bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of SCCmec type in resistance to the synergistic activity of oxacillin and cefoxitin in MRSA
Authors: Reichmann Nathalie T. , Pinho Mariana G. 
Published: July 2017

Abstractβ-lactam antibiotics target penicillin-binding proteins (PBPs) preventing peptidoglycan synthesis and this inhibition is circumvented in methicillin resistant Staphylococcus aureus (MRSA) strains through the expression of an additional PBP, named PBP2A. This enzyme is encoded by the mecA gene located within the Staphylococcal Chromosome Cassette mec (SCCmec) mobile genetic element, of which there are 12 types described to date. Previous investigations aimed at analysing the synergistic activity of two β-lactams, oxacillin and cefoxitin, found that SCCmec type IV community-acquired MRSA strains exhibited increased susceptibility to oxacillin in the presence of cefoxitin, while hospital-acquired MRSA strains were unaffected. However, it is not clear if these differences in β-lactam resistance are indeed a consequence of the presence of the different SCCmec types. To address this question, we have exchanged the SCCmec type I in COL (HA-MRSA) for the SCCmec type IV from MW2 (CA-MRSA). This exchange did not decrease the resistance of COL against oxacillin and cefoxitin, as observed in MW2, indicating that genetic features residing outside of the SCCmec element are likely to be responsible for the discrepancy in oxacillin and cefoxitin synergy against these MRSA strains.
Deficient glutamate biosynthesis triggers a concerted upregulation of ribosomal protein genes in Arabidopsis
Authors: Muñoz-Nortes Tamara , Pérez-Pérez José Manuel , Sarmiento-Mañús Raquel , Candela Héctor , Micol José Luis 
Published: July 2017

AbstractBiomass production requires the coordination between growth and metabolism. In a large-scale screen for mutants affected in leaf morphology, we isolated the orbiculata1 (orb1) mutants, which exhibit a pale green phenotype and reduced growth. The combination of map-based cloning and next-generation sequencing allowed us to establish that ORB1 encodes the GLUTAMATE SYNTHASE 1 (GLU1) enzyme, also known as FERREDOXIN-DEPENDENT GLUTAMINE OXOGLUTARATE AMINOTRANSFERASE 1 (Fd-GOGAT1). We performed an RNA-seq analysis to identify global gene expression changes in the orb1–3 mutant. We found altered expression levels of genes encoding enzymes involved in nitrogen assimilation and amino acid biosynthesis, such as glutamine synthetases, asparagine synthetases and glutamate dehydrogenases, showing that the expression of these genes depends on the levels of glutamine and/or glutamate. In addition, we observed a concerted upregulation of genes encoding subunits of the cytosolic ribosome. A gene ontology (GO) analysis of the differentially expressed genes between Ler and orb1–3 showed that the most enriched GO terms were ‘translation’, ‘cytosolic ribosome’ and ‘structural constituent of ribosome’. The upregulation of ribosome-related functions might reflect an attempt to keep protein synthesis at optimal levels even when the pool of glutamate is reduced.
Electronic Structure of Polyethylene: Role of Chemical, Morphological and Interfacial Complexity
Authors: Chen Lihua , Huan Tran Doan , Ramprasad Rampi 
Published: July 2017

AbstractThe electronic structure of an insulator encodes essential signatures of its short-term electrical performance and long-term reliability. A critical long-standing challenge though is that key features of the electronic structure of an insulator (and its evolution) under realistic conditions have not been entirely accessible, either via experimental or computational approaches, due to the inherent complexities involved. In this comprehensive study, we reveal the role of chemical and morphological imperfections that inevitably exist within the technologically important prototypical and pervasive insulator, polyethylene (PE), and at electrode/PE interfaces. Large-scale density functional theory computations and long-time molecular dynamics simulations were employed to accurately recover, explain and unravel a wide variety of experimental data obtained during the electrical degradation of PE. This scheme has allowed us to directly and realistically address the role of chemical, morphological and interfacial complexity in determining electronic structure. These efforts take us a step closer to understanding and potentially controlling dielectric degradation and breakdown.
High-fidelity de novo synthesis of pathways using microchip-synthesized oligonucleotides and general molecular biology equipment
Authors: Wan Wen , Lu Min , Wang Dongmei , Gao Xiaolian , Hong Jiong 
Published: July 2017

AbstractEngineering and evaluation of synthetic routes for generating valuable compounds require accurate and cost-effective de novo synthesis of genetic pathways. Here, we present an economical and streamlined de novo DNA synthesis approach for engineering a synthetic pathway with microchip-synthesized oligonucleotides (oligo). The process integrates entire oligo pool amplification, error-removal, and assembly of long DNA molecules. We utilized this method to construct a functional lycopene biosynthetic pathway (11.9 kb encoding 10 genes) in Escherichia coli using a highly error-prone microchip-synthesized oligo pool (479 oligos) without pre-purification, and the error-frequency was reduced from 14.25/kb to 0.53/kb. This low-equipment-dependent and cost-effective method can be widely applied for rapid synthesis of biosynthetic pathways in general molecular biology laboratories.
Nanoscale Investigation of Generation 1 PAMAM Dendrimers Interaction with a Protein Nanopore
Authors: Asandei Alina , Ciuca Andrei , Apetrei Aurelia , Schiopu Irina , Mereuta Loredana , Seo Chang Ho , Park Yoonkyung , Luchian Tudor 
Published: July 2017

AbstractHerein, we describe at uni-molecular level the interactions between poly(amidoamine) (PAMAM) dendrimers of generation 1 and the α-hemolysin protein nanopore, at acidic and neutral pH, and ionic strengths of 0.5 M and 1 M KCl, via single-molecule electrical recordings. The results indicate that kinetics of dendrimer-α-hemolysin reversible interactions is faster at neutral as compared to acidic pH, and we propose as a putative explanation the fine interplay among conformational and rigidity changes on the dendrimer structure, and the ionization state of the dendrimer and the α-hemolysin. From the analysis of the dendrimer’s residence time inside the nanopore, we posit that the pH- and salt-dependent, long-range electrostatic interactions experienced by the dendrimer inside the ion-selective α-hemolysin, induce a non-Stokesian diffusive behavior of the analyte inside the nanopore. We also show that the ability of dendrimer molecules to adapt their structure to nanoscopic spaces, and control the flow of matter through the α-hemolysin nanopore, depends non-trivially on the pH- and salt-induced conformational changes of the dendrimer.
Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders
Authors: Mozzi Alessandra , Forni Diego , Cagliani Rachele , Pozzoli Uberto , Clerici Mario , Sironi Manuela 
Published: July 2017

AbstractIn addition to high intelligence, humans evolved specialized social-cognitive skills, which are specifically affected in children with autism spectrum disorder (ASD). Genes affected in ASD represent suitable candidates to study the evolution of human social cognition. We performed an evolutionary analysis on 68 genes associated to neurodevelopmental disorders; our data indicate that genetic diversity was shaped by distinct selective forces, including natural selection and introgression from archaic hominins. We discuss the possibility that segregation distortion during spermatogenesis accounts for a subset of ASD mutations. Finally, we detected modern-human-specific alleles in DYRK1A and TCF4. These variants are located within regions that display chromatin features typical of transcriptional enhancers in several brain areas, strongly suggesting a regulatory role. These SNPs thus represent candidates for association with neurodevelopmental disorders, and await experimental validation in future studies.
Short-chain fatty acids and inulin, but not guar gum, prevent diet-induced obesity and insulin resistance through differential mechanisms in mice
Authors: Weitkunat Karolin , Stuhlmann Christin , Postel Anna , Rumberger Sandra , Fankhänel Maria , Woting Anni , Petzke Klaus Jürgen , Gohlke Sabrina , Schulz Tim J. , Blaut Michael , Klaus Susanne , Schumann Sara 
Published: July 2017

AbstractThe role of dietary fibre and short-chain fatty acids (SCFA) in obesity development is controversially discussed. Here, we investigated how various types of dietary fibre and different SCFA ratios affect metabolic syndrome-related disorders. Male mice (B6) were fed high-fat diets supplemented with dietary fibres (either cellulose, inulin or guar gum) or different Ac:Pr ratios (high acetate (HAc) or propionate (HPr)) for 30 weeks. Body-fat gain and insulin resistance were greatly reduced by inulin, but not by guar gum, and completely prevented by SCFA supplementation. Only inulin and HAc increased body temperature, possibly by the induction of beige/browning markers in WAT. In addition, inulin and SCFA lowered hepatic triglycerides and improved insulin sensitivity. Both, inulin and HAc reduced hepatic fatty acid uptake, while only inulin enhanced mitochondrial capacity and only HAc suppressed lipogenesis in liver. Interestingly, HPr was accompanied by the induction of Nrg4 in BAT. Fermentable fibre supplementation increased the abundance of bifidobacteria;B.animaliswas particularly stimulated by inulin andB.pseudolongumby guar gum. We conclude that in contrast to guar gum, inulin and SCFA prevent the onset of diet-induced weight gain and hepatic steatosis by different mechanisms on liver and adipose tissue metabolism.
Gestational age-specific sex difference in mortality and morbidities of preterm infants: A nationwide study
Authors: Shim So-Yeon , Cho Su Jin , Kong Kyoung Ae , Park Eun Ae 
Published: July 2017

AbstractThis study aims to determine whether male sex has adverse effect on mortality and morbidities in very low birth weight infants (VLBWI) <30 weeks of gestation and to ascertain this sex effect, stratified by gestational age, adjusting for perinatal risk factors. This is a population-based study from Korean Neonatal Network for VLBWI born at 23+0 and 29+6 weeks of gestation between January 2013 and December 2014. The primary outcome was gestation-specific sex difference in the occurrence of mortality, combined morbidities, and individual morbidity. A total of 2228 VLBWI were enrolled (males, 51.7%). Mortality was not different between sexes. The risk of bronchopulmonary dysplasia and combined morbidities was significantly higher in males ≤25 weeks of gestation (odds ratio [OR] 2.08, 95% confidence interval [CI] 1.35–3.20 and OR 2.00, CI 1.19–3.39, respectively). Males had a significantly higher incidence of periventricular leukomalacia at 23 and 29 weeks of gestation. The risk of severe retinopathy of prematurity was higher in females >25 weeks of gestation. Although both sexes have similar risk for mortality, male sex remains an independent risk for major morbidities, especially at ≤25 weeks of gestation. The risk of each outcome for males has a specific pattern with increasing gestational age.
Inductively powered wireless pacing via a miniature pacemaker and remote stimulation control system
Authors: Abiri Parinaz , Abiri Ahmad , Packard René R. Sevag , Ding Yichen , Yousefi Alireza , Ma Jianguo , Bersohn Malcolm , Nguyen Kim-Lien , Markovic Dejan , Moloudi Shervin , Hsiai Tzung K. 
Published: July 2017

AbstractPacemakers have existed for decades as a means to restore cardiac electrical rhythms. However, lead-related complications have remained a clinical challenge. While market-released leadless devices have addressed some of the issues, their pacer-integrated batteries cause new health risks and functional limitations. Inductive power transfer enables wireless powering of bioelectronic devices; however, Specific Absorption Rate and size limitations reduce power efficiency for biomedical applications. We designed a remote-controlled system in which power requirements were significantly reduced via intermittent power transfer to control stimulation intervals. In parallel, the cardiac component was miniaturized to facilitate intravascular deployment into the anterior cardiac vein. Given size constraints, efficiency was optimal via a circular receiver coil wrapped into a half-cylinder with a meandering tail. The pacemaker was epicardially tested in a euthanized pig at 60 beats per minute, 2 V amplitude, and 1 ms pulse width, restoring mean arterial pressure from 0 to 37 mmHg. Power consumption was 1 mW at a range of > 3 cm with no misalignment and at 2 cm with 45° displacement misalignment, 45° x-axis angular misalignment, or 45° y-axis angular misalignment. Thus, we demonstrated a remote-controlled miniaturized pacing system with low power consumption, thereby providing a basis for the next generation of wireless implantable devices.
RNAi screening identifies Trypanosoma brucei stress response protein kinases required for survival in the mouse
Authors: Fernandez-Cortes Fernando , Serafim Tiago D. , Wilkes Jonathan M. , Jones Nathaniel G. , Ritchie Ryan , McCulloch Richard , Mottram Jeremy C. 
Published: July 2017

AbstractProtein kinases (PKs) are a class of druggable targets in Trypanosoma brucei, the causative agent of Human African Trypanosomiasis (sleeping sickness), yet little is known about which PKs are essential for survival in mammals. A recent kinome-wide RNAi screen with 176 individual bloodstream form Trypanosoma brucei lines identified PKs required for proliferation in culture. In order to assess which PKs are also potential virulence factors essential in vivo, lines were pooled, inoculated into mice, and screened for loss of fitness after 48 h RNAi. The presence of trypanosomes in the bloodstream was assessed using RNAi target sequencing (RITseq) and compared to growth in culture. We identified 49 PKs with a significant loss of fitness in vivo in two independent experiments, and a strong correlation between in vitro and in vivo loss of fitness for the majority. Nine PKs had a more pronounced growth defect in vivo, than in vitro. Amongst these PKs were several with putative functions related to stress responses mediated through the PI3K/TOR or MAPK signaling cascades, which act to protect the parasite from complement-mediated and osmotic lysis. Identification of these virulence-associated PKs provides new insights into T. brucei-host interaction and reveals novel potential protein kinase drug targets.
Impact of Natural Blind Spot Location on Perimetry
Authors: Wang Mengyu , Shen Lucy Q. , Boland Michael V. , Wellik Sarah R. , De Moraes Carlos Gustavo , Myers Jonathan S. , Bex Peter J. , Elze Tobias 
Published: July 2017

AbstractWe study the spatial distribution of natural blind spot location (NBSL) and its impact on perimetry. Pattern deviation (PD) values of 11,449 reliable visual fields (VFs) that are defined as clinically unaffected based on summary indices were extracted from 11,449 glaucoma patients. We modeled NBSL distribution using a two-dimensional non-linear regression approach and correlated NBSL with spherical equivalent (SE). Additionally, we compared PD values of groups with longer and shorter distances than median, and larger and smaller angles than median between NBSL and fixation. Mean and standard deviation of horizontal and vertical NBSL were 14.33° ± 1.37° and −2.06° ± 1.27°, respectively. SE decreased with increasing NBSL (correlation: r = −0.14, p < 0.001). For NBSL distances longer than median distance (14.32°), average PD values decreased in the upper central (average difference for significant points (ADSP): −0.18 dB) and increased in the lower nasal VF region (ADSP: 0.14 dB). For angles in the direction of upper hemifield relative to the median angle (−8.13°), PD values decreased in lower nasal (ADSP: −0.11 dB) and increased in upper temporal VF areas (ADSP: 0.19 dB). In conclusion, we demonstrate that NBSL has a systematic effect on the spatial distribution of VF sensitivity.
Revealing higher than expected meiofaunal diversity in Antarctic sediments: a metabarcoding approach
Authors: Fonseca V. G. , Sinniger F. , Gaspar J. M. , Quince C. , Creer S. , Power Deborah M. , Peck Lloyd S. , Clark Melody S. 
Published: July 2017

AbstractAn increasing number of studies are showing that Antarctic mega- and macrofauna are highly diverse, however, little is known about meiofaunal biodiversity in sediment communities, which are a vital part of a healthy and functional ecosystem. This is the first study to analyse community DNA (targeting meiofauna) using metabarcoding to investigate biodiversity levels in sediment communities of the Antarctic Peninsula. The results show that almost all of the meiofaunal biodiversity in the benthic habitat has yet to be characterised, levels of biodiversity were higher than expected and similar to temperate regions, albeit with the existence of potentially new and locally adapted species never described before at the molecular level. The Rothera meiofaunal sample sites showed four dominant eukaryotic groups, the nematodes, arthropods, platyhelminthes, and the annelids; some of which could comprise species complexes. Comparisons with deep-sea data from the same region suggest little exchange of Operational Taxonomic Units (OTUs) between depths with the nematodes prevalent at all depths, but sharing the shallow water benthos with the copepods. This study provides a preliminary analysis of benthic Antarctic Peninsula meiofauna using high throughput sequencing which substantiates how little is known on the biodiversity of one of the most diverse, yet underexplored communities of the Antarctic: the benthos.
Language Sampling With Adolescents: Building a Normative Database With Fables
Authors: Nippold Marilyn A. , Vigeland Laura M. , Frantz-Kaspar Megan W. , Ward-Lonergan Jeannene M. 
Published: July 2017

Purpose
The goal of the study was to create a language sampling task appropriate for adolescents and to contribute normative data from speakers with typical language development.

Method
Thirty adolescents (mean age = 14 years, 1 month) participated in an interview that involved the retelling and interpretation of 4 Greek fables. Each speaker's performance on the task was audio-recorded, transcribed verbatim, and entered into the Systematic Analysis of Language Transcripts computer program (Miller & Iglesias, 2015). Samples were analyzed statistically for language productivity and syntactic complexity. In addition, each participant's perspective on the moral messages of the fables was examined informally.

Results
The Fables task was effective in prompting adolescents to use complex language and in encouraging them to express their opinions about the moral messages. Although boys and girls did not differ in their performance on the task, some fables were more effective than others at eliciting spoken language and complex syntax. Moreover, the adolescents tended to agree with the moral messages of the fables and appeared to find them relevant to their lives.

Conclusion
The Fables task has potential for clinical use with adolescents. Research is necessary to expand the normative database to include larger and more diverse groups of adolescents.
Superantigen staphylococcal enterotoxin C1 inhibits the growth of bladder cancer
Authors: Liu Tao , Li Lin , Yin Lei , Yu Hongyuan , Jing Hongwei , Liu Yang , Kong Chuize , Xu Mingkai 
Published: July 2017

AbstractSuperantigens can induce cell-mediated cytotoxicity preferentially against MHC II-positive target cells with large amounts of inflammatory cytokines releasing. In this study, superantigen staphylococcal enterotoxin C (SEC) 1 was investigated to evaluate its potential in bladder cancer immunotherapy in vitro and in vivo. Our results revealed that SEC1 could stimulate the proliferation of human peripheral blood mononuclear cells (PBMCs) in a dose-dependent manner, accompanied with the release of interleukin-2, interferon-γ, and tumor necrosis factor-α, and increased the population of CD4+ T cells and CD8+ T cells. PBMCs stimulated by SEC1 could initiate significant cytotoxicity towards human bladder cancer cells in vitro. The results of in vivo antitumor experiment indicated that SEC1 could decrease the rate of tumor formation and prolong the survival time of tumor-bearing mice. Our study demonstrated that SEC1 inhibited the growth of bladder cancer. And it is also suggested that SEC1 may become a candidate for bladder cancer immunotherapy.
Time Operator in Relativistic Quantum Mechanics
Authors: Khorasani Sina 
Published: July 2017

Abstract

It is first shown that the Dirac’s equation in a relativistic frame could be modified to allow discrete time, in agreement to a recently published upper bound. Next, an exact self-adjoint 4 × 4 relativistic time operator for spin-1/2 particles is found and the time eigenstates for the non-relativistic case are obtained and discussed. Results confirm the quantum mechanical speculation that particles can indeed occupy negative energy levels with vanishingly small but non-zero probablity, contrary to the general expectation from classical physics. Hence, Wolfgang Pauli’s objection regarding the existence of a self-adjoint time operator is fully resolved. It is shown that using the time operator, a bosonic field referred here to as energons may be created, whose number state representations in non-relativistic momentum space can be explicitly found.
Enhanced tau pathology via RanBP9 and Hsp90/Hsc70 chaperone complexes
Authors: Woo Jung A , Liu Tian , Zhao Xingyu , Trotter Courtney , Yrigoin Ksenia , Cazzaro Sara , Narvaez Emilio De , Khan Hirah , Witas Richard , Bukhari Anusha , Makati Kamal , Wang Xinming , Dickey Chad , Kang David E 
Published: July 2017

Abstract
Accumulation of amyloid β (Aβ) and tau represent the two major pathological hallmarks of Alzheimer’s disease (AD). Despite the critical importance of Aβ accumulation as an early event in AD pathogenesis, multiple lines of evidence indicate that tau is required to mediate Aβ-induced neurotoxic signals in neurons. We have previously shown that the scaffolding protein Ran-binding protein 9 (RanBP9), which is highly elevated in brains of AD and AD mouse models, both enhances Aβ production and mediates Aβ-induced neurotoxicity. However, it is unknown whether and how RanBP9 transmits Aβ-induced neurotoxic signals to tau. Here we show for the first time that overexpression or knockdown of RanBP9 directly enhances and reduces tau levels, respectively, in vitro and in vivo. Such changes in tau levels are associated with the ability of RanBP9 to physically interact with tau and heat shock protein 90/heat shock cognate 70 (Hsp90/Hsc70) complexes. Meanwhile, both RanBP9 and tau levels are simultaneously reduced by Hsp90 or Hsc70 inhibitors, whereas overexpression or knockdown of RanBP9 significantly diminishes the anti-tau potency of Hsp90/Hsc70 inhibitors as well as Hsc70 variants (WT & E175S). Further, RanBP9 increases the capacity for Hsp90 and Hsc70 complexes to bind ATP and enhances their ATPase activities in vitro. These observations in vitro and cell lines are recapitulated in primary neurons and in vivo, as genetic reduction in RanBP9 not only ameliorates tauopathy in Tau-P301S mice but also rescues the deficits in synaptic integrity and plasticity.