bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of prognostic gene signature associated with microenvironment of lung adenocarcinoma
Authors: Yue Cheng , Ma Hongtao , Zhou Yubai 
Published: November 2019

Background
Lung cancer has the highest morbidity and mortality worldwide, and lung adenocarcinoma (LADC) is the most common pathological subtype. Accumulating evidence suggests the tumor microenvironment (TME) is correlated with the tumor progress and the patient’s outcome. As the major components of TME, the tumor-infiltrated immune cells and stromal cells have attracted more and more attention. In this study, differentially expressed immune and stromal signature genes were used to construct a TME-related prognostic model for predicting the outcomes of LADC patients.

Methods
The expression profiles of LADC samples with clinical information were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The differentially expressed genes (DEGs) related to the TME of LADC were identified using TCGA dataset by Wilcoxon rank sum test. The prognostic effects of TME-related DEGs were analyzed using univariate Cox regression. Then, the least absolute shrinkage and selection operator (LASSO) regression was performed to reduce the overfit and the number of genes for further analysis. Next, the prognostic model was constructed by step multivariate Cox regression and risk score of each sample was calculated. Then, survival and Receiver Operating Characteristic (ROC) analyses were conducted to validate the model using TCGA and GEO datasets, respectively. The Kyoto Encyclopedia of Genes and Genomes analysis of gene signature was performed using Gene Set Enrichment Analysis (GSEA). Finally, the overall immune status, tumor purity and the expression profiles of HLA genes of high- and low-risk samples was further analyzed to reveal the potential mechanisms of prognostic effects of the model.

Results
A total of 93 TME-related DEGs were identified, of which 23 DEGs were up-regulated and 70 DEGs were down-regulated. The univariate cox analysis indicated that 23 DEGs has the prognostic effects, the hazard ratio ranged from 0.65 to 1.25 (p < 0.05). Then, seven genes were screened out from the 23 DEGs by LASSO regression method and were further analyzed by step multivariate Cox regression. Finally, a three-gene (ADAM12, Bruton Tyrosine Kinase (BTK), ERG) signature was constructed, and ADAM12, BTK can be used as independent prognostic factors. The three-gene signature well stratified the LADC patients in both training (TCGA) and testing (GEO) datasets as high-risk and low-risk groups, the 3-year area under curve (AUC) of ROC curves of three GEO sets were 0.718 (GSE3141), 0.646 (GSE30219) and 0.643 (GSE50081). The GSEA analysis indicated that highly expressed ADAM12, BTK, ERG mainly correlated with the activation of pathways involving in focal adhesion, immune regulation. The immune analysis indicated that the low-risk group has more immune activities and higher expression of HLA genes than that of the high-risk group. In sum, we identified and constructed a three TME-related DEGs signature, which could be used to predict the prognosis of LADC patients.
Characteristics of the vaginal microbiome in cross-border female sex workers in China: a case-control study
Authors: Hong Xiang , Fang Shenghao , Huang Kaiping , Yin Jiechen , Chen Jianshuang , Xuan Yan , Zhu Jing , Ma Jun , Qin Pengfei , Peng Danhong , Wang Ning , Wang Bei 
Published: November 2019

BackgroundFemale sex workers (FSWs) are key groups in the transmission of sexual transmitted infections (STI), and vaginal microbiome variations play an important role in transmission. We aimed to explore the characteristics of vaginal microbiome among FSWs.Materials and MethodsA total of 24 cross-border FSWs were randomly selected from a cross-sectional survey for female sex workers in southwest China. Thirty-seven female non-sex workers (FNSWs) were randomly selected from the gynecology clinic and health examination center. Vaginal swabs were collected, bacterial DNA extracted and 16S rRNA genes were sequenced. Differences in the vaginal microbiome between both groups were compared using bioinformatics analysis.ResultsOne DNA sample was excluded due to unqualified concentration, therefore 60 samples were sequenced. FSWs had significantly different vaginal microbiota β diversity, but undifferentiated α diversity when compared with non-sex workers. The average relative abundance ofSneathia,Shigella,Neisseria,Chlamydia,Prevotella,EnterococcusandUreaplasmaamong FSWs was higher than FNSWs, and relative abundance ofAtopobiumin FSWs was lower than FNSWs. TheLactobacillusgenus was the major genus in both groups. At the species level,Lactobacllus crispatus,Lactobacllus gasseriandLactobacllus jensenii, in female sex workers, were lower when compared to FNSWs.ConclusionThere were distinct differences in vaginal bacteria variety between FSWs and FNSWs. Some disease-related genus were also more abundant in FSWs. Based on these observations, further research is required to identify microbiome communities related to high STI risks and other diseases in these cohorts.
Modeling of Neutral Red Adsorption on Apple Peel Based Activated Carbon
Authors: Demir Canan , Yıldız Halime , Kul Ali Rıza , Keskin Sıddık 
Published: November 2019

Neutral red is used in textile industry as dyestuff. Dyestuffs which remain unchanged throughout the process in the wastewater treatment plants have toxic effects. In this study, removal of neutral red dyestuff from aqueous medium of active carbon obtained from apple peel waste was investigated. For this purpose, the apple peel was pretreated into 2 mm pieces. Chemical Activation of apple peel with ZnCl2 was used in activated carbon preparation. The amount of adsorbed material at different temperatures (25, 35, 45°C) and concentrations (100, 150, 200 ppm) was determined. In addition to the linear model, 4 different nonlinear models were used to model the adsorbed material. From these models, the best estimate for all temperature values and concentrations gave the cubic model.
Microbiological Examination and Physicochemical Analysis of Estuary Water Used as a Point of Source Drinking Water
Authors: O. Edet U. , P. Antai S. , A. Brooks A. , D. Asitok A. 
Published: November 2019

Introduction: Access to potable water is a fundamental human right. However, this is hardly the case in the rural areas of oil producing communities of the Niger Delta.
Aim of Study: The primary aim of this study was therefore to evaluate the physicochemical and microbiological qualities of estuary water used as potable water.
Method: Estuary water samples were collected from Eastern Obolo community in Akwa Ibom State, Niger Delta, Nigeria and analysed for physiochemical using standard techniques, and microbiological parameters using standard cultural and metagenomics techniques. Replicate data from microbiological and physicochemical analyses were analyzed using analysis of variance (ANOVA) while bioinformatic analyses were done using Vecton NTI suite 9 (InforMax, Inc.), NCBI-BLAST-2.2.24 and CLC bio Genomics workbench v7.5.1.
Results: Physicochemical analysis showed that the levels of metals such as chromium, nickel, zinc and iron and as well as turbidity were significantly higher than acceptable standards. Bacterial counts ranged from 0.64 to 1.00 (x 105) cfu/ml. Fungal counts ranged from 2.00 to 4.00 (x 102) cfu/ml. Esherichia coli, Citrobacter, Bacillus, Micrococcus, Pseudomonas and Flavobacterium, Shigella, Salmonella and Vibrio species were isolated using cultural means. Total coliforms counts were higher in location E6 which was closest to the community. Metagenomics analysis gave a total of six kingdoms namely bacteria, unknown, protozoa, archae, plantae and fungi in decreasing order of read counts. Furthermore, it revealed a total of 16 phyla, 24 classes, 38 orders, 39 families and 209 species of bacteria. Some pathogens not captured by cultural means such as Clostridium species, Vibrio alginolyticus, Vibrio neresis, Staphylococcus kloosii, Corynebacterium diptheriae, and uncultured species such as uncultured Helicobacter were all captured by metagenomics.
Conclusion: Although, cultural methods used in this study were able to capture water borne disease pathogens, metagenomics captured much more kingdoms and species. Where possible, both techniques should be used in the microbiological examination of water samples.
Bacteriological Assessment of Chicken Meat, Chicken Meat Products and Its Impact of Human Enteric Infections in Taif Governorate
Authors: Mansour Ahmed M. A. 
Published: November 2019

From different shops and supermarkets at Taif governorate in KSA; a total number of 105 samples were collected. They were 35 samples from raw chicken meat, 35 samples from frozen chicken meat burger and 35 samples from chicken meat luncheon. The samples were examined for their organoleptic and bacteriological quality; the results revealed that, 8.6% and 2.9% of the examined raw chicken meat and frozen chicken burger were unaccepted while all examined samples of chicken-luncheon were accepted.
The bacteriological examination revealed that, the bacterial counts in frozen chicken burger samples were higher than that detected in raw chicken meat and chicken luncheon samples whereas 51.4%, of the frozen chicken burger were exceeded the permissible limit, but 45.7% of the raw chicken meat samples exceeded the permissible limit, while 20% from the chicken luncheon samples exceeded the permissible limit, moreover, E. coli, Enterobacter aerogenes, Enterobacter cloaca, Klebsiella aerogenes, Citrobacter freundii, Proteus vulgaris, Morganella morganii, Providencia stuartii and Providencia rettergii could be isolated from the examined samples of raw chicken meat and frozen chicken burger in varying percentages ranged from 2.86 to 22.85% and 2.86 to 20.00% respectively, while Enterobacter aerogenes, Klebsiella aerogenes, Citrobacter freundii, P. vulgaris and Morganella morganii only were detected in chicken luncheon in a percentage varying from 5.17 to 17.14%.
Furthermore, Campylobacter jejuni were isolated in a percentage of 14.3, 8.8 and 2.9% from the former examined samples respectively, while Salmonella organism were detected in raw chicken meat samples in a percentage of 5.7% but failed to be isolated from frozen chicken burger and chicken luncheon samples.
The relationship between total aerobic count and the incidence of Campylobacter jejuni and Salmonella pathogens as well as the public health significance of the isolated organisms and preventive measures to improve the quality of the products were discussed.
Silver Nanofilament Formation Dynamics in a Polymer‐Ionic Liquid Thin Film by Direct Write
Authors: Chao Zhongmou , Sezginel Kutay B. , Xu Ke , Crouch Garrison M. , Gray Abigale E. , Wilmer Christopher E. , Bohn Paul W. , Go David B. , Fullerton‐Shirey Susan K. 
Published: November 2019

AbstractSilver nanofilament formation dynamics are reported for an ionic liquid (IL)‐filled solid polymer electrolyte prepared by a direct‐write process using a conductive atomic force microscope (C‐AFM). Filaments are electrochemically formed at hundreds of xy locations on a ≈40 nm thick polymer electrolyte, polyethylene glycol diacrylate (PEGDA)/[BMIM]PF6. Although the formation time generally decreases with increasing bias from 0.7 to 3.0 V, an unexpected non‐monotonic maximum is observed ≈2.0 V. At voltages approaching this region of inverted kinetics, IL electric double layers (EDLs) become detectable; thus, the increased nanofilament formation time can be attributed to electric field screening, which hinders silver electromigration and deposition. Scanning electron microscopy confirms that nanofilaments formed in this inverted region have significantly more lateral and diffuse features. Time‐dependent formation currents reveal two types of nanofilament growth dynamics: abrupt, where the resistance decreases sharply over as little as a few ms, and gradual where it decreases more slowly over hundreds of ms. Whether the resistance change is abrupt or gradual depends on the extent to which the EDL screens the electric field. Tuning the formation time and growth dynamics using an IL opens the range of accessible resistance states, which is useful for neuromorphic applications.
Development of Injectable Amniotic Membrane Matrix for Postmyocardial Infarction Tissue Repair
Authors: Henry Jeffrey J. D. , Delrosario Lawrence , Fang Jun , Wong Sze Yue , Fang Qizhi , Sievers Richard , Kotha Surya , Wang Aijun , Farmer Diana , Janaswamy Praneeth , Lee Randall J. , Li Song 
Published: November 2019

AbstractIschemic heart disease represents the leading cause of death worldwide. Heart failure following myocardial infarction (MI) is associated with severe fibrosis formation and cardiac remodeling. Recently, injectable hydrogels have emerged as a promising approach to repair the infarcted heart and improve heart function through minimally invasive administration. Here, a novel injectable human amniotic membrane (hAM) matrix is developed to enhance cardiac regeneration following MI. Human amniotic membrane is isolated from human placenta and engineered to be a thermoresponsive, injectable gel around body temperature. Ultrasound‐guided injection of hAM matrix into rat MI hearts significantly improves cardiac contractility, as measured by ejection fraction (EF), and decrease fibrosis. The results of this study demonstrate the feasibility of engineering as an injectable hAM matrix and its efficacy in attenuating degenerative changes in cardiac function following MI, which may have broad applications in tissue regeneration.
Novel Organophosphate‐Derived Dual‐Layered Interface Enabling Air‐Stable and Dendrite‐Free Lithium Metal Anode
Authors: Liu Xuejun , Liu Jie , Qian Tao , Chen Hongli , Yan Chenglin 
Published: November 2019

AbstractLithium (Li) metal, as a promising candidate for next‐generation energy storage systems, suffers from an extremely unstable interface that is prone to crack, causing serious corrosion of Li metal and dendrite growth. To address this, a novel dual‐layered interface on the Li metal anode is reported, which is featured with organics (COPO3, (CO)2PO2, and (CO)3PO) on the top and inorganics (Li3PO4) at the bottom. The flexible organic layer with reduced Young's modulus (≈550 MPa) contributes to maintain structural integrity, while the rigid inorganic layer with improved Young's modulus of ≈12 GPa is beneficial to suppress the Li dendrite growth. Accordingly, the protected Li is stabilized to maintain successive electrodeposition over 800 cycles of plating/stripping process at a current density of 2 mA cm−2. Furthermore, the uniform dual‐layered interface tends to prevent the corrosion of air to Li metal, exhibiting almost the same performance as the Li metal treated in the inert atmosphere.
Coupling Topological Insulator SnSb2Te4 Nanodots with Highly Doped Graphene for High‐Rate Energy Storage
Authors: Wu Zhibin , Liang Gemeng , Pang Wei Kong , Zhou Tengfei , Cheng Zhenxiang , Zhang Wenchao , Liu Ye , Johannessen Bernt , Guo Zaiping 
Published: November 2019

AbstractTopological insulators have spurred worldwide interest, but their advantageous properties have scarcely been explored in terms of electrochemical energy storage, and their high‐rate capability and long‐term cycling stability still remain a significant challenge to harvest. p‐Type topological insulator SnSb2Te4 nanodots anchoring on few‐layered graphene (SnSb2Te4/G) are synthesized as a stable anode for high‐rate lithium‐ion batteries and potassium‐ion batteries through a ball‐milling method. These SnSb2Te4/G composite electrodes show ultralong cycle lifespan (478 mAh g−1 at 1 A g−1 after 1000 cycles) and excellent rate capability (remaining 373 mAh g−1 even at 10 A g−1) in Li‐ion storage owing to the rapid ion transport accelerated by the PN heterojunction, virtual electron highways provided by the conductive topological surface state, and extraordinary pseudocapacitive contribution, whose excellent phase reversibility is confirmed by synchrotron in situ X‐ray powder diffraction. Surprisingly, durable lifespan even at practical levels of mass loading (>10 mg cm−2) for Li‐ion storage and excellent K‐ion storage performance are also observed. This work provides new insights for designing high‐rate electrode materials by boosting conductive topological surfaces, atomic doping, and the interface interaction.
Comparison ofArachis monticolawith Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut
Authors: Yin Dongmei , Ji Changmian , Song Qingxin , Zhang Wanke , Zhang Xingguo , Zhao Kunkun , Chen Charles Y. , Wang Chuantang , He Guohao , Liang Zhe , Ma Xingli , Li Zhongfeng , Tang Yueyi , Wang Yuejun , Li Ke , Ning Longlong , Zhang Hui , Zhao Kai , Li Xuming , Yu Haiyan , Lei Yan , Wang Mingcheng , Ma Liming , Zheng Hongkun , Zhang Yijing , Zhang Jinsong , Hu Wei , Chen Z. Jeffrey 
Published: November 2019

AbstractLike many important crops, peanut is a polyploid that underwent polyploidization, evolution, and domestication. The wild allotetraploid peanut speciesArachis monticola(A. monticola) is an important and unique link from the wild diploid species to cultivated tetraploid species in theArachislineage. However, little is known aboutA. monticolaand its role in the evolution and domestication of this important crop. A fully annotated sequence of ≈2.6 GbA. monticolagenome and comparative genomics of theArachisspecies is reported. Genomic reconstruction of 17 wild diploids from AA, BB, EE, KK, and CC groups and 30 tetraploids demonstrates a monophyletic origin of A and B subgenomes in allotetraploid peanuts. The wild and cultivated tetraploids undergo asymmetric subgenome evolution, including homoeologous exchanges, homoeolog expression bias, and structural variation (SV), leading to subgenome functional divergence during peanut domestication. Significantly, SV‐associated homoeologs tend to show expression bias and correlation with pod size increase from diploids to wild and cultivated tetraploids. Moreover, genomic analysis of disease resistance genes shows the unique alleles present in the wild peanut can be introduced into breeding programs to improve some resistance traits in the cultivated peanuts. These genomic resources are valuable for studying polyploid genome evolution, domestication, and improvement of peanut production and resistance.
Dysprosium Iron Garnet Thin Films with Perpendicular Magnetic Anisotropy on Silicon
Authors: Bauer Jackson J. , Rosenberg Ethan R. , Kundu Subhajit , Mkhoyan K. Andre , Quarterman Patrick , Grutter Alexander J. , Kirby Brian J. , Borchers Julie A. , Ross Caroline A. 
Published: November 2019

AbstractMagnetic insulators, such as the rare‐earth iron garnets, are promising materials for energy‐efficient spintronic memory and logic devices, and their anisotropy, magnetization, and other properties can be tuned over a wide range through selection of the rare‐earth ion. Films are typically grown as epitaxial single crystals on garnet substrates, but integration of these materials with conventional electronic devices requires growth on Si. The growth, magnetic, and spin transport properties of polycrystalline films of dysprosium iron garnet (DyIG) with perpendicular magnetic anisotropy (PMA) on Si substrates and as single crystal films on garnet substrates are reported. PMA originates from magnetoelastic anisotropy and is obtained by controlling the strain state of the film through lattice mismatch or thermal expansion mismatch with the substrates. DyIG/Si exhibits large grain sizes and bulk‐like magnetization and compensation temperature. Polarized neutron reflectometry demonstrates a small interfacial nonmagnetic region near the substrate. Spin Hall magnetoresistance measurements conducted on a Pt/DyIG/Si heterostructure demonstrate a large interfacial spin mixing conductance between the Pt and DyIG comparable to other garnet/Pt heterostructures.
Increased produce enrichment reduces trauma in socially‐housed captive rhesus macaques (Macaca mulatta)
Authors: Wooddell Lauren J. , Beisner Brianne , Hannibal Darcy L. , Nathman Amy C. , McCowan Brenda 
Published: November 2019

AbstractDue to primate adaptations for sociality, captive rhesus macaques have optimal welfare and utility as a biomedical model when they can be maintained in outdoor social groups. As a despotic species; however, aggression can result in costly injuries and may result in temporary or permanent removal of specific individuals from social housing. Enrichment items, such as toys, climbing structures, and foraging material, are employed to keep captive animals occupied. We hypothesized that produce enrichment that requires more processing to extract may reduce socially‐derived injuries by keeping animals occupied. We tested the effects of additional weekly produce (corn‐in‐husk, whole melon, or whole squash) on trauma incidence in an outdoor social group of rhesus macaques across two distinct seasons (mating and birthing seasons) at the California National Primate Research Center. Aggression and status behavioral data, food resource use and proximity, and trauma incidence were collected over two 16‐week periods, with eight control and treatment conditions alternating biweekly. Mixed‐effects regression modeling was used to determine the best predictors of trauma risk and severe aggression at the group level and at an individual level. We found that food resource use was an important predictor of trauma risk at both group and individual levels; greater use of food resources reduced trauma risk. Produce enrichment did not; however, reduce severe aggression. We suggest that other captive social groups of rhesus macaques with high levels of trauma may benefit from supplemental produce enrichment that increases animal engagement with food resources.
A 3.3 Å‐Resolution Structure of Hyperthermophilic Respiratory Complex III Reveals the Mechanism of Its Thermal Stability
Authors: Zhu Guoliang , Zeng Hui , Zhang Shuangbo , Juli Jana , Pang Xiaoyun , Hoffmann Jan , Zhang Yan , Morgner Nina , Zhu Yun , Peng Guohong , Michel Hartmut , Sun Fei 
Published: November 2019

AbstractRespiratory chain complexes convert energy by coupling electron flow to transmembrane proton translocation. Owing to a lack of atomic structures of cytochrome bc1 complex (Complex III) from thermophilic bacteria, little is known about the adaptations of this macromolecular machine to hyperthermophilic environments. In this study, we purified the cytochrome bc1 complex of Aquifex aeolicus, one of the most extreme thermophilic bacteria known, and determined its structure with and without an inhibitor at 3.3 Å resolution. Several residues unique for thermophilic bacteria were detected that provide additional stabilization for the structure. An extra transmembrane helix at the N‐terminus of cyt. c1 was found to greatly enhance the interaction between cyt. b and cyt. c1, and to bind a phospholipid molecule to stabilize the complex in the membrane. These results provide the structural basis for the hyperstability of the cytochrome bc1 complex in an extreme thermal environment.