bluuebunny/crossref_metadata_2025_split huggingface dataset:
PD-L1 enhances migration and invasion of trophoblasts by upregulating ARHGDIB via transcription factor PU.1
Authors: Zhang Ruonan , Jia Linyan , Meng Lulu , Peng Hao , Zhang Donghai , He Qizhi , Duan Tao , Wang Kai 
Published: September 2022

AbstractAs the main constituent cells of the human placenta, trophoblasts proliferate, differentiate, and invade the uterine endometrium via a series of processes, which are regulated exquisitely through intercellular signaling mediated by hormones, cytokines, and growth factors. Programmed cell death ligand 1 (PD-L1) is a biomarker of the response to immune checkpoint inhibitors and can regulate maternal-fetal immune tolerance during pregnancy progression. Recently, it was found that PD-L1 may regulate obstetric complications by affecting the function of trophoblasts. Therefore, we examined the expression and localization of PD-L1 in the human placenta and observed the effects of PD-L1 on trophoblasts migration and invasion in both the trophoblasts line HTR-8/SVneo and an extravillous explant culture model. Finally, we explored the molecular mechanisms underlying PD-L1-regulated trophoblasts migration and invasion through RNA sequencing and bioinformatics analysis. Our data showed that PD-L1 was mainly expressed in syncytiotrophoblasts and that its protein levels increased with gestational age. Interestingly, the protein expression of PD-L1 was significantly decreased in placentas from pregnancies with preeclampsia compared with normal placentas. Importantly, the migration and invasion abilities of trophoblasts were significantly changed after knockdown or overexpression of PD-L1 in HTR-8/SVneo cells and an extravillous explant culture model, which was partially mediated through the transcription factor PU.1 (encoded by Spi1)-regulated Rho GDP-dissociation inhibitor beta (ARHGDIB) expression. These results suggested that PD-L1 was highly involved in the regulation of trophoblasts migration and invasion, providing a potential target for the diagnosis and treatment of placenta-derived pregnancy disorders.
Tropical modulation of East Asia air pollution
Authors: Jung Myung-Il , Son Seok-Woo , Kim Hyemi , Chen Deliang 
Published: September 2022

AbstractUnderstanding air pollution in East Asia is of great importance given its high population density and serious air pollution problems during winter. Here, we show that the day-to-day variability of East Asia air pollution, during the recent 21-year winters, is remotely influenced by the Madden–Julian Oscillation (MJO), a dominant mode of subseasonal variability in the tropics. In particular, the concentration of particulate matter with aerodynamic diameter less than 10 micron (PM10) becomes significantly high when the tropical convections are suppressed over the Indian Ocean (MJO phase 5–6), and becomes significantly low when those convections are enhanced (MJO phase 1–2). The station-averaged PM10 difference between these two MJO phases reaches up to 15% of daily PM10 variability, indicating that MJO is partly responsible for wintertime PM10 variability in East Asia. This finding helps to better understanding the wintertime PM10 variability in East Asia and monitoring high PM10 days.
A meta-analysis of acetogenic and methanogenic microbiomes in microbial electrosynthesis
Authors: Mills Simon , Dessì Paolo , Pant Deepak , Farràs Pau , Sloan William T. , Collins Gavin , Ijaz Umer Zeeshan 
Published: September 2022

AbstractA meta-analysis approach was used, to study the microbiomes of biofilms and planktonic communities underpinning microbial electrosynthesis (MES) cells. High-throughput DNA sequencing of 16S rRNA gene amplicons has been increasingly applied to understand MES systems. In this meta-analysis of 22 studies, we find that acetogenic and methanogenic MES cells share 80% of a cathodic core microbiome, and that different inoculum pre-treatments strongly affect community composition. Oxygen scavengers were more abundant in planktonic communities, and several key organisms were associated with operating parameters and good cell performance. We suggest Desulfovibrio sp. play a role in initiating early biofilm development and shaping microbial communities by catalysing H2 production, to sustain either Acetobacterium sp. or Methanobacterium sp. Microbial community assembly became more stochastic over time, causing diversification of the biofilm (cathodic) community in acetogenic cells and leading to re-establishment of methanogens, despite inoculum pre-treatments. This suggests that repeated interventions may be required to suppress methanogenesis.
Parkinson’s disease-associated, sex-specific changes in DNA methylation at PARK7 (DJ-1), SLC17A6 (VGLUT2), PTPRN2 (IA-2β), and NR4A2 (NURR1) in cortical neurons
Authors: Kochmanski Joseph , Kuhn Nathan C. , Bernstein Alison I. 
Published: September 2022

AbstractEvidence for epigenetic regulation playing a role in Parkinson’s disease (PD) is growing, particularly for DNA methylation. Approximately 90% of PD cases are due to a complex interaction between age, genes, and environmental factors, and epigenetic marks are thought to mediate the relationship between aging, genetics, the environment, and disease risk. To date, there are a small number of published genome-wide studies of DNA methylation in PD, but none accounted for cell type or sex in their analyses. Given the heterogeneity of bulk brain tissue samples and known sex differences in PD risk, progression, and severity, these are critical variables to account for. In this genome-wide analysis of DNA methylation in an enriched neuronal population from PD postmortem parietal cortex, we report sex-specific PD-associated methylation changes inPARK7(DJ-1),SLC17A6(VGLUT2),PTPRN2(IA-2β),NR4A2(NURR1), and other genes involved in developmental pathways, neurotransmitter packaging and release, and axon and neuron projection guidance.
Network hub centrality and working memory performance in schizophrenia
Authors: Eryilmaz Hamdi , Pax Melissa , O’Neill Alexandra G. , Vangel Mark , Diez Ibai , Holt Daphne J. , Camprodon Joan A. , Sepulcre Jorge , Roffman Joshua L. 
Published: September 2022

AbstractCognitive impairment, and working memory deficits in particular, are debilitating, treatment-resistant aspects of schizophrenia. Dysfunction of brain network hubs, putatively related to altered neurodevelopment, is thought to underlie the cognitive symptoms associated with this illness. Here, we used weighted degree, a robust graph theory metric representing the number of weighted connections to a node, to quantify centrality in cortical hubs in 29 patients with schizophrenia and 29 age- and gender-matched healthy controls and identify the critical nodes that underlie working memory performance. In both patients and controls, elevated weighted degree in the default mode network (DMN) was generally associated with poorer performance (accuracy and reaction time). Higher degree in the ventral attention network (VAN) nodes in the right superior temporal cortex was associated with better performance (accuracy) in patients. Degree in several prefrontal and parietal areas was associated with cognitive performance only in patients. In regions that are critical for sustained attention, these correlations were primarily driven by between-network connectivity in patients. Moreover, a cross-validated prediction analysis showed that a linear model using a summary degree score can be used to predict an individual’s working memory accuracy (r = 0.35). Our results suggest that schizophrenia is associated with dysfunctional hubs in the cortical systems supporting internal and external cognition and highlight the importance of topological network analysis in the search of biomarkers for cognitive deficits in schizophrenia.
Public opinion towards global distribution of COVID-19 vaccines - Data from Germany and the United States
Authors: Klumpp Matthias , Monfared Ida G. , Vollmer Sebastian 
Published: September 2022

AbstractThis study gathered evidence from Germany and the United States on public opinion towards fair distribution of COVID-19 vaccines across the world. Analytical Hierarchy Process and discrete choice experiments were used for this purpose. The sample is nationally representative of adults (aged 18 and above) for both countries using quotas on age, gender, education, state, and COVID-19 vaccination rates at the time of the fieldwork (25 May 2021 to 26 June 2021). Overall 1,003 responses in Germany and 1,000 in the United States were collected.
Clinical and molecular characterization of primary hyperoxaluria in Egypt
Authors: Soliman Neveen A. , Elmonem Mohamed A. , Abdelrahman Safaa M. , Nabhan Marwa M. , Fahmy Yosra A. , Cogal Andrea , Harris Peter C. , Milliner Dawn S. 
Published: September 2022

AbstractPrimary hyperoxaluria (PH) is an autosomal recessive disorder of oxalate metabolism caused by pathogenic variants in either of three genes (AGXT, GRHPR or HOGA1). The study aimed at characterizing the clinical phenotypes as well as the genotypic spectrum of PH in Egypt. We screened 25 Egyptian patients suspected of PH for the three responsible genes by Sanger sequencing. We diagnosed 20 patients from 18 unrelated families, in which the natural history, family history, clinical features and genotypes were evaluated. PH patients were 15 males and 5 females ranging in age from 4 months to 31 years (median 8 years). Fifteen families were consanguineous (83%) and familial clustering was reported in six families (33%). Pathogenic variants in all 40 alleles were in AGXT, with none detected in GRHPR or HOGA1. We detected two novel pathogenic variants c.166-1_172dupGATCATGG (p.Asp58Glyfs*65) and c.766delC (p.Gln256fs*16) and seven previously reported variants in our cohort. This is the first study reporting the genotype of a considerable number of PH1 patients from Egypt. Our detected variants in the AGXT gene could form the basis for future genetic counseling and prenatal diagnosis in Egypt and surrounding populations.
Actin cable formation and epidermis–dermis positional relationship during complete skin regeneration
Authors: Takaya Kento , Okabe Keisuke , Ishigami Ayaka , Imbe Yuka , Kanazawa Hideko , Sakai Shigeki , Aramaki-Hattori Noriko , Kishi Kazuo 
Published: September 2022

AbstractUp to a certain developmental stage, a fetus can completely regenerate wounds in the skin. To clarify the mechanism of fetal skin regeneration, identifying when the skin switches from fetal-type wound regeneration to adult-type wound repair is necessary. We hypothesized that this switch occurs at several time points and that complete skin regeneration requires epidermal–dermal interactions and the formation of actin cables. We compared normal skin and wound morphology at each developmental stage. We examined two parameters: epidermal texture and dermal structure. We found that the three-dimensional structure of the skin was completely regenerated in full-thickness skin incisions made before embryonic day (E) 13. However, the skin texture did not regenerate in wounds made after E14. We also found that the dermal structure regenerates up to E16, but wounds created after E17 heal as scars with dermal fibrosis. By controlling the activity of AMP-activated protein kinase and altering actin cable formation, we could regulate scar formation in utero. These findings may contribute to therapies that allow complete skin regeneration without scarring.
A 3D image-based modelling approach for understanding spatiotemporal processes in phosphorus fertiliser dissolution, soil buffering and uptake by plant roots
Authors: Williams K. A. , McKay Fletcher D. M. , Petroselli C. , Ruiz S. A. , Roose T. 
Published: September 2022

AbstractPhosphorus (P) is a key yield-limiting nutrient for crops, but the main source of P fertiliser is finite. Therefore, efficient fertilisation is crucial. Optimal P application requires understanding of the dynamic processes affecting P availability to plants, including fertiliser dissolution rate and soil buffer power. However, standard soil testing methods sample at fixed time points, preventing a mechanistic understanding of P uptake variability. We used image-based modelling to investigate the effects of fertiliser dissolution rate and soil buffer power on P uptake by wheat roots imaged using X-ray CT. We modelled uptake based on 1-day, 1-week, and 14-week dissolution of a fixed quantity of total P for two common soil buffer powers. We found rapid fertiliser dissolution increased short-term root uptake, but total uptake from 1-week matched 1-day dissolution. We quantified the large effects root system architecture had on P uptake, finding that there were trade-offs between total P uptake and uptake per unit root length, representing a carbon investment/phosphorus uptake balance. These results provide a starting point for predictive modelling of uptake from different P fertilisers in different soils. With the addition of further X-ray CT image datasets and a wider range of conditions, our simulation approach could be developed further for rapid trialling of fertiliser-soil combinations to inform field-scale trials or management.
Quantification of ovarian lesion and fallopian tube vasculature using optical-resolution photoacoustic microscopy
Authors: Leng Xiandong , Kou Sitai , Lin Yixiao , Hagemann Andrea R. , Hagemann Ian S. , Thaker Premal H. , Kuroki Lindsay M. , McCourt Carolyn K. , Mutch David G. , Siegel Cary , Powell Matthew A. , Zhu Quing 
Published: September 2022

AbstractThe heterogeneity in the pathological and clinical manifestations of ovarian cancer is a major hurdle impeding early and accurate diagnosis. A host of imaging modalities, including Doppler ultrasound, MRI, and CT, have been investigated to improve the assessment of ovarian lesions. We hypothesized that pathologic conditions might affect the ovarian vasculature and that these changes might be detectable by optical-resolution photoacoustic microscopy (OR-PAM). In our previous work, we developed a benchtop OR-PAM and demonstrated it on a limited set of ovarian and fallopian tube specimens. In this study, we collected data from over 50 patients, supporting a more robust statistical analysis. We then developed an efficient custom analysis pipeline for characterizing the vascular features of the samples, including the mean vessel diameter, vascular density, global vascular directionality, local vascular definition, and local vascular tortuosity/branchedness. Phantom studies using carbon fibers showed that our algorithm was accurate within an acceptable error range. Between normal ovaries and normal fallopian tubes, we observed significant differences in five of six extracted vascular features. Further, we showed that distinct subsets of vascular features could distinguish normal ovaries from cystic, fibrous, and malignant ovarian lesions. In addition, a statistically significant difference was found in the mean vascular tortuosity/branchedness values of normal and abnormal tubes. The findings support the proposition that OR-PAM can help distinguish the severity of tubal and ovarian pathologies.
A machine learning approach for predicting suicidal ideation in post stroke patients
Authors: Song Seung Il , Hong Hyeon Taek , Lee Changwoo , Lee Seung Bo 
Published: September 2022

AbstractCurrently, the identification of stroke patients with an increased suicide risk is mainly based on self‐report questionnaires, and this method suffers from a lack of objectivity. This study developed and validated a suicide ideation (SI) prediction model using clinical data and identified SI predictors. Significant variables were selected through traditional statistical analysis based on retrospective data of 385 stroke patients; the data were collected from October 2012 to March 2014. The data were then applied to three boosting models (Xgboost, CatBoost, and LGBM) to identify the comparative and best performing models. Demographic variables that showed significant differences between the two groups were age, onset, type, socioeconomic, and education level. Additionally, functional variables also showed a significant difference with regard to ADL and emotion (p < 0.05). The CatBoost model (0.900) showed higher performance than the other two models; and depression, anxiety, self-efficacy, and rehabilitation motivation were found to have high importance. Negative emotions such as depression and anxiety showed a positive relationship with SI and rehabilitation motivation and self-efficacy displayed an inverse relationship with SI. Machine learning-based SI models could augment SI prevention by helping rehabilitation and medical professionals identify high-risk stroke patients in need of SI prevention intervention.
Expression of the immune checkpoint modulator OX40 indicates poor survival in acute myeloid leukemia
Authors: Marconato Maddalena , Kauer Joseph , Salih Helmut R. , Märklin Melanie , Heitmann Jonas S. 
Published: September 2022

AbstractDespite therapeutic advances, mortality of Acute Myeloid Leukemia (AML) is still high. Currently, the determination of prognosis which guides treatment decisions mainly relies on genetic markers. Besides molecular mechanisms, the ability of malignant cells to evade immune surveillance influences the disease outcome and, among others, the expression of checkpoints modulators contributes to this. In AML, functional expression of the checkpoint molecule OX40 was reported, but the prognostic relevance of OX40 and its ligand OX40L axis has so far not been investigated. Here we described expression and prognostic relevance of the checkpoint modulators OX40 and OX40L, analyzed on primary AML cells obtained from 92 therapy naïve patients. Substantial expression of OX40 and OX40L on AML blasts was detected in 29% and 32% of the investigated subjects, respectively, without correlation between the expression of the receptor and its ligand. Whereas OX40L expression was not associated with different survival, patients with high expression levels of the receptor (OX40high) on AML blasts survived significantly shorter than OX40low patients (p = 0.009, HR 0.46, 95% CI 0.24–0.86), which identifies OX40 as novel prognostic marker and a potential therapeutic target in AML patients.
The correction factor of Monterey No. 0/30 sample with fines content liquefaction resistance between cyclic triaxial and cyclic hollow cylinder tests
Authors: Liu Jungang , Chen Geng 
Published: September 2022

AbstractSoil liquefaction is one of the most detrimental forms of earthquake-induced ground failure that can result in catastrophic damage to engineering structures. For the seismic safety evaluation of foundations and high-rise structures, it is the most critical way to assess liquefaction resistance. In this paper, an array number of isotropically consolidated undrained cyclic triaxial tests (CTT) and cyclic hollow cylinder tests (CHCT) have been performed to evaluate soil liquefaction resistance. Thirty-seven isotopically consolidated undrained cyclic triaxial tests and thirty-seven cyclic hollow cylinder tests were run on the uniform medium Monterey No. 0/30 sand and it is with four different percentages of fine content. By using cyclic triaxial and cyclic hollow cylinder tests for evaluating liquefaction resistance, it helps us better understand the relationship between two types of tests on uniform clean Monterey No. 0/30 sand and soil sample with five different percentages of fines content. Four different relative densities of 30%, 45%, 50%, and 60%, two confining pressure of 103 kpa and 207 kpa, and five cyclic stress ratios (0.15, 0.2, 0.25, 0.3, and 0.4) have been used for a series of cyclic triaxial tests and cyclic hollow cylinder tests. At the same relative densities of 30% and 60%, the correction factor between CTT and CHCT evaluated ranged from 0.46 to 0.63 on the uniform clean Monterey No. 0/30 sand. Statistical analyses were performed to formulate functional relationships for predicting the correction factor of soil liquefaction resistance between CTT and CHCT tests.
Genetic abnormalities in fetal congenital heart disease with aberrant right subclavian artery
Authors: Sun Hairui , Han Lu , Hao Xiaoyan , Chen Zhaoyi , Wang Jingyi , Yi Tong , Zhou Xiaoxue , Gu Xiaoyan , Han Jiancheng , Zhang Ye , Sun Lin , Liu Xiaowei , Zhang Siyao , Guo Yong , Zhang Hongjia , He Yihua 
Published: September 2022

AbstractFetal aberrant right subclavian artery (ARSA) is a relatively common sonographic finding. Congenital heart disease (CHD) is the most common structural abnormality in patients with ARSA. We aimed to assess the prevalence of genetic abnormalities, particularly sequence variants, in fetuses with CHD and ARSA. By clinical phenotyping and genomic sequencing, we retrospectively reviewed all fetuses with a prenatal diagnosis of CHD combined with ARSA at a single center. As a result, we identified 30 fetuses with ARSA combined with CHD, with conotruncal anomalies being the most common (n = 12, 40%), followed by left ventricular outflow tract obstruction (n = 6, 20%) and atrioventricular septal defects (n = 6, 20%). Overall, 18 (60%) cases had a genetic diagnosis. Copy number variation sequencing analysis identified six (20%) fetuses with aneuploidy and seven (23%) with pathogenic copy-number variants. Whole-exome sequencing (WES) analysis of the remaining 17 cases revealed diagnostic genetic variants in five (29%) cases, indicating that the diagnostic yield of WES for the entire cohort was 17% (5/30). Our findings reveal the high burden of genetic abnormalities in fetal CHD with ARSA. Single-gene disorders contribute substantially to the genetic etiology of fetal CHD with ARSA.
Finite-state parameter space maps for pruning partitions in modularity-based community detection
Authors: Gibson Ryan A. , Mucha Peter J. 
Published: September 2022

AbstractPartitioning networks into communities of densely connected nodes is an important tool used widely across different applications, with numerous methods and software packages available for community detection. Modularity-based methods require parameters to be selected (or assume defaults) to control the resolution and, in multilayer networks, interlayer coupling. Meanwhile, most useful algorithms are heuristics yielding different near-optimal results upon repeated runs (even at the same parameters). To address these difficulties, we combine recent developments into a simple-to-use framework for pruning a set of partitions to a subset that are self-consistent by an equivalence with the objective function for inference of a degree-corrected planted partition stochastic block model (SBM). Importantly, this combined framework reduces some of the problems associated with the stochasticity that is inherent in the use of heuristics for optimizing modularity. In our examples, the pruning typically highlights only a small number of partitions that are fixed points of the corresponding map on the set of somewhere-optimal partitions in the parameter space. We also derive resolution parameter upper bounds for fitting a constrained SBM of K blocks and demonstrate that these bounds hold in practice, further guiding parameter space regions to consider. With publicly available code (http://github.com/ragibson/ModularityPruning), our pruning procedure provides a new baseline for using modularity-based community detection in practice.