bluuebunny/crossref_metadata_2025_split huggingface dataset:
SparsePro: an efficient genome-wide fine-mapping method integrating summary statistics and functional annotations
Authors: Zhang Wenmin , Najafabadi Hamed , Li Yue 
Published: January 2022

Abstract
Identifying causal variants from genome-wide association studies (GWASs) is challenging due to widespread linkage disequilibrium (LD). Functional annotations of the genome may help prioritize variants that are biologically relevant and thus improve fine-mapping of GWAS results. However, classical fine-mapping methods have a high computational cost, particularly when the underlying genetic architecture and LD patterns are complex. Here, we propose a novel approach, SparsePro, to efficiently conduct genome-wide fine-mapping. Our method enjoys two major innovations: First, by creating a sparse low-dimensional projection of the high-dimensional genotype data, we enable a linear search of causal variants instead of a combinatorial search of causal configurations used in most existing methods; Second, we adopt a probabilistic framework with a highly efficient variational expectation-maximization algorithm to integrate statistical associations and functional priors. We evaluate SparsePro through extensive simulations using resources from the UK Biobank. Compared to state-of-the-art methods, SparsePro achieved more accurate and well-calibrated posterior inference with greatly reduced computation time. We demonstrate the utility of SparsePro by investigating the genetic architecture of five functional biomarkers of vital organs. We show that, compared to other methods, the causal variants identified by SparsePro are highly enriched for expression quantitative trait loci and explain a larger proportion of trait heritability. We also identify potential causal variants contributing to the genetically encoded coordination mechanisms between vital organs, and pinpoint target genes with potential pleiotropic effects. In summary, we have developed an efficient genome-wide fine-mapping method with the ability to integrate functional annotations. Our method may have wide utility in understanding the genetics of complex traits as well as in increasing the yield of functional follow-up studies of GWASs. SparsePro software is available on GitHub at https://github.com/zhwm/SparsePro.
Design of Frustrated Lewis Pair in Defective TiO2 for Photocatalytic Non-Oxidative Methane Coupling
Authors: Ma Jiayu , Zhang Qingqing , Chen Ziyu , Kang Kai , Pan Lihan , Wu Shiqun , Chen Chen , Wu Zhiqin , Zhang Jinlong , Wang Lingzhi 
Published: January 2022

Abstract
The efficient C-H polarization is the prerequisite for the low-temperature photocatalytic CH4 conversion, which however is restricted by the poor stretching ability of short-distanced lattice atoms. Herein, frustrated Lewis pair (FLP) composed of doped ion in TiO2 as Lewis acid (LA) and neighboring Ti-OH as Lewis base (LB) with a long distance (0.31-0.37 nm) were designed through DFT calculation and fabricated by hydrogenation treatment of metal-doped TiO2-SiO2 with macroporous-mesoporous structure. Benefitting from the long LA-LB distance and matched acid-base intensity, hydrogenated Ga-doped composite achieves superior C-H stretching with a high CH4 conversion rate (139 µmol g−1 h−1) to ethane. The photo-irradiation causes the electron excitation from Ga to Ti-OH according to the time-dependent DFT calculation and in situ EPR analysis, which promotes the formation and coupling of ·CH3. This work provides a key underpinning for regulating the characteristics of FLP for C-H activation and C-C coupling via light irradiation.
Evaluation of Rap1GAP and Epac1 Gene Expression in Endometriosis
Authors: Dehghanian Mehran , Yarahmadi Ghafour , Sandoghsaz Reyhaneh Sadat , Shamsi Farimah , Khodadadian Ali , Mehrjardi Mohammad Yahya Vahidi 
Published: January 2022

Abstract
Objective: Endometriosis is a female reproductive system disease in which endometrial tissue are found in other women organs. Various factors are effective in the development of endometriosis and due to the interaction of genetics and environmental factors, this disease is a multifactorial disease. MAPK/ERK and PI3K/Akt/mTOR pathways are activated by growth factors and steroid hormones and known as two important pathways involved in the processes of growth, proliferation and survival of endometriosis cells. Raps, monomeric GTPase of Ras family, are able to activate these pathways independently of Ras. The goal of our study was to evaluated the expression level of Rap1GAP and Epac1 gene, as two important RapGAPs (GTPase-activating proteins) and RapGEFs (guanine nucleotide exchange factors) respectively, in endometriosis tissues and normal endometrium tissues.Materials and Methods: In this study, 15 samples of women without signs of endometriosis were taken as control samples, 15 ectopic and 15 eutopic samples were taken from women with endometriosis using laparoscopic surgery. The expression of Epac1 and Rap1GAP genes was investigated by Real-time PCR technique and results were analysis by One-Way ANOVA test.Results: Epac1 upregulated significantly in ectopic tissues compared to eutopic and control tissues (Their P-value were <0.0001). Rap1GAP expression was lower in ectopic tissues compared to control samples (P-value was 0.003) and eutopic tissues (P-value was 0.001).Conclusion: Based on these results, it may be concluded that changes in the expression of the Rap1GAP and Epca1 genes may play role in the pathways involved in the pathogenesis, displacement, and migration of endometriosis cells.
Steady increase in geomagnetic reversal frequency after the Cretaceous Normal Superchron
Authors: Yoshimura Yutaka , Ishizuka Osamu , Yamazaki Toshitsugu , Yamamoto Yuhji , Ahn Hyeon-Seon , Kidane Tesfaye , Otofuji Yo-ichiro , Sekimoto Shun 
Published: January 2022

Abstract
The Earth's core is constantly and efficiently cooled by mantle convection. The heat flux transferred from the core to the mantle through the core-mantle boundary (CMB) is critical for understanding the dynamics of solid Earth. Although it is difficult to estimate the CMB heat flux, its history could be reconstructed from geomagnetic reversal frequency. However, overlooked short geomagnetic reversals may exist in the geomagnetic polarity time scale (GPTS), which affects the estimation of the heat flux history. Here, we report four new high-precision 40Ar/39Ar ages of the Oligocene Ethiopian traps. The traps may contain undiscovered reversals in marine magnetic anomaly. Based on the ages, we identified new reversals in Chron C12n, which was not found in marine magnetic anomalies. Our non-parametric analysis of GPTS suggests four potential periods of missing geomagnetic reversals, which correspond to long polarity intervals in GPTS. We found that C12n correspond to one of the periods. This indicates that several undetected reversals may exist within or near the edge of long polarity intervals after the Cretaceous Normal Superchron (prolonged stable polarity period). Considering the undetected reversals, we conclude that the CMB heat flux increased more slowly and monotonically after the Superchron than that ever estimated.
Palau’s warmest reefs harbor a thermally tolerant coral lineage that thrives across different habitats
Authors: Rivera Hanny , Cohen Anne , Thompson Janelle , Baums Iliana , Fox Michael , Meyer Kirstin 
Published: January 2022

Abstract
Ocean warming is killing corals, but heat-tolerant populations exist; if protected, they could replenish affected reefs naturally or through restoration. Palau’s Rock Islands experience chronically higher temperatures and extreme heatwaves, yet their diverse coral communities bleach less than those on Palau’s cooler outer reefs. Here, we combined genetic analyses, bleaching histories and growth rates of Porites cf. lobata colonies to identify thermally tolerant genotypes, map their distribution, and investigate potential growth trade-offs. We identified four P cf. lobata genetic lineages. On Palau’s outer reefs, a thermally sensitive lineage dominates. The Rock Islands harbor two lineages with enhanced thermal tolerance and no consistent growth trade-off. One of these lineages also occurs on several outer reefs. This suggests that the Rock Islands provide naturally tolerant larvae to neighboring areas. Finding and protecting such sources of thermally-tolerant corals is key to reef survival under 21st century climate change.
Impact of urban expansion on continental- to regional-scale warming
Authors: Chakraborty TC , Qian Yun 
Published: January 2022

Abstract
Although the influence of land use/land cover change on climate has become increasingly apparent, cities and other built-up areas are usually ignored when estimating large-scale historical climate change or for future projections since cities cover a small fraction of the terrestrial land surface1,2. As such, ground-based observations of urban near-surface meteorology are rare and most earth system models do not represent historical or future urban land cover3–7. Here, by combining global satellite observations of land surface temperature with historical estimates of built-up area, we demonstrate that the urban temperature signal on continental- to regional-scale warming has become non-negligible, especially for rapidly urbanizing regions in Asia. Consequently, expected urban expansion over the next century suggest further increased urban influence on surface climate under all future climate scenarios. Based on these results, we argue that, in line with other forms of land use/land cover change, urbanization should be explicitly included in future climate change assessments. This would require extensive model development to incorporate urban extent and biophysics in current-generation earth system models to quantify potential urban feedbacks on the climate system at multiple scales.
Association between effector-type regulatory T cells and immune checkpoint expression on CD8+ T cells in malignant ascites from epithelial ovarian cancer
Authors: Sato Sho , Matsushita Hirokazu , Shintani Daisuke , Fujieda Nao , Yabuno Akira , Nishikawa Tadaaki , Fujiwara Keiichi , Kakimi Kazuhiro , Hasegawa Kosei 
Published: January 2022

Abstract
Background

Regulatory T cells (Tregs) play an important role in the antitumor immune response in epithelial ovarian cancer (EOC). To understand the immune-inhibitory networks of EOC, we addressed the association between Tregs and immune checkpoint expression on T cells in the tumor microenvironment of EOC
Methods

A total of 41 patients with stage IIIC and IV EOC were included in the analysis. We harvested cells from malignant ascites and investigated them using multi-color flow cytometry. We categorized the Tregs into 3 groups: effector-type Tregs, naïve Tregs and non-Tregs, based on the expression patterns of CD45RA and Foxp3 in CD4+ T cells. Furthermore, the relationships between the expression of various immune checkpoint molecules, such as PD-1, on CD8+T cells and each of the Treg subtypes was also evaluated.
Results

The median frequency of naïve Tregs, effector-type Tregs and non-Tregs were 0.2% (0-0.8), 2.0% (0-11.4) and 1.5% (0.1-6.3) in CD4+ T cells of malignant ascites from EOC patients, respectively. A high frequency of effector-type Tregs was associated with high-grade serous carcinoma compared with the other histotypes. Patients with higher proportions of effector-type Tregs showed a trend towards increased progression-free survival. We also demonstrated a correlation between a higher proportion of effector-type Tregs and increased PD-1 expression on CD8+ T cells. In addition, C-C chemokine receptor 4 expression was also observed in effector-type Tregs.
Conclusion

These data suggest that multiple immune-inhibitory networks exist in malignant ascites from EOC patients, suggesting an approach towards combinational immunotherapies for advanced EOC patients.
Two Current Systems in the Preliminary Phase of Sudden Commencements in the Magnetosphere
Authors: Fujita Shigeru , Tanaka Takashi 
Published: January 2022

Abstract
The geomagnetic variations of the preliminary impulse (PI) of the sudden commencement (SC) are known to show a time delay of the peak displacement and longer duration time in the higher latitudes in the pre-noon and post-noon sectors of the polar region. This peculiar behavior of the PI geomagnetic variation is associated with temporal deformation of the ionospheric PI field-aligned current (FAC) distribution into a crescent shape; its lower-latitude edge extends toward the anti-sunward direction, and its higher-latitude edge almost stays on the same longitude near noon. Numerical simulations revealed that the deformation of the FAC distribution is derived from different behaviors of the two PI current systems. The first current system consists of the FAC connected to the PI FAC in the lower latitude side of the ionosphere, the cross-magnetopause current, and the magnetosheath current (type L current system). The cross-magnetopause current is the inertia current generated in the acceleration front of the solar wind due to the sudden compression of the magnetosheath. Thus, the longitudinal speed of the type L current system in the ionosphere is the solar wind speed in the magnetosheath projected into the ionosphere. In contrast, the PI current system connected to the PI FAC at higher latitude (type H current system) consists of the upward/downward FAC in the pre-noon/post-noon sector, respectively, and dawn-to-dusk field-perpendicular current (FPC) along the dayside magnetopause. The dawn-to-dusk FPC moves to the higher latitudes in the outer magnetosphere over time. The FAC of the type H current system is converted from the FPC due to convergence of the return FPC heading toward the sunward direction in the outer magnetosphere; the return FPC is the inertia current driven by the magnetospheric plasma flow associated with compression of the magnetopause behind the front region of the accelerated solar wind. The acceleration front spreads concentrically from the subsolar point. Consequently, as the return FPC is converted to the FAC of the type H current system, it does not move much in the longitudinal direction over time because the dawn-to-dusk FPC of the type H current system moves to the higher latitudes. Therefore, the high-latitude edge of the PI current distribution in the ionosphere moves only slightly. Finally, we clarified that the FPC-FAC conversion of the type L current system mainly occurs in the region where the Alfvén speed starts to increase toward the Earth. A region with a steep gradient of the Alfvén speed like the plasmapause is not always necessary for conversion from the FPC to the FAC. We also suggest the possible field-aligned structure of the standing Alfvén wave that may occur in the PI phase.
A 2-Gene Host Signature for Improved Accuracy of COVID-19 Diagnosis Agnostic to Viral Variants
Authors: Albright Jack , Mick Eran , Sanchez-Guerrero Estella , Kamm Jack , Mitchell Anthea , Detweiler Angela , Neff Norma , Tsitsiklis Alexandra , Serpa Paula , Ratnasiri Kalani , Havlir Diane , Kistler Amy , DeRisi Joseph , Pisco Angela Oliveira , Langelier Charles 
Published: January 2022

Abstract
The continued emergence of SARS-CoV-2 variants is one of several factors that may cause false negative viral PCR test results. Such tests are also susceptible to false positive results due to trace contamination from high viral titer samples. Host immune response markers provide an orthogonal indication of infection that can mitigate these concerns when combined with direct viral detection. Here, we leverage nasopharyngeal swab RNA-seq data from patients with COVID-19, other viral acute respiratory illnesses and non-viral conditions (n=318) to develop support vector machine classifiers that rely on a parsimonious 2-gene host signature to predict COVID-19. Optimal classifiers achieve an area under the receiver operating characteristic curve (AUC) greater than 0.9 when evaluated on an independent RNA-seq cohort (n=553). We show that a classifier relying on a single interferon-stimulated gene, such as IFI6 or IFI44, measured in RT-qPCR assays (n=144) achieves AUC values as high as 0.88. Addition of a second gene, such as GBP5, significantly improves the specificity compared to other respiratory viruses. The performance of a clinically practical 2-gene RT-qPCR classifier is robust across common SARS-CoV-2 variants, including Omicron, and is unaffected by cross-contamination, demonstrating its utility for improving accuracy of COVID-19 diagnostics.
The Plasmodium falciparum protein PfMRP1 functions as an influx ABC transporter
Authors: Silva Miguel , Calçada Carla , Osório Nuno , Baptista Vitória , Thathy Vandana , Teixeira Miguel , Reid Adam , Ferreira Pedro , Fidock David , Veiga Maria 
Published: January 2022

Abstract
Adenosine triphosphate (ATP)-binding cassette (ABC) transporters play an important role in mediating solute or drug transport across cellular membranes. Although this class of transporters has been well characterized in diverse organisms little is known about the physiological roles in Plasmodium falciparum, the deadliest malaria parasite species. We studied the Plasmodium falciparum Multidrug Resistance-associated Protein 1 (PfMRP1; PF3D7_0112200), an ABC transporter localized to the parasite plasma membrane, generating genetic disrupted parasites. We demonstrate that parasites with disrupted pfmrp1 are resistant to folate analogs, methotrexate and aminopterin, with antimalarial activity. This phenotype occurs due to reduction in compound accumulation in the parasite cytoplasm. Phylogenetic analysis supports pfmrp1 being distantly related to ABC transporters in other eukaryotes, suggesting an unusual function. We propose that PfMRP1 can act as a solute importer, a function not previously observed in this organism.
Interaction between gene polymorphisms in MLL3 gene and TGF-β signal pathway with the susceptibility of type B aortic dissection in the Chinese population
Authors: Yuan qinghua , Chang Yafei , Jiang Peipei , Sun Ling , Ma Yitong , Ma Xiang 
Published: January 2022

Abstract
Objective: To investigate the impact of MLL3 polymorphisms and Transforming growth factor-β (TGF-β) pathway additional their interactions with type B aortic dissection (AD) risk based on the Chinese population. ﻿Methods: We investigated the MLL3 (rs10244604, rs6963460, rs1137721), TGFβ1 (rs1800469), TGFβ2 (rs900), TGFR1 (rs1626340) and TGFR2 (rs4522809) gene polymorphisms analysis. Logistic regression was performed to investigate the association between 7 SNPs and Type B AD. GMDR software was used to analyze gene-gene and gene-environment interactions. Odds ratio (OR) with a 95% confidence interval (CI) was employed to evaluate the association of genes and Type B AD risk. Results: Genotypes and alleles distribution in case and control groups showed significant differences (P<0.05). Logistic regression has shown that the Type B AD risk was the highest in those with rs1137721 CT genotype, (OR=4.33, 95%CI=1.51-12.40). Meanwhile, WBC, Drinking, Hypertension, TG, and LDL-C were independent risk factors for Type B AD. Respectively, Logistic regression showed that the Type B AD risk was the highest in those with rs1137721-TT+CT and rs4522809-AA genotype (OR=6.72, 95% CI=1.56-29.84), and was lowest in those with rs1137721-CC and rs4522809-AA+GG genotype (OR=4.38, 95%CI=0.92-20.83). However, 55-month median long-term follow-up were not show significant.Conclusion: MLL3 (rs1137721) with TGFβ1 (rs4522809) polymorphisms may be closely related to the development of Type B AD. Inflammation reaction and lipid metabolism were associated with the morbility of Type B AD. Moreover, there exist gene-gene interactions among these susceptibility genes. These may become new diagnostic and research goal for Type B AD.
Poor prognosis of stage I lung adenocarcinoma patients determined by elevated expression over pre/minimally invasive status of COL11A1 and THBS2 in the focal adhesion pathway
Authors: Shi Leming , Shang Jun , Zhao Yue , Jiang He , Yang Jingcheng , Zhang Naixin , Ren Luyao , Chen Qingwang , Yu Ying , Chen Haiquan , Zheng Yuanting 
Published: January 2022

Abstract
Patients with adenocarcinomas in situ (AIS) and minimally invasive (MIA) lung adenocarcinoma (LUAD) are curable by surgery, whereas 20% stage I patients die within five years post-operative. We hypothesize that poor-prognosis stage I patients may exhibit key molecular characteristics deviating from AIS/MIA. Focal adhesion (FA) was identified as the only pathway significantly perturbed at both genomic and transcriptomic levels by comparing 98 AIS/MIA and 99 LUAD. Then, two FA genes (COL11A1 and THBS2) were found strongly upregulated from AIS/MIA to stage I while steadily expressed from normal to AIS/MIA. Furthermore, unsupervised clustering separated stage I patients into two molecularly and prognostically distinct subtypes (S1 and S2) based on COL11A1 and THBS2 expressions (FA2). Subtype S1 resembled AIS/MIA, whereas S2 exhibited more somatic alterations and activated cancer-associated fibroblast. The simple knowledge-driven model was validated with 12 external datasets, showing potential in identifying high-risk stage I patients for more intensive post-surgery treatment.
Mussel-inspired Coating of α-AlH3: A Compact Structure with Highly Enhanced Stability
Authors: Qin Mingna , Yao Bingjie , Shi Qiang , Tang Wang , Chen Shaoli , Guo Tao , Qiu Shaojun , Zhang Yan , Ge Zhongxue 
Published: January 2022

Abstract
we present a novel surfacing coating to resolve the stability of α-AlH3. Inspired by the strong chemical adhesion of mussels, the polymerization of dopamine was first introduced to coat α-AlH3 through a simple situ polymerization. The α-AlH3 was used as a substrate. In-depth characterizations confirmed compact formation with PDA on α-AlH3 surface. The coated α-AlH3 sample was characterized by XRD XPS and SEM . The results show that a strong PDA film is formed on the surface of α-AlH3, the PDA@α-AlH3 retained primary morphology. The crystal form of α-AlH3 does not change after coated by PDA. The results of XPS analysis show that N1s appears on the material after coated by PDA, indicating that polydopamine is formed on the surface of α-AlH3. The moisture absorption tests show that the moisture absorption rate of α-AlH3 is greatly reduced after being coated with PDA. The excellent intact ability of PDA prevent α-AlH3 reacting with watered in the air. The thermal stability of α-AlH3 before and after coating was analyzed by DSC. This work demonstrates the successful applications of dopamine chemistry to α-AlH3, thereby providing a potential method for the metastable materials.
Detection of Face Mask in Real-Time Using Deep Convolutional Networks with Alert System
Authors: S Renugadevi A , B Nihila , A Rakesh , M priyadharshini 
Published: January 2022

Abstract
Owing to the spread of covid-19 in and around all the areas, the people are advised to wear masks regularly, maintain social distancing and to sanitize the hands frequently. But most of the people are not properly following the wearing of masks in all the places including the crowdest areas. While the causes are complicated, there is a widespread belief that there is insufficient evidence to justify the use of face masks, particularly among the general people in a community environment. Detection of face mask is a difficult computer vision research subject due to the tiny size of the face cover region. The availability of appropriate datasets for this problem is rare so the way of finding solution is difficult. Considering all the drawbacks in the existing methodologies, The proposed method uses a innovative dataset that contains the images of masks and also the dataset includes 5,821 images of both the persons with masks and without masks that helps to classify in the different labels such as having mask and does not have mask. The box is bounded over the persons with and without masks. For detection, the system employs the YOLO v4 model, which has been shown to outperform prior versions of the YOLO and RESNET50 models.