bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental challenge of pregnant cattle with the putative abortifacient Waddlia chondrophila
Authors: Wheelhouse Nicholas , Flockhart Allen , Aitchison Kevin , Livingstone Morag , Finlayson Jeanie , Flachon Virginie , Sellal Eric , Dagleish Mark P. , Longbottom David 
Published: November 2016

AbstractWaddlia chondrophila is a Gram-negative intracellular bacterial organism that is related to classical chlamydial species and has been implicated as a cause of abortion in cattle. Despite an increasing number of observational studies linking W. chondrophila infection to cattle abortion, little direct experimental evidence exists. Given this paucity of direct evidence the current study was carried out to investigate whether experimental challenge of pregnant cattle with W. chondrophila would result in infection and abortion. Nine pregnant Friesian-Holstein heifers received 2 × 108 inclusion forming units (IFU) W. chondrophila intravenously on day 105–110 of pregnancy, while four negative-control animals underwent mock challenge. Only one of the challenged animals showed pathogen-associated lesions, with the organism being detected in the diseased placenta. Importantly, the organism was re-isolated and its identity confirmed by whole genome sequencing, confirming Koch’s third and fourth postulates. However, while infection of the placenta was observed, the experimental challenge in this study did not confirm the abortifacient potential of the organism.
Inversion of inherited thrusts by wastewater injection induced seismicity at the Val d’Agri oilfield (Italy)
Authors: Buttinelli M. , Improta L. , Bagh S. , Chiarabba C. 
Published: November 2016

AbstractSince 2006 wastewater has been injected below the Val d’Agri Quaternary basin, the largest on-land oilfield in Europe, inducing micro-seismicity in the proximity of a high-rate injection well. In this study, we have the rare opportunity to revise a massive set of 2D/3D seismic and deep borehole data in order to investigate the relationship between the active faults that bound the basin and the induced earthquakes. Below the injection site we identify a Pliocene thrusts and back-thrusts system inherited by the Apennines compression, with no relation with faults bounding the basin. The induced seismicity is mostly confined within the injection reservoir, and aligns coherently with a NE-dipping back-thrust favorably oriented within the current extensional stress field. Earthquakes spread upwards from the back-thrust deep portion activating a 2.5-km wide patch. Focal mechanisms show a predominant extensional kinematic testifying to an on-going inversion of the back-thrust, while a minor strike-slip compound suggests a control exerted by a high angle inherited transverse fault developed within the compressional system, possibly at the intersection between the two fault sets. We stress that where wastewater injection is active, understanding the complex interaction between injection-linked seismicity and pre-existing faults is a strong requisite for safe oilfield exploitation.
Development of functional human oral mucosal epithelial stem/progenitor cell sheets using a feeder-free and serum-free culture system for ocular surface reconstruction
Authors: Nakamura Takahiro , Yokoo Seiichi , Bentley Adams J. , Nagata Maho , Fullwood Nigel J. , Inatomi Tsutomu , Sotozono Chie , Yamagami Satoru , Kinoshita Shigeru 
Published: November 2016

AbstractOcular surface reconstruction (OSR) using tissue-engineered cultivated oral mucosal epithelial cell sheets (COMECS) is a promising newly developed treatment for patients with severe ocular surface disease. Until now, this technique has used exogenic and undefined components such as mouse-derived 3T3 feeder cells and fetal bovine serum. To minimize associated risks of zoonotic infection or transmission of unknown pathogens and so establish a safe and effective protocol for the next generation of treatment modality, we developed a novel technique for the COMECS protocol, using a feeder-free and serum-free (FFSF) culture system. Following this new protocol, COMECS exhibited 4–5 layers of well-stratified and differentiated cells, and we successfully produced functional COMECS that included holoclone-type stem cells. Immunohistochemistry confirmed the presence of markers for cell junction (ZO1, Desmoplakin), basement membrane assembly (Collagen 7, Laminin 5), differentiation (K13, K3), proliferation (Ki67) and stem/progenitor cells (p75) in the FFSF COMECS. When transplanted to the ocular surfaces of rabbits, the tissue survived for up to 2 weeks. This study represents a first step toward assessing the development of functional FFSF COMECS for safe and ideal OSR.
The effect of alloying elements on the corrosion resistance of brass
Authors: Claesson E. , Rod O. 
Published: November 2016

A systematic study has been performed on the effect of alloying elements arsenic (As), antimony (Sb) and phosphorus (P) on the dezincification resistance of α-phase in brass. The result showed that P formed particles with Al and Fe already at relatively high temperatures, leaving no P in solid solution and thus no protection against dezincification. Arsenic only formed particles at lower temperatures and offers a satisfactory protecting. However, with increasing As levels grain boundary attack was observed. Samples alloyed with Sb show a satisfactory resistance to dezincification and no grain boundary attack. Finally, a combination of As and Sb at low alloying levels provided an excellent dezincification resistance for brass containing typical impurity levels. This paper is part of a Themed Issue on Brass Alloys.
Practical large-scale production of dihydrocapsiate, a nonpungent capsaicinoid-like substance
Authors: Kurosawa Wataru , Nakano Takashi , Amino Yusuke 
Published: November 2016

Abstract
Capsinoids represent a novel group of capsaicinoid-like substances found in a nonpungent cultivar, Capsicum annuum “CH-19 Sweet.” They have capsaicinoid-like physiological and biological properties while lacking the harmful stimuli of capsaicinoids. A large-scale synthesis of dihydrocapsiate (DCT) is established in this work. 8-Methynonanoic acid (MNA) was synthesized by copper-catalyzed cross-coupling of ethyl 6-bromohexanoate with isobutylmagnesium bromide and subsequent hydrolysis. Lipase-catalyzed chemoselective esterification of vanillyl alcohol and MNA was performed at 50 °C under reduced pressure to remove water without solvents or drying agents. A slightly larger stoichiometric amount of MNA was used and the purification in the final stage was simplified to leave a small amount of MNA in the product, because we found that the presence of a small amount of MNA is necessary to stabilize DCT. DCT was synthesized according to the production, and stabilization methods described here has been filed as a new dietary ingredient.
The Barratt Impulsiveness Scale - 11 Among a Portuguese Sample of Female Juvenile Delinquents and Community Youths
Authors: Pechorro Pedro , Ayala-Nunes Lara , Nunes Cristina , Maia Ângela , Gonçalves Rui Abrunhosa 
Published: November 2016

Impulsivity among incarcerated female juvenile offenders is an understudied area of research. The aim of this study was to examine the psychometric properties of the Barratt Impulsiveness Scale version 11 (BIS-11) among a Portuguese sample of female participants (N = 377, mean age = 16.23 years, SD = 1.38) recruited from forensic and school contexts. Confirmatory factor analysis revealed the expected six-factor first-order structure, but not the three-factor second-order structure. Acceptable levels of internal consistency were mostly obtained, but some dimensions showed somewhat lower than expected values. Convergent validity with measures of psychopathic and callous-unemotional traits, and discriminant validity with a measure of social anxiety was demonstrated. In terms of criterion-related validity significant associations were found with relevant variables (e.g., age of crime onset, conduct disorder symptoms, alcohol, and drug use). The use of the BIS-11 among female juvenile delinquents and community youth is psychometrically justified and it can be considered a useful measure to identify impulsive adolescents.
Computing structure-based lipid accessibility of membrane proteins withmp_lipid_accin RosettaMP
Authors: Koehler Leman Julia , Lyskov Sergey , Bonneau Richard 
Published: November 2016

AbstractBackgroundMembrane proteins are vastly underrepresented in structural databases, which has led to a lack of computational tools and the corresponding inappropriate use of tools designed for soluble proteins. For membrane proteins, lipid accessibility is an essential property. Even though programs are available for sequence-based prediction of lipid accessibility and structure-based identification of solvent-accessible surface area, the latter does not distinguish between water accessible and lipid accessible residues in membrane proteins.ResultsHere we presentmp_lipid_acc, the first method to identify lipid accessible residues from the protein structure, implemented in the RosettaMP framework and available as a webserver. Our method uses protein structures transformed in membrane coordinates, for instance from PDBTM or OPM databases, and a defined membrane thickness to classify lipid accessibility of residues.mp_lipid_accis applicable to both α-helical and β-barrel membrane proteins of diverse architectures with or without water-filled pores and uses a concave hull algorithm for classification. We further provide a manually curated benchmark dataset, on which our method achieves prediction accuracies of 90%.ConclusionWe present a novel tool to classify lipid accessibility from the protein structure, which is applicable to proteins of diverse architectures and achieves prediction accuracies of 90% on a manually curated database.mp_lipid_accis part of the Rosetta software suite, available atwww.rosettacommons.org. The webserver is available athttp://rosie.graylab.jhu.edu/mp_lipid_acc/submitand the benchmark dataset is available athttp://tinyurl.com/mp-lipid-acc-dataset.Supplementary informationSupplementary information is available atBMC Bioinformatics.
Spike interval coding of translatory optic flow and depth from motion in the fly visual system
Authors: Longden Kit D. , Wicklein Martina , Hardcastle Ben J. , Huston Stephen J. , Krapp Holger G. 
Published: November 2016

SummaryMany animals use the visual motion generated by travelling straight, the translatory optic flow, to successfully navigate obstacles: near objects appear larger and to move more quickly than distant objects. Flies are expert at navigating cluttered environments, and while their visual processing of rotatory optic flow is understood in exquisite detail, how they process translatory optic flow remains a mystery. Here, we present novel cell types that have motion receptive fields matched to translation self-motion, the vertical translation (VT) cells. One of these, the VT1 cell, encodes forward sideslip self-motion, and fires action potentials in clusters - spike bursts. We show that the spike burst coding is size and speed-tuned, and is selectively modulated by motion parallax - the relative motion experienced during translation. These properties are spatially organized, so that the cell is most excited by clutter rather than isolated objects. When the fly is presented with a simulation of flying past an elevated object, the spike burst activity is modulated by the height of the object, and the single spike rate is unaffected. When the moving object alone is experienced, the cell is weakly driven. Meanwhile, the VT2-3 cells have motion receptive fields matched to the lift axis. In conjunction with previously described horizontal cells, the VT cells have properties well-suited to the visual navigation of clutter and to encode the fly’s movements along near cardinal axes of thrust, lift and forward sideslip.HighlightsVT1 is a novel cell encoding sideslip translatory optic flow with spike burstsSpike burst rate is modulated by size, speed and motion parallax to detect clutterThese properties enable spike bursting to signal object depth from motionVT2-3 are complementary novel cells with receptive fields matching lift translation
lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets
Authors: Gong Yixiao , Huang Hsuan-Ting , Liang Yu , Trimarchi Thomas , Aifantis Iannis , Tsirigos Aristotelis 
Published: November 2016

ABSTRACTLong non-coding RNAs (lncRNAs) have emerged as a class of factors that are important for regulating development and cancer. Computational prediction of lncRNAs from ultra-deep RNA sequencing has been successful in identifying candidate lncRNAs. However, the complexity of handling and integrating different types of genomics data poses significant challenges to experimental laboratories that lack extensive genomics expertise. To address this issue, we have developed lncRNA-screen, a comprehensive pipeline for computationally screening putative lncRNA transcripts over large multimodal datasets. The main objective of this work is to facilitate the computational discovery of lncRNA candidates to be further examined by functional experiments. lncRNA-screen provides a fully automated easy-to-run pipeline which performs data download, RNA-seq alignment, assembly, quality assessment, transcript filtration, novel lncRNA identification, coding potential estimation, expression level quantification, histone mark enrichment profile integration, differential expression analysis, annotation with other type of segmented data (CNVs, SNPs, Hi-C, etc.) and visualization. Importantly, lncRNA-screen generates an interactive report summarizing all interesting lncRNA features including genome browser snapshots and lncRNA-mRNA interactions based on Hi-C data. In summary, our pipeline provides a comprehensive solution for lncRNA discovery and an intuitive interactive report for identifying promising lncRNA candidates. lncRNA-screen is available as free open-source software on GitHub.
Y-RNA and tRNA Cleavage by RNase L Mediates Terminal dsRNA Response
Authors: Donovan Jesse , Rath Sneha , Kolet-Mandrikov David , Korennykh Alexei 
Published: November 2016

AbstractDouble-stranded RNA (dsRNA) is a danger signal that triggers endonucleolytic degradation of RNA inside infected and stressed mammalian cells. This mechanism inhibits growth and ultimately removes problematic cells via apoptosis. To elucidate the molecular functions of this program and understand the connection between RNA cleavage and programmed cell death, we visualized dsRNA-induced degradation of human small RNAs using RtcB ligase-assisted RNA sequencing (RtcB RNA-seq). RtcB RNA-seq revealed strong cleavage of select transfer RNAs (tRNAs) and autoantigenic Y-RNAs, and identified the innate immune receptor RNase L as the responsible endoribonuclease. RNase L cleaves the non-coding RNA (ncRNA) targets site-specifically, releasing abundant ncRNA fragments, and downregulating full-length tRNAs and Y-RNAs. The depletion of a single Y-RNA, RNY1, appears particularly important and the loss of this Y-RNA is sufficient to initiate apoptosis. Site-specific cleavage of small ncRNA by RNase L thus emerges as an important terminal step in dsRNA surveillance.
A Preliminary Study of Insect Succession in Al‐Ahsaa Oasis, in the Eastern Region of the Kingdom of Saudi Arabia
Authors: Shaalan Essam A. , El‐Moaty Zeinab A. , Abdelsalam Salaheldin , Anderson Gail S. 
Published: November 2016

AbstractRabbit carcass decomposition was examined in four seasons in Al‐Ahsaa Oasis. Decomposition rate was significantly faster in summer compared with other seasons. Fourteen insect species from four orders and seven families were recorded: Calliphoridae, Muscidae, Sarcophagidae, Formicidae, Histeridae, Dermestidae, and Tenebrionidae. Most of the fly maggots collected were Calliphoridae with only one species from both Muscidae and Sarcophagidae. Maggots of Calliphora vicina (R.‐D.) and Chrysomya albiceps (Wiedemann) colonized the carcasses in all seasons while both Ch. bezziana (Villeneuve) and Lucilia sericata (Meigen) were found in all seasons except for winter. Maggots of Chrysomya megacephala (F.) and Phormia regina (Meigen) were only collected in the summer and autumn, respectively. Four coleopteran species were collected: Hymenorus sp., Saprinus chacites (Illiger), Dermestes maculatus DeGeer and Blaps sp. One formicidian species, Pheidole megacephala (F.), was observed in all seasons. Insect richness was greater, and decomposition rate was faster in summer compared with other seasons.
Impact of Swift and Certain Sanctions
Authors: Hamilton Zachary , Campbell Christopher M. , van Wormer Jacqueline , Kigerl Alex , Posey Brianne 
Published: November 2016

Research SummaryIn the wake of the mass incarceration movement, many states must now manage the rebound of decarceration. Thermodynamic forces of the justice system, however, have pushed former fiscal pressures of institutions onto that of community corrections. Encouraged by the positive findings of recently piloted innovations, several jurisdictions have taken great interest in the implementation of deterrence‐based sanctioning models when dealing with supervision violations. Among the first to implement a statewide turn to this style of sanctioning, Washington State's swift‐and‐certain (SAC) policy was implemented in June 2012. The intent of SAC was to expand the model found in Hawaii's Opportunity Probation and Enforcement (HOPE) to a wider criminal justice population, while emphasizing the reduction of confinement costs. This study focused on the impact of SAC with regard to supervision outcomes for participants. By using a quasi‐experimental design, we examined confinement, recidivism, treatment, violation, and costs outcomes of SAC participants. Findings reveal that SAC participants were found to incur fewer sanctioned incarceration days after a violation, reduced odds of recidivism, possessed greater treatment program utilization, reduced their propensity of committing violations over time, and as a result, imposed lower correctional and associated costs. The SAC model provides noteworthy positive effects and no appreciable negative impacts on public safety.Policy ImplicationsWe further discuss the impact of SAC in the context of deterrence‐based sanctioning. Specifically, we explain how practices such as SAC may impact the future of sanctioning community supervision conditions. Although many policies that emphasize deterrence demonstrate inconsistent findings, immediate advantages of SAC take the form of fiscal savings, indicating that these novel methods provide a form of justice reinvestment. Additionally, connecting deterrence‐based supervision methods to reductions in most recidivism measures suggests that proportionality and quality assurance may increase the effectiveness of these policies. We recommend ways that such nuanced implementation may be fruitful, as well as suggest ways of conceptualizing the theory of deterrence. Policy makers can appropriately work its components into supervision practice without depreciating the importance of treatment and addressing criminogenic needs.
Foetal Ureaplasma parvum bacteraemia as a function of gestation‐dependent complement insufficiency: Evidence from a sheep model of pregnancy
Authors: Kemp Matthew W. , Ahmed Shatha , Beeton Michael L. , Payne Matthew S. , Saito Masatoshi , Miura Yuichiro , Usuda Haruo , Kallapur Suhas G. , Kramer Boris W. , Stock Sarah J. , Jobe Alan H. , Newnham John P. , Spiller Owen B. 
Published: November 2016

ProblemComplement is a central defence against sepsis, and increasing complement insufficiency in neonates of greater prematurity may predispose to increased sepsis. Ureaplasma spp. are the most frequently cultured bacteria from preterm blood samples.Method of studyA sheep model of intrauterine Ureaplasma parvum infection was used to examine in vivo Ureaplasma bacteraemia at early and late gestational ages. Complement function and Ureaplasma killing assays were used to determine the correlation between complement potency and bactericidal activity of sera ex vivo.ResultsUreaplasma was cultured from 50% of 95‐day gestation lamb cord blood samples compared to 10% of 125‐day gestation lambs. Bactericidal activity increased with increased gestational age, and a direct correlation between functional complement activity and bactericidal activity (R2=.86; P<.001) was found for 95‐day gestational lambs.ConclusionsUreaplasma bacteraemia in vivo was confined to early preterm lambs with low complement function, but Ureaplasma infection itself did not diminish complement levels.
Bodies That Walk, Bodies That Talk, Bodies That Love: Palestinian Women Refugees, Affectivity, and the Politics of the Ordinary
Authors: Salih Ruba 
Published: November 2016

AbstractIn this article I interrogate what is lost in war and displacement through the affective memories of Palestinian refugee women who remember through their body and what their body has endured. I reflect on how bodies and spaces connect and disconnect at violent junctures, and on the vital forces vulnerability and precariousness ignite in displacement. Throughout the geography of separations and shifting shelters, refugee women engaged in place‐making, transforming the transience enforced by their continuous evictions into the permanence of home, not as a static identity‐place‐nation, but as a site of dynamic affective, social relations and connections. Read through Michael Hardt's metaphor of “social muscles”, as bodily and emotional drives that blur the boundaries of intimate and social spaces, affective memories can serve as a political horizon that redesigns, in Arendtian terms, the love for the nation as love for concrete relations and for existing in the world.
Study of Greek children and youths with cystic fibrosis identifies immunisation gaps and delays
Authors: Maltezou Helena C. , Doudounakis Stavros , Lekaditi Maria , Tanou Kalliopi , Katerelos Panos , Theodoridou Maria 
Published: November 2016

AbstractAimData about immunisation rates in cystic fibrosis (CF) patients are scarce. We estimated the rates and timeliness of immunisations in CF patients aged 0.55–22 years.MethodsWe studied 122 subjects at a hospital in Greece in 2014. A standard questionnaire was used to collect data and parents' opinions about immunisations.ResultsThe complete immunisation rates were 92.6% for diphtheria–tetanus–acellular pertussis‐inactivated poliomyelitis‐Haemophilus influenzae (DTaP‐IPV‐Hib), 96.7% for hepatitis A, 97.4% for hepatitis B, 97.4% for measles–mumps–rubella, 85.1% for the varicella zoster virus, 85.1% for the meningococcus C conjugate, 84.3% for the pneumococcus conjugate and 58.9% for the bacillus Calmette‐Guérin vaccine. Immunisation rates in youths were 64.4% for DTaP‐IPV, 26.8% for the tetravalent meningococcus conjugate vaccine and 54.1% for the human papilloma virus vaccine. In addition, 30.1% received the 23‐valent pneumococcal polysaccharide vaccine and 45.6% received annual influenza vaccines. Complete, up‐to‐date immunisation rates fell from 61.4% at 12 months of age to 14.5% at six and 12 years. All vaccines experienced delays. Most parents believed vaccines were necessary to protect their child's health.ConclusionOur study of children with CF found immunisation gaps with no catch‐up immunisations and these need to be administered at follow‐up visits.