024

AbstractBackgroundSchizophrenia is associated with hypoactivation of reward sensitive brain areas during reward anticipation. However, it is unclear whether these neural functions are similarly impaired in other disorders with psychotic symptomatology or individuals with genetic liability for psychosis. If abnormalities in reward sensitive brain areas are shared across individuals with psychotic psychopathology and people with heightened genetic liability for psychosis, there may be a common neural basis for symptoms of diminished pleasure and motivation.MethodsWe compared performance and neural activity in 123 people with a history of psychosis (PwP), 81 of their first-degree biological relatives, and 49 controls during a modified Monetary Incentive Delay task during fMRI.ResultsPwP exhibited hypoactivation of the striatum and anterior insula (AI) during cueing of potential future rewards with each diagnostic group showing hypoactivations during reward anticipation compared to controls. Despite normative task performance, relatives demonstrated caudate activation intermediate between controls and PwP, nucleus accumbens activation more similar to PwP than controls, but putamen activation on par with controls. Across diagnostic groups of PwP there was less functional connectivity between bilateral caudate and several regions of the salience network (medial frontal gyrus, anterior cingulate, AI) during reward anticipation.ConclusionsFindings implicate less activation and connectivity in reward processing brain regions across a spectrum of disorders involving psychotic psychopathology. Specifically, aberrations in striatal and insular activity during reward anticipation seen in schizophrenia are partially shared with other forms of psychotic psychopathology and associated with genetic liability for psychosis.
Chariots, mail coaches and wagons in the Arabic dialect of Qaṭrāyīth (“in Qatari”) in early Islamic eastern Arabia
Authors: Kozah Mario 
Published: January 2024

AbstractThis paper will present the evidence for two newly discovered words, gawzag and shagar, meaning “two-horse chariot/mail coach” and “wagon” respectively in the eastern Arabian dialect of Qaṭrāyīth (Syriac for “in Qatari”) of the seventh and eighth centuries ce. They reveal the continued local knowledge of wheeled transport in Arabia and possible use long after its supposed disappearance in the Near East between the fourth and sixth centuries according to Richard Bulliet's well-known thesis in his seminal work The Camel and the Wheel (New York: Columbia University Press, 1990). The fact that this vernacular maintained two specific words for two different modes of wheeled transport likely suggests a practical need for them in everyday communication among the inhabitants of the Beth Qaṭraye region (Syriac for “region of the Qataris” in north-eastern Arabia). Moreover, their use in an Arabic dialect reveals that native words were developed for wheeled vehicles in the local language spoken by the inhabitants of the area well before the adoption of markabah as a neologism to mean chariot in nineteenth-century Arabic, according to Michael Macdonald's stimulating article “Wheels in a land of camels” (Arabian Archaeology and Epigraphy 20/2, 2009). Thus, the various rock drawings of two-wheeled carts and chariots in northern Arabia may in fact not only have been known but also used nearby in eastern Arabia, rather than being inaccurate representations reflecting a distant awareness of the existence of chariots elsewhere such as in Mesopotamia and Egypt as had been previously thought. This is a literary, philological. and historical study that aims at presenting newly discovered vocabulary in context for further analysis by linguists and others.
Expert Bias and Democratic Erosion: Assessing Expert Perceptions of Contemporary American Democracy
Authors: Bergeron-Boutin Olivier , Carey John M. , Helmke Gretchen , Rau Eli 
Published: January 2024

ABSTRACTIn an important contribution to scholarship on measuring democratic performance, Little and Meng suggest that bias among expert coders accounts for erosion in ratings of democratic quality and performance observed in recent years. Drawing on 19 waves of survey data on US democracy from academic experts and from the public collected by Bright Line Watch (BLW), this study looks for but does not find manifestations of the type of expert bias that Little and Meng posit. Although we are unable to provide a direct test of Little and Meng’s hypothesis, several analyses provide reassurance that expert samples are an informative source to measure democratic performance. We find that respondents who have participated more frequently in BLW surveys, who have coded for V-Dem, and who are vocal about the state of American democracy on Twitter are no more pessimistic than other participants.
Measuring Backsliding with Observables: Observable-to-Subjective Score Mapping
Authors: Weitzel Daniel , Gerring John , Pemstein Daniel , Skaaning Svend-Erik 
Published: January 2024

ABSTRACTMultiple well-known democracy-rating projects—including Freedom House, Polity, and Varieties of Democracy (V-Dem)—have identified apparent global regression in recent years. These measures rely on partly subjective indicators, which—in principle—could suffer from rater bias. For instance, Little and Meng (2023) argue that shared beliefs driven by the current zeitgeist could lead to shared biases that produce the appearance of democratic backsliding in subjectively coded measures. To assess this argument and the strength of the evidence for global democratic backsliding, we propose an observable-to-subjective score mapping (OSM) methodology that uses only easily observable features of democracy to predict existing indices of democracy. Applying this methodology to three prominent democracy indices, we find evidence of backsliding—but beginning later and not as pronounced as suggested by some of the original indices. Our approach suggests that the Freedom House measure particularly does not track with the recent patterns in observable indicators and that there has been a stasis or—at most—a modest decline in the average level of democracy.
Numerical Simulation of Falling‐Snow Deposition Pattern Over 3D‐Hill
Authors: Huang Ning , Yu Yang , Shao Yaping , Zhang Jie 
Published: January 2024

AbstractSnow distribution over complex terrain is an important input quantity for hydrological modeling. Earlier numerical studies on falling‐snow deposition pattern mostly focused on two‐dimensional (2D) hills. This is simulated over a three‐dimensional (3D) hill using a large‐eddy simulation model. It is shown that for both 2D and 3D cases, the hill blocking effect leads to the formation of a snow accumulation zone on the windward slope. For the 3D case, the maximum snow deposition occurs on the leeward toe, but not for the 2D case under the same background conditions. The main reason for these differences is that the spanwise terrain change in the 3D case weakens this hill blocking effect and concurrently generates terrain‐scale vortices which cause spatially variable snow depositions. It is found that an additional snow accumulation zone forms on the leeward slope of the 3D‐hill due to the presence of a horseshoe vortex there. The low wind velocity regime bracketed by the vorticity streamers forms another large snow accumulation zone on the leeward toe. While the results here are only applicable to small hills in a mountain chain, they provide the necessary information for the parameterization of large‐scale snow patterns for hydrological modeling.
Sedimentological Evidence for Pre‐Early Permian Continental Subduction in the Dabie Orogen, Central‐East China
Authors: Deng Tao , Hu Xiumian , Chew David , Wang Qin , Yu Jinhai , Drakou Foteini 
Published: January 2024

AbstractHow to constrain the onset of continental subduction and prograde metamorphism in an orogen remains a fundamental question. The widespread Triassic ultrahigh‐pressure (UHP) metamorphic rocks in the Dabie orogen in central‐east China are generally attributed to continental subduction. The earliest Triassic peripheral basins (the Huangshi, Yueshan and Nanjing basins) around the Dabie orogen represent an ideal archive to reconstruct the early evolution of the orogen. Here we present a multidisciplinary provenance study on these Triassic strata, including framework petrography and heavy mineral analyses combined with U‐Pb age and trace‐element analyses of detrital zircon, rutile and apatite. The abundant metapelitic lithics and muscovite grains, a heavy mineral population dominated by metamorphic apatite, and a significant Permian (270–290 Ma) age peak from U‐Pb age spectra of detrital zircon, rutile and apatite imply an Early Permian medium‐high grade metamorphic source in the uppermost structural levels of the Dabie orogen. Our provenance data indicate that the onset of northward continental subduction of the South China Block commenced no later than the Early Permian (c. 290 Ma). This event is clearly earlier and distinct from the more widespread Triassic UHP metamorphism of the Dabie orogen, suggesting that continental subduction and mountain‐basin interaction were protracted processes (>55 Myr, c. 290–235 Ma). When combined with other geological evidence, our results show that the prolonged continental subduction is not always preceded by subduction of oceanic crust.
Brine Drying and Salt Precipitation in Porous Media: A Microfluidics Study
Authors: Zhang Hui , Sun Zhonghao , Zhang Nan , Zhao Budi 
Published: January 2024

AbstractDrying and salt precipitation in porous media impact various engineering disciplines, including carbon geological storage in brine reservoirs, with considerable hydraulic and mechanical effects. However, understanding the underlying mechanisms and controlling factors is limited due to the lack of pore‐scale observation and quantitative analysis. We design radial flow microfluidic chips with varying pore heterogeneity and wettability and quantify the pore‐scale dynamics of brine drying and salt precipitation using time‐lapse images and image processing techniques. The gas injection process determines the distribution of residual (drying) brine and is influenced by pore heterogeneity. Higher concentrations of residual brine are observed near the injection well in more heterogeneous porous media. Capillary backflow replenishes evaporative losses near the well during drying in hydrophilic chips. Brine clusters induced by gas injection connect through brine films and reconnect by capillary backflow. Two types of pore habits of salt precipitation are identified: bulk salt within brine clusters and aggregated salt at the air‐brine interface. Salt precipitation, particularly near the injection well, significantly reduces injectivity, with less impact observed in the porous media with uniform pore structure and hydrophobic surfaces.
Intellectual disability and autism in propionic acidemia: a biomarker-behavioral investigation implicating dysregulated mitochondrial biology
Authors: Shchelochkov Oleg A. , Farmer Cristan A. , Chlebowski Colby , Adedipe Dee , Ferry Susan , Manoli Irini , Pass Alexandra , McCoy Samantha , Van Ryzin Carol , Sloan Jennifer , Thurm Audrey , Venditti Charles P. 
Published: January 2024

AbstractPropionic acidemia (PA) is an autosomal recessive condition (OMIM #606054), wherein pathogenic variants inPCCAandPCCBimpair the activity of propionyl-CoA carboxylase. PA is associated with neurodevelopmental disorders, including intellectual disability (ID) and autism spectrum disorder (ASD); however, the correlates and mechanisms of these outcomes remain unknown. Using data from a subset of participants with PA enrolled in a dedicated natural history study (n = 33), we explored associations between neurodevelopmental phenotypes and laboratory parameters. Twenty (61%) participants received an ID diagnosis, and 12 of the 31 (39%) who were fully evaluated received the diagnosis of ASD. A diagnosis of ID, lower full-scale IQ (sample mean = 65 ± 26), and lower adaptive behavior composite scores (sample mean = 67 ± 23) were associated with several biomarkers. Higher concentrations of plasma propionylcarnitine, plasma total 2-methylcitrate, serum erythropoietin, and mitochondrial biomarkers plasma FGF21 and GDF15 were associated with a more severe ID profile. Reduced 1-13C-propionate oxidative capacity and decreased levels of plasma and urinary glutamine were also associated with a more severe ID profile. Only two parameters, increased serum erythropoietin and decreased plasma glutamine, were associated with ASD. Plasma glycine, one of the defining features of PA, was not meaningfully associated with either ID or ASD. Thus, while both ID and ASD were commonly observed in our PA cohort, only ID was robustly associated with metabolic parameters. Our results suggest that disease severity and associated mitochondrial dysfunction may play a role in CNS complications of PA and identify potential biomarkers and candidate surrogate endpoints.
Translational implications of CHRFAM7A, an elusive human-restricted fusion gene
Authors: Ihnatovych Ivanna , Saddler Ruth-Ann , Sule Norbert , Szigeti Kinga 
Published: January 2024

AbstractGenes restricted to humans may contribute to human-specific traits and provide a different context for diseases.CHRFAM7Ais a uniquely human fusion gene and a negative regulator of the α7 nicotinic acetylcholine receptor (α7 nAChR). The α7 nAChR has been a promising target for diseases affecting cognition and higher cortical functions, however, the treatment effect observed in animal models failed to translate into human clinical trials. AsCHRFAM7Awas not accounted for in preclinical drug screens it may have contributed to the translational gap. Understanding the complex genetic architecture of the locus, deciphering the functional impact of CHRFAM7A on α7 nAChR neurobiology and utilizing human-relevant models may offer novel approaches to explore α7 nAChR as a drug target.
Placental transcriptomic signatures of prenatal and preconceptional maternal stress
Authors: Baker Brennan H. , Freije Sophie , MacDonald James W. , Bammler Theo K. , Benson Ciara , Carroll Kecia N. , Enquobahrie Daniel A. , Karr Catherine J. , LeWinn Kaja Z. , Zhao Qi , Bush Nicole R. , Sathyanarayana Sheela , Paquette Alison G. 
Published: January 2024

AbstractPrenatal exposure to maternal psychological stress is associated with increased risk for adverse birth and child health outcomes. Accumulating evidence suggests that preconceptional maternal stress may also be transmitted intergenerationally to negatively impact offspring. However, understanding of mechanisms linking these exposures to offspring outcomes, particularly those related to placenta, is limited. Using RNA sequencing, we identified placental transcriptomic signatures associated with maternal prenatal stressful life events (SLEs) and childhood traumatic events (CTEs) in 1 029 mother-child pairs in two birth cohorts from Washington state and Memphis, Tennessee. We evaluated individual gene-SLE/CTE associations and performed an ensemble of gene set enrichment analyses combing across 11 popular enrichment methods. Higher number of prenatal SLEs was significantly (FDR < 0.05) associated with increased expression of ADGRG6, a placental tissue-specific gene critical in placental remodeling, and decreased expression of RAB11FIP3, an endocytosis and endocytic recycling gene, and SMYD5, a histone methyltransferase. Prenatal SLEs and maternal CTEs were associated with gene sets related to several biological pathways, including upregulation of protein processing in the endoplasmic reticulum, protein secretion, and ubiquitin mediated proteolysis, and down regulation of ribosome, epithelial mesenchymal transition, DNA repair, MYC targets, and amino acid-related pathways. The directional associations in these pathways corroborate prior non-transcriptomic mechanistic studies of psychological stress and mental health disorders, and have previously been implicated in pregnancy complications and adverse birth outcomes. Accordingly, our findings suggest that maternal exposure to psychosocial stressors during pregnancy as well as the mother’s childhood may disrupt placental function, which may ultimately contribute to adverse pregnancy, birth, and child health outcomes.
Early prediction of pediatric asthma in the Canadian Healthy Infant Longitudinal Development (CHILD) birth cohort using machine learning
Authors: He Ping , Moraes Theo J. , Dai Darlene , Reyna-Vargas Myrtha E. , Dai Ruixue , Mandhane Piush , Simons Elinor , Azad Meghan B. , Hoskinson Courtney , Petersen Charisse , Del Bel Kate L. , Turvey Stuart E. , Subbarao Padmaja , Goldenberg Anna , Erdman Lauren 
Published: January 2024

Abstract
Background
Early identification of children at risk of asthma can have significant clinical implications for effective intervention and treatment. This study aims to disentangle the relative timing and importance of early markers of asthma.

Methods
Using the CHILD Cohort Study, 132 variables measured in 1754 multi-ethnic children were included in the analysis for asthma prediction. Data up to 4 years of age was used in multiple machine learning models to predict physician-diagnosed asthma at age 5 years. Both predictive performance and variable importance was assessed in these models.

Results
Early-life data (≤1 year) has limited predictive ability for physician-diagnosed asthma at age 5 years (area under the precision-recall curve (AUPRC) < 0.35). The earliest reliable prediction of asthma is achieved at age 3 years, (area under the receiver-operator curve (AUROC) > 0.90) and (AUPRC > 0.80). Maternal asthma, antibiotic exposure, and lower respiratory tract infections remained highly predictive throughout childhood. Wheezing status and atopy are the most important predictors of early childhood asthma from among the factors included in this study.

Conclusions
Childhood asthma is predictable from non-biological measurements from the age of 3 years, primarily using parental asthma and patient history of wheezing, atopy, antibiotic exposure, and lower respiratory tract infections.

Impact

Machine learning models can predict physician-diagnosed asthma in early childhood (AUROC > 0.90 and AUPRC > 0.80) using ≥3 years of non-biological and non-genetic information, whereas prediction with the same patient information available before 1 year of age is challenging.

Wheezing, atopy, antibiotic exposure, lower respiratory tract infections, and the child’s mother having asthma were the strongest early markers of 5-year asthma diagnosis, suggesting an opportunity for earlier diagnosis and intervention and focused assessment of patients at risk for asthma, with an evolving risk stratification over time.
Medical and genetic correlates of long-term buprenorphine treatment in the electronic health records
Authors: Niarchou Maria , Sanchez-Roige Sandra , Reddy India A. , Reese Thomas J. , Marcovitz David , Davis Lea K. 
Published: January 2024

AbstractDespite the benefits associated with longer buprenorphine treatment duration (i.e., >180 days) (BTD) for opioid use disorder (OUD), retention remains poor. Research on the impact of co-occurring psychiatric issues on BTD has yielded mixed results. It is also unknown whether the genetic risk in the form of polygenic scores (PGS) for OUD and other comorbid conditions, including problematic alcohol use (PAU) are associated with BTD. We tested the association between somatic and psychiatric comorbidities and long BTD and determined whether PGS for OUD-related conditions was associated with BTD. The study included 6686 individuals with a buprenorphine prescription that lasted for less than 6 months (short-BTD) and 1282 individuals with a buprenorphine prescription that lasted for at least 6 months (long-BTD). Recorded diagnosis of substance addiction and disorders (Odds Ratio (95% CI) = 22.14 (21.88–22.41), P = 2.8 × 10−116), tobacco use disorder (OR (95% CI) = 23.4 (23.13–23.68), P = 4.5 × 10−111), and bipolar disorder (OR(95% CI) = 9.70 (9.48–9.92), P = 1.3 × 10−91), among others, were associated with longer BTD. The PGS of OUD and several OUD co-morbid conditions were associated with any buprenorphine prescription. A higher PGS for OUD (OR per SD increase in PGS (95%CI) = 1.43(1.16–1.77), P = 0.0009), loneliness (OR(95% CI) = 1.39(1.13–1.72), P = 0.002), problematic alcohol use (OR(95%CI) = 1.47(1.19–1.83), P = 0.0004), and externalizing disorders (OR(95%CI) = 1.52(1.23 to 1.89), P = 0.0001) was significantly associated with long-BTD. Associations between BTD and the PGS of depression, chronic pain, nicotine dependence, cannabis use disorder, and bipolar disorder did not survive correction for multiple testing. Longer BTD is associated with diagnoses of psychiatric and somatic conditions in the EHR, as is the genetic score for OUD, loneliness, problematic alcohol use, and externalizing disorders.