bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum majorization and a complete set of entropic conditions for quantum thermodynamics
Authors: Gour Gilad , Jennings David , Buscemi Francesco , Duan Runyao , Marvian Iman 
Published: December 2018

AbstractWhat does it mean for one quantum process to be more disordered than another? Interestingly, this apparently abstract question arises naturally in a wide range of areas such as information theory, thermodynamics, quantum reference frames, and the resource theory of asymmetry. Here we use a quantum-mechanical generalization of majorization to develop a framework for answering this question, in terms of single-shot entropies, or equivalently, in terms of semi-definite programs. We also investigate some of the applications of this framework, and remarkably find that, in the context of quantum thermodynamics it provides the first complete set of necessary and sufficient conditions for arbitrary quantum state transformations under thermodynamic processes, which rigorously accounts for quantum-mechanical properties, such as coherence. Our framework of generalized thermal processes extends thermal operations, and is based on natural physical principles, namely, energy conservation, the existence of equilibrium states, and the requirement that quantum coherence be accounted for thermodynamically.
Myopathy associated BAG3 mutations lead to protein aggregation by stalling Hsp70 networks
Authors: Meister-Broekema Melanie , Freilich Rebecca , Jagadeesan Chandhuru , Rauch Jennifer N. , Bengoechea Rocio , Motley William W. , Kuiper E. F. Elsiena , Minoia Melania , Furtado Gabriel V. , van Waarde Maria A. W. H. , Bird Shawn J. , Rebelo Adriana , Zuchner Stephan , Pytel Peter , Scherer Steven S. , Morelli Federica F. , Carra Serena , Weihl Conrad C. , Bergink Steven , Gestwicki Jason E. , Kampinga Harm H. 
Published: December 2018

AbstractBAG3 is a multi-domain hub that connects two classes of chaperones, small heat shock proteins (sHSPs) via two isoleucine-proline-valine (IPV) motifs and Hsp70 via a BAG domain. Mutations in either the IPV or BAG domain of BAG3 cause a dominant form of myopathy, characterized by protein aggregation in both skeletal and cardiac muscle tissues. Surprisingly, for both disease mutants, impaired chaperone binding is not sufficient to explain disease phenotypes. Recombinant mutants are correctly folded, show unaffected Hsp70 binding but are impaired in stimulating Hsp70-dependent client processing. As a consequence, the mutant BAG3 proteins become the node for a dominant gain of function causing aggregation of itself, Hsp70, Hsp70 clients and tiered interactors within the BAG3 interactome. Importantly, genetic and pharmaceutical interference with Hsp70 binding completely reverses stress-induced protein aggregation for both BAG3 mutations. Thus, the gain of function effects of BAG3 mutants act as Achilles heel of the HSP70 machinery.
Proteasomal degradation of NOD2 by NLRP12 in monocytes promotes bacterial tolerance and colonization by enteropathogens
Authors: Normand Sylvain , Waldschmitt Nadine , Neerincx Andreas , Martinez-Torres Ruben Julio , Chauvin Camille , Couturier-Maillard Aurélie , Boulard Olivier , Cobret Laetitia , Awad Fawaz , Huot Ludovic , Ribeiro-Ribeiro Andre , Lautz Katja , Ruez Richard , Delacre Myriam , Bondu Clovis , Guilliams Martin , Scott Charlotte , Segal Anthony , Amselem Serge , Hot David , Karabina Sonia , Bohn Erwin , Ryffel Bernhard , Poulin Lionel F. , Kufer Thomas A. , Chamaillard Mathias 
Published: December 2018

AbstractMutations in the nucleotide-binding oligomerization domain protein 12 (NLRP12) cause recurrent episodes of serosal inflammation. Here we show that NLRP12 efficiently sequesters HSP90 and promotes K48-linked ubiquitination and degradation of NOD2 in response to bacterial muramyl dipeptide (MDP). This interaction is mediated by the linker-region proximal to the nucleotide-binding domain of NLRP12. Consequently, the disease-causing NLRP12 R284X mutation fails to repress MDP-induced NF-κB and subsequent activity of the JAK/STAT signaling pathway. While NLRP12 deficiency renders septic mice highly susceptible towards MDP, a sustained sensing of MDP through NOD2 is observed among monocytes lacking NLRP12. This loss of tolerance in monocytes results in greater colonization resistance towards Citrobacter rodentium. Our data show that this is a consequence of NOD2-dependent accumulation of inflammatory mononuclear cells that correlates with induction of interferon-stimulated genes. Our study unveils a relevant process of tolerance towards the gut microbiota that is exploited by an attaching/effacing enteric pathogen.
SOX9 regulated matrix proteins are increased in patients serum and correlate with severity of liver fibrosis
Authors: Athwal Varinder S. , Pritchett James , Martin Katherine , Llewellyn Jessica , Scott Jennifer , Harvey Emma , Zaitoun Abed M. , Mullan Aoibheann F. , Zeef Leo A. H. , Friedman Scott L. , Irving William L. , Hanley Neil A. , Guha Indra N. , Piper Hanley Karen 
Published: December 2018

AbstractExtracellular matrix (ECM) deposition and resultant scar play a major role in the pathogenesis and progression of liver fibrosis. Identifying core regulators of ECM deposition may lead to urgently needed diagnostic and therapetic strategies for the disease. The transcription factor Sex determining region Y box 9 (SOX9) is actively involved in scar formation and its prevalence in patients with liver fibrosis predicts progression. In this study, transcriptomic approaches of Sox9-abrogated myofibroblasts identified >30% of genes regulated by SOX9 relate to the ECM. Further scrutiny of these data identified a panel of highly expressed ECM proteins, including Osteopontin (OPN), Osteoactivin (GPNMB), Fibronectin (FN1), Osteonectin (SPARC) and Vimentin (VIM) as SOX9 targets amenable to assay in patient serum. In vivo all SOX-regulated targets were increased in human disease and mouse models of fibrosis and decreased following Sox9-loss in mice with parenchymal and biliary fibrosis. In patient serum samples, SOX9-regulated ECM proteins were altered in response to fibrosis severity, whereas comparison with established clinical biomarkers demonstrated superiority for OPN and VIM at detecting early stages of fibrosis. These data support SOX9 in the mechanisms underlying fibrosis and highlight SOX9 and its downstream targets as new measures to stratify patients with liver fibrosis.
Syntactic and non-syntactic sources of interference by music on language processing
Authors: Fiveash Anna , McArthur Genevieve , Thompson William Forde 
Published: December 2018

AbstractMusic and language are complex hierarchical systems in which individual elements are systematically combined to form larger, syntactic structures. Suggestions that music and language share syntactic processing resources have relied on evidence that syntactic violations in music interfere with syntactic processing in language. However, syntactic violations may affect auditory processing in non-syntactic ways, accounting for reported interference effects. To investigate the factors contributing to interference effects, we assessed recall of visually presented sentences and word-lists when accompanied by background auditory stimuli differing in syntactic structure and auditory distraction: melodies without violations, scrambled melodies, melodies that alternate in timbre, and environmental sounds. In Experiment 1, one-timbre melodies interfered with sentence recall, and increasing both syntactic complexity and distraction by scrambling melodies increased this interference. In contrast, three-timbre melodies reduced interference on sentence recall, presumably because alternating instruments interrupted auditory streaming, reducing pressure on long-distance syntactic structure building. Experiment 2 confirmed that participants were better at discriminating syntactically coherent one-timbre melodies than three-timbre melodies. Together, these results illustrate that syntactic processing and auditory streaming interact to influence sentence recall, providing implications for theories of shared syntactic processing and auditory distraction.
Transcriptome profiling of human oocytes experiencing recurrent total fertilization failure
Authors: Suo Lun , Zhou Yu xiao , Jia Li ling , Wu Hai bo , Zheng Jin , Lyu Qi feng , Sun Li hua , Sun Han , Kuang Yan ping 
Published: December 2018

AbstractThere exist some patients who face recurrent total fertilization failure during assisted reproduction treatment, but the pathological mechanism underlying is elusive. Here, by using sc-RNA-seq method, the transcriptome profiles of ten abnormally fertilized zygotes were assessed, including five zygotes from one patient with recurrent Poly-PN zygotes, and five zygotes from a patient with pronuclear fusion failure. Four zygotes with three pronuclear (Tri-PN) were collected from four different patients as controls. After that, we identified 951 and 1697 significantly differentially expressed genes (SDEGs) in Poly-PN and PN arrest zygotes, respectively as compared with the control group. KEGG analyses indicated down regulated genes in the Poly-PN group included oocyte meiosis related genes, such as PPP2R1B, YWHAZ, MAD2L1, SPDYC, SKP1 and CDC27, together with genes associated with RNA processing, such as SF3B1, LOC645691, MAGOHB, PHF5A, PRPF18, DDX5, THOC1 and BAT1. In contrast, down regulated genes in the PN arrest group, included cell cycle genes, such as E2F4, DBF4, YWHAB, SKP2, CDC23, SMC3, CDC25A, CCND3, BUB1B, MDM2, CCNA2 and CDC7, together with homologous recombination related genes, such as NBN, XRCC3, SHFM1, RAD54B and RAD51. Thus, our work provides a better understanding of transcriptome profiles underlying RTFF, although it based on a limited number of patients.
Comparative shotgun metagenomic data of the silkworm Bombyx mori gut microbiome
Authors: Chen Bosheng , Yu Ting , Xie Sen , Du Kaiqian , Liang Xili , Lan Yahua , Sun Chao , Lu Xingmeng , Shao Yongqi 
Published: December 2018

AbstractLepidoptera (butterflies and moths) is a major insect order including important pollinators and agricultural pests, however their microbiomes are little studied. Here, using next-generation sequencing (NGS)-based shotgun metagenomics, we characterize both the biodiversity and functional potential of gut microbiota of a lepidopteran model insect, the silkworm Bombyx mori. Two metagenomes, including the standard inbred strain Dazao (P50) and an improved hybrid strain Qiufeng × Baiyu (QB) widely used in commercial silk production, were generated, containing 45,505,084 and 69,127,002 raw reads, respectively. Taxonomic analysis revealed that a total of 663 bacterial species were identified in P50 silkworms, while 322 unique species in QB silkworms. Notably, Enterobacter, Acinetobacter and Enterococcus were dominated in both strains. The further functional annotation was performed by both BlastP and MG-RAST against various databases including Nr, COG, KEGG, CAZy and SignalP, which revealed >5 × 106 protein-coding genes. These datasets not only provide first insights into all bacterial genes in silkworm guts, but also help to generate hypotheses for subsequently testing functional traits of gut microbiota in an important insect group.
Transcriptome profiling of a beach-adapted wild legume for dissecting novel mechanisms of salinity tolerance
Authors: Zhang Hengyou , Zuelsdorf Christine , Penneys Darin , Fan Shoujin , Kofsky Janice , Song Bao-Hua 
Published: December 2018

AbstractStrophostyles helvola is a close relative to common bean (Phaseolus vulgaris) and inhabits both coastal and non-coastal regions in North America. However, the mechanism of saline adaptation in S. helvola remains unclear. A transcriptome profiling would facilitate dissecting the underlying molecular mechanisms in salinity-adapted S. helvola. In this study, we reported the RNA-seq analyses of two genotypes (a salt-tolerant beach genotype and a salt-sensitive inland genotype) of S. helvola stressed with salt. S. helvola plants were grown in pots and treated with half lethal-guided dose of NaCl solution for 3 h, 24 h, and 7d. The plants supplied with the same amount of water were used as controls. The whole roots sampled from the three time points were equally pooled as one biological replicate, and three replicates were used for library construction and transcriptome sequencing on Illumina Hiseq 2500. The comparative analyses of root transcriptomes presented here provides a valuable resource for discovery of genes and networks involved in salt tolerance in S. helvola.
Structure and nucleotide-induced conformational dynamics of the Chlorobium tepidum Roco protein
Authors: Deyaert Egon , Leemans Margaux , Singh Ranjan Kumar , Gallardo Rodrigo , Steyaert Jan , Kortholt Arjan , Lauer Janelle , Versées Wim 
Published: December 2018

Abstract
The LRR (leucine-rich repeat)–Roc (Ras of complex proteins)–COR (C-terminal of Roc) domains are central to the action of nearly all Roco proteins, including the Parkinson's disease-associated protein LRRK2 (leucine-rich repeat kinase 2). We previously demonstrated that the Roco protein from Chlorobium tepidum (CtRoco) undergoes a dimer–monomer cycle during the GTPase reaction, with the protein being mainly dimeric in the nucleotide-free and GDP (guanosine-5′-diphosphate)-bound states and monomeric in the GTP (guanosine-5′-triphosphate)-bound state. Here, we report a crystal structure of CtRoco in the nucleotide-free state showing for the first time the arrangement of the LRR–Roc–COR. This structure reveals a compact dimeric arrangement and shows an unanticipated intimate interaction between the Roc GTPase domains in the dimer interface, involving residues from the P-loop, the switch II loop, the G4 region and a loop which we named the ‘Roc dimerization loop’. Hydrogen–deuterium exchange coupled to mass spectrometry (HDX-MS) is subsequently used to highlight structural alterations induced by individual steps along the GTPase cycle. The structure and HDX-MS data propose a pathway linking nucleotide binding to monomerization and relaying the conformational changes via the Roc switch II to the LRR and COR domains. Together, this work provides important new insights in the regulation of the Roco proteins.
Procaspase activating compound 1 controls tetracycline repressor-regulated gene expression system
Authors: Song Chiman , Kim Namkyoung , Park Miri , Lee Jiyeon , Oh Ki-Bong , Sim Taebo 
Published: December 2018

Abstract
The tetracycline repressor (TetR)-regulated system is a widely used tool to study gene functions through control of its expression. Various effectors such as tetracycline (Tc) and doxycycline (Dox) quickly induce or shut down gene expression, but reversing gene expression has not been eligible due to long half-lives of such effectors. Here, we found that procaspase activating compound 1 (PAC-1) rapidly reduces transient expression of TetR-regulated green fluorescent protein (GFP) in mammalian cells. Next, we applied PAC-1 to control of expression of transient receptor potential melastatin 7 (TRPM7) protein, whose downstream cellular events can be monitored by cell morphological changes. We observed that PAC-1 quickly reduces TRPM7 expression, consequently affecting cell morphology regulated by TRPM7. The present study demonstrates the first small molecule that efficiently turns off the TetR-regulated gene expression in mammalian cells, thereby precisely regulating the expression level of target gene.
Heme oxygenase-1 induction by hemin prevents oxidative stress-induced acute cholestasis in the rat
Authors: Martín Pamela L. , Ceccatto Paula , Razori María V. , Francés Daniel E.A. , Arriaga Sandra M.M. , Pisani Gerardo B. , Martínez Alejandra I. , Sánchez Pozzi Enrique J. , Roma Marcelo G. , Basiglio Cecilia L. 
Published: December 2018

AbstractWe previously demonstrated in in vitro and ex vivo models that physiological concentrations of unconjugated bilirubin (BR) prevent oxidative stress (OS)-induced hepatocanalicular dysfunction and cholestasis. Here, we aimed to ascertain, in the whole rat, whether a similar cholestatic OS injury can be counteracted by heme oxygenase-1 (HO-1) induction that consequently elevates endogenous BR levels. This was achieved through the administration of hemin, an inducer of HO-1, the rate-limiting step in BR generation. We found that BR peaked between 6 and 8 h after hemin administration. During this time period, HO-1 induction fully prevented the pro-oxidant tert-butylhydroperoxide (tBuOOH)-induced drop in bile flow, and in the biliary excretion of bile salts and glutathione, the two main driving forces of bile flow; this was associated with preservation of the membrane localization of their respective canalicular transporters, bile salt export pump (Bsep) and multidrug resistance-associated protein 2 (Mrp2), which are otherwise endocytosed by OS. HO-1 induction counteracted the oxidation of intracellular proteins and membrane lipids induced by tBuOOH, and fully prevented the increase in the oxidized-to-total glutathione (GSHt) ratio, a sensitive parameter of hepatocellular OS. Compensatory elevations of the activity of the antioxidant enzymes catalase (CAT) and superoxide dismutase (SOD) were also prevented. We conclude that in vivo HO-1 induction protects the liver from acute oxidative injury, thus preventing consequent cholestasis. This reveals an important role for the induction of HO-1 and the consequently elevated levels of BR in preserving biliary secretory function under OS conditions, thus representing a novel therapeutic tool to limit the cholestatic injury that bears an oxidative background.
Analysis, design, and performance evaluation of zero‐voltage‐ripple buck dc–dc converter
Authors: Ayachit Agasthya , Saini Dalvir K. , Salvatierra Thomas , Kazimierczuk Marian K. 
Published: December 2018

A buck dc–dc converter with ripple reduction has been proposed previously. However, detailed characterisation and performance analysis were not conducted. This study presents steady‐state analysis, design, and performance evaluation of the zero‐voltage ripple (ZVR) buck dc–dc converter in continuous conduction mode (CCM). The ZVR buck converter is capable of eliminating the output voltage ripple by employing a two‐winding auto‐transformer. The expressions for steady‐state current and voltage waveforms are given. The equations for the design of the converter components are derived. A step‐by‐step procedure to design the auto‐transformer for the ZVR buck converter using the area‐product method is introduced. Derivations of expressions for the power losses in passive components, magnetic core, windings, and semiconductor devices are presented. A laboratory prototype of the ZVR buck converter in CCM with input voltage 12 V, output voltage 5 V, output power 10 W, and switching frequency 500 kHz was designed, built, and tested. Simulation results showing the superior performance of the ZVR buck converter over the poly‐phase converters are given. Experimental results are provided to validate the theory. It was observed that the ZVR buck converter produces nearly zero ripples at any duty cycle with efficiency in the order of 90%.
Multiple positive bound states for critical Schrödinger-Poisson systems
Authors: Cerami Giovanna , Molle Riccardo 
Published: December 2018

Using variational methods we prove some results about existence and multiplicity of positive bound states of to the following Schrödinger-Poisson system:
[see formula in PDF]
We remark that (SP) exhibits a “double” lack of compactness because of the unboundedness of ℝ3 and the critical growth of the nonlinear term and that in our assumptions ground state solutions of (SP) do not exist.
Ski Mountaineering – Evaluation of a Sports Specific Performance Diagnosis
Authors: Schöffl Volker , Pöppelmeier Olaf , Emmler Julia , Schöffl Isabelle , Küpper Thomas , Lutter Christoph 
Published: December 2018

AbstractSki mountaineering (skimo) has recently gained popularity and established itself as a competition sport. It requires a specific training with a high hypoxic load. Although a variety of sport specific performance test protocols have been developed, a specific method for ski mountaineering (skimo) is pending. After the development of a sport specific ergometric protocol with recreational athletes in pre-tests a standard sport specific protocol was defined, concerning treadmill speed, slope and step test variables. This protocol was evaluated for its effectivity with members of the German national skimo team (6 male, 2 female). All athletes performed two spiroergometry test protocols, a standard bike test profile followed by sport specific spiroergometry. This skimo-specific test involved an incremental step test with skis on a treadmill, using a standard incline of 20° with an stepwise speed increase. Spiroergometry and blood lactate (BL) data were recorded and the first and second ventilatory thresholds (VT1 and VT2) were determined. All athletes could complete the test without any technical problems and reached cardiopulmonary exhaustion. The mean test break off BL was 9.98 ± 2.0 mmol/L for the bike test, and 9.28 ± 2.3 mmol/L for the skimo test. The heart rate at VT1 as a percentage of the maximum heart rate did not differ significantly between protocols. Heart rates at VT2 did not significantly differ between both protocols, but varied in both directions. In three athletes, VO2max was higher in the skimo tests than in the bike tests, while the remaining five athletes exhibited the opposite situation. VO2max did not differ significantly between skimo and bike tests (p = 0.35), but it varied in both directions. Motion analysis revealed motoric deficits in two cases. The study indicates that skimo and bike tests are not fully comparable. The skimo and bike test results vary with respect to the majority of test parameters and statistical findings, nevertheless these findings were not statistically significant. These differences were furthermore found to be inconsistent, which is the most valuable finding of the study. It can thus be concluded that a sport specific test is important for both optimal exercise testing and the development of training recommendations for skimo athletes.