bluuebunny/crossref_metadata_2025_split huggingface dataset:
Islamic Culture, Oil, and Women's Rights Revisited
Authors: Rørbæk Lasse Lykke 
Published: February 2016

AbstractAccording to recent research, oil abundance is the principal explanation for women's poor human rights record in many Muslim societies. However, this study argues that resistance to gender equality in the Muslim world originates in its specific historical trajectory and that the critical juncture precedes the extraction of oil by a thousand years. The study assesses data on women's economic, social, and political rights in 166 countries from 1999–2008 and shows that whereas the negative effect of oil is driven by the 11 members of the Organization of Arab Petroleum Exporting Countries, Muslim countries consistently underperform even when oil and gas rents and other relevant factors such as income and democracy are accounted for. The study concludes that persisting orthodox tendencies in Islamic culture provide the best explanation for Muslim women's limited empowerment.
αTAT1 downregulation induces mitotic catastrophe in HeLa and A549 cells
Authors: Chien J-Y , Tsen S-D , Chien C-C , Liu H-W , Tung C-Y , Lin C-H 
Published: February 2016

Abstractα-Tubulin acetyltransferase 1 (αTAT1) controls reversible acetylation on Lys40 of α-tubulin and modulates multiple cellular functions. αTAT1 depletion induced morphological defects of touch receptor neurons in Caenorhabditis elegans and impaired cell adhesion and contact inhibition in mouse embryonic fibroblasts, however, no morphological or proliferation defects in human RPE-hTERT cells were found after αTAT1-specific siRNA treatment. Here, we compared the effect of three αTAT1-specific shRNAs on proliferation and morphology in two human cell lines, HeLa and A549. The more efficient two shRNAs induced mitotic catastrophe in both cell lines and the most efficient one also decreased F-actin and focal adhesions. Further analysis revealed that αTAT1 downregulation increased γ-H2AX, but not other DNA damage markers p-CHK1 and p-CHK2, along with marginal change in microtubule outgrowth speed and inter-kinetochore distance. Overexpression of αTAT1 could not precisely mimic the distribution and concentration of endogenous acetylated α-tubulin (Ac-Tu), although no overt phenotype change was observed, meanwhile, this could not completely prevent αTAT1 downregulation-induced deficiencies. We therefore conclude that efficient αTAT1 downregulation could impair actin architecture and induce mitotic catastrophe in HeLa and A549 cells through mechanisms partly independent of Ac-Tu.
Off-stoichiometry improves the photostructuring of thiol–enes through diffusion-induced monomer depletion
Authors: Hillmering Mikael , Pardon Gaspard , Vastesson Alexander , Supekar Omkar , Carlborg Carl Fredrik , Brandner Birgit D. , van der Wijngaart Wouter , Haraldsson Tommy 
Published: February 2016

AbstractThiol–enes are a group of alternating copolymers with highly ordered networks and are used in a wide range of applications. Here, “click” chemistry photostructuring in off-stoichiometric thiol–enes is shown to induce microscale polymeric compositional gradients due to species diffusion between non-illuminated and illuminated regions, creating two narrow zones with distinct compositions on either side of the photomask feature boundary: a densely cross-linked zone in the illuminated region and a zone with an unpolymerized highly off-stoichiometric monomer composition in the non-illuminated region. Using confocal Raman microscopy, it is here explained how species diffusion causes such intricate compositional gradients in the polymer and how off-stoichiometry results in improved image transfer accuracy in thiol–ene photostructuring. Furthermore, increasing the functional group off-stoichiometry and decreasing the photomask feature size is shown to amplify the induced gradients, which potentially leads to a new methodology for microstructuring.
Prediction of an arc-tunable Weyl Fermion metallic state in MoxW1−xTe2
Authors: Chang Tay-Rong , Xu Su-Yang , Chang Guoqing , Lee Chi-Cheng , Huang Shin-Ming , Wang BaoKai , Bian Guang , Zheng Hao , Sanchez Daniel S. , Belopolski Ilya , Alidoust Nasser , Neupane Madhab , Bansil Arun , Jeng Horng-Tay , Lin Hsin , Zahid Hasan M. 
Published: February 2016

AbstractA Weyl semimetal is a new state of matter that hosts Weyl fermions as emergent quasiparticles. The Weyl fermions correspond to isolated points of bulk band degeneracy, Weyl nodes, which are connected only through the crystal’s boundary by exotic Fermi arcs. The length of the Fermi arc gives a measure of the topological strength, because the only way to destroy the Weyl nodes is to annihilate them in pairs in the reciprocal space. To date, Weyl semimetals are only realized in the TaAs class. Here, we propose a tunable Weyl state in MoxW1−xTe2 where Weyl nodes are formed by touching points between metallic pockets. We show that the Fermi arc length can be changed as a function of Mo concentration, thus tuning the topological strength. Our results provide an experimentally feasible route to realizing Weyl physics in the layered compound MoxW1−xTe2, where non-saturating magneto-resistance and pressure-driven superconductivity have been observed.
GAME9 regulates the biosynthesis of steroidal alkaloids and upstream isoprenoids in the plant mevalonate pathway
Authors: Cárdenas Pablo D. , Sonawane Prashant D. , Pollier Jacob , Vanden Bossche Robin , Dewangan Veena , Weithorn Efrat , Tal Lior , Meir Sagit , Rogachev Ilana , Malitsky Sergey , Giri Ashok P. , Goossens Alain , Burdman Saul , Aharoni Asaph 
Published: February 2016

AbstractSteroidal glycoalkaloids (SGAs) are cholesterol-derived molecules produced by solanaceous species. They contribute to pathogen defence but are toxic to humans and considered as anti-nutritional compounds. Here we show that GLYCOALKALOID METABOLISM 9 (GAME9), an APETALA2/Ethylene Response Factor, related to regulators of alkaloid production in tobacco and Catharanthus roseus, controls SGA biosynthesis. GAME9 knockdown and overexpression in tomato and potato alters expression of SGAs and upstream mevalonate pathway genes including the cholesterol biosynthesis gene STEROL SIDE CHAIN REDUCTASE 2 (SSR2). Levels of SGAs, C24-alkylsterols and the upstream mevalonate and cholesterol pathways intermediates are modified in these plants. Δ(7)-STEROL-C5(6)-DESATURASE (C5-SD) in the hitherto unresolved cholesterol pathway is a direct target of GAME9. Transactivation and promoter-binding assays show that GAME9 exerts its activity either directly or cooperatively with the SlMYC2 transcription factor as in the case of the C5-SD gene promoter. Our findings provide insight into the regulation of SGA biosynthesis and means for manipulating these metabolites in crops.
Non-equilibrium behaviour in coacervate-based protocells under electric-field-induced excitation
Authors: Yin Yudan , Niu Lin , Zhu Xiaocui , Zhao Meiping , Zhang Zexin , Mann Stephen , Liang Dehai 
Published: February 2016

AbstractAlthough numerous strategies are now available to generate rudimentary forms of synthetic cell-like entities, minimal progress has been made in the sustained excitation of artificial protocells under non-equilibrium conditions. Here we demonstrate that the electric field energization of coacervate microdroplets comprising polylysine and short single strands of DNA generates membrane-free protocells with complex, dynamical behaviours. By confining the droplets within a microfluidic channel and applying a range of electric field strengths, we produce protocells that exhibit repetitive cycles of vacuolarization, dynamical fluctuations in size and shape, chaotic growth and fusion, spontaneous ejection and sequestration of matter, directional capture of solute molecules, and pulsed enhancement of enzyme cascade reactions. Our results highlight new opportunities for the study of non-equilibrium phenomena in synthetic protocells, provide a strategy for inducing complex behaviour in electrostatically assembled soft matter microsystems and illustrate how dynamical properties can be activated and sustained in microcompartmentalized media.
Directed block copolymer self-assembly implemented via surface-embedded electrets
Authors: Wu Mei-Ling , Wang Dong , Wan Li-Jun 
Published: February 2016

AbstractBlock copolymer (BCP) nanolithography is widely recognized as a promising complementary approach to circumvent the feature size limits of conventional photolithography. The directed self-assembly of BCP thin film to form ordered nanostructures with controlled orientation and localized pattern has been the key challenge for practical nanolithography applications. Here we show that BCP nanopatterns can be directed on localized surface electrets defined by electron-beam irradiation to realize diverse features in a simple, effective and non-destructive manner. Charged electrets can generate a built-in electric field in BCP thin film and induce the formation of perpendicularly oriented microdomain of BCP film. The electret-directed orientation control of BCP film can be either integrated with mask-based patterning technique or realized by electron-beam direct-writing method to fabricate microscale arbitrary lateral patterns down to single BCP cylinder nanopattern. The electret-directed BCP self-assembly could provide an alternative means for BCP-based nanolithography, with high resolution.
Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea
Authors: Baker Brett J. , Saw Jimmy H. , Lind Anders E. , Lazar Cassandre Sara , Hinrichs Kai-Uwe , Teske Andreas P. , Ettema Thijs J. G. 
Published: February 2016

AbstractThe subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes1. Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface2–4, the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are unknown. Here, we report the metabolic capabilities of this enigmatic group as inferred from genomic reconstructions. Four high-quality (63–90% complete) genomes were obtained from White Oak River estuary and Yellowstone National Park hot spring sediment metagenomes. Phylogenomic analyses place SAGMEG Archaea as a deeply rooting sister clade of the Thermococci, leading us to propose the name Hadesarchaea for this new Archaeal class. With an estimated genome size of around 1.5 Mbp, the genomes of Hadesarchaea are distinctly streamlined, yet metabolically versatile. They share several physiological mechanisms with strict anaerobic Euryarchaeota. Several metabolic characteristics make them successful in the subsurface, including genes involved in CO and H2 oxidation (or H2 production), with potential coupling to nitrite reduction to ammonia (DNRA). This first glimpse into the metabolic capabilities of these cosmopolitan Archaea suggests they are mediating key geochemical processes and are specialized for survival in the subsurface biosphere.
Gain of function of mutant p53: R282W on the peak?
Authors: Zhang Y , Coillie S V , Fang J-Y , Xu J 
Published: February 2016

AbstractMutant p53 proteins commonly lose their tumor suppression function and gain novel oncogenic functions (gain of function (GOF)). Different p53 mutations are often considered in one class in biological and clinical studies. However, recent studies have revealed that p53 mutations are biologically and clinically distinct. The R282W mutant associates with earlier onset of familial cancers and poorer outcome of cancer patients, suggesting a more prominent GOF effect of this specific mutant. Here we discuss our current understanding on the multifaceted effects of R282W mutation, including its structural features, signaling pathways and clinical implications. The destabilizing nature, aggregation proneness, altered transcriptome and interactome may collaboratively contribute to the unique phenotype of R282W mutation. The quest for mechanistic insights into the unique GOF effects of R282W mutation would further our understanding of the biology of mutant proteins in cancers, and enforce the development of more effective targeted therapies.
Gr/gr deletions on Y-chromosome correlate with male infertility: an original study, meta-analyses and trial sequential analyses
Authors: Bansal Sandeep Kumar , Jaiswal Deepika , Gupta Nishi , Singh Kiran , Dada Rima , Sankhwar Satya Narayan , Gupta Gopal , Rajender Singh 
Published: February 2016

AbstractWe analyzed the AZFc region of the Y-chromosome for complete (b2/b4) and distinct partial deletions (gr/gr, b1/b3, b2/b3) in 822 infertile and 225 proven fertile men. We observed complete AZFc deletions in 0.97% and partial deletions in 6.20% of the cases. Among partial deletions, the frequency of gr/gr deletions was the highest (5.84%). The comparison of partial deletion data between cases and controls suggested a significant association of the gr/gr deletions with infertility (P = 0.0004); however, the other partial deletions did not correlate with infertility. In cohort analysis, men with gr/gr deletions had a relatively poor sperm count (54.20 ± 57.45 million/ml) in comparison to those without deletions (72.49 ± 60.06), though the difference was not statistically significant (p = 0.071). Meta-analysis also suggested that gr/gr deletions are significantly associated with male infertility risk (OR = 1.821, 95% CI = 1.39–2.37, p = 0.000). We also performed trial sequential analyses that strengthened the evidence for an overall significant association of gr/gr deletions with the risk of male infertility. Another meta-analysis suggested a significant association of the gr/gr deletions with low sperm count. In conclusion, the gr/gr deletions show a strong correlation with male infertility risk and low sperm count, particularly in the Caucasian populations.
Correlation between topological band character and chemical bonding in a Bi14Rh3I9-based family of insulators
Authors: Rasche Bertold , Isaeva Anna , Ruck Michael , Koepernik Klaus , Richter Manuel , van den Brink Jeroen 
Published: February 2016

AbstractRecently the presence of topologically protected edge-states in Bi14Rh3I9 was confirmed by scanning tunnelling microscopy consolidating this compound as a weak 3D topological insulator (TI). Here, we present a density-functional-theory-based study on a family of TIs derived from the Bi14Rh3I9 parent structure via substitution of Ru, Pd, Os, Ir and Pt for Rh. Comparative analysis of the band-structures throughout the entire series is done by means of a unified minimalistic tight-binding model that evinces strong similarity between the quantum-spin-Hall (QSH) layer in Bi14Rh3I9 and graphene in terms of "Equation missing"-molecular orbitals. Topologically non-trivial energy gaps are found for the Ir-, Rh-, Pt- and Pd-based systems, whereas the Os- and Ru-systems remain trivial. Furthermore, the energy position of the metal "Equation missing"-band centre is identified as the parameter which governs the evolution of the topological character of the band structure through the whole family of TIs. The "Equation missing"-band position is shown to correlate with the chemical bonding within the QSH layers, thus revealing how the chemical nature of the constituents affects the topological band character.
Asymmetric Preorganization of Inverted Pair Residues in the Sodium-Calcium Exchanger
Authors: Giladi Moshe , Almagor Lior , van Dijk Liat , Hiller Reuben , Man Petr , Forest Eric , Khananshvili Daniel 
Published: February 2016

AbstractIn analogy with many other proteins, Na+/Ca2+ exchangers (NCX) adapt an inverted twofold symmetry of repeated structural elements, while exhibiting a functional asymmetry by stabilizing an outward-facing conformation. Here, structure-based mutant analyses of the Methanococcus jannaschii Na+/Ca2+ exchanger (NCX_Mj) were performed in conjunction with HDX-MS (hydrogen/deuterium exchange mass spectrometry) to identify the structure-dynamic determinants of functional asymmetry. HDX-MS identified hallmark differences in backbone dynamics at ion-coordinating residues of apo-NCX_Mj, whereas Na+or Ca2+ binding to the respective sites induced relatively small, but specific, changes in backbone dynamics. Mutant analysis identified ion-coordinating residues affecting the catalytic capacity (kcat/Km), but not the stability of the outward-facing conformation. In contrast, distinct “noncatalytic” residues (adjacent to the ion-coordinating residues) control the stability of the outward-facing conformation, but not the catalytic capacity. The helix-breaking signature sequences (GTSLPE) on the α1 and α2 repeats (at the ion-binding core) differ in their folding/unfolding dynamics, while providing asymmetric contributions to transport activities. The present data strongly support the idea that asymmetric preorganization of the ligand-free ion-pocket predefines catalytic reorganization of ion-bound residues, where secondary interactions with adjacent residues couple the alternating access. These findings provide a structure-dynamic basis for ion-coupled alternating access in NCX and similar proteins.
Tissue Metabonomic Phenotyping for Diagnosis and Prognosis of Human Colorectal Cancer
Authors: Tian Yuan , Xu Tangpeng , Huang Jia , Zhang Limin , Xu Shan , Xiong Bin , Wang Yulan , Tang Huiru 
Published: February 2016

AbstractColorectal cancer (CRC) is one of the leading causes of cancer-related death worldwide and prognosis based on the conventional histological grading method for CRC remains poor. To better the situation, we analyzed the metabonomic signatures of 50 human CRC tissues and their adjacent non-involved tissues (ANIT) using high-resolution magic-angle spinning (HRMAS) 1H NMR spectroscopy together with the fatty acid compositions of these tissues using GC-FID/MS. We showed that tissue metabolic phenotypes not only discriminated CRC tissues from ANIT, but also distinguished low-grade tumor tissues (stages I-II) from the high-grade ones (stages III-IV) with high sensitivity and specificity in both cases. Metabonomic phenotypes of CRC tissues differed significantly from that of ANIT in energy metabolism, membrane biosynthesis and degradations, osmotic regulations together with the metabolism of proteins and nucleotides. Amongst all CRC tissues, the stage I tumors exhibited largest differentiations from ANIT. The combination of the differentiating metabolites showed outstanding collective power for differentiating cancer from ANIT and for distinguishing CRC tissues at different stages. These findings revealed details in the typical metabonomic phenotypes associated with CRC tissues nondestructively and demonstrated tissue metabonomic phenotyping as an important molecular pathology tool for diagnosis and prognosis of cancerous solid tumors.
Selective potentiation of 2-APB-induced activation of TRPV1–3 channels by acid
Authors: Gao Luna , Yang Pu , Qin Peizhong , Lu Yungang , Li Xinxin , Tian Quan , Li Yang , Xie Chang , Tian Jin-bin , Zhang Chengwei , Tian Changlin , Zhu Michael X. , Yao Jing 
Published: February 2016

AbstractTemperature-sensitive TRP channels are important for responses to pain and inflammation, to both of which tissue acidosis is a major contributing factor. However, except for TRPV1, acid-sensing by other ThermoTRP channels remains mysterious. We show here that unique among TRPV1–3 channels, TRPV3 is directly activated by protons from cytoplasmic side. This effect is very weak and involves key cytoplasmic residues L508, D512, S518, or A520. However, mutations of these residues did not affect a strong proton induced potentiation of TRPV3 currents elicited by the TRPV1–3 common agonist, 2-aminoethoxydiphenyl borate (2-APB), no matter if the ligand was applied from extracellular or cytoplasmic side. The acid potentiation was common among TRPV1–3 and only seen with 2-APB-related ligands. Using 1H-nuclear magnetic resonance to examine the solution structures of 2-APB and its analogs, we observed striking structural differences of the boron-containing compounds at neutral/basic as compared to acidic pH, suggesting that a pH-dependent configuration switch of 2-APB-based drugs may underlie their functionality. Supporting this notion, protons also enhanced the inhibitory action of 2-APB on TRPM8. Collectively, our findings reveal novel insights into 2-APB action on TRP channels, which should facilitate the design of new drugs for these channels.
Critical POU domain residues confer Oct4 uniqueness in somatic cell reprogramming
Authors: Jin Wensong , Wang Lei , Zhu Fei , Tan Weiqi , Lin Wei , Chen Dahua , Sun Qinmiao , Xia Zongping 
Published: February 2016

AbstractThe POU domain transcription factor Oct4 plays critical roles in self-renewal and pluripotency of embryonic stem cells (ESCs). Together with Sox2, Klf4 and c-Myc, Oct4 can reprogram any other cell types to pluripotency, in which Oct4 is the only factor that cannot be functionally replaced by other POU family members. To investigate the determinant elements of Oct4 uniqueness, we performed Ala scan on all Ser, Thr, Tyr, Lys and Arg of murine Oct4 by testing their capability in somatic cell reprogramming. We uncovered a series of residues that are important for Oct4 functionality, in which almost all of these key residues are within the POU domains making direct interaction with DNA. The Oct4 N- and C-terminal transactivation domains (TADs) are not unique and could be replaced by the Yes-associated protein (YAP) TAD domain to support reprogramming. More importantly, we uncovered two important residues that confer Oct4 uniqueness in somatic cell reprogramming. Our systematic structure-function analyses bring novel mechanistic insight into the molecular basis of how critical residues function together to confer Oct4 uniqueness among POU family for somatic cell reprogramming.
Hydrogen Sulfide—Mechanisms of Toxicity and Development of an Antidote
Authors: Jiang Jingjing , Chan Adriano , Ali Sameh , Saha Arindam , Haushalter Kristofer J. , Lam Wai-Ling Macrina , Glasheen Megan , Parker James , Brenner Matthew , Mahon Sari B. , Patel Hemal H. , Ambasudhan Rajesh , Lipton Stuart A. , Pilz Renate B. , Boss Gerry R. 
Published: February 2016

AbstractHydrogen sulfide is a highly toxic gas—second only to carbon monoxide as a cause of inhalational deaths. Its mechanism of toxicity is only partially known and no specific therapy exists for sulfide poisoning. We show in several cell types, including human inducible pluripotent stem cell (hiPSC)-derived neurons, that sulfide inhibited complex IV of the mitochondrial respiratory chain and induced apoptosis. Sulfide increased hydroxyl radical production in isolated mouse heart mitochondria and F2-isoprostanes in brains and hearts of mice. The vitamin B12 analog cobinamide reversed the cellular toxicity of sulfide and rescued Drosophila melanogaster and mice from lethal exposures of hydrogen sulfide gas. Cobinamide worked through two distinct mechanisms: direct reversal of complex IV inhibition and neutralization of sulfide-generated reactive oxygen species. We conclude that sulfide produces a high degree of oxidative stress in cells and tissues and that cobinamide has promise as a first specific treatment for sulfide poisoning.