bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inclusion of infrared dielectric screening in the GW method from polaron energies to charge mobilities
Authors: Umari Paolo 
Published: July 2022

AbstractWe introduce in the many-body GW scheme the modulation of the screened Coulomb interactionWarising from the macroscopic dielectric response in the infrared. We derive expressions for the polaron binding energies, the renormalization of the effective masses and for the electron and hole relaxation times. Electron and hole mobilities are then obtained from the incorporation of appropriate scattering rules. Zinc-blende GaN and orthorhombic MAPbI3are used as test beds finding fair agreement with results from rigorous electron-phonon coupling approaches. Although limited to polar phonons, our method has a negligible computational cost.
XGBoost model for electrocaloric temperature change prediction in ceramics
Authors: Gong Jie , Chu Sharon , Mehta Rohan K. , McGaughey Alan J. H. 
Published: July 2022

AbstractAn eXtreme Gradient Boosting (XGBoost) machine learning model is built to predict the electrocaloric (EC) temperature change of a ceramic based on its composition (encoded by Magpie elemental properties), dielectric constant, Curie temperature, and characterization conditions. A dataset of 97 EC ceramics is assembled from the experimental literature. By sampling data from clusters in the feature space, the model can achieve a coefficient of determination of 0.77 and a root mean square error of 0.38 K for the test data. Feature analysis shows that the model captures known physics for effective EC materials. The Magpie features help the model to distinguish between materials, with the elemental electronegativities and ionic charges identified as key features. The model is applied to 66 ferroelectrics whose EC performance has not been characterized. Lead-free candidates with a predicted EC temperature change above 2 K at room temperature and 100 kV/cm are identified.
Coloured filters can simulate colour deficiency in normal vision but cannot compensate for congenital colour vision deficiency
Authors: Álvaro Leticia , Linhares João M. M. , Formankiewicz Monika A. , Waugh Sarah J. 
Published: July 2022

AbstractRed-green colour vision deficiency (CVD) affects ~ 4% of Caucasians. Notch filters exist to simulate CVD when worn by colour vision normal (CVN) observers (simulation tools), or to improve colour discrimination when worn by CVD observers (compensation tools). The current study assesses effects of simulation (Variantor) and compensation (EnChroma) filters on performance in a variety of tasks. Experiments were conducted on 20 CVN and 16 CVD participants under no-filter and filter conditions (5 CVN used Variantor; 15 CVN and 16 CVD used EnChroma). Participants were tested on Ishihara and Farnsworth-Munsell 100 hue tests, CVA-UMinho colour discrimination and colour naming tasks and a board-game colour-sorting task. Repeated-measures ANOVAs found Variantor filters to significantly worsen CVN performance, mimicking protanopia. Mixed-model and repeated-measures ANOVAs demonstrate that EnChroma filters do not significantly enhance performance in CVD observers. Key EnChroma results were replicated in 8 CVD children (Ishihara test) and a sub-sample of 6 CVD adults (CVA-UMinho colour discrimination and colour naming tasks) for a smaller stimulus size. Pattern similarity exists across hue for discrimination thresholds and naming errors. Variantor filters are effective at mimicking congenital colour vision defects in CVN observers for all tasks, however EnChroma filters do not significantly compensate for CVD in any.
Association of the triglyceride-glucose index with weight-adjusted appendicular lean mass in Chinese adolescents aged 12–18 years old
Authors: Zhou Jinyu , Bai Ling , Tong Lingling , Jia Leina , Ding Wenqing 
Published: July 2022

AbstractThere is no study exploring the association between triglyceride-glucose (TyG) index and skeletal muscle mass in Chinese adolescents. Therefore, the objective of this study is to explore the association between TyG index and appendicular lean mass (ALM) in Chinese adolescents. In this study, 1336 adolescents (805 boys, 60.25%) aged 12–18 years in China were randomly selected through a stratified cluster sampling. According to the tertiles of TyG index, we separated all participants into three groups, and LM was measured by Bioelectrical Impedance Analysis. The TyG index was negatively related to ALM/weight in Chinese adolescents whether stratified by gender (boys: β = − 0.293; girls: β = − 0.195; all P < 0.001). After adjusting for age and BMI, a significant correlation between the TyG index and ALM/weight was observed only in boys (β = − 0.169, P = 0.001). The highest TyG index tertile was significantly associated with low ALM/weight after adjusting for all covariates in the full sample (OR = 3.04, 95% CI 1.12–8.26, P = 0.029) and boys (OR = 4.68, 95% CI 1.22–17.95, P = 0.025) only in overweight/obese group. Our findings suggested elevated levels of TyG index may be a risk factor of low ALM/weight in Chinese adolescents, especially in boys.
Physiological responses and adaptations to high methane production in Japanese Black cattle
Authors: Kim Minji , Masaki Tatsunori , Ikuta Kentaro , Iwamoto Eiji , Nishihara Koki , Hirai Makoto , Uemoto Yoshinobu , Terada Fuminori , Roh Sanggun 
Published: July 2022

AbstractIn this study, using enteric methane emissions, we investigated the metabolic characteristics of Japanese Black cattle. Their methane emissions were measured at early (age 13 months), middle (20 months), and late fattening phases (28 months). Cattle with the highest and lowest methane emissions were selected based on the residual methane emission values, and their liver transcriptome, blood metabolites, hormones, and rumen fermentation characteristics were analyzed. Blood β-hydroxybutyric acid and insulin levels were high, whereas blood amino acid levels were low in cattle with high methane emissions. Further, propionate and butyrate levels differed depending on the enteric methane emissions. Hepatic genes, such as SERPINI2, SLC7A5, ATP6, and RRAD, which were related to amino acid transport and glucose metabolism, were upregulated or downregulated during the late fattening phase. The above mentioned metabolites and liver transcriptomes could be used to evaluate enteric methanogenesis in Japanese Black cattle.
Oncogenic role and potential regulatory mechanism of topoisomerase IIα in a pan-cancer analysis
Authors: Wang Xiaobo , Wang Jinhua , Lyu Li , Gao Xin , Cai Yinuo , Tang Bo 
Published: July 2022

AbstractTopoisomerase IIα (TOP2A) plays an oncogenic role in multiple tumor types. However, no pan-cancer analysis about the function and the upstream molecular mechanism of TOP2A is available. For the first time, we analyzed potential oncogenic roles of TOP2A in 33 cancer types via The Cancer Genome Atlas (TCGA) database. Overexpression of TOP2A was existed in almost all cancer types, and related to poor prognosis and advanced pathological stages in most cases. Besides, the high frequency of TOP2A genetic alterations was observed in several cancer types, and related to prognosis in some cases. Moreover, we conduct upstream miRNAs and lncRNAs of TOP2A to establish ceRNA networks in kidney renal clear cell carcinoma (SNHG3-miR-139-5p), kidney renal papillary cell carcinoma (TMEM147-AS1/N4BP2L2-IT2/THUMPD3-AS1/ERICD/TTN-AS1/SH3BP5-AS1/THRB-IT1/SNHG3/NEAT1-miR-139-5p), liver hepatocellular carcinoma (SNHG3/THUMPD3-AS1/NUTM2B-AS1/NUTM2A-AS1-miR-139-5p and SNHG6/GSEC/SNHG1/SNHG14/LINC00265/MIR3142HG-miR-101-3p) and lung adenocarcinoma (TYMSOS/HELLPAR/SNHG1/GSEC/SNHG6-miR-101-3p). TOP2A expression was generally positively correlated with cancer associated fibroblasts, M0 and M1 macrophages in most cancer types. Furthermore, TOP2A was positively associated with expression of immune checkpoints (CD274, CTLA4, HAVCR2, LAG3, PDCD1 and TIGIT) in most cancer types. Our first TOP2A pan-cancer study contributes to understanding the prognostic roles, immunological roles and potential upstream molecular mechanism of TOP2A in different cancers.
Amelioration for an ignored pitfall in reference gene selection by considering the mean expression and standard deviation of target genes
Authors: Esfandiarpour Ghazal , Mokhtari Mohammad , Javadirad Seyed-Morteza , Kolahdouzan Mohsen , Almuslimawi Ahmed 
Published: July 2022

AbstractRoutine tissue-specific reference genes are often used in expression studies, but target genes are not taken into account. Using the relative RT-qPCR approach, we evaluated the expression of three target genes. At the same time, meta-analyses were conducted in various ethnic groups, genders, and thyroid cancer subtypes. When eight common reference genes were examined, it was discovered that some of them not only lacked consistent expression but also had considerable expression variance. It is worth noting that while choosing a reference gene, the mean gene expression and its standard deviation should be carefully addressed. An equation was developed based on this, and it was used to perform statistical analysis on over 25,000 genes. According to the subtype of thyroid cancer and, of course, the target genes in this investigation, appropriate reference genes were proposed. The intuitive choice of GAPDH as a common reference gene caused a major shift in the quantitative expression data of target genes, inverting the relative expression values. As a result, choosing the appropriate reference gene(s) for quantification of transcription data, and especially for relative studies of the expression of target gene(s), is critical and should be carefully considered during the study design.
Characteristics and mortality of 561,379 hospitalized COVID-19 patients in Germany until December 2021 based on real-life data
Authors: Kloka Jan Andreas , Blum Lea Valeska , Old Oliver , Zacharowski Kai , Friedrichson Benjamin 
Published: July 2022

AbstractThe ongoing SARS-CoV-2 pandemic is characterized by poor outcome and a high mortality especially in the older patient cohort. Up to this point there is a lack of data characterising COVID-19 patients in Germany admitted to intensive care (ICU) vs. non-ICU patients. German Reimbursement inpatient data covering the period in Germany from January 1st, 2020 to December 31th, 2021 were analyzed. 561,379 patients were hospitalized with COVID-19. 24.54% (n = 137,750) were admitted to ICU. Overall hospital mortality was 16.69% (n = 93,668) and 33.36% (n = 45,947) in the ICU group. 28.66% (n = 160,881) of all patients suffer from Cardiac arrhythmia and 17.98% (n = 100,926) developed renal failure. Obesity showed an odds-ratio ranging from 0.83 (0.79–0.87) for WHO grade I to 1.13 (1.08–1.19) for grade III. Mortality-rates peaked in April 2020 and January 2021 being 21.23% (n = 4539) and 22.99% (n = 15,724). A third peak was observed November and December 2021 (16.82%, n = 7173 and 16.54%, n = 9416). Hospitalized COVID-19 patient mortality in Germany is lower than previously shown in other studies. 24.54% of all patients had to be treated in the ICU with a mortality rate of 33.36%. Congestive heart failure was associated with a higher risk of death whereas low grade obesity might have a protective effect on patient survival. High admission numbers are accompanied by a higher mortality rate.
Dissecting the roles of Haspin and VRK1 in histone H3 phosphorylation during mitosis
Authors: Cartwright Tyrell N. , Harris Rebecca J. , Meyer Stephanie K. , Mon Aye M. , Watson Nikolaus A. , Tan Cheryl , Marcelot Agathe , Wang Fangwei , Zinn-Justin Sophie , Traktman Paula , Higgins Jonathan M. G. 
Published: July 2022

AbstractProtein kinases that phosphorylate histones are ideally-placed to influence the behavior of chromosomes during cell division. Indeed, a number of conserved histone phosphorylation events occur prominently during mitosis and meiosis in most eukaryotes, including on histone H3 at threonine-3 (H3T3ph). At least two kinases, Haspin and VRK1 (NHK-1/ballchen in Drosophila), have been proposed to carry out this modification. Phosphorylation of H3 by Haspin has defined roles in mitosis, but the significance of VRK1 activity towards histones in dividing cells has been unclear. Here, using in vitro kinase assays, KiPIK screening, RNA interference, and CRISPR/Cas9 approaches, we were unable to substantiate a direct role for VRK1, or its paralogue VRK2, in the phosphorylation of threonine-3 or serine-10 of Histone H3 in mitosis, although loss of VRK1 did slow cell proliferation. We conclude that the role of VRKs, and their more recently identified association with neuromuscular disease and importance in cancers of the nervous system, are unlikely to involve mitotic histone kinase activity. In contrast, Haspin is required to generate H3T3ph during mitosis.
Identification of pyroptosis-related long non-coding RNAs with prognosis and therapy in lung squamous cell carcinoma
Authors: Zhang Yi , Wang Yuzhi , Yin Xiaoqing , Huang Yi 
Published: July 2022

AbstractPyroptosis is a type of programmed cell death with an intense inflammatory response. Previous studies have shown that pyroptosis plays an important role in the pathogenesis and progression of lung cancer. However, the prognostic value and drug targets of pyroptosis-related lncRNAs in lung squamous cell carcinoma (LSCC) have never been studied. In the present study, we identified 1468 pyroptosis-related lncRNAs in LSCC by performing Pearson correlation analysis between the pyroptosis-related genes and the lncRNAs from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. The whole set was divided into a training and a test set with a 1:1 ratio. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) analyses were conducted to establish an 11 multilncRNA signature in the three sets. The signature divided LSCC patients into the low-risk and the high-risk groups. Kaplan–Meier analysis and receiver operating characteristic (ROC) indicated that the prognostic signature had a promising predictive capability for LSCC patients. Besides, the association of microenvironment and immunotherapy response with signature was also analyzed. Moreover, 28 potential compounds targeting signature were screened as possible drugs to treat LSCC. Finally, a nomogram model was constructed to offer the quantitative prediction and net benefit for the prognosis of LSCC patients. In conclusion, the 11 pyroptosis-related lncRNAs and their signature may be promising prognostic factors and therapeutic targets for patients with LSCC.
The efficiency of a clinical pathway to guide combined applications of interventional pulmonology in undiagnosed pleural effusions
Authors: Liu Yuan , Geng Lili , Xu Jian , Sun Mei , Gao Na , Zhao Jing , Han Xue , Zhang Xiaolin , Zhao Xiaohui , Jiang Ling , Zhao Junjun 
Published: July 2022

AbstractThe diagnostic procedure of pleural effusion (PEs) is challenging due to low detection rates and numerous aetiologies. Hence, any attempt to enhance diagnosis is worthwhile. We present a clinical pathway to guide combined application of interventional pulmonology (IP) for tracing causes of undiagnosed PEs. Subjects with undiagnosed PEs were identified in the Hospital Information System of Dalian Municipal Central Hospital from January 1, 2012, to December 31, 2018. Eligible subjects were divided into a group of combined tests and a group of medical thoracoscopy (MT). Optimal and subsequent diagnostic tests were performed depending on the guidance of the clinical pathway by matching profitable chest lesions with the respective adaptation. As the guidance of clinical pathway, common bronchoscopy would be preferentially selected if pulmonary lesions involved or within the central bronchus, EBUS-TBNA was favoured when pulmonary lesions were adjacent to the central bronchus or with the enlarged mediastinal/hilar lymph nodes, guided bronchoscopy would be preferred if pulmonary nodules/masses were larger than 20 mm with discernible bronchus signs, CT-assisted transthoracic core biopsy was preferred if pulmonary nodules were less than 20 mm, image guided cutting needle biopsy was the recommendation if the pleural thickness was larger than 10 mm and pulmonary lesions were miliary. MT was preferred only when undiagnosed PEs was the initial symptom and pulmonary lesions were miliary or absent. A total of 83.57% cases of undiagnosed PEs were eligible for the clinical pathway, and 659 and 216 subjects were included in the combined tests and MT groups, respectively, depending on the optimal recommendation of the clinical pathway. The total diagnostic yields in the combined tests and MT groups were 95.99% and 91.20%, respectively, and the difference in total diagnostic yield was statistically significant (χ2 = 7.510, p = 0.006). Overall, clinical pathway guidance of the combined application of IP is useful for tracing the causes of undiagnosed PEs. The diagnostic yield of undiagnosed PEs is significantly increased compared with that of MT alone.
Resting-state functional connectivity of salience network in schizophrenia and depression
Authors: Huang Huan , Chen Cheng , Rong Bei , Wan Qirong , Chen Jingang , Liu Zhongchun , Zhou Yuan , Wang Gaohua , Wang Huiling 
Published: July 2022

AbstractTo explore the salience network (SN) functional alterations in schizophrenia and depression, resting-state functional magnetic resonance imaging (rs-fMRI) data from 29 patients with schizophrenia (SCH), 28 patients with depression (DEP) and 30 healthy controls (HC) were obtained. The SN was derived from data-driven group independent component analysis (gICA). ANCOVA and post hoc tests were performed to discover the FC differences of SN between groups. The ANCOVA demonstrated a significant group effect in FC with right inferior and middle temporal gyrus (ITG and MTG), left caudate, and right precentral gyrus. Post-hoc analyses revealed an opposite altered FC pattern between SN and right ITG and MTG for both patient groups. The DEP group showed a reduced FC between SN and right ITG and MTG compared with HC whereas the SCH group showed an increased FC. In addition, the SCH group showed decreased FC between SN and left caudate, and enhanced FC between SN and right precentral gyrus compared to the other two groups. Our findings suggest distinct FC of SN in schizophrenia and depression, supporting that the resting-state FC pattern of SN may be a transdiagnostic difference between depression and schizophrenia and may play a critical role in the pathogenesis of these two disorders.
Comparing methods for immobilizing HIV-1 SOSIPs in ELISAs that evaluate antibody binding
Authors: Dam Kim-Marie A. , Mutia Patricia S. , Bjorkman Pamela J. 
Published: July 2022

AbstractEnzyme-linked immunosorbent assays (ELISAs) are used to evaluate binding of broadly neutralizing antibodies (bNAbs) and polyclonal sera to native-like HIV-1 Env SOSIPs. Methods for immobilizing SOSIPs on plates differ, which can lead to variable or, in some cases, misleading results. Three methods used to immobilize SOSIPs were compared to determine how antigen immobilization methods affect Env conformation and ELISA results. HIV-1 SOSIPs were directly coated on polystyrene plates, captured by a monoclonal antibody against a C-terminal affinity tag, or randomly biotinylated and coated on a streptavidin plate. Binding of bNAbs with known epitopes were compared for each immobilization method. Binding of bNAbs targeting the V1V2, V3, CD4 binding site, and gp120/gp41 interface was comparable for all antigen immobilization methods. However, directly coated HIV-1 SOSIP ELISAs showed detectable binding of 17b, a CD4-induced antibody that binds a V3 epitope that is concealed on closed prefusion Env trimers in the absence of added CD4, whereas antibody-immobilized and randomly biotinylated Env-coated ELISAs did not show detectable binding of 17b in the absence of CD4. We conclude direct coating of HIV-1 SOSIPs on ELISA plates can result in exposure of CD4-induced antibody epitopes, suggesting disruption of Env structure and exposure of epitopes that are hidden in the closed, prefusion trimer.
Cardiovascular changes after pneumonia in a dual disease mouse model
Authors: Bartlett Benjamin , Ludewick Herbert P. , Verma Shipra , Corrales-Medina Vicente F. , Waterer Grant , Lee Silvia , Dwivedi Girish 
Published: July 2022

AbstractResidual inflammation in cardiovascular organs is thought to be one of the catalysts for the increased risk of cardiovascular complications seen following pneumonia. To test this hypothesis, we investigated changes in plaque characteristics and inflammatory features in ApoE−/− mouse aorta and heart following pneumonia. Male ApoE−/− mice were fed a high fat diet for 8 weeks before intranasal inoculation with either Streptococcus pneumoniae serotype 4 (test group) or phosphate buffered saline (control group). Mice were sacrificed at 2-, 7- and 28-days post-challenge. Changes in plaque burden and characteristics in aortic root and thoracic aorta were characterized by Oil red O and Trichrome stains. Inflammatory changes were investigated by FDG-PET imaging and immunofluorescence staining. We found TIGR4-infected mice present with increased plaque presence in the aortic root and thoracic aorta at 2- and 28-days post-inoculation, respectively. Aortic wall remodelling was also more pronounced in mice challenged with pneumococci at 28 days post-inoculation. Aortic root plaques of infected mice had reduced collagen and smooth muscle cells, consistent with an unstable plaque phenotype. Pneumonia alters plaque burden, plaque characteristics, and aortic wall remodelling in ApoE−/− mice. These effects caused by Streptococcus pneumoniae TIGR4, may contribute to the increased risk of cardiovascular complications seen in survivors of this infection.
Ergodic capacity analysis of multiple IRS‐aided dual‐hop DF relaying system
Authors: Qian Panpan , Sun Qiang , Zhang Zihan , Zhao Huan 
Published: July 2022

AbstractIntelligent reflecting surface (IRS) is regarded as a promising emerging technology, which has shown enormous potentials for performance enhancement. This paper investigates the multiple IRS‐aided dual‐hop DF relaying system for both single‐user and multi‐user scenarios over Nakagami‐m fading. Based on a scenario with non‐orthogonal multiple access users, tight upper bounds for the ergodic capacity in perfect channel state information(pCSI) scenario are first derived, and then approximate expressions are obtained in imperfect CSI (ipCSI) mode. Moreover, the performance of multiple IRS‐aided DF relaying system are compared with multi‐IRSs‐only system and DF relaying‐only system. Finally, all the analytical results are verified using Monte Carlo simulations.
On the achievable secrecy transmission rates by Alamouti space‐time block coding in time‐selective fading channels
Authors: Kim Dongjin , Kwon Girim , Lee Hoojin , Chae Seong Ho 
Published: July 2022

AbstractIn this letter, the authors study the security performance of Alamouti space‐time block coding (STBC) with two different linear detection strategies, linear maximum likelihood (LML) and zero‐forcing (ZF), over time‐selective Rayleigh fading channels. Specifically, the connection and secrecy outage probabilities for general temporal correlation when the legitimate receiver and eavesdropper adopt the LML and ZF detectors are first derived. Then the secrecy transmission rates for various combinations of LML and ZF detectors at the legitimate receiver and eavesdropper are derived. The authors also found that the optimal control of the codeword rate and secrecy rate can maximize the secrecy transmission rates.