bluuebunny/crossref_metadata_2025_split huggingface dataset:
Superconductor to Mott insulator transition in YBa2Cu3O7/LaCaMnO3 heterostructures
Authors: Gray B. A. , Middey S. , Conti G. , Gray A. X. , Kuo C.-T. , Kaiser A. M. , Ueda S. , Kobayashi K. , Meyers D. , Kareev M. , Tung I. C. , Liu Jian , Fadley C. S. , Chakhalian J. , Freeland J. W. 
Published: September 2016

AbstractThe superconductor-to-insulator transition (SIT) induced by means such as external magnetic fields, disorder or spatial confinement is a vivid illustration of a quantum phase transition dramatically affecting the superconducting order parameter. In pursuit of a new realization of the SIT by interfacial charge transfer, we developed extremely thin superlattices composed of high Tc superconductor YBa2Cu3O7 (YBCO) and colossal magnetoresistance ferromagnet La0.67Ca0.33MnO3 (LCMO). By using linearly polarized resonant X-ray absorption spectroscopy and magnetic circular dichroism, combined with hard X-ray photoelectron spectroscopy, we derived a complete picture of the interfacial carrier doping in cuprate and manganite atomic layers, leading to the transition from superconducting to an unusual Mott insulating state emerging with the increase of LCMO layer thickness. In addition, contrary to the common perception that only transition metal ions may respond to the charge transfer process, we found that charge is also actively compensated by rare-earth and alkaline-earth metal ions of the interface. Such deterministic control of Tc by pure electronic doping without any hindering effects of chemical substitution is another promising route to disentangle the role of disorder on the pseudo-gap and charge density wave phases of underdoped cuprates.
Extension of the classical classification of β-turns
Authors: de Brevern Alexandre G. 
Published: September 2016

AbstractThe functional properties of a protein primarily depend on its three-dimensional (3D) structure. These properties have classically been assigned, visualized and analysed on the basis of protein secondary structures. The β-turn is the third most important secondary structure after helices and β-strands. β-turns have been classified according to the values of the dihedral angles φ and ψ of the central residue. Conventionally, eight different types of β-turns have been defined, whereas those that cannot be defined are classified as type IV β-turns. This classification remains the most widely used. Nonetheless, the miscellaneous type IV β-turns represent 1/3rdof β-turn residues. An unsupervised specific clustering approach was designed to search for recurrent new turns in the type IV category. The classical rules of β-turn type assignment were central to the approach. The four most frequently occurring clusters defined the new β-turn types. Unexpectedly, these types, designated IV1, IV2, IV3and IV4, represent half of the type IV β-turns and occur more frequently than many of the previously established types. These types show convincing particularities, in terms of both structures and sequences that allow for the classical β-turn classification to be extended for the first time in 25 years.
The Tetraodon nigroviridis reference transcriptome: developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome
Authors: Basu Swaraj , Hadzhiev Yavor , Petrosino Giuseppe , Nepal Chirag , Gehrig Jochen , Armant Olivier , Ferg Marco , Strahle Uwe , Sanges Remo , Müller Ferenc 
Published: September 2016

AbstractPufferfish such as fugu and tetraodon carry the smallest genomes among all vertebrates and are ideal for studying genome evolution. However, comparative genomics using these species is hindered by the poor annotation of their genomes. We performed RNA sequencing during key stages of maternal to zygotic transition of Tetraodon nigroviridis and report its first developmental transcriptome. We assembled 61,033 transcripts (23,837 loci) representing 80% of the annotated gene models and 3816 novel coding transcripts from 2667 loci. We demonstrate the similarities of gene expression profiles between pufferfish and zebrafish during maternal to zygotic transition and annotated 1120 long non-coding RNAs (lncRNAs) many of which differentially expressed during development. The promoters for 60% of the assembled transcripts result validated by CAGE-seq. Despite the extreme compaction of the tetraodon genome and the dramatic loss of transposons, the length of lncRNA exons remain comparable to that of other vertebrates and a small set of lncRNAs appears enriched for transposable elements suggesting a selective pressure acting on lncRNAs length and composition. Finally, a set of lncRNAs are microsyntenic between teleost and vertebrates, which indicates potential regulatory interactions between lncRNAs and their flanking coding genes. Our work provides a fundamental molecular resource for vertebrate comparative genomics and embryogenesis studies.
High steady-state column density of I(2P3/2) atoms from I2 photodissociation at 532 nm: Towards parity non-conservation measurements
Authors: Katsoprinakis G. E. , Chatzidrosos G. , Kypriotakis J. A. , Stratakis E. , Rakitzis T. P. 
Published: September 2016

AbstractSteady-state column densities of 1017 cm−2 of I(2P3/2) atoms are produced from photodissociation of I2 vapour at 290.5 K using 5 W of 532 nm laser light. Recombination of the I(2P3/2) atoms at the cell walls is minimized by coating the cell surface with a hydrophobic silane (dimethyldichlorosilane/DMDCS). Operation at room temperature, and at an I2 vapour pressure of ~0.2 mbar, without using a buffer gas, allows relatively low Lorentz and Doppler widths of ~2π × 1.5 (FWHM) and ~2π × 150 (HW at 1/e2) Mrad/s, respectively, at the "Equation missing" M1 transition of atomic iodine at 1315 nm. These high column densities and low linewidths are favorable for parity nonconservation optical rotation measurements near this M1 transition. Furthermore, as the cell is completely sealed, this method of production of high-density 127I(2P3/2) atoms is also compatible with using iodine radioisotopes, such as for the production of high-density 129I(2P3/2).
α-Synuclein is a Novel Microtubule Dynamase
Authors: Cartelli Daniele , Aliverti Alessandro , Barbiroli Alberto , Santambrogio Carlo , Ragg Enzio M. , Casagrande Francesca V.M. , Cantele Francesca , Beltramone Silvia , Marangon Jacopo , De Gregorio Carmelita , Pandini Vittorio , Emanuele Marco , Chieregatti Evelina , Pieraccini Stefano , Holmqvist Staffan , Bubacco Luigi , Roybon Laurent , Pezzoli Gianni , Grandori Rita , Arnal Isabelle , Cappelletti Graziella 
Published: September 2016

Abstractα-Synuclein is a presynaptic protein associated to Parkinson’s disease, which is unstructured when free in the cytoplasm and adopts α helical conformation when bound to vesicles. After decades of intense studies, α-Synuclein physiology is still difficult to clear up due to its interaction with multiple partners and its involvement in apletoraof neuronal functions. Here, we looked at the remarkably neglected interplay between α-Synuclein and microtubules, which potentially impacts on synaptic functionality. In order to identify the mechanisms underlying these actions, we investigated the interaction between purified α-Synuclein and tubulin. We demonstrated that α-Synuclein binds to microtubules and tubulin α2β2tetramer; the latter interaction inducing the formation of helical segment(s) in the α-Synuclein polypeptide. This structural change seems to enable α-Synuclein to promote microtubule nucleation and to enhance microtubule growth rate and catastrophe frequency, bothin vitroandin cell. We also showed that Parkinson’s disease-linked α-Synuclein variants do not undergo tubulin-induced folding and cause tubulin aggregation rather than polymerization. Our data enable us to propose α-Synuclein as a novel, foldable, microtubule-dynamase, which influences microtubule organisation through its binding to tubulin and its regulating effects on microtubule nucleation and dynamics.
Global analysis of differential gene expression related to long-term sperm storage in oviduct of Chinese Soft-Shelled Turtle Pelodiscus sinensis
Authors: Liu Tengfei , Yang Ping , Chen Hong , Huang Yufei , Liu Yi , Waqas Yasir , Ahmed Nisar , Chu Xiaoya , Chen Qiusheng 
Published: September 2016

AbstractImportant evolutionary and ecological consequences arise from the ability of female turtles to store viable spermatozoa for an extended period. Although previous morphological studies have observed the localization of spermatozoa inPelodiscus sinensisoviduct, no systematic study on the identification of genes that are involved in long-term sperm storage has been performed. In this study, the oviduct ofP. sinensisat different phases (reproductive and hibernation seasons) was prepared for RNA-Seq and gene expression profiling. In total, 2,662 differentially expressed genes (DEGs) including 1,224 up- and 1,438 down-regulated genes were identified from two cDNA libraries. Functional enrichment analysis indicated that many genes were predominantly involved in the immune response, apoptosis pathway and regulation of autophagy. RT-qPCR, ELISA, western blot and IHC analyses showed that the expression profiles of mRNA and protein in selected DEGs were in consistent with results from RNA-Seq analysis. Remarkably, TUNEL analysis revealed the reduced number of apoptotic cells during sperm storage. IHC and TEM analyses found that autophagy occurred in the oviduct epithelial cells, where the spermatozoa were closely attached. The outcomes of this study provide fundamental insights into the complex sperm storage regulatory process and facilitate elucidating the mechanism of sperm storage inP. sinensis.
CenH3 evolution reflects meiotic symmetry as predicted by the centromere drive model
Authors: Zedek František , Bureš Petr 
Published: September 2016

AbstractThe centromere drive model explaining rapid evolution of eukaryotic centromeres predicts higher frequency of positive selection acting on centromeric histone H3 (CenH3) in clades with asymmetric meiosis compared to the clades with only symmetric meiosis. However, despite the impression one might get from the literature, this key prediction of the centromere drive model has not only never been confirmed, but it has never been tested, because all the previous studies dealt only with the presence or absence instead of the frequency of positive selection. To provide evidence for or against different frequencies of positively selected CenH3 in asymmetrics and symmetrics, we have inferred the selective pressures acting on CenH3 in seventeen eukaryotic clades, including plants, animals, fungi, ciliates and apicomplexa, using codon-substitution models, and compared the inferred frequencies between asymmetrics and symmetrics in a quantitative manner. We have found that CenH3 has been evolving adaptively much more frequently in clades with asymmetric meiosis compared with clades displaying only symmetric meiosis which confirms the prediction of centromere drive model. Our findings indicate that the evolution of asymmetric meiosis required CenH3 to evolve adaptively more often to counterbalance the negative consequences of centromere drive.
Comparative DNA Methylation Profiling Reveals an Immunoepigenetic Signature of HIV-related Cognitive Impairment
Authors: Corley Michael J. , Dye Christian , D’Antoni Michelle L. , Byron Mary Margaret , Yo Kaahukane Leite-Ah , Lum-Jones Annette , Nakamoto Beau , Valcour Victor , SahBandar Ivo , Shikuma Cecilia M. , Ndhlovu Lishomwa C. , Maunakea Alika K. 
Published: September 2016

AbstractMonocytes/macrophages contribute to the neuropathogenesis of HIV-related cognitive impairment (CI); however, considerable gaps in our understanding of the precise mechanisms driving this relationship remain. Furthermore, whether a distinct biological profile associated with HIV-related CI resides in immune cell populations remains unknown. Here, we profiled DNA methylomes and transcriptomes of monocytes derived from HIV-infected individuals with and without CI using genome-wide DNA methylation and gene expression profiling. We identified 1,032 CI-associated differentially methylated loci in monocytes. These loci related to gene networks linked to the central nervous system (CNS) and interactions with HIV. Most (70.6%) of these loci exhibited higher DNA methylation states in the CI group and were preferentially distributed over gene bodies and intergenic regions of the genome. CI-associated DNA methylation states at 12 CpG sites associated with neuropsychological testing performance scores. CI-associated DNA methylation also associated with gene expression differences including CNS genes CSRNP1 (P = 0.017), DISC1 (P = 0.012), and NR4A2 (P = 0.005); and a gene known to relate to HIV viremia, THBS1 (P = 0.003). This discovery cohort data unveils cell type-specific DNA methylation patterns related to HIV-associated CI and provide an immunoepigenetic DNA methylation “signature” potentially useful for corroborating clinical assessments, informing pathogenic mechanisms, and revealing new therapeutic targets against CI.
Long-term adaptation of the influenza A virus by escaping cytotoxic T-cell recognition
Authors: Woolthuis Rutger G. , van Dorp Christiaan H. , Keşmir Can , de Boer Rob J. , van Boven Michiel 
Published: September 2016

AbstractThe evolutionary adaptation of the influenza A virus (IAV) to human antibodies is well characterised. Much less is known about the long-term evolution of cytotoxic T lymphocyte (CTL) epitopes, which are important antigens for clearance of infection. We construct an antigenic map of IAVs of all human subtypes using a compendium of 142 confirmed CTL epitopes, and show that IAV evolved gradually in the period 1932–2015, with infrequent antigenic jumps in the H3N2 subtype. Intriguingly, the number of CTL epitopes per virus decreases with more than one epitope per three years in the H3N2 subtype (from 84 epitopes per virus in 1968 to 64 in 2015), mostly attributed to the loss of HLA-B epitopes. We confirm these observations with epitope predictions. Our findings indicate that selection pressures imposed by CTL immunity shape the long-term evolution of IAV.
Oncogenic Mutations Differentially Affect Bax Monomer, Dimer, and Oligomeric Pore Formation in the Membrane
Authors: Zhang Mingzhen , Zheng Jie , Nussinov Ruth , Ma Buyong 
Published: September 2016

AbstractDysfunction of Bax, a pro-apoptotic regulator of cellular metabolism is implicated in neurodegenerative diseases and cancer. We have constructed the first atomistic models of the Bax oligomeric pore consisting with experimental residue-residue distances. The models are stable, capturing well double electron-electron resonance (DEER) spectroscopy measurements and provide structural details in line with the DEER data. Comparison with the latest experimental results revealed that our models agree well with both Bax and Bak pores, pointed to a converged structural arrangement for Bax and Bak pore formation. Using multi-scale molecular dynamics simulations, we probed mutational effects on Bax transformation from monomer → dimer → membrane pore formation at atomic resolution. We observe that two cancer-related mutations, G40E and S118I, allosterically destabilize the monomer and stabilize an off-pathway swapped dimer, preventing productive pore formation. This observation suggests a mechanism whereby the mutations may work mainly by over-stabilizing the monomer → dimer transformation toward an unproductive off-pathway swapped-dimer state. Our observations point to misfolded Bax states, shedding light on the molecular mechanism of Bax mutation-elicited cancer. Most importantly, the structure of the Bax pore facilitates future study of releases cytochrome C in atomic detail.
SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics
Authors: Chen Dana , Orenstein Yaron , Golodnitsky Rada , Pellach Michal , Avrahami Dorit , Wachtel Chaim , Ovadia-Shochat Avital , Shir-Shapira Hila , Kedmi Adi , Juven-Gershon Tamar , Shamir Ron , Gerber Doron 
Published: September 2016

AbstractTranscription factors (TFs) alter gene expression in response to changes in the environment through sequence-specific interactions with the DNA. These interactions are best portrayed as a landscape of TF binding affinities. Current methods to study sequence-specific binding preferences suffer from limited dynamic range, sequence bias, lack of specificity and limited throughput. We have developed a microfluidic-based device for SELEX Affinity Landscape MAPping (SELMAP) of TF binding, which allows high-throughput measurement of 16 proteins in parallel. We used it to measure the relative affinities of Pho4, AtERF2 and Btd full-length proteins to millions of different DNA binding sites, and detected both high and low-affinity interactions in equilibrium conditions, generating a comprehensive landscape of the relative TF affinities to all possible DNA 6-mers, and even DNA10-mers with increased sequencing depth. Low quantities of both the TFs and DNA oligomers were sufficient for obtaining high-quality results, significantly reducing experimental costs. SELMAP allows in-depth screening of hundreds of TFs, and provides a means for better understanding of the regulatory processes that govern gene expression.
Charge transport mechanism in lead oxide revealed by CELIV technique
Authors: Semeniuk O. , Juska G. , Oelerich J.-O. , Wiemer M. , Baranovskii S. D. , Reznik A. 
Published: September 2016

AbstractAlthough polycrystalline lead oxide (PbO) belongs to the most promising photoconductors for optoelectronic and large area detectors applications, the charge transport mechanism in this material still remains unclear. Combining the conventional time-of-flight and the photo-generated charge extraction by linear increasing voltage (photo-CELIV) techniques, we investigate the transport of holes which are shown to be the faster carriers in poly-PbO. Experimentally measured temperature and electric field dependences of the hole mobility suggest a highly dispersive transport. In order to analyze the transport features quantitatively, the theory of the photo-CELIV is extended to account for the dispersive nature of charge transport. While in other materials with dispersive transport the amount of dispersion usually depends on temperature, this is not the case in poly-PbO, which evidences that dispersive transport is caused by the spatial inhomogeneity of the material and not by the energy disorder.
Y chromosome haplogroups based genome-wide association study pinpoints revelation for interactions on non-obstructive azoospermia
Authors: Lu Chuncheng , Wen Yang , Hu Weiyue , Lu Feng , Qin Yufeng , Wang Ying , Li Shilin , Yang Shuping , Lin Yuan , Wang Cheng , Jin Li , Shen Hongbing , Sha Jiahao , Wang Xinru , Hu Zhibin , Xia Yankai 
Published: September 2016

AbstractThe Y chromosome has high genetic variability with low rates of parallel and back mutations, which make up the most informative haplotyping system. To examine whether Y chromosome haplogroups (Y-hgs) could modify the effects of autosomal variants on non-obstructive azoospermia (NOA), based on our previous genome-wide association study (GWAS), we conducted a genetic interaction analysis in GWAS subjects. Logistic regression analysis demonstrated a protective effect of Y-hg O3e* on NOA. Then, we explored the potential interaction between Y-hg O3e* and autosomal variants. Our results demonstrated that there was a suggestively significant interaction between Y-hg O3e* and rs11135484 on NOA (Pinter = 9.89 × 10−5). Bioinformatic analysis revealed that genes annotated by significant single nucleotide polymorphisms (SNPs) were mainly enriched in immunological pathways. This is the first study of interactions between Y-hgs and autosomal variants on a genome-wide scale, which addresses the missing heritability in spermatogenic impairment and sheds new light on the pathogenesis of male infertility.
Molecular Dynamics Simulations of the Permeation of Bisphenol A and Pore Formation in a Lipid Membrane
Authors: Chen Liang , Chen Junlang , Zhou Guoquan , Wang Yu , Xu Can , Wang Xiaogang 
Published: September 2016

AbstractBisphenol A (BPA) is particularly considered as one of the most suspicious endocrine disruptors. Exposure to BPA may bring about possible human toxicities, such as cancerous tumors, birth defects and neoteny. One of the key issues to understand its toxicities is how BPA enters cells. In this paper, we perform molecular dynamics simulations to explore the interactions between BPA and a phospholipid membrane (dipalmitoylphosphatidylcholine, DPPC bilayer). The simulation results show that BPA can easily enter the membrane from the aqueous phase. With the increasing concentrations of BPA in the membrane, BPA tends to aggregate and form into cluster. Meanwhile, several DPPC lipids are pulled out from each leaflet and adsorbed on the cluster surface, leading to pore formation. Detailed observations indicate that the lipid extraction results mainly from the dispersion interactions between BPA cluster and lipid tails, as well as weak electrostatic attractions between lipid headgroups and the two hydroxyl groups on BPA. The lipid extraction and pore formation may cause cell membrane damage and are of great importance to uncover BPA’s cytotoxicity.
Solar-rechargeable battery based on photoelectrochemical water oxidation: Solar water battery
Authors: Kim Gonu , Oh Misol , Park Yiseul 
Published: September 2016

AbstractAs an alternative to the photoelectrochemical water splitting for use in the fuel cells used to generate electrical power, this study set out to develop a solar energy rechargeable battery system based on photoelectrochemical water oxidation. We refer to this design as a “solar water battery”. The solar water battery integrates a photoelectrochemical cell and battery into a single device. It uses a water oxidation reaction to simultaneously convert and store solar energy. With the solar water battery, light striking the photoelectrode causes the water to be photo-oxidized, thus charging the battery. During the discharge process, the solar water battery reduces oxygen to water with a high coulombic efficiency (>90%) and a high average output voltage (0.6 V). Because the reduction potential of oxygen is more positive [E0 (O2/H2O) = 1.23 V vs. NHE] than common catholytes (e.g., iodide, sulfur), a high discharge voltage is produced. The solar water battery also exhibits a superior storage ability, maintaining 99% of its specific discharge capacitance after 10 h of storage, without any evidence of self-discharge. The optimization of the cell design and configuration, taking the presence of oxygen in the cell into account, was critical to achieving an efficient photocharge/discharge.