bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transformation from Film to Nanorod via a Sacrifical Layer: Pulsed Laser Deposition of ZnO for Enhancing Photodetector Performance
Authors: Ou Sin-Liang , Yu Fei-Peng , Wuu Dong-Sing 
Published: October 2017

AbstractA novel fabrication method for single crystalline ZnO nanorods by pulsed laser deposition (PLD) using a chemical-bath-deposited ZnS seed layer is proposed. For the substrate temperature (Ts) lower than 700 °C, the PLD-ZnO showed a polycrystalline phase and film-type morphology, resulting from the ZnS seed layer with a cubic phase. However, the ZnS film became a sacrifical layer and single crystalline ZnO(002) nanorods can be achieved at Ts of 900 °C, where ZnS was decomposed to zinc metals and sulfur fumes. The transformation from ZnO film to nanorod microstructure was demonstrated with the change of ZnS layer into Zn grains. Enhanced performance of the metal-semiconductor-metal photodetectors were fabricated with ZnO/ZnS samples grown at Ts of 500, 700, and 900 °C. The responsivities (@1 V and 370 nm) of these three devices were 1.71, 6.35, and 98.67 A/W, while their UV-to-visible discrimination ratios were 7.2, 16.5, and 439.1, respectively. Obviously, a higher light-capturing efficiency was obtained in the 900 °C-grown ZnO/ZnS device owing to its one-dimensional nanostructure with high crystal quality. The results indicate PLD combined with a sacrifical nanostructure is a promising method for obtaining high-quality ZnO nanorods, which paves the way for the fabrication of high performance ZnO-based devices.
UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq
Authors: Sun Zhifu , Nair Asha , Chen Xianfeng , Prodduturi Naresh , Wang Junwen , Kocher Jean-Pierre 
Published: October 2017

AbstractLong non-coding RNA (lncRNA) is a large class of gene transcripts with regulatory functions discovered in recent years. Many more are expected to be revealed with accumulation of RNA-seq data from diverse types of normal and diseased tissues. However, discovering novel lncRNAs and accurately quantifying known lncRNAs is not trivial from massive RNA-seq data. Herein we describe UClncR, an Ultrafast and Comprehensive lncRNA detection pipeline to tackle the challenge. UClncR takes standard RNA-seq alignment file, performs transcript assembly, predicts lncRNA candidates, quantifies and annotates both known and novel lncRNA candidates, and generates a convenient report for downstream analysis. The pipeline accommodates both un-stranded and stranded RNA-seq so that lncRNAs overlapping with other genes can be predicted and quantified. UClncR is fully parallelized in a cluster environment yet allows users to run samples sequentially without a cluster. The pipeline can process a typical RNA-seq sample in a matter of minutes and complete hundreds of samples in a matter of hours. Analysis of predicted lncRNAs from two test datasets demonstrated UClncR’s accuracy and their relevance to sample clinical phenotypes. UClncR would facilitate researchers’ novel lncRNA discovery significantly and is publically available at http://bioinformaticstools.mayo.edu/research/UClncR.
A missense mutation in SLC26A3 is associated with human male subfertility and impaired activation of CFTR
Authors: Wedenoja Satu , Khamaysi Ahlam , Shimshilashvili Liana , Anbtawe-Jomaa Shireen , Elomaa Outi , Toppari Jorma , Höglund Pia , Aittomäki Kristiina , Holmberg Christer , Hovatta Outi , Tapanainen Juha S. , Ohana Ehud , Kere Juha 
Published: October 2017

AbstractChloride absorption and bicarbonate excretion through exchange by the solute carrier family 26 member 3 (SLC26A3) and cystic fibrosis transmembrane conductance regulator (CFTR) are crucial for many tissues including sperm and epithelia of the male reproductive tract. HomozygousSLC26A3mutations cause congenital chloride diarrhea with male subfertility, while homozygousCFTRmutations cause cystic fibrosis with male infertility. Some homozygous or heterozygousCFTRmutations only manifest as male infertility. Accordingly, we studied the influence ofSLC26A3on idiopathic infertility by sequencing exons ofSLC26A3in 283 infertile and 211 control men. A heterozygous mutation c.2062 G > C (p.Asp688His) appeared in nine (3.2%) infertile men, and additionally, in two (0.9%) control men, whose samples revealed a sperm motility defect. The p.Asp688His mutation is localized in the CFTR-interacting STAS domain of SLC26A3 and enriched in Finland, showing a significant association with male infertility in comparison with 6,572 Finnish (P < 0.05) and over 120,000 global alleles (P < 0.0001) (ExAC database). Functional studies showed that while SLC26A3 is a strong activator of CFTR-dependent anion transport, SLC26A3-p.Asp688His mutant retains normal Cl−/HCO3−exchange activity but suppresses CFTR, despite unaffected domain binding and expression. These results suggest a novel mechanism for human male infertility─impaired anion transport by the coupled SLC26A3 and CFTR.
Embodiment in a virtual body that speaks produces agency over the speaking but does not necessarily influence subsequent real speaking
Authors: Banakou Domna , Slater Mel 
Published: October 2017

AbstractPrevious results have shown that body ownership, induced through first-person perspective (1PP) over a virtual body (VB) that moves synchronously with real body movements, can lead to illusory agency over VB utterances even though the participant does not speak. It was also found that when participants later speak they follow the fundamental frequency (FF) of the voice of their VB, indicating a new motor plan for speaking. To eliminate the contribution of veridical agency over the VB movements, we conducted a study where we induced body ownership using visuotactile (VT) synchrony rather than visuomotor. Participants saw a life-sized VB from 1PP and reflected in a virtual mirror, that spoke with corresponding lip movements. Half of the 36 experimental participants experienced synchronous (Sync) passive VT on their hands and abdomen, and the other half asynchronous (Async). We found that both VT Sync and Async conditions resulted in a strong subjective illusion of body ownership and agency over the VB, but not, however, changes in voice FF in subsequent speaking. This shows that although illusory agency may be associated with body ownership, a change in motor plan is likely to be a generalisation from veridical agency over whole body movements.
SFRP4 gene expression is increased in aggressive prostate cancer
Authors: Sandsmark Elise , Andersen Maria K. , Bofin Anna M. , Bertilsson Helena , Drabløs Finn , Bathen Tone F. , Rye Morten B. , Tessem May-Britt 
Published: October 2017

AbstractIncreased knowledge of the molecular differences between indolent and aggressive prostate cancer is needed for improved risk stratification and treatment selection. Secreted frizzled-related protein 4 (SFRP4) is a modulator of the cancer-associated Wnt pathway, and previously suggested as a potential marker for prostate cancer aggressiveness. In this study, we investigated and validated the association between SFRP4 gene expression and aggressiveness in nine independent cohorts (n = 2157). By differential expression and combined meta-analysis of all cohorts, we detected significantly higher SFRP4 expression in cancer compared with normal samples, and in high (3–5) compared with low (1–2) Grade Group samples. SFRP4 expression was a significant predictor of biochemical recurrence in six of seven cohorts and in the overall analysis, and was a significant predictor of metastatic event in one cohort. In our study cohort, where metabolic information was available, SFRP4 expression correlated significantly with the concentrations of citrate and spermine, two previously suggested biomarkers for aggressive prostate cancer. SFRP4 immunohistochemistry in an independent cohort (n = 33) was not associated with aggressiveness. To conclude, high SFRP4 gene expression is associated with high Grade Group and recurrent prostate cancer after surgery. Future studies investigating the mechanistic and clinical usefulness of SFRP4 in prostate cancer are warranted.
Hemoglobin variants shape the distribution of malaria parasites in human populations and their transmission potential
Authors: Gonçalves Bronner P. , Sagara Issaka , Coulibaly Mamadou , Wu Yimin , Assadou Mahamadoun H. , Guindo Agnes , Ellis Ruth D. , Diakite Mahamadou , Gabriel Erin , Prevots D. Rebecca , Doumbo Ogobara K. , Duffy Patrick E. 
Published: October 2017

AbstractHemoglobin variants C and S protect against severe malaria but their influence on parameters not directly linked to disease severity such as gametocyte carriage and infection chronicity is less well understood. To assess whether these infection-related phenotypes depend on the host hemoglobin genotype, we followed 500 Malian individuals over 1–2 years and determined their parasitological status during monthly visits and incidental clinical episodes. While adults heterozygous for hemoglobin S mutation were less often parasitemic compared to AA adults (odds ratio [OR] 0.50 95% confidence interval [CI] 0.31–0.79, P = 0.003), schoolchildren (but not toddlers or adults) with AC genotype carried parasites, including gametocytes, more often than their AA counterparts (OR 3.01 95% CI 1.38–6.57, P = 0.006). AC children were also likelier to be parasite-positive during the dry season, suggesting longer infections, and were more infectious in mosquito skin feeding assays than AA children. Notably, AC school-aged children, who comprise ~5% of the population, harbor a third of infections with patent gametocytes between May and August, when transmission transitions from very low to intense. These findings indicate that schoolchildren with hemoglobin C mutation might contribute disproportionately to the seasonal malaria resurgence in parts of West Africa where the HbC variant is common.
Electronic Cigarette Smoke Impairs Normal Mesenchymal Stem Cell Differentiation
Authors: Shaito A. , Saliba J. , Husari A. , El-Harakeh M. , Chhouri H. , Hashem Y. , Shihadeh A. , El-Sabban M. 
Published: October 2017

AbstractElectronic cigarettes (e-cigarettes) are promoted as low-risk alternatives to combustible cigarettes. However, the effects of chronic inhalation of potential toxicants emitted by ecigarettes remain largely unexamined. It is conceivable that smoking-induced chronic diseases result in cellular injury, in the absence of effective repair by stem cells. This study evaluates the effect of cigarette and e-cigarette aerosol extracts on the survival and differentiation of bone marrow-derived mesenchymal stem cells (MSCs). MSC growth and osteogenic differentiation were examined after exposure to smoke extracts. Data revealed detrimental effects of both cigarette and e-cigarette extracts on MSC morphology and growth. Levels and activity of alkaline phosphatase, an osteogenic marker, decreased and induction of osteoblastic differentiation was impaired. Both smoke extracts prevented osteogenic differentiation from progressing, evident by decreased expression of terminal osteogenic markers and mineralization. Elevated levels of reactive oxygen species (ROS) were detected in cells exposed to smoke extracts. Moreover, decreased differentiation potential was concomitant with severe down-regulation of Connexin 43 expression, leading to the loss of gap junction-mediated communication, which together with elevated ROS levels, could explain decreased proliferation and loss of differentiation potential. Hence, e-cigarettes present similar risk as combustible cigarettes with respect to tissue repair impairment.
Yeast diversity in relation to the production of fuels and chemicals
Authors: Wu Jia , Elliston Adam , Le Gall Gwenaelle , Colquhoun Ian J. , Collins Samuel R. A. , Dicks Jo , Roberts Ian N. , Waldron Keith W. 
Published: October 2017

AbstractIn addition to ethanol, yeasts have the potential to produce many other industrially-relevant chemicals from numerous different carbon sources. However there remains a paucity of information about overall capability across the yeast family tree. Here, 11 diverse species of yeasts with genetic backgrounds representative of different branches of the family tree were investigated. They were compared for their abilities to grow on a range of sugar carbon sources, to produce potential platform chemicals from such substrates and to ferment hydrothermally pretreated rice straw under simultaneous saccharification and fermentation conditions. The yeasts differed considerably in their metabolic capabilities and production of ethanol. A number could produce significant amounts of ethyl acetate, arabinitol, glycerol and acetate in addition to ethanol, including from hitherto unreported carbon sources. They also demonstrated widely differing efficiencies in the fermentation of sugars derived from pre-treated rice straw biomass and differential sensitivities to fermentation inhibitors. A new catabolic property of Rhodotorula mucilaginosa (NCYC 65) was discovered in which sugar substrate is cleaved but the products are not metabolised. We propose that engineering this and some of the other properties discovered in this study and transferring such properties to conventional industrial yeast strains could greatly expand their biotechnological utility.
A Hybrid Gate Dielectrics of Ion Gel with Ultra-Thin Passivation Layer for High-Performance Transistors Based on Two-Dimensional Semiconductor Channels
Authors: Jo Hyunjin , Choi Jeong-Hun , Hyun Cheol-Min , Seo Seung-Young , Kim Da Young , Kim Chang-Min , Lee Myoung-Jae , Kwon Jung-Dae , Moon Hyoung-Seok , Kwon Se-Hun , Ahn Ji-Hoon 
Published: October 2017

AbstractWe propose a hybrid gate structure for ion gel dielectrics using an ultra-thin Al2O3 passivation layer for realizing high-performance devices based on electric-double-layer capacitors. Electric-double-layer transistors can be applied to practical devices with flexibility and transparency as well as research on the fundamental physical properties of channel materials; however, they suffer from inherent unwanted leakage currents between electrodes, especially for channel materials with low off-currents. Therefore, the Al2O3 passivation layer was introduced between the metal electrodes and ion gel film as a leakage current barrier; this simple approach effectively reduced the leakage current without capacitance degradation. In addition, we confirmed that a monolayer MoS2 transistor fabricated with the proposed hybrid gate dielectric exhibited remarkably enhanced device properties compared to a transistor using a normal ion gel gate dielectric. Our findings on a simple method to improve the leakage current properties of ion gels could be applied extensively to realize high-performance electric-double-layer transistors utilizing various channel materials.
The role of Thyroid Transcription Factor-1 and Tumor differentiation in Resected Lung Adenocarcinoma
Authors: Huang Tsai-Wang , Lin Ke- Feng , Lee Chien-Hsing , Chang Hung , Lee Shih-Chun , Shieh Yi-Shing 
Published: October 2017

AbstractTo investigate the role of thyroid transcription factor-1 (TTF-1) and tumor differentiation in resected lung adenocarcinoma. A total of 520 patients with clinical early stage lung adenocarcinoma who underwent surgical resection were reviewed retrospectively. Clinical data and outcomes were evaluated with an average follow-up of 117 months. The results were validated via lung cancer cell line studies. The clinical parameters did not differ between relapse and nonrelapse patients. Exceptions were tumor differentiation, lymphovascular space invasion, F18-fluorodeoxyglucose maximum standard uptake value, tumor size, and pathological stage (p < 0.001). Poor tumor differentiation was the independent prognostic factor (odds ratio: 2.937,p = 0.026). The expression of TTF-1 was correlated with tumor differentiation in resected lung adenocarcinoma patients (p < 0.001). Five-year survival was 60.0% for score 1 TTF-1 expression patients, 80.1% for score 2 TTF-1 expression patients, and 86.1% for score 3 TTF-1 expression group patients. The lung cancer cell line study of knockdown and overexpression of TTF-1 revealed TTF-1 mediated High Mobility Group AT-Hook 2 (HMGA2) protein involved with epithelium-mesenchymal transformation. The chromatin immunoprecipitation revealed TTF-1 regulated HMGA2 via direct binding. TTF-1/HMGA2 axis was associated with tumor differentiation and mediated the aggressiveness of the tumor and prognosis.
Development of a Curative Therapeutic Vaccine (TheraVac) for the Treatment of Large Established Tumors
Authors: Nie Yingjie , Yang De , Trivett Anna , Han Zhen , Xin Haiyun , Chen Xin , Oppenheim Joost J. 
Published: October 2017

AbstractHarnessing immune system to treat cancer requires simultaneous generation of tumor-specific CTLs and curtailment of tumor immunosuppressive environment. Here, we developed an immunotherapeutic regimen capable of eliminating large established mouse tumors using HMGN1, a DC-activating TLR4 agonist capable of inducing anti-tumor immunity. Intratumoral delivery of HMGN1 with low dose of Cytoxan cured mice bearing small (∅ ≈ 0.5 cm), but not large (∅ ≈ 1.0 cm) CT26 tumors. Screening for activators capable of synergizing with HMGN1 in activating DC identified R848. Intratumoral delivery of HMGN1 and R848 plus Cytoxan eradicated large established CT26 tumors. The resultant tumor-free mice were resistant to subsequent challenge with CT26, indicating the generation of CT26-specific protective immunity. This immunotherapeutic regimen caused homing of tumor-infiltrating DC to draining lymph nodes and increased infiltration of T cells into tumor tissues. Cytoxan in this regimen could be replaced by anti-CTLA4) or anti-PD-L1. Importantly, this immunotherapeutic regimen was also curative for large established mouse Renca and EG7 tumors. Thus, we have developed a curative therapeutic vaccination regimen dubbed ‘TheraVac’ consisting of HMGN1 and R848 plus a checkpoint inhibitor, that can, without using exogenous tumor-associated antigen(s), eliminate various large tumors and induce tumor-specific immunity.
High potential thermoelectric figure of merit in ternary La3Cu3X4 (X = P, As, Sb and Bi) compounds
Authors: Pandey Tribhuwan , Parker David S. 
Published: October 2017

AbstractWe investigate the thermoelectric properties of the relatively unexplored rare-earth ternary compounds La3Cu3X4 (X = Bi, Sb, As, and P) using first principles electronic structure and Boltzmann transport calculations. These compounds, of which the La3Cu3Sb4 and La3Cu3Bi4 have previously been synthesized, are all predicted to be semiconductors and present a wide range of bandgaps varying from 0.24 eV (for the Bi compound) to 0.87 eV (for the P compound). We further find a mixture of light and heavy bands, which results in a high thermoelectric power factor. In addition, as discussed in our previous study (Phys. Rev. B 95 (22), 224306, 2017) at high temperatures of 1000 K these compounds exhibit lattice thermal conductivity less than 1 W/mK. The combination of low thermal conductivity and good transport properties results in a predicted ZT as high as ~1.5 for both La3Cu3P4 and La3Cu3As4, under high p-type doping. This predicted high performance makes these compounds promising candidates for high temperature thermoelectric applications and thus merits further experimental investigation.
Retinal Pigment Epithelium Sequelae Caused by Blunt Ocular Trauma: Incidence, Visual Outcome, and Associated Factors
Authors: Ahn Seong Joon , Woo Se Joon , Park Kyu Hyung , Lee Byung Ro 
Published: October 2017

AbstractVision loss can occur in eyes with blunt ocular trauma, but the causes have not been elucidated fully. We encountered cases of retinal pigment epithelium (RPE) sequelae following blunt ocular trauma associated with permanent vision loss in our cohort of patients with blunt ocular trauma. In this multicentre retrospective cohort study on 129 patients with retinal abnormalities caused by acute blunt ocular trauma, we investigated the incidence of RPE sequelae and evaluated associated factors and visual outcomes. RPE sequelae, which typically presented as hyperpigmentation within well-demarcated hypopigmented lesions, occurred in 29 (22.5%) patients within 1 month of trauma. Optical coherence tomography (OCT) revealed complete photoreceptor loss over the abnormal RPE. Final visual outcomes were significantly different between eyes with and without RPE sequelae. Logistic regression analysis revealed a significant association between the presence of subretinal fluid and RPE sequelae. In conclusion, RPE sequelae occurred in approximately 20% of patients with blunt ocular trauma and was associated with permanent photoreceptor defects and visual loss. Clinical evaluation using OCT may help predict RPE sequelae and visual outcomes in eyes with blunt trauma.
Oligomerization and ATP stimulate condensin-mediated DNA compaction
Authors: Keenholtz Ross A. , Dhanaraman Thillaivillalan , Palou Roger , Yu Jia , D’Amours Damien , Marko John F. 
Published: October 2017

AbstractLarge-scale chromatin remodeling during mitosis is catalyzed by a heteropentameric enzyme known as condensin. The DNA-organizing mechanism of condensin depends on the energy of ATP hydrolysis but how this activity specifically promotes proper compaction and segregation of chromosomes during mitosis remains poorly understood. Purification of budding yeast condensin reveals that it occurs not only in the classical heteropentameric “monomer” form, but that it also adopts much larger configurations consistent with oligomerization. We use a single-DNA magnetic tweezers assay to study compaction of DNA by yeast condensin, with the result that only the multimer shows ATP-enhanced DNA-compaction. The compaction reaction involves step-like events of 200 nm (600 bp) size and is strongly suppressed by forces above 1 pN, consistent with a loop-capture mechanism for initial binding and compaction. The compaction reactions are largely insensitive to DNA torsional stress. Our results suggest a physiological role for oligomerized condensin in driving gradual chromatin compaction by step-like and slow “creeping” dynamics consistent with a loop-extrusion mechanism.
Genetic diversity and structure of wild and cultivated Amorphophallus paeoniifolius populations in southwestern China as revealed by RAD-seq
Authors: Gao Yong , Yin Si , Wu Lifang , Dai Dongqin , Wang Haibo , Liu Chao , Tang Lizhou 
Published: October 2017

AbstractAmorphophallus paeoniifolius, is a commercially important vegetable crop because of its high production potential. In this study, we generated a total of 166 Gb of genomic data from 16 wild and 20 cultivated A. paeoniifolius individuals in southwestern China using restriction site associated DNA sequencing (RAD-seq). We compared the genome-wide variations between the wild and cultivated populations. Wild populations exhibited higher genetic diversity than did cultivated populations based on private allele number, expected heterozygosity, observed heterozygosity and nucleotide diversity. STRUCTURE analysis, principal component analysis (PCA) and a maximum likelihood (ML) tree indicated that A. paeoniifolius populations could be divided into three groups (a cultivated group and two wild groups) with significant genetic differentiation. The low genetic diversity and shallow genetic differentiation found within cultivated populations are likely caused by continuous selection and the clonal propagation methods used during domestication. The significant differentiation between the wild populations may suggest strong genetic drift due to small populations and human disturbance. The genome-wide single nucleotide polymorphisms (SNPs) identified in our study will provide a valuable resource for further breeding improvement and effective use of the germplasm.