bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of linkage disequilibrium region suggests association of the ancient haplotype, hX with neural function
Authors: Shimada Makoto , Kanasashi Tsutomu 
Published: July 2019

AbstractModern human populations are known to contain "ancient haplotypes" that originated from archaic humans by hybridization. Some of them had been reported before the development of human genomic diversity databases, such as HapMap. Consequently, some of them have no information about linkage disequilibrium (LD) regions. Because genetic information within LD is tightly linked, to know LD region containing ancient haplotypes will be useful to estimate basic parameters of admixture events, and to infer biological functions that linked with the ancient haplotypes. One of these ancient haplotypes, haplotype X (hX) was found in a 10.1 kb-region located on Xp11.22, which diverged at 1.4 M years ago, with low diversity within the cluster in gene genealogy and worldwide distribution in low frequency. We determined the LD region around the ancient haplotypes using LD information obtained in the HapMap project. The LD determination presents that the LD region surrounding the hX is stable and contains genic regions that may associate with neural and brain functions.
The genomic landscape of Epstein-Barr virus-associated pulmonary lymphoepithelioma-like carcinoma
Authors: Hong Shaodong , Liu Dongbing , Luo Shuzhen , Fang Wenfeng , Zhan Jianhua , Fu Sha , Zhang Yaxiong , Wu Xuan , Zhou Huaqiang , Chen Xi , Chen Gang , Zhang Zhonghan , Zheng Qiufan , Li Xiaobo , Chen Jinghao , Liu Xingmin , Lei Mengyue , Ye Chen , Wang Jian , Yang Huanming , Xu Xun , Zhu Shida , Yang Yunpeng , Zhao Yuanyuan , Zhou Ningning , Zhao Hongyun , Huang Yan , Zhang Lanjun , Wu Kui , Zhang Li 
Published: July 2019

AbstractPulmonary lymphoepithelioma-like carcinoma (LELC) is a rare and distinct subtype of primary lung cancer characterized by Epstein-Barr virus (EBV) infection. Herein, we reported the mutational landscape of pulmonary LELC using whole-exome sequencing, targeted deep sequencing and single-nucleotide polymorphism arrays. We identify a low degree of somatic mutation but widespread existence of copy number variations. We reveal predominant signature 2 mutations and frequent loss of type I interferon genes that are involved in the host-virus counteraction. Integrated analysis shows enrichment of genetic lesions affecting several critical pathways, including NF-κB, JAK/STAT, and cell cycle. Notably, multi-dimensional comparison unveils that pulmonary LELC resemble NPC but are clearly different from other lung cancers, natural killer/T-cell lymphoma or EBV-related gastric cancer in terms of genetic features. In all, our study illustrates a distinct genomic landscape of pulmonary LELC and provides a road map to facilitate genome-guided personalized treatment.
High density oilfield wastewater disposal causes deeper, stronger, and more persistent earthquakes
Authors: Pollyea Ryan M. , Chapman Martin C. , Jayne Richard S. , Wu Hao 
Published: July 2019

AbstractOilfield wastewater disposal causes fluid pressure transients that induce earthquakes. Here we show that, in addition to pressure transients related to pumping, there are pressure transients caused by density differences between the wastewater and host rock fluids. In northern Oklahoma, this effect caused earthquakes to migrate downward at ~0.5 km per year during a period of high-rate injections. Following substantial injection rate reductions, the downward earthquake migration rate slowed to ~0.1 km per year. Our model of this scenario shows that the density-driven pressure front migrates downward at comparable rates. This effect may locally increase fluid pressure below injection wells for 10+ years after substantial injection rate reductions. We also show that in north-central Oklahoma the relative proportion of high-magnitude earthquakes increases at 8+ km depth. Thus, our study implies that, following injection rate reductions, the frequency of high-magnitude earthquakes may decay more slowly than the overall earthquake rate.
Microbial spatial footprint as a driver of soil carbon stabilization
Authors: Kravchenko A. N. , Guber A. K. , Razavi B. S. , Koestel J. , Quigley M. Y. , Robertson G. P. , Kuzyakov Y. 
Published: July 2019

AbstractIncreasing the potential of soil to store carbon (C) is an acknowledged and emphasized strategy for capturing atmospheric CO2. Well-recognized approaches for soil C accretion include reducing soil disturbance, increasing plant biomass inputs, and enhancing plant diversity. Yet experimental evidence often fails to support anticipated C gains, suggesting that our integrated understanding of soil C accretion remains insufficient. Here we use a unique combination of X-ray micro-tomography and micro-scale enzyme mapping to demonstrate for the first time that plant-stimulated soil pore formation appears to be a major, hitherto unrecognized, determinant of whether new C inputs are stored or lost to the atmosphere. Unlike monocultures, diverse plant communities favor the development of 30–150 µm pores. Such pores are the micro-environments associated with higher enzyme activities, and greater abundance of such pores translates into a greater spatial footprint that microorganisms make on the soil and consequently soil C storage capacity.
Systematic allelic analysis defines the interplay of key pathways in X chromosome inactivation
Authors: Nesterova Tatyana B. , Wei Guifeng , Coker Heather , Pintacuda Greta , Bowness Joseph S. , Zhang Tianyi , Almeida Mafalda , Bloechl Bianca , Moindrot Benoit , Carter Emma J. , Alvarez Rodrigo Ines , Pan Qi , Bi Ying , Song Chun-Xiao , Brockdorff Neil 
Published: July 2019

AbstractXist RNA, the master regulator of X chromosome inactivation, acts in cis to induce chromosome-wide silencing. Whilst recent studies have defined candidate silencing factors, their relative contribution to repressing different genes, and their relationship with one another is poorly understood. Here we describe a systematic analysis of Xist-mediated allelic silencing in mouse embryonic stem cell-based models. Using a machine learning approach we identify distance to the Xist locus and prior gene expression levels as key determinants of silencing efficiency. We go on to show that Spen, recruited through the Xist A-repeat, plays a central role, being critical for silencing of all except a subset of weakly expressed genes. Polycomb, recruited through the Xist B/C-repeat, also plays a key role, favouring silencing of genes with pre-existing H3K27me3 chromatin. LBR and the Rbm15/m6A-methyltransferase complex make only minor contributions to gene silencing. Together our results provide a comprehensive model for Xist-mediated chromosome silencing.
Superior Photo-thermionic electron Emission from Illuminated Phosphorene Surface
Authors: Madas S. , Mishra S. K. , Kahaly S. , Kahaly M. Upadhyay 
Published: July 2019

AbstractThis work demonstrates that black phosphorene, a two dimensional allotrope of phosphorus, has the potential to be an efficient photo-thermionic emitter. To investigate and understand the novel aspects we use a combined approach in which ab initio quantum simulation tools are utilized along with semiclassical description for the emission process. First by using density functional theory based formalism, we study the band structure of phosphorene. From the locations of electronic bands, and band edges, we estimate the Fermi level and work function. This leads us to define a valid material specific parameter space and establish a formalism for estimating thermionic electron emission current from phosphorene. Finally we demonstrate how the emission current can be enhanced substantially under the effect of photon irradiation. We observe that photoemission flux to strongly dominate over its coexisting counterpart thermionic emission flux. Anisotropy in phosphorene structure plays important role in enhancing the flux. The approach which is valid over a much wider range of parameters is successfully tested against recently performed experiments in a different context. The results open up a new possibility for application of phosphorene based thermionic and photo-thermionic energy converters.
A Pilot Proof-Of-Principle Analysis Demonstrating Dielectrophoresis (DEP) as a Glioblastoma Biomarker Platform
Authors: Lewis Jean , Alattar Ali A. , Akers Johnny , Carter Bob S. , Heller Michael , Chen Clark C. 
Published: July 2019

AbstractExtracellular vesicles (EVs) are small, membrane-bound particles released by all cells that have emerged as an attractive biomarker platform. We study the utility of a dielectrophoretic (DEP) micro-chip device for isolation and characterization of EVs derived from plasma specimens from patients with brain tumors. EVs were isolated by DEP chip and subjected to on-chip immunofluorescence (IF) staining to determine the concentration of glial fibrillary acidic protein (GFAP) and Tau. EVs were analyzed from the plasma samples isolated from independent patient cohorts. Glioblastoma cell lines secrete EVs enriched for GFAP and Tau. These EVs can be efficiently isolated using the DEP platform. Application of DEP to clinical plasma samples afforded discrimination of plasma derived from brain tumor patients relative to those derived from patients without history of brain cancer. Sixty-five percent (11/17) of brain tumor patients showed higher EV-GFAP than the maximum observed in controls. Ninety-four percent (16/17) of tumor patients showed higher EV-Tau than the maximum observed in controls. These discrimination thresholds were applied to plasma isolated from a second, independent cohort of 15 glioblastoma patients and 8 controls. For EV-GFAP, we observed 93% sensitivity, 38% specificity, 74% PPV, 75% NPV, and AUC of 0.65; for EV-Tau, we found 67% sensitivity, 75% specificity 83% PPV, 55% NPV, and AUC of 0.71 for glioblastoma diagnosis. This proof-of-principle study provides support for DEP-IF of plasma EVs for diagnosis of glioblastoma.
Observation of treated iris neovascularization by swept-source-based en-face anterior-segment optical coherence tomography angiography
Authors: Shiozaki Daiki , Sakimoto Susumu , Shiraki Akihiko , Wakabayashi Taku , Fukushima Yoko , Oie Yoshinori , Usui Shinichi , Sato Shigeru , Sakaguchi Hirokazu , Nishida Kohji 
Published: July 2019

AbstractWe evaluated regression of iris neovascularization (INV) using en-face anterior-segment optical coherence tomography angiography (AS-OCTA) after anti-vascular endothelial growth factor (VEGF) therapy. Seven consecutive eyes with INV were examined before and after anti-VEGF therapy, and all AS-OCTA scans were obtained using a swept-source OCTA system with an anterior-segment lens adapter. Slit-lamp microscopy photography and anterior indocyanine green angiography also were performed. Quantitative analyses of the vascular density, vascular lacunarity, and fractal dimension on AS-OCTA images were performed. AS-OCTA visualized the INV as signals around the pupillary margin, which corresponded to the vasculature confirmed by slit-lamp microscopy. After anti-VEGF drug injection, regression of INV was observed by AS-OCTA in all eyes (100%). The vascular density decreased and vascular lacunarity increased significantly after anti-VEGF therapy. This pilot study demonstrated the ability of AS-OCTA not only to detect but also to evaluate INV. Further study is warranted to improve the algorithm for delineating the iris vasculature to decrease artifacts.
Glucose, adrenaline and palmitate antagonistically regulate insulin and glucagon secretion in human pseudoislets
Authors: Lorza-Gil Estela , Gerst Felicia , Oquendo Morgana Barroso , Deschl Ulrich , Häring Hans-Ulrich , Beilmann Mario , Ullrich Susanne 
Published: July 2019

AbstractIsolated human islets do not always meet the quality standards required for transplant survival and reliable functional in vitro studies. The formation of pseudoislets, i.e. the reaggregation of a defined number of islet cells after dissociation, improves insulin secretion. We present a simple method of pseudoislet formation from human islet cells and assess the transcriptome and function of isolated human islets and pseudoislets from the same organ donors. Following pseudoislet formation, insulin content/DNA and mRNA/RPS13 resembled that of islets. In pseudoislets, glucose-stimulated insulin secretion (GSIS) was significantly higher (8–13-fold) than in islets (2–4-fold). GSIS of pseudoislets was partly inhibited by the glucagon-like peptide-1 receptor (GLP-1R) antagonist exendin-9. The stimulatory effects of palmitate and forskolin at 12 mM glucose were also significantly higher in pseudoislets than in islets. Further analysis of pseudoislets revealed that regulation of secretion and insulin and glucagon content was maintained over a longer culture period (6–14 d). While adrenaline inhibited GSIS, adrenaline together with palmitate stimulated glucagon secretion 2-fold at low glucose, an effect suppressed by high glucose. Transcriptome analysis revealed that, unlike islets, pseudoislets were deprived of exocrine and endothelial cells. In conclusion, pseudoislet formation restores functional integrity of human islet cells and allows long-term in vitro testing.
New perspectives for simultaneous attraction of Chrysoperla and Chrysopa lacewing species for enhanced biological control (Neuroptera: Chrysopidae)
Authors: Koczor Sándor , Szentkirályi Ferenc , Tóth Miklós 
Published: July 2019

AbstractGreen lacewings (Chrysopidae) are important predators of many soft-bodied pest insects, for instance aphids. Previous studies reported attraction of Chrysoperla carnea species-complex to a ternary floral bait. The larvae of these lacewings are important generalist predators in agroecosystems, however adults are non-predatory, they feed on pollen, nectar or honeydew. Squalene, a plant originated compound was previously reported to be attractive to the nearctic Chrysopa nigricornis. In the current study squalene was tested alone and in combination with the ternary bait in field experiments in Hungary. In our experiments, traps baited with squalene attracted predatory males of Chrysopa formosa. Traps baited with squalene and the ternary floral bait attracted adults of both C. formosa and C. carnea complex lacewings. To our knowledge this is the first report of a bait combination attractive to both Chrysoperla and Chrysopa species. This finding is of special interest considering the remarkably different feeding habits of the adults of these lacewings. Potential perspectives in biological control are discussed.
Presence of Histatin-1 in Human Tears and Association with Aqueous Deficient Dry Eye Diagnosis: A Preliminary Study
Authors: Kalmodia Sushma , Son Kyung-No , Cao Dingcai , Lee Bao-Shiang , Surenkhuu Bayasgalan , Shah Dhara , Ali Marwan , Balasubramaniam Arun , Jain Sandeep , Aakalu Vinay Kumar 
Published: July 2019

AbstractThe aims of this study were to determine if histatin-1 (H1) is present in normal human tears and whether tear levels of H1 varied between normal patients and those with aqueous deficient dry eye disease (ADDE). Patient samples were obtained from 11 normal patients and 11 severe ADDE patients. Relevant patient characteristics, including age, sex, and dry eye disease (DED) diagnostic parameters were collected. Multiple qualitative and quantitative methods were used to compare the concentration of H1 between patient groups. Mixed linear modeling was used to compare H1 levels between groups, and diagnostic performance was assessed using the receiver-operator-characteristic (ROC). ADDE patients had significantly lower H1 concentrations (85.9 ± 63.7 ng/ml) than the normal group (891.6 ± 196.5 ng/ml) (p < 0.001), while controlling for age and sex. ROC analysis indicated that H1 concentration is potentially a biomarker for ADDE (area under curve = 0.96). Reclassification of patients by DED parameters including, Ocular Surface Disease Index (OSDI) (≤13, >13) and Schirmer I (without anesthesia) (<10 mm, ≥10 mm) showed significant differences in H1 level (OSDI, p = 0.004) and Schirmer I ((p = 0.010). In conclusion, this is the first preliminary report of the presence of H1 in human tears. H1 concentrations are lower in ADDE patients and H1 may have diagnostic potential in evaluation ADDE patients.
Lithium and GADL1 regulate glycogen synthase kinase-3 activity to modulate KCTD12 expression
Authors: Wu Tai-Na , Chen Chih-Ken , Lee Chau-Shoun , Wu Bo-Jian , Sun Hsiao-Ju , Chang Chieh-Hsing , Chen Chun-Ying , Wu Lawrence Shih-Hsin , Cheng Andrew Tai-Ann 
Published: July 2019

AbstractPotassium channel tetramerization domain containing 12 (KCTD12), the auxiliary GABAB receptor subunit, is identified as a susceptibility gene for bipolar I (BPI) disorder in the Han Chinese population. Moreover, the single-nucleotide polymorphism (SNP) rs17026688 in glutamate decarboxylase–like protein 1 (GADL1) is shown to be associated with lithium response in Han Chinese BPI patients. In this study, we demonstrated for the first time the relationship among lithium, GADL1, and KCTD12. In circulating CD11b+ macrophage cells, BPI patients showed a significantly higher percentage of KCTD12 expression than healthy controls. Among BPI patients, carriers of the ‘T’ allele (i.e., CT or TT) at site rs17026688 were found to secrete lower amounts of GADL1 but higher amounts of GABA b receptor 2 (GABBR2) in the plasma. In human SH-SY5Y neuroblastoma cells, lithium treatment increased the percentage of KCTD12 expression. Through inhibition of glycogen synthase kinase-3 (GSK-3), lithium induced cyclic AMP-response element binding protein (CREB)–mediated KCTD12 promoter activation. On the other hand, GADL1 overexpression enhanced GSK-3 activation and inhibited KCTD12 expression. We found that lithium induced, whereas GADL1 inhibited, KCTD12 expression. These findings suggested that KCTD12 may be an important gene with respect to neuron excitability and lithium response in BPI patients. Therefore, targeting GSK-3 activity and/or KCTD12 expression may constitute a possible therapeutic strategy for treating patients with BPI disorder.
Ge nanoparticles in SiO2 for near infrared photodetectors with high performance
Authors: Stavarache Ionel , Teodorescu Valentin Serban , Prepelita Petronela , Logofatu Constantin , Ciurea Magdalena Lidia 
Published: July 2019

AbstractIn this work we prepared films of amorphous germanium nanoparticles embedded in SiO2 deposited by magnetron sputtering on Si and quartz heated substrates at 300, 400 and 500 °C. Structure, morphology, optical, electrical and photoconduction properties of all films were investigated. The Ge concentration in the depth of the films is strongly dependent on the deposition temperature. In the films deposited at 300 °C, the Ge content is constant in the depth, while films deposited at 500 °C show a significant decrease of Ge content from interface of the film with substrate towards the film free surface. From the absorption curves we obtained the Ge band gap of 1.39 eV for 300 °C deposited films and 1.44 eV for the films deposited at 500 °C. The photocurrents are higher with more than one order of magnitude than the dark ones. The photocurrent spectra present different cutoff wavelengths depending on the deposition temperature, i.e. 1325 nm for 300 °C and 1267 nm for 500 °C. These films present good responsivities of 2.42 AW−1 (52 μW incident power) at 300 °C and 0.69 AW−1 (57 mW) at 500 °C and high internal quantum efficiency of ∼445% for 300 °C and ∼118% for 500 °C.
Uncovering bacterial and functional diversity in macroinvertebrate mitochondrial-metagenomic datasets by differential centrifugation
Authors: Macher Jan-Niklas , Speksnijder Arjen , Choo Le Qin , van der Hoorn Berry , Renema Willem 
Published: July 2019

AbstractPCR-free techniques such as meta-mitogenomics (MMG) can recover taxonomic composition of macroinvertebrate communities, but suffer from low efficiency, as >90% of sequencing data is mostly uninformative due to the great abundance of nuclear DNA that cannot be identified with current reference databases. Current MMG studies do not routinely check data for information on macroinvertebrate-associated bacteria and gene functions. However, this could greatly increase the efficiency of MMG studies by revealing yet overlooked diversity within ecosystems and making currently unused data available for ecological studies. By analysing six ‘mock’ communities, each containing three macroinvertebrate taxa, we tested whether this additional data on bacterial taxa and functional potential of communities can be extracted from MMG datasets. Further, we tested whether differential centrifugation, which is known to greatly increase efficiency of macroinvertebrate MMG studies by enriching for mitochondria, impacts on the inferred bacterial community composition. Our results show that macroinvertebrate MMG datasets contain a high number of mostly endosymbiont bacterial taxa and associated gene functions. Centrifugation reduced both the absolute and relative abundance of highly abundant Gammaproteobacteria, thereby facilitating detection of rare taxa and functions. When analysing both taxa and gene functions, the number of features obtained from the MMG dataset increased 31-fold (‘enriched’) respectively 234-fold (‘not enriched’). We conclude that analysing MMG datasets for bacteria and gene functions greatly increases the amount of information available and facilitates the use of shotgun metagenomic techniques for future studies on biodiversity.
Regulatory mechanisms leading to differential Acyl-CoA synthetase 4 expression in breast cancer cells
Authors: Dattilo Melina A. , Benzo Yanina , Herrera Lucía M. , Prada Jesica G. , Castillo Ana F. , Orlando Ulises D. , Podesta Ernesto J. , Maloberti Paula M. 
Published: July 2019

AbstractAcyl-CoA synthetase 4 (ACSL4) overexpression plays a causal role in the aggressiveness of triple negative breast cancer. In turn, a negative correlation has been established between ACSL4 and estrogen receptor alpha (ERα) expression. However, the upstream regulatory mechanisms leading to differential ACSL4 expression between triple negative breast cancer and ERα-positive cells remained unknown. We performed the characterization of the human ACSL4 promoter and the identification of transcription factors involved. Deletional analysis demonstrated the proximal 43 base pairs of the promoter are involved in overexpression. By site directed mutagenesis we describe that retinoid-related orphan receptor alpha (RORα), Sp1 and E2F elements are involved in the promoter activity. We established for the first time that estrogen-related receptor alpha (ERRα) is a transcription factor involved in the higher activation of the human ACSL4 promoter in breast cancer cells. Furthermore, a combination of inhibitors of ACSL4 and ERRα produced a synergistic decrease in MDA-MB-231 cell proliferation. We also demonstrated that ERα restoration in triple negative breast cancer cells downregulates ACSL4 expression. The results presented in this manuscript demonstrated transcriptional mechanism is involved in the different expression of ACSL4 in human breast cancer cell lines of different aggressiveness.