bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metagenomic Analysis Reveals Associations between Salivary Microbiota and Body Composition in Early Childhood
Authors: Coker Modupe , Lebeaux Rebecca , Hoen Anne , Moroishi Yuka , Gilbert-Diamond Diane , Dade Erika , Palys Thomas , Madan Juliette , Karagas Margaret 
Published: September 2021

Abstract
Several studies have shown that body mass index is strongly associated with differences in gut microbiota, but the relationship between body weight and oral microbiota is less clear. Among more than 200 toddlers in the New Hampshire Birth Cohort Study, we characterized the association between multiple anthropometric measures of body mass/growth longitudinally and used shotgun metagenomics to taxonomically and functionally profile the oral microbiome. We found that within-sample diversity was inversely related to body mass measurements while community composition was not associated. Certain taxa were consistently associated with growth and modified by sex. Functional examination also showed concordance between microbial metabolic pathways and child growth metrics. Further exploration of the functional significance of this relationship will enhance our understanding of the intersection between weight gain, microbiota, and energy metabolism and the potential role of these relationships on the onset of obesity-associated diseases in later life.
Multiple Sites of Thrombosis Without Thrombocytopenia After a Second Dose of Pfizer-BioNTech COVID-19 Vaccine
Authors: Scendoni Roberto , Petrelli Cristina , Giustozzi Mauro , Logullo Francesco Ottavio 
Published: September 2021

Abstract
BackgroundIn the current international scientific panorama rare cases of venous thrombotic complications following mRNA vaccine administration have been reported, consisting of cerebral sinus thromboses and acute venous thromboembolism. Case presentationThe present paper describes the case of a 75-year-old woman in good health who developed cerebral venous thrombosis (CVT), deep venous thrombosis (DVT) and bilateral pulmonary emboli (PE) after receiving a second dose of Pfizer-BioNTech COVID-19 vaccine. A series of laboratory tests performed during the hospitalization yielded interesting results, allowing us to exclude thrombophilic risk factors and certify the absence of thrombocytopenia in the patient.ConclusionAlthough COVID-19 vaccination is the most important tool in stopping the pandemic, pharmacovigilance is crucial for detecting potential multisystem thrombotic events, even for mRNA vaccines.
Effect of Microwave Heating On The Mechanical Properties and Energy Dissipation Characteristics of Hard Rock
Authors: Yang Jianming , Liu Jiantian , Guo Hongchen , LI Qingwen , Wang Wei 
Published: September 2021

Abstract
To study the effect of microwave on the weakening mechanism of hard rock, uniaxial compression tests were conducted on granite samples after microwave treatment, and an acoustic emission system was established to monitor the fracture evolution in such rock samples. The effects of microwave irradiation on the stress-strain curve, acoustic emission characteristics, and energy dissipation characteristics of granite were investigated in the experiment. The results show that: 1) With the continuous increase of microwave irradiation power and time, the compaction stage and crack development stage of the sample gradually increase, and the elastic stage gradually becomes shorter; the trend of post-peak stress drop becomes slower, changing from “cliff type” to multi-step type “. The failure of the sample indicates that they become less brittle and more ductile; 2) Microwave irradiation reduces the strength. The overall acoustic emission count rate is weak before the peak and increases rapidly near the peak. The count rate has also changed from sparse to dense, and with the increase in the irradiation power and time, the total acoustic emission count rate increases; 3) From the energy point of view, the weakening of granite by microwave irradiation will not only decrease the energy-storage limit of granite and increase the proportion of dissipated energy in the failure process, but also decrease the rate of release of elastic energy after the peak. Therefore, microwave irradiation will not only reduce the mechanical energy dissipated during damage, but also reduce the intensity of potential dynamic disasters.
Q-Mer Analysis: A Generalized Method for Analyzing RNA-Seq Data
Authors: Shoji Tatsuma , Sato Yoshiharu 
Published: September 2021

Abstract
Background: RNA-Seq data are usually summarized by counting the number of transcript reads aligned to each gene. However, count-based methods do not take alignment information, where and how each read was mapped in the gene, into account. This information is essential to characterize samples accurately. In this study, we developed a method to summarize RNA-Seq data without losing alignment information. Results: To include alignment information, we introduce “q-mer analysis,” which summarizes RNA-Seq data with 4q kinds of q-length oligomers. Using publicly available RNA-Seq datasets, we demonstrate that at least q ≧ 9 is required for capturing alignment information in Homo sapiens. It should be noted that 49 = 262,144 is approximately 10 times larger than the number of genes in H. sapiens (20,022 genes). Furthermore, principal component analysis showed that q-mer analysis with q = 14 linearly distinguished samples from controls, while a count-based method failed. These results indicate that alignment information is essential to characterize transcriptomics samples. Conclusions: In conclusion, we introduce q-mer analysis to include alignment information in RNA-Seq analysis and demonstrate the superiority of q-mer analysis over count-based methods in that q-mer analysis can distinguish case samples from controls. Combining RNA-Seq research with q-mer analysis could be useful for identifying distinguishing transcriptomic features that could provide hypotheses for disease mechanisms.
Exploring ALDH2 Expression and Its Immune Infiltration in HNSC and Its Prognositic Correlation With Gender or Alcohol Intake
Authors: Yao Senbang , Yin Xiangxiang , Chen Tingting , Chen Wenjun , Zuo He , Bi Ziran , Zhang Xiuqing , Jing Yanyan , Pang Lulian , Cheng Huaidong 
Published: September 2021

Abstract
Aldehyde dehydrogenase 2 (ALDH2) point mutation ALDH2*2 is the common frequent human gene variant, espically in East Asians. However, nothing is known about their expression and mechanism of action in HNSC. This research tried to explore the clinical significance and immune characteristics of ALDH2 in HNSC. The receiver operating characteristic (ROC) curve was analysed to assessment the diagnostic value of ALDH2 expression. ALDH2 expression in normal tissues and HNSC tissues were evaluated by IHC. Also we analyzed ALDH2 gene expression in 4 HNSC cell lines. ALDH2 expression was significantly reduced in HNSC tissues (p< 0.05). HNSC patients with highly expressed ALDH2 have a better prognosis (p< 0.05). Then, GSEA analysis result pointed that these gene sets were connected with signaling pathways including JAK-STAT signaling pathway. We unexpectedly found a significant prognostic effect of ALDH2 in alcohol consumption and male HNSC patients. The correlation between ALDH2 expression and immunoinhibitors showed a effect for ALDH2 in modifying tumor immunology in HNSC and there may be a possible mechanism by which ALDH2 regulates functions of T cell in HNSC. We developed a nomogram prognostic model for HNSC patients. Moreover, low ALDH2 expression was a poor prognostic factor in male alcoholics of HNSC.
Ultrasonic Diagnostic Strategy for the Causes of Coronary Artery Dilatation in Infants
Authors: Hu Jinling , Ren Weidong 
Published: September 2021

Abstract
Objective:To explore a differential diagnosis strategy for the causes of coronary artery dilatation (CAD) in infants．Methods: Clinical and echocardiography data for 243 infants with CAD from the Shengjing Hospital of China Medical University were analyzed retrospectively. The patients were divided into congenital and acquired groups according to the CAD causes.Results: The lesion detection rate for CAD in 22,925 infants who underwent echocardiography was 1.06% (243/22,925). The acquired group accounted for 84.77% (206/243) of participants, all of which had Kawasaki disease. The congenital group accounted for 15.23% (37/243) of patients, including coronary artery fistula [12.35% (30/243)], anomalous origin of the coronary artery [2.06% (5/243)], severe pulmonary stenosis [0.41% (1/243)], and moderate aortic stenosis [0.41% (1/243)]. There was no significant difference in the Z-score for CAD between the two groups of children (P>0.05). There were differences in the scope and shape of CAD between the two groups (all P<0. 05). Acquired causes mainly manifested as segmental dilatation, while congenital causes manifested as tubular dilatation. The sensitivity and specificity of segmental dilatation in predicting acquired causes were 97.57% and 100%, respectively, and that of tubular dilatation in predicting congenital causes were 97.30% and 98.06%, respectively. Conclusion: It is particularly important to diagnose the cause of CAD because its treatment depends on its etiology. When an echocardiography examination identifies CAD in infants, comprehensive and systematic analysis can quickly and accurately determine the cause of CAD according to the diagnostic strategy process and evaluation of dilatation and cardiac structure characteristics.
A Comparative Study of the Chloroplast Genomes of Five Lepidium Medicinal Plants
Authors: Zhou Qian , Chen Yun , Li Mingyuan , Zeng Weijun , Wang Jilian , Wang Yuzhou , Li Yanhong , Zhao Huixin 
Published: September 2021

Abstract
Background

Herb genomics is a rapidly developing field of medicinal plant research and development. Plant genomic studies demonstrate the unique advantage of employing plants in medicinal therapy. The genus Lepidium falls under the Brassicaceae family and it includes crucial medicinal plants. Herein, we sequenced the complete chloroplast (cp) genomes of Lepidium apetalum (LA) and Lepidium perfoliatum (LP) and assessed their genetic profiles against the reported profiles of Lepidium sativum (LS), Lepidium meyenii (LM), and Lepidium virginicum (LV).
Results

In particular, we examined genomic arrangement, gene number, type, and repeat sequences. Based on our annotation data, both LA and LP possessed 130 distinct genes that included 85 protein-coding, 37 transfer RNA (tRNA), and 8 ribosomal RNA (rRNA) genes. Our repeat analyses revealed that LA harbored 20 forward repeats, 16 palindrome repeats, 30 tandem repeats, and 87 simple sequence repeats, whereas LP had 15 forward repeats, 20 palindrome repeats,4 reverse repeats, 21 tandem repeats, and 98 simple sequence repeats. Using syntenic analysis, we also revealed a high degree of sequence similarity within the coding regions of Lepidium cp genomes and a remarkably high degree of divergence among the intergenic spacers. Pairwise alignment and single-nucleotide polymorphism (SNP) examinations further revealed certain Lepidium-specific gene fragments, particularly in the intergenic regions of the trnK-atpA, trnC-psbC, trnT-rbcL, ndhF-ndhH, ycf1-trnR, accD, ccsA, matK, ndhF, rpoB, rpoC2, and ycf1 genes. Moreover, following codon usage analysis, we observed that codon 14 was the most frequently used codon in the Lepidium CDS. In addition, correlation investigations revealed that the ENC (the effective number of codon) content was strongly associated with GC3, GC3s, and N.
Conclusion

Based on these data, LA and LP originate from very similar genetic backgrounds. Furthermore, neutrality, ENC, and PR2-plots analyses demonstrated that the CUB (the codon usage bias) of Lepidium cp genome was strongly influenced by mutation and natural selection. Our analysis of the cp genomic sequences of LA and LP will likely enhance breeding, species recognition, phylogenetic evolution, and cp genetic engineering of the Lepidium medicinal plants.
Seismic Site Response of A Large Deep-seated Rock Slope Revealed by Field Monitoring and Geophysical Methods
Authors: Wang Hui , Cui Shenghua , Pei Xiangjun , Zhu Ling , Yang Qingwen , Huang Runqiu 
Published: September 2021

Abstract
Shidaguan Slope (hereinafter short for SDG Slope) is an unstable rock slope with an area of 30.78×104 m2 and a deformation depth of 30-70 m in Maoxian County, Sichuan Province, China. Three seismometers (P2-P4) with high sensitivity were installed at different locations on the unstable part of the slope. P2 and P3 were almost at the same elevation (2221 m and 2247 m), while P4 was the lowest (at 2140 m). Another seismometer (P1) sat in a stable location at a higher elevation (2373 m). 99 shallow earthquakes were analyzed. According to the peak acceleration ratios of three seismometers (P2-P4) on the unstable part and another seismometer (P1) on the stable part, the points at lower elevations showed greater seismic amplification (with the amplification coefficient of 2.64-3.51) than one at a higher elevation. And points at relatively thinner part (23 m thick) of unstable slope showed greater seismic amplification than ones at thick part (60-75 m thick). The same rule was also found in studying the site-epicenter azimuth and earthquake magnitude data. Based on the relationship between amplification coefficient and resistivity and rock core, the seismic response amplification was affected by the lithofacies difference. The lithofacies with resistivity values of 50-100 Ohm.m and RQD values of 0-50 % incurred seismic response amplification, which was restrained by the below lithofacies with resistivity values of 10-50 Ohm.m and ROD values of 0 %. When building on slope areas, the lithofacies difference should be taken into full consideration.
Estimating Malaria Attributable Fractions With Changing Transmission Intensity: Bayesian Latent Class Vs Logistic Models
Authors: Mwai Kennedy , Nkumama Irene , Thairu Amos , Mburu James , Odera Dennis , Kimathi Rinter , Nyamako Lydia , Tuju James , Kinyanjui Samson , Musenge Eustasius , Osier Faith 
Published: September 2021

Abstract
Background Asymptomatic carriage of malaria parasites is common in high transmission intensity areas and confounds clinical case definitions for research studies. This is important for investigations that aim to identify immune correlates of protection from clinical malaria. The proportion of fevers attributable to malaria parasites is widely used to define different thresholds of parasite density associated with febrile episodes. We investigated whether varying intensity of malaria transmission had a significant impact on parasite density thresholds. We used the same dataset to explore an alternative statistical approach using the probability of developing fevers as a choice over threshold cut-offs as the former has been reported to increase predictive power. Methods Data from children monitored longitudinally between 2005 and 2017 from Junju and Chonyi in Kilifi, Kenya were analysed. We compare the performance of Bayesian-latent class and logistic power models in estimating malaria attributable fractions and probabilities of having fever given a parasite density with changing malaria transmission intensity. Zero-inflated beta regressions were used to assess the impact of using probabilities to evaluate anti-merozoite antibodies as correlates of protection compared with multilevel binary regression.ResultsMalaria transmission intensity declined from over 49% to 5% between 2006 and 2017 respectively. During this period, malaria attributable fraction varied between 27%-59% using logistic regression compared to 10%-36% using the Bayesian latent class approach. Both models estimated similar patterns of fevers attributable to malaria with changing transmission intensities. The former performed well in estimating the probabilities of having fever, while the latter was efficient in determining the parasite density threshold. However, compared to the logistic power model, the Bayesian algorithm yielded lower estimates for both attributable fractions and probabilities of fever. In modelling the association of merozoite antibodies and clinical malaria, both approaches resulted in comparable estimates, but the utilization of probabilities had a better statistical fit. ConclusionsMalaria attributable fractions varied with an overall decline in the malaria transmission intensity in this setting but did not significantly impact the outcomes of analyses aimed at identifying immune correlates of protection. These data confirm the statistical advantage of using probabilities over binary data.
Empagliflozin Restores Cardiac Metabolic Flexibility in Diet-induced Obese C57BL6/J Mice
Authors: Xie Bingxian , Ramirez Wesley , Mills Amanda M. , Huckestein Brydie R. , Anderson Moira , Pangburn Martha M. , Lang Eric Y. , Mullet Steven J. , Chuan Byron W. , Guo Lanping , Sipula Ian , O’Donnell Christopher P. , Wendell Stacy G. , Scott Iain , Jurczak Michael 
Published: September 2021

Abstract
BackgroundSodium-glucose co-transporter type 2 (SGLT2) inhibitor therapy to treat type 2 diabetes unexpectedly reduced all-cause mortality and hospitalization due to heart failure in several large-scale clinical trials, and has since been shown to produce similar cardiovascular disease-protective effects in patients without diabetes. How SGLT2 inhibitor therapy improves cardiovascular disease outcomes remains incompletely understood. Metabolic flexibility refers to the ability of a cell or organ to adjust its use of metabolic substrates, such as glucose or fatty acids, in response to physiological or pathophysiological conditions, and is a feature of a healthy heart that may be lost during diabetic cardiomyopathy and in the failing heart. While several studies have addressed metabolic changes in hearts in response to SGLT2 inhibitor therapy, none have specifically assessed metabolic flexibility in an in vivo system. We therefore undertook the described studies to determine the effects of SGLT2 inhibitor therapy on cardiac metabolic flexibility in vivo in obese, insulin resistant mice.MethodsDiet-induced obese mice were treated with the SGLT2 inhibitor empagliflozin (EMPA; 10 mg/kg/d) for four weeks prior to study and compared with untreated obese and lean controls. We assessed changes in body weight and composition, plasma metabolites in response to fasting/re-feeding, cardiac hypertrophy by echocardiography, the response to ischemic stress following coronary artery ligation, as well as cardiac-specific rates of relative glucose and fatty acid utilization using a [U13C]-glucose infusion during fasting and hyperinsulinemic euglycemic clamp.ResultsEMPA-treated mice presented with reduced cardiac hypertrophy and protection from ischemic stress compared with obese controls. In the fasted state, relative rates of cardiac glucose and fatty acid utilization were similar in control and EMPA-treated mice. During the hyperinsulinemic euglycemic clamp, rates of cardiac glucose utilization and metabolic flexibility were reduced in obese compared with lean mice, and EMPA-treatment partially restored both features. ConclusionsSGLT2 inhibitor therapy restored cardiac metabolic flexibility in obese, insulin resistant mice, and was associated with reduced cardiac hypertrophy and protection from ischemia. These observations suggest that the cardiovascular disease-protective effects of SGLT2 inhibitors may in part be explained by beneficial effects on cardiac metabolic substrate selection.
Enhanced All-optical Y-shaped Plasmonic NAND Gate Model, Analysis, and Simulation for High Speed Computations
Authors: Charles Ipshitha , Sreev Alluru , Krishna SabbiVamshi , Swarnakar Sandip , Kumar Santosh 
Published: September 2021

Abstract
In this digital era, all-optical logic gates (OLGs) proved its effectiveness in execution of high-speed computations. A unique construction for all optical NAND gate based on the notion of power combiner employing metal–insulator–metal (MIM) waveguide in the Y-shape in a minimal imprint of 6.2 µm × 3 µm is presented and the structure is evaluated by finite-difference time-domain (FDTD) technique. The insertion loss (IL) and extinction-ratio (ER) for proposed model are 6 dB and 27.76 dB. The simplified model is used in the construction of complex circuits to achieve greater efficiency, which contributes to the emergence of a new technique for designing plasmonic integrated circuits.
Prevalence, molecular characterization and anti-microbial resistance pattern of Staphylococcus species isolates from buck semen
Authors: Kumaresan Gururaj , Gangwar Chetna , Mishra Anil Kumar , Kumar Ashok , Kharche Suresh Dinkar , Singh Narendra Pratap , Pachoori Anjali 
Published: September 2021

Abstract
Staphylococcus aureus is one of the most prevalent pathogens, and a causative agent of a variety of infections in humans and animals. A total of 48 semen samples were collected from healthy bucks of different breeds to investigate the prevalence of S. aureus . Antimicrobial resistance and virulence of the Staphylococcus isolates were determined to assess the adverse effects of them on buck fertility. The bacterial isolates were tentatively confirmed as Staphylococcus spp. based on the Gram’s staining, growth on Mannitol salt agar and catalase test. Overall, 75% (n = 36) of the samples were positive for Staphylococcus spp. from the total 48 buck semen ejaculates from different breeds. Out of 36 staphylococcal isolates, 23 (47.92%) were coagulase negative (CoNS) and 13 (27.08%) were coagulase positive Staphylococcus (CoPS) based on the slide coagulase test. In the current study, on the basis of molecular characterization, we identified S. aureus , S. chromogenes, S. haemolyticus, S. sciuri, S. simulans and S. epidermidis amongst the staphylococcal isolates in the buck semen. This study revealed a high prevalence of Staphylococcus species in semen of the healthy bucks. The isolates exhibited varying degrees of multidrug resistance genotypically as well as phenotypically. The presence of antibiotic resistance and virulence genes may pose a potential threat to reproductive health of animals, highlighting the need for vigilant monitoring of these isolates at the time of semen cryopreservation.
Prediction Poverty Levels of College Students Using a Machine Learning Model
Authors: Sheng Wang , Yumei Shi 
Published: September 2021

Abstract
Nowadays, poverty-stricken college students have become a special group among the college students and occupied higher proportion in it. How to accurately identify poverty levels of college students and provide funding is a new problem for universities. In this manuscript, a novel model that combined Random Forest with Principle Components Analysis (RF-PCA) is proposed prediction poverty levels of college students. To build this model, data was firstly collected to establish datasets including 4 classed of poverty levels and 21 features of poverty-stricken college students. Then, feature dimension reduction includes two steps: the first step we selected the top 16 features with the ranking of feature, according to the Gini importance and Shapley Additive explanations (SHAP) values of features based on Random Forest (RF); the second step of feature extraction through Principle Components Analysis (PCA) extracted 11 dimensions. Finally, confusion metrics and receiver operating characteristic (ROC) curves were used to evaluate the performance of the proposed model, the accuracy of the model achieved 78.61%. Furthermore, compared with seven different classification algorithms, the model has a higher prediction accuracy, the result has great potential to identify the poverty levels of college students.