bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons
Authors: Weinert Tobias , Olieric Natacha , Cheng Robert , Brünle Steffen , James Daniel , Ozerov Dmitry , Gashi Dardan , Vera Laura , Marsh May , Jaeger Kathrin , Dworkowski Florian , Panepucci Ezequiel , Basu Shibom , Skopintsev Petr , Doré Andrew S. , Geng Tian , Cooke Robert M. , Liang Mengning , Prota Andrea E. , Panneels Valerie , Nogly Przemyslaw , Ermler Ulrich , Schertler Gebhard , Hennig Michael , Steinmetz Michel O. , Wang Meitian , Standfuss Jörg 
Published: September 2017

AbstractHistorically, room-temperature structure determination was succeeded by cryo-crystallography to mitigate radiation damage. Here, we demonstrate that serial millisecond crystallography at a synchrotron beamline equipped with high-viscosity injector and high frame-rate detector allows typical crystallographic experiments to be performed at room-temperature. Using a crystal scanning approach, we determine the high-resolution structure of the radiation sensitive molybdenum storage protein, demonstrate soaking of the drug colchicine into tubulin and native sulfur phasing of the human G protein-coupled adenosine receptor. Serial crystallographic data for molecular replacement already converges in 1,000–10,000 diffraction patterns, which we collected in 3 to maximally 82 minutes. Compared with serial data we collected at a free-electron laser, the synchrotron data are of slightly lower resolution, however fewer diffraction patterns are needed for de novo phasing. Overall, the data we collected by room-temperature serial crystallography are of comparable quality to cryo-crystallographic data and can be routinely collected at synchrotrons.
Engineered factor Xa variants retain procoagulant activity independent of direct factor Xa inhibitors
Authors: Verhoef Daniël , Visscher Koen M. , Vosmeer C. Ruben , Cheung Ka Lei , Reitsma Pieter H. , Geerke Daan P. , Bos Mettine H. A. 
Published: September 2017

AbstractThe absence of an adequate reversal strategy to prevent and stop potential life-threatening bleeding complications is a major drawback to the clinical use of the direct oral inhibitors of blood coagulation factor Xa. Here we show that specific modifications of the substrate-binding aromatic S4 subpocket within the factor Xa active site disrupt high-affinity engagement of the direct factor Xa inhibitors. These modifications either entail amino-acid substitution of S4 subsite residues Tyr99 and/or Phe174 (chymotrypsinogen numbering), or extension of the 99-loop that borders the S4 subsite. The latter modifications led to the engineering of a factor Xa variant that is able to support coagulation in human plasma spiked with (supra-)physiological concentrations of direct factor Xa inhibitors. As such, this factor Xa variant has the potential to be employed to bypass the direct factor Xa inhibitor-mediated anticoagulation in patients that require restoration of blood coagulation.
Functional organization of cytoplasmic inclusion bodies in cells infected by respiratory syncytial virus
Authors: Rincheval Vincent , Lelek Mickael , Gault Elyanne , Bouillier Camille , Sitterlin Delphine , Blouquit-Laye Sabine , Galloux Marie , Zimmer Christophe , Eleouet Jean-François , Rameix-Welti Marie-Anne 
Published: September 2017

AbstractInfection of cells by respiratory syncytial virus induces the formation of cytoplasmic inclusion bodies (IBs) where all the components of the viral RNA polymerase complex are concentrated. However, the exact organization and function of these IBs remain unclear. In this study, we use conventional and super-resolution imaging to dissect the internal structure of IBs. We observe that newly synthetized viral mRNA and the viral transcription anti-terminator M2-1 concentrate in IB sub-compartments, which we term “IB-associated granules” (IBAGs). In contrast, viral genomic RNA, the nucleoprotein, the L polymerase and its cofactor P are excluded from IBAGs. Live imaging reveals that IBAGs are highly dynamic structures. Our data show that IBs are the main site of viral RNA synthesis. They further suggest that shortly after synthesis in IBs, viral mRNAs and M2-1 transiently concentrate in IBAGs before reaching the cytosol and suggest a novel post-transcriptional function for M2-1.
Oxytocin stimulates hippocampal neurogenesis via oxytocin receptor expressed in CA3 pyramidal neurons
Authors: Lin Yu-Ting , Chen Chien-Chung , Huang Chiung-Chun , Nishimori Katsuhiko , Hsu Kuei-Sen 
Published: September 2017

AbstractIn addition to the regulation of social and emotional behaviors, the hypothalamic neuropeptide oxytocin has been shown to stimulate neurogenesis in adult dentate gyrus; however, the mechanisms underlying the action of oxytocin are still unclear. Taking advantage of the conditional knockout mouse model, we show here that endogenous oxytocin signaling functions in a non-cell autonomous manner to regulate survival and maturation of newly generated dentate granule cells in adult mouse hippocampus via oxytocin receptors expressed in CA3 pyramidal neurons. Through bidirectional chemogenetic manipulations, we also uncover a significant role for CA3 pyramidal neuron activity in regulating adult neurogenesis in the dentate gyrus. Retrograde neuronal tracing combined with immunocytochemistry revealed that the oxytocin neurons in the paraventricular nucleus project directly to the CA3 region of the hippocampus. Our findings reveal a critical role for oxytocin signaling in adult neurogenesis.
Late Permian wood-borings reveal an intricate network of ecological relationships
Authors: Feng Zhuo , Wang Jun , Rößler Ronny , Ślipiński Adam , Labandeira Conrad 
Published: September 2017

AbstractBeetles are the most diverse group of macroscopic organisms since the mid-Mesozoic. Much of beetle speciosity is attributable to myriad life habits, particularly diverse-feeding strategies involving interactions with plant substrates, such as wood. However, the life habits and early evolution of wood-boring beetles remain shrouded in mystery from a limited fossil record. Here we report new material from the upper Permian (Changhsingian Stage, ca. 254–252 million-years ago) of China documenting a microcosm of ecological associations involving a polyphagan wood-borer consuming cambial and wood tissues of the conifer Ningxiaites specialis. This earliest evidence for a component community of several trophically interacting taxa is frozen in time by exceptional preservation. The combination of an entry tunnel through bark, a cambium mother gallery, and up to 11 eggs placed in lateral niches—from which emerge multi-instar larval tunnels that consume cambium, wood and bark—is ecologically convergent with Early Cretaceous bark-beetle borings 120 million-years later.
Room-temperature 2D semiconductor activated vertical-cavity surface-emitting lasers
Authors: Shang Jingzhi , Cong Chunxiao , Wang Zilong , Peimyoo Namphung , Wu Lishu , Zou Chenji , Chen Yu , Chin Xin Yu , Wang Jianpu , Soci Cesare , Huang Wei , Yu Ting 
Published: September 2017

AbstractTwo-dimensional (2D) semiconductors are opening a new platform for revitalizing widely spread optoelectronic applications. The realisation of room-temperature vertical 2D lasing from monolayer semiconductors is fundamentally interesting and highly desired for appealing on-chip laser applications such as optical interconnects and supercomputing. Here, we present room-temperature low-threshold lasing from 2D semiconductor activated vertical-cavity surface-emitting lasers (VCSELs) under continuous-wave pumping. 2D lasing is achieved from a 2D semiconductor. Structurally, dielectric oxides were used to construct the half-wavelength-thick cavity and distributed Bragg reflectors, in favour of single-mode operation and ultralow optical loss; in the cavity centre, the direct-bandgap monolayer WS2was embedded as the gain medium, compatible with the planar VCSEL configuration and the monolithic integration technology. This work demonstrates 2D semiconductor activated VCSELs with desirable emission characteristics, which represents a major step towards practical optoelectronic applications of 2D semiconductor lasers.
Inherent aggressive character of invasive and non-invasive cells dictates the in vitro migration pattern of multicellular spheroid
Authors: Gayan Sukanya , Teli Abhishek , Dey Tuli 
Published: September 2017

AbstractCellular migration, a process relevant to metastasis, is mostly studied in the conventional 2D condition. However, cells cultured in the 3D condition assumed to mimic the in vivo conditions better. The current study is designed to compare an invasive and non-invasive adenocarcinoma cell with an invasive fibrosarcoma cell to understand the migration pattern of the multicellular spheroid. It is observed that conventional haplotaxis, chemotactic and pseudo-3D migration assay cannot distinguish between the invasive and non-invasive cells conclusively under 2D condition. Invasive spheroids migrate rapidly in sprouting assay in comparison to non-invasive spheroids. Effects of cytochalasin B, marimastat and blebbistatin are tested to determine the influence of different migration modality namely actin polymerization, matrix metalloprotease and acto-myosin in both culture conditions. Altered mRNA profile of cellular migration related genes (FAK, Talin, Paxillin, p130cas and Vinculin) is observed between 2D and 3D condition followed by the changed expression of matrix metallo proteases. A distinct difference is observed in distribution and formation of focal adhesion complex under these culture conditions. This study demonstrates the efficacy of multicellular spheroids in identifying the intrinsic aggressive behavior of different cell lines as a proof of concept and recognizes the potential of spheroids as a migration model.
Enhancement of water diffusion and compression performance of crosslinked alginate films with a minuscule amount of graphene oxide
Authors: Serrano-Aroca Ángel , Ruiz-Pividal Juan-Francisco , Llorens-Gámez Mar 
Published: September 2017

AbstractA series of calcium alginate composite hydrogels with several calcium chloride contents ranging from 3 to 18 wt.% with and without 0.1 wt.% of graphene oxide (GO) was prepared in order to study the effect of crosslinking and nanofilling on water diffusion and compression performance. Thus, for high crosslinker contents, these composite hydrogels exhibited ultrafast diffusion of liquid water and excellent compression properties as compared with control (0 wt.% GO and the same crosslinking). These remarkable results are produced due to calcium cations are able to crosslink alginate and also graphene oxide nanosheets to form large crosslinked GO networks inside the calcium alginate hydrogels. Besides, these crosslinked GO/calcium alginate networks present nanochannels, as confirmed by electron microscopy, able to improve significantly water diffusion. Thus, these composite materials are very promising for many industrial applications demanding low-cost hydrogels with improved mechanical and water diffusion properties.
Transcriptome analysis of developing lens reveals abundance of novel transcripts and extensive splicing alterations
Authors: Srivastava Rajneesh , Budak Gungor , Dash Soma , Lachke Salil A. , Janga Sarath Chandra 
Published: September 2017

AbstractLens development involves a complex and highly orchestrated regulatory program. Here, we investigate the transcriptomic alterations and splicing events during mouse lens formation using RNA-seq data from multiple developmental stages, and construct a molecular portrait of known and novel transcripts. We show that the extent of novelty of expressed transcripts decreases significantly in post-natal lens compared to embryonic stages. Characterization of novel transcripts into partially novel transcripts (PNTs) and completely novel transcripts (CNTs) (novelty score ≥ 70%) revealed that the PNTs are both highly conserved across vertebrates and highly expressed across multiple stages. Functional analysis of PNTs revealed their widespread role in lens developmental processes while hundreds of CNTs were found to be widely expressed and predicted to encode for proteins. We verified the expression of four CNTs across stages. Examination of splice isoforms revealed skipped exon and retained intron to be the most abundant alternative splicing events during lens development. We validated by RT-PCR and Sanger sequencing, the predicted splice isoforms of several genes Banf1, Cdk4, Cryaa, Eif4g2, Pax6, and Rbm5. Finally, we present a splicing browser Eye Splicer (http://www.iupui.edu/~sysbio/eye-splicer/), to facilitate exploration of developmentally altered splicing events and to improve understanding of post-transcriptional regulatory networks during mouse lens development.
Honeycomb-like ZnO Mesoporous Nanowall Arrays Modified with Ag Nanoparticles for Highly Efficient Photocatalytic Activity
Authors: Feng Yimeng , Wang Guojing , Liao Jiecui , Li Wei , Chen Chienhua , Li Mingyang , Li Zhengcao 
Published: September 2017

AbstractA new structure of honeycomb-like ZnO mesoporous nanowall arrays (MNWAs) with highly efficient photocatalytic activity was designed and successfully synthesized on Al foil by hydrothermal method. The nanowalls of ZnO-MNWAs have mesopores, which possess a large surface area. The visible light absorption of ZnO-MNWAs was efficiently stronger than ZnO nanowire, resulting in that the photocatalytic activity of ZnO-MNWAs, whose bandgap energy was 3.12 eV, was 5.97 times than that of ZnO nanowires in the degradation of methyl orange. Besides, Al foil acted as a good electron conductor which was beneficial to the separation of photo-induced electron-hole pairs. After modifying ZnO-MNWAs with a proper amount of Ag nanoparticles (NPs), photocatalytic activity could be further enhanced. The photocatalytic activity of ZnO-MNWAs with the optimal amount of Ag NPs was 9.08 times than that of ZnO nanowires and 1.52 times than that of pure ZnO-MNWAs.
Qubit-mediated deterministic nonlinear gates for quantum oscillators
Authors: Park Kimin , Marek Petr , Filip Radim 
Published: September 2017

AbstractQuantum nonlinear operations for harmonic oscillator systems play a key role in the development of analog quantum simulators and computers. Since strong highly nonlinear operations are often unavailable in the existing physical systems, it is a common practice to approximate them by using conditional measurement-induced methods. The conditional approach has several drawbacks, the most severe of which is the exponentially decreasing success rate of the strong and complex nonlinear operations. We show that by using a suitable two level system sequentially interacting with the oscillator, it is possible to resolve these issues and implement a nonlinear operation both nearly deterministically and nearly perfectly. We explicitly demonstrate the approach by constructing self-Kerr and cross-Kerr couplings in a realistic situation, which require a feasible dispersive coupling between the two-level system and the oscillator.
Systematic review and meta-analysis of differentially expressed miRNAs in experimental and human temporal lobe epilepsy
Authors: Korotkov A. , Mills J. D. , Gorter J. A. , van Vliet E. A. , Aronica E. 
Published: September 2017

AbstractTemporal lobe epilepsy (TLE) is a common chronic neurological disease in humans. A number of studies have demonstrated differential expression of miRNAs in the hippocampus of humans with TLE and in animal models of experimental epilepsy. However, the dissimilarities in experimental design have led to largely discordant results across these studies. Thus, a comprehensive comparison is required in order to better characterize miRNA profiles obtained in various post-status epilepticus (SE) models. We therefore created a database and performed a meta-analysis of differentially expressed miRNAs across 3 post-SE models of epileptogenesis (electrical stimulation, pilocarpine and kainic acid) and human TLE with hippocampal sclerosis (TLE-HS). The database includes data from 11 animal post-SE studies and 3 human TLE-HS studies. A total of 378 differentially expressed miRNAs were collected (274 up-regulated and 198 down-regulated) and analyzed with respect to the post-SE model, time point and animal species. We applied the novel robust rank aggregation method to identify consistently differentially expressed miRNAs across the profiles. It highlighted common and unique miRNAs at different stages of epileptogenesis. The pathway analysis revealed involvement of these miRNAs in key pathogenic pathways underlying epileptogenesis, including inflammation, gliosis and deregulation of the extracellular matrix.
PHF7, a novel male gene influences female fecundity and population growth in Nilaparvata lugens Stål (Hemiptera: Delphacidae)
Authors: Ge Lin-Quan , Xia Ting , Huang Bo , Gu Hao-Tian , Song Qi-Sheng , Yang Guo-Qing , Liu Fang , Wu Jin-Cai 
Published: September 2017

AbstractPHF7 exhibits male-specific expression in early germ cells, germline stem cells and spermatogonia in insects, and its expression promotes spermatogenesis in germ cells when they are present in a male soma. However, the influence of male-specific PHF7 on female reproductive biology via mating remains unclear. Thus, we investigated the potential impacts of male PHF7, existed in seminal fluid of Nilaparvata lugens (NlPHF7), on fecundity and population growth via mating. Our results revealed that suppressing male NlPHF7 expression by RNAi led to decreases in body weight, soluble accessory gland protein content, arginine content, and reproductive organ development in males, resulting in significant reduction of oviposition periods and fecundity in females, and significant decrease in body weight, fat body and ovarian protein content, yeast-like symbionts abundance, ovarian development and vitellogenin gene expression in their female mating partners. Similarly, suppression of NlPHF7 expression in males mated with the control female reduced population growth and egg hatching rate, but did not influence gender ratio. We infer that NlPHF7 play a role important in stimulating female fecundity via mating. This study provides valuable information by identifying a potentially effective target gene for managing BPH population through RNAi.
Thermodynamics of nanodisc formation mediated by styrene/maleic acid (2:1) copolymer
Authors: Grethen Anne , Oluwole Abraham Olusegun , Danielczak Bartholomäus , Vargas Carolyn , Keller Sandro 
Published: September 2017

AbstractStyrene/maleic acid copolymers (SMA) have recently attracted great interest for in vitro studies of membrane proteins, as they self-insert into and fragment biological membranes to form polymer-bounded nanodiscs that provide a native-like lipid-bilayer environment. SMA copolymers are available in different styrene/maleic acid ratios and chain lengths and, thus, possess different charge densities, hydrophobicities, and solubilisation properties. Here, we studied the equilibrium solubilisation properties of the most commonly used copolymer, SMA(2:1), by monitoring the formation of nanodiscs from phospholipid vesicles using 31P nuclear magnetic resonance spectroscopy, dynamic light scattering, and differential scanning calorimetry. Comparison of SMA(2:1) phase diagrams with those of SMA(3:1) and diisobutylene/maleic acid (DIBMA) revealed that, on a mass concentration scale, SMA(2:1) is the most efficient membrane solubiliser, despite its relatively mild effects on the thermotropic phase behaviour of solubilised lipids. In contrast with previous kinetic studies, our equilibrium experiments demonstrate that the solubilisation of phospholipid bilayers by SMA(2:1) is most efficient at moderately alkaline pH values. This pH dependence was also observed for the solubilisation of native Escherichia coli membranes, for which SMA(2:1) again turned out to be the most powerful solubiliser in terms of the total amounts of membrane proteins extracted.
Role of RKKY torque on domain wall motion in synthetic antiferromagnetic nanowires with opposite spin Hall angles
Authors: Krishnia S. , Sethi P. , Gan W. L. , Kholid F. N. , Purnama I. , Ramu M. , Herng T. S. , Ding J. , Lew W. S. 
Published: September 2017

AbstractWe experimentally show the effect of enhanced spin-orbit and RKKY induced torques on the current-induced motion of a pair of domain walls (DWs), which are coupled antiferromagnetically in synthetic antiferromagnetic (SAF) nanowires. The torque from the spin Hall effect (SHE) rotates the Néel DWs pair into the transverse direction, which is due to the fact that heavy metals of opposite spin Hall angles are deposited at the top and the bottom ferromagnetic interfaces. The rotation of both DWs in non-collinear fashion largely perturbs the antiferromagnetic coupling, which in turn stimulates an enhanced interlayer RKKY exchange torque that improved the DW velocity. The interplay between the SHE-induced torque and the RKKY exchange torque is validated via micromagnetic simulations. In addition, the DW velocity can be further improved by increasing the RKKY exchange strength.
Novel insight into streptozotocin-induced diabetic rats from the protein misfolding perspective
Authors: Leyva-García Edgar , Lara-Martínez Reyna , Morán-Zanabria Liborio , Revilla-Monsalve Cristina , Jiménez-García Luis Felipe , Oviedo Norma , Murata Chiharu , Garrido-Magaña Eulalia , Altamirano-Bustamante Nelly F. , Altamirano-Bustamante Myriam M. 
Published: September 2017

AbstractProtein folding is a process of self-assembly defined by the sequence of the amino acids of the protein involved. Additionally, proteins tend to unfold, misfold and aggregate due to both intrinsic and extrinsic causes. Human islet amyloid polypeptide (hIAPP) aggregation is an early step in diabetes mellitus. However, the aggregation of rat IAPP (rIAPP) remains an open question. Adult female Sprague-Dawley rats weighing 150–250 g were divided into two groups. The experimental group (streptozotocin [STZ]) (n = 21) received an intraperitoneal injection of a single dose of 40 mg/kg STZ. We used the mouse anti-IAPP antibody and the anti-amyloid oligomer antibody to study the temporal course of rIAPP oligomerization during STZ-induced diabetes using a wide array of methods, strategies and ideas derived from biochemistry, cell biology, and proteomic medicine. Here, we demonstrated the tendency of rIAPP to aggregate and trigger cooperative processes of self-association or hetero-assembly that lead to the formation of amyloid oligomers (trimers and hexamers). Our results are the first to demonstrate the role of rIAPP amyloid oligomers in the development of STZ-induced diabetes in rats. The IAPP amyloid oligomers are biomarkers of the onset and progression of diabetes and could play a role as therapeutic targets.