bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonreciprocal charge transport in topological kagome superconductor CsV3Sb5
Authors: Wu Yueshen , Wang Qi , Zhou Xiang , Wang Jinghui , Dong Peng , He Jiadian , Ding Yifan , Teng Bolun , Zhang Yiwen , Li Yifei , Zhao Chenglong , Zhang Hongti , Liu Jianpeng , Qi Yanpeng , Watanabe Kenji , Taniguchi Takashi , Li Jun 
Published: November 2022

AbstractNonreciprocal charge transport phenomena are widely studied in two-dimensional superconductors, which demonstrate unidirectional-anisotropy magnetoresistances as a result of symmetry breaking. Here, we report a strong nonreciprocal transport phenomenon in superconducting CsV3Sb5 thin flakes. The second harmonic voltages, mainly originating from the rectification effect of vortex motion, are unambiguously developed with in-plane and out-of-plane magnetic fields, and their magnitudes are comparable to those in noncentrosymmetric superconductors. The second harmonic magnetoresistances split into several peaks and some of them reverse their signs by ramping the magnetic field or the current within the superconducting transition. The nonreciprocity suggests a strong asymmetry in CsV3Sb5. The centrosymmetric structure and symmetric electronic phases in CsV3Sb5 can hardly induce the distinct nonreciprocal transport phenomenon, which could be correlated to a symmetry breaking from an unconventional superconducting order parameter symmetry.
DYNAMIC cohort study evaluating metabolic predictors of influenza vaccine immune response in older adults
Authors: Sadarangani Sapna P. , Young Barnaby E. , Lian Weixiang , Phua Hwee Pin , Chen Mark I.-C. , Barr Ian , Yeo Tsin Wen , Dalan Rinkoo , Chow Angela 
Published: November 2022

AbstractImmunosenescence (age-related immune dysfunction) and inflamm-aging contribute to suboptimal immune responses in older adults to standard-dose influenza vaccines, which may be exacerbated in those with metabolic co-morbidities. We sought to investigate metabolic factors/predictors of influenza vaccine immune response in an older adult (age ≥65 years) cohort in Singapore, where influenza typically circulates year-round. The primary outcome for the DYNAMIC prospective cohort study was haemagglutination-inhibition titer (HAI) response to each of the trivalent inactivated influenza vaccine strains at day 28 (D28) compared to baseline (D0), as assessed by seroconversion and D28/D0 log2 HAI fold rise. Baseline blood samples were tested for total Vitamin D (25-(OH) D) levels. We enrolled 234 participants in June–Dec 2017. Two hundred twenty completed all study visits. The median age was 71 [IQR 68–75] years, 67 (30.5%) had diabetes mellitus (DM), and the median BMI was 24.9 [IQR 22.2–27.8] kg/m2. Median baseline totals 25-(OH) D was 29 [IQR: 21–29] ng/ml. Age, DM, obesity, and baseline 25-(OH) D were not associated with HAI fold rise in multivariable analysis. More recent prior influenza vaccination and higher baseline HAI titers were associated with lower HAI fold rise for influenza A/HK/H3N2. Physical activity was associated with a higher HAI fold rise for influenza A/HK/H3N2 in a dose-response relationship (p-test for trend = 0.015). Older adults with well-controlled metabolic co-morbidities retain HAI response to the influenza vaccine, and physical activity had a beneficial effect on immune response, particularly for influenza A/HK/H3N2.
Exploring the mechanism of andrographolide in the treatment of gastric cancer through network pharmacology and molecular docking
Authors: Yadav Ravi Prakash , Sadhukhan Susanta , Saha Makhan Lal , Ghosh Sudakshina , Das Madhusudan 
Published: November 2022

AbstractGastric cancer has emerged as a key challenge in oncology research as a malignant tumour with advanced stage detection. Apart from surgical management, a pharmacotherapeutic approach to stomach cancer treatment is an appealing option to consider. Andrographolide has been shown to have anticancer and chemosensitizer properties in a variety of solid tumors, including stomach cancer but the exact molecular mechanism is skeptical. In this study, we identified and validated pharmacological mechanism involved in the treatment of GC with integrated approach of network pharmacology and molecular docking. The targets of andrographolide and GC were obtained from databases. The intersected targets between andrographolide and GC-related genes were used to construct protein–protein interaction (PPI) network. Furthermore, mechanism of action of the targets was predicted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Finally, these results were validated by molecular docking experiments, mRNA and protein expression level. A total of 197 targets were obtained for andrographolide treating GC. Functional enrichment analysis revealed that the target genes were exerted promising therapeutic effects on GC by HIF-1 and PI3K-Akt signaling pathway. The possible mechanism of action is by inactivation of HIF-1 signaling pathway which is dependent on the inhibition of upstream PI3K-AKT pathway. The PPI network identified SRC, AKT1, TP53, STAT3, PIK3CA, MAPK1, MAPK3, VEGFA, JUN and HSP90AA1 as potential hub targets. In addition, these results were further validated with molecular docking experiments. Survival analysis indicated that the expression levels of the hub genes were significantly associated with the clinical prognosis of GC. This study provided a novel approach to reveal the therapeutic mechanisms of andrographolide on GC, making future clinical application of andrographolide in the treatment of GC.
Explainable analytics: understanding causes, correcting errors, and achieving increasingly perfect accuracy from the nature of distinguishable patterns
Authors: Pai Hao-Ting , Hsu Chung-Chian 
Published: November 2022

AbstractIn addition to pursuing accurate analytics, it is invaluable to clarify how and why inaccuracy exists. We propose a transparent classification (TC) method. In training, data consist of positive and negative observations. To obtain positive patterns, we find the intersection between each of the two positive observations. The negative patterns are obtained in the same manner. Next, pure positive and pure negative patterns are established by selecting patterns that appear in only one type. In testing, such pure positive and pure negative patterns are used for scoring observations. Next, an observation is classified as positive if its positive score is not zero or if both its positive and negative scores are zero; otherwise, it is classified as negative. By experiment, TC can identify all positive (e.g., malignant) observations at low ratios of training to testing data, e.g., 1:9 using the Breast Cancer Wisconsin (Original) and 3:7 using the Contraceptive Method Choice. Without fine-tuned parameters and random selection, the uncertainty of the methodology is eliminated when using TC. TC can visualize causes, and therefore, prediction errors in a network are traceable and can be corrected. Furthermore, TC shows potential in identifying whether the ground truth is incorrect (e.g., identifying diagnostic errors).
Slope stability analysis considering the strength anisotropy of c-φ soil
Authors: He Yi , Li Zhi , Wang Wenfa , Yuan Ran , Zhao Xiaoyan , Nikitas Nikolaos 
Published: November 2022

AbstractIn traditional slope stability analyses, soil is usually approximated as isotropic. However, naturally cohesive soil deposits are inherently anisotropic, primarily due to the directional arrangement of soil particles during their deposition process. In this paper, a generalized anisotropic constitutive model forc–φsoil is introduced to evaluate the influence of varying shear strength on slope stability. In this model, the initial strength anisotropy is defined by the variety of friction angles to the direction of the principle stress. This model is utilized by two approaches to estimate the slope stability. Firstly, the upper bound limit analysis solution for slope stability is developed, and the safety factor of the slopes is studied. Secondly, this model is coupled with the finite element method to get insight of the influence of anisotropy on slope stability. One typical slope case of slope is studied by numerical analyses. It is found that the slope stability is largely overestimated when the strength anisotropy is ignored, and the overestimation, in terms of safety factors, can reach up to 32.9%. The complex interrelations between the degree of anisotropy and evolution of the ensuing safety factor are revealed by a series of parametric studies in terms of different degrees of anisotropy.
HIV-1 Rev-RRE functional activity in primary isolates is highly dependent on minimal context-dependent changes in Rev
Authors: Dzhivhuho Godfrey , Holsey Jordan , Honeycutt Ethan , O’Farrell Heather , Rekosh David , Hammarskjold Marie-Louise , Jackson Patrick E. H. 
Published: November 2022

AbstractDuring HIV infection, intron-containing viral mRNAs are exported from the cell nucleus to the cytoplasm to complete the replication cycle. Cellular restrictions on the export of incompletely spliced transcripts are overcome by a viral protein, Rev, and an RNA structure found in all unspliced and incompletely spliced viral mRNAs, the Rev Response Element (RRE). Primary HIV isolates display substantial variation in the sequence and functional activity of Rev proteins. We analyzed Rev from two primary isolates with disparate activity that resulted in differences in in vitro fitness of replication-competent viral constructs. The results showed that amino acid differences within the oligomerization domain, but not the arginine-rich motif or the nuclear export signal, determined the level of Rev activity. Two specific amino acid substitutions were sufficient to alter the low-activity Rev to a high-activity phenotype. Other mutations in Rev sequences had unpredictable effects on activity that differed between the two Rev backbones. The sensitivity of Rev function level to small sequence changes likely permits modulation of Rev-RRE activity during HIV infection, which may play a role in pathogenesis. The functional consequences of Rev mutations differed between primary isolates, highlighting the challenge of generalizing studies of Rev conducted using laboratory HIV strains.
A two-step pre-processing tool to remove Gaussian and ectopic noise for heart rate variability analysis
Authors: Saleem Shiza , Khandoker Ahsan H. , Alkhodari Mohanad , Hadjileontiadis Leontios J. , Jelinek Herbert F. 
Published: November 2022

AbstractArtifacts in the Electrocardiogram (ECG) degrade the quality of the recorded signal and are not conducive to heart rate variability (HRV) analysis. The two types of noise most often found in ECG recordings are technical and physiological artifacts. Current preprocessing methods primarily attend to ectopic beats but do not consider technical issues that affect the ECG. A secondary aim of this study was to investigate the effect of increasing increments of artifacts on 24 of the most used HRV measures. A two-step preprocessing approach for denoising HRV is introduced which targets each type of noise separately. First, the technical artifacts in the ECG are eliminated by applying complete ensemble empirical mode decomposition with adaptive noise. The second step removes physiological artifacts from the HRV signal using a combination filter of single dependent rank order mean and an adaptive filtering algorithm. The performance of the two-step pre-processing tool showed a high correlation coefficient of 0.846 and RMSE value of 7.69 × 10–5for 6% of added ectopic beats and 6 dB Gaussian noise. All HRV measures studied except HF peak and LF peak are significantly affected by both types of noise. Frequency measures of Total power, HF power, and LF power and fragmentation measures; PAS, PIP, and PSS are the most sensitive to both types of noise.
Testis-expressed gene 11 inhibits cisplatin-induced DNA damage and contributes to chemoresistance in testicular germ cell tumor
Authors: Kitayama Sachi , Ikeda Kazuhiro , Sato Wataru , Takeshita Hideki , Kawakami Satoru , Inoue Satoshi , Horie Kuniko 
Published: November 2022

AbstractTesticular germ cell tumor (TGCT) is a rare cancer but the most common tumor among adolescent and young adult males. Patients with advanced TGCT often exhibit a worse prognosis due to the acquisition of therapeutic resistance. Cisplatin-based chemotherapy is a standard treatment for advanced TGCTs initially sensitive to cisplatin, as exemplified by embryonal carcinoma. The acquisition of cisplatin resistance, however, could be a fatal obstacle for TGCT management. To identify cisplatin resistance-related genes, we performed transcriptome analysis for cisplatin-resistant TGCT cells compared to parental cells. In two types of cisplatin-resistant TGCT cell models that we established from patient-derived TGCT cells, and from the NEC8 cell line, we found that mRNA levels of the high-mobility-group nucleosome-binding gene HMGN5 and meiosis-related gene TEX11 were remarkably upregulated compared to those in the corresponding parental cells. We showed that either HMGN5 or TEX11 knockdown substantially reduced the viability of cisplatin-resistant TGCT cells in the presence of cisplatin. Notably, TEX11 silencing in cisplatin-resistant TGCT cells increased the level of cleaved PARP1 protein, and the percentage of double-strand break marker γH2AX-positive cells. We further demonstrated the therapeutic efficiency of TEX11-specific siRNA on in vivo xenograft models derived from cisplatin-resistant patient-derived TGCT cells. Taken together, the present study provides a potential insight into a mechanism of cisplatin resistance via TEX11-dependent pathways that inhibit apoptosis and DNA damage. We expect that our findings can be applied to the improvement of cisplatin-based chemotherapy for TGCT, particularly for TEX11-overexpressing tumor.
Selective conversion of methane to cyclohexane and hydrogen via efficient hydrogen transfer catalyzed by GaN supported platinum clusters
Authors: Tan Lida , Su Hui , Han Jingtan , Liu Mingxin , Li Chao-Jun 
Published: November 2022

AbstractNon-oxidative liquefaction of methane at room temperature and ambient pressure has long been a scientific “holy grail” of chemical research. Herein, we exploit an unprecedented catalytic transformation of methane exclusively to cyclohexane and hydrogen evolution through effective surface-hydrogen-transfer (SHT) at the heterojunctions boundary consisting of electron-rich platinum cluster (Pt) loaded on methane-activating gallium nitride (GaN) host. The experimental analysis demonstrates that the interface-induced overall reaction starts with methane aromatization to benzene and surface-bound hydrogen initiated by the Ga–N pairs, followed by the hydrogenation of benzene to cyclohexane with surface-bound hydrogen. The in-situ activated hydrogen at electron-rich metal Pt cluster is crucial for the hydrogenation and enables an outstanding selectivity (up to 92%) and productivity (41 μmol g−1) towards cyclohexane and hydrogen evolution concurrently at 300 °C, which is well-delivered after 5 recycling runs.
Predicting walking-to-work using street-level imagery and deep learning in seven Canadian cities
Authors: Doiron Dany , Setton Eleanor M. , Brook Jeffrey R. , Kestens Yan , McCormack Gavin R. , Winters Meghan , Shooshtari Mahdi , Azami Sajjad , Fuller Daniel 
Published: November 2022

AbstractNew ‘big data’ streams such as street-level imagery are offering unprecedented possibilities for developing health-relevant data on the urban environment. Urban environmental features derived from street-level imagery have been used to assess pedestrian-friendly neighbourhood design and to predict active commuting, but few such studies have been conducted in Canada. Using 1.15 million Google Street View (GSV) images in seven Canadian cities, we applied image segmentation and object detection computer vision methods to extract data on persons, bicycles, buildings, sidewalks, open sky (without trees or buildings), and vegetation at postal codes. The associations between urban features and walk-to-work rates obtained from the Canadian Census were assessed. We also assessed how GSV-derived urban features perform in predicting walk-to-work rates relative to more widely used walkability measures. Results showed that features derived from street-level images are better able to predict the percent of people walking to work as their primary mode of transportation compared to data derived from traditional walkability metrics. Given the increasing coverage of street-level imagery around the world, there is considerable potential for machine learning and computer vision to help researchers study patterns of active transportation and other health-related behaviours and exposures.
IL-1 β gene (+3954 C/T, exon 5, rs1143634) and NOS2 (exon 22) polymorphisms associate with early aseptic loosening of arthroplasties
Authors: López-Anglada Esteban , Collazos Julio , Montes A. Hugo , Pérez-Is Laura , Pérez-Hevia Imanol , Jiménez-Tostado Sergio , Suárez-Zarracina Tomás , Alvarez Victoria , Valle-Garay Eulalia , Asensi Víctor 
Published: November 2022

AbstractAseptic prosthetic loosening (APL) and prosthetic joint infections (PJI) are frequent complications of hip and knee implants. Polymorphisms of cytokines and nitric oxide (NO), key inflammatory molecules in APL and PJI pathogenesis, could explain individual susceptibility to these complications. Three cytokines (IL-1-a, IL-1-β, TNF-α) and two nitric oxide synthase (NOS2, NOS3) genes polymorphisms were genotyped in 77 APL and 117 PJI patients and 145 controls with aseptic hip or knee implants that were implanted for > 16 years. Plasma cytokines and nitrate-nitrite (NOx) levels also were measured. The TT genotype and T allele of (+3954 C/T, exon 5, rs1143634) IL-1β polymorphism were more frequent in APL patients compared to controls (P = 0.03 and P = 0.02, respectively). No genotypic associations in PJI patients were observed. Plasma IL-6, TNF-α and NOx were significantly different between APL and controls (P < 0.0001). Plasma IL-1β and IL-6 were significantly higher in APL T allele carriers vs. non-carriers (P < 0.03). Knee implant (HR 2.488, 95% CI 1.307–4.739, P = 0.005), male gender (HR 2.252, 95% CI 1.121–4.525, P = 0.023), carriages of the TT genotype of the (+3954 C/T) IL-1β polymorphism (HR 3.704, 95% CI 1.274–10.753, P = 0.016) and AA genotype of the (exon 22) NOS2 polymorphism (HR 3.509, 95% CI 1.266–9.709, P = 0.016) were independently associated with a shorter implant survival by Cox regression. No genotypic associations in PJI patients were observed. Genotyping of IL-1β (+3954 C/T, exon 5, rs1143634) and NOS2 (exon 22) polymorphisms could be useful as predictors of early hip or knee APL.
Cost effectiveness analysis of single and sequential testing strategies for tuberculosis infection in adults living with HIV in the United States
Authors: Fekadu Ginenus , Yao Jiaqi , You Joyce H. S. 
Published: November 2022

AbstractTuberculosis infection (TBI) frequently progresses to tuberculosis (TB) disease in people co-infected with human immunodeficiency virus (HIV). We examined the cost-effectiveness of single, sequential and no testing (total 12) strategies of TBI in HIV-infected people from the perspective of US healthcare provider. A decision-analytic model (20-year timeframe) was constructed to simulate TB-related outcomes: Direct medical cost and quality-adjusted life-years (QALYs). In the base-case analysis, the “confirm negative TST followed by QFT-Plus” strategy gained 0.1170 QALY at a total cost of USD3377. In the probabilistic sensitivity analysis of 10,000 Monte Carlo simulations, the probability of “confirm negative TST followed by QFT-Plus” to be accepted as cost-effective was the highest of all 12 strategies when the willingness-to-pay threshold exceeded 2340 USD/QALY. In conclusion, the strategy of “confirm negative TST followed by QFT-Plus” appears to be the preferred cost-effective option for TBI testing in HIV-infected people from the US healthcare provider’s perspective.
A novel refined pyroptosis and inflammasome-related genes signature for predicting prognosis and immune microenvironment in pancreatic ductal adenocarcinoma
Authors: Zuo Jieliang , Yi Chenhe , Chen Zhenmei , Zhou Bo , Yang Tingsong , Lin Jing 
Published: November 2022

AbstractPyroptosis is an inflammatory form of cell death, which plays a key role in the development of auto-inflammation and cancer. This study aimed to construct a pyroptosis and inflammasome-related genes for predicting prognosis of the pancreatic ductal adenocarcinoma (PDAC). This study was based primarily on the one-way analysis of variance, univariate Cox regression analysis, Least absolute shrinkage and selection operator (LASSO) Cox regression, a risk-prognostic signature, gene set variation analysis (GSVA), and immune microenvironment analysis, using PDAC data from The Cancer Genome Atlas and International Cancer Genome Consortium databases for the analysis of the role of 676 pyroptosis and inflammasome-related genes in PDAC retrieved from the Reactome and GeneCards databases. Lastly, we collected six paired PDAC and matched normal adjacent tissue samples to verify the expression of signature genes by quantitative real-time PCR (qRT-PCR). We identified 18 candidate pyroptosis and inflammasome-related genes that differed significantly between pathologic grades (stages) of PDAC patients. The univariate Cox and LASSO analyses pointed to six genes as the best variables for constructing a prognostic signature, including ACTA2, C1QTNF9, DNAH8, GATM, LBP, and NGF. The results of the risk prognostic model indicated that the AUCs at 1, 3, and 5 years were greater than 0.62. GSVA revealed that ‘GLYCOLYSIS’, ‘P53 PATHWAY’, ‘KRAS SIGNALING UP’, and ‘INFLAMMATORY RESPONSE’ hallmark gene sets were associated with the risk score. The high-risk group was associated with poor prognosis and was characterized by a lower infiltration of cells involved in anti-tumor immunity; whereas the low-risk group with higher T cells, NK cells, and macrophages showed relatively better survival and significantly higher upregulation of cytolytic scores and inflammation scores. Additionally, crucial pyroptosis and inflammasome-related genes were further validated by qRT-PCR. Our study revealed the prognostic role of the pyroptosis and inflammasome-related genes in PDAC for the first time. Simultaneously, the biological and prognostic heterogeneity of PDAC had been demonstrated, deepening our molecular understanding of this tumor.
Reference genes expression stability in Avena sativa L. during compatible and incompatible interactions with Puccinia graminis
Authors: Sowa Sylwia , Sozoniuk Magdalena , Toporowska Joanna , Kowalczyk Krzysztof , Paczos-Grzęda Edyta 
Published: November 2022

AbstractA reliable qPCR experiment requires the selection of reference genes with a stable level of expression in a given experimental system. This study attempts to determine the reference genes (RGs) for the A. sativa–P. graminis experimental setup. We evaluated nine candidate reference genes in A. sativa (oat line Pg4 and the cultivar Kasztan) during compatible and incompatible interactions with different pathotypes of Puccinia graminis f. sp. avenae in six time points post-inoculation. The identification of genes with high expression stability was performed by four algorithms (geNorm, NormFinder, BestKeeper and ΔCt method). We found that the most appropriate combination of RGs for RT-qPCR data normalization were HNR (heterogeneous nuclear ribonucleoprotein 27C) + EF1A (elongation factor 1-alpha) + EIF4A (eukaryotic initiation factor 4A-3). The worst candidates for normalization in this dataset were CYP (cyclophilin) and TUA (alpha tubulin). Identified reference genes are suitable candidates for the standardization of gene expression studies in the A. sativa–P. graminis interaction system and potentially other related pathogens. To date, this is the first report of RGs selection in this pathosystem.