bluuebunny/crossref_metadata_2025_split huggingface dataset:
Organization of the multiaminoacyl‐tRNA synthetase complex and the cotranslational protein folding
Authors: Berezovsky Igor N. , Zheng Zejun , Kurotani Atsushi , Tokmakov Alexander A. , Kurochkin Igor V. 
Published: June 2015

AbstractAminoacyl‐tRNA synthetases (ARSs) play an essential role in the protein synthesis by catalyzing an attachment of their cognate amino acids to tRNAs. Unlike their prokaryotic counterparts, ARSs in higher eukaryotes form a multiaminoacyl‐tRNA synthetase complex (MARS), consisting of the subset of ARS polypeptides and three auxiliary proteins. The intriguing feature of MARS complex is the presence of only nine out of twenty ARSs, specific for Arg, Asp, Gln, Glu, Ile, Leu, Lys, Met, and Pro, regardless of the organism, cell, or tissue types. Although existence of MARSs complex in higher eukaryotes has been already known for more than four decades, its functional significance remains elusive. We found that seven of the nine corresponding amino acids (Arg, Gln, Glu, Ile, Leu, Lys, and Met) together with Ala form a predictor of the protein α‐helicity. Remarkably, all amino acids (besides Ala) in the predictor have the highest possible number of side‐chain rotamers. Therefore, compositional bias of a typical α‐helix can contribute to the helix's stability by increasing the entropy of the folded state. It also appears that position‐specific α‐helical propensity, specifically periodic alternation of charged and hydrophobic residues in the helices, may well be provided by the structural organization of the complex. Considering characteristics of MARS complex from the perspective of the α‐helicity, we hypothesize that specific composition and structure of the complex represents a functional mechanism for coordination of translation with the fast and correct folding of amphiphilic α‐helices.
Estimating first‐passage time distributions from weighted ensemble simulations and non‐Markovian analyses
Authors: Suárez Ernesto , Pratt Adam J. , Chong Lillian T. , Zuckerman Daniel M. 
Published: June 2015

AbstractFirst‐passage times (FPTs) are widely used to characterize stochastic processes such as chemical reactions, protein folding, diffusion processes or triggering a stock option. In previous work (Suarez et al., JCTC 2014;10:2658‐2667), we demonstrated a non‐Markovian analysis approach that, with a sufficient subset of history information, yields unbiased mean first‐passage times from weighted‐ensemble (WE) simulations. The estimation of the distribution of the first‐passage times is, however, a more ambitious goal since it cannot be obtained by direct observation in WE trajectories. Likewise, a large number of events would be required to make a good estimation of the distribution from a regular “brute force” simulation. Here, we show how the previously developed non‐Markovian analysis can generate approximate, but highly accurate, FPT distributions from WE data. The analysis can also be applied to any other unbiased trajectories, such as from standard molecular dynamics simulations. The present study employs a range of systems with independent verification of the distributions to demonstrate the success and limitations of the approach. By comparison to a standard Markov analysis, the non‐Markovian approach is less sensitive to the user‐defined discretization of configuration space.
Structural mapping of the ClpBATPases of Plasmodium falciparum: Targeting protein folding and secretion for antimalarial drug design
Authors: AhYoung Andrew P. , Koehl Antoine , Cascio Duilio , Egea Pascal F. 
Published: June 2015

AbstractCaseinolytic chaperones and proteases (Clp) belong to the AAA+ protein superfamily and are part of the protein quality control machinery in cells. The eukaryotic parasite Plasmodium falciparum, the causative agent of malaria, has evolved an elaborate network of Clp proteins including two distinct ClpB ATPases. ClpB1 and ClpB2 are involved in different aspects of parasitic proteostasis. ClpB1 is present in the apicoplast, a parasite‐specific and plastid‐like organelle hosting various metabolic pathways necessary for parasite growth. ClpB2 localizes to the parasitophorous vacuole membrane where it drives protein export as core subunit of a parasite‐derived protein secretion complex, the Plasmodium Translocon of Exported proteins (PTEX); this process is central to parasite virulence and survival in the human host. The functional associations of these two chaperones with parasite‐specific metabolism and protein secretion make them prime drug targets. ClpB proteins function as unfoldases and disaggregases and share a common architecture consisting of four domains—a variable N‐terminal domain that binds different protein substrates, followed by two highly conserved catalytic ATPase domains, and a C‐terminal domain. Here, we report and compare the first crystal structures of the N terminal domains of ClpB1 and ClpB2 from Plasmodium and analyze their molecular surfaces. Solution scattering analysis of the N domain of ClpB2 shows that the average solution conformation is similar to the crystalline structure. These structures represent the first step towards the characterization of these two malarial chaperones and the reconstitution of the entire PTEX to aid structure‐based design of novel anti‐malarial drugs.
An ALS disease mutation in Cdc48/p97 impairs 20S proteasome binding and proteolytic communication
Authors: Barthelme Dominik , Jauregui Ruben , Sauer Robert T. 
Published: June 2015

AbstractCdc48 (also known as p97 or VCP) is an essential and highly abundant, double‐ring AAA+ ATPase, which is ubiquitous in archaea and eukaryotes. In archaea, Cdc48 ring hexamers play a direct role in quality control by unfolding and translocating protein substrates into the degradation chamber of the 20S proteasome. Whether Cdc48 and 20S cooperate directly in protein degradation in eukaryotic cells is unclear. Two regions of Cdc48 are important for 20S binding, the pore‐2 loop at the bottom of the D2 AAA+ ring and a C‐terminal tripeptide. Here, we identify an aspartic acid in the pore‐2 loop as an important element in 20S recognition. Importantly, mutation of this aspartate in human Cdc48 has been linked to familial amyotrophic lateral sclerosis (ALS). In archaeal or human Cdc48 variants, we find that mutation of this pore‐2 residue impairs 20S binding and proteolytic communication but does not affect the stability of the hexamer or rates of ATP hydrolysis and protein unfolding. These results suggest that human Cdc48 interacts functionally with the 20S proteasome.
Effect of plasma composition on nanocrystalline diamond layers deposited by a microwave linear antenna plasma‐enhanced chemical vapour deposition system
Authors: Taylor Andrew , Ashcheulov Petr , Čada Martin , Fekete Ladislav , Hubík Pavel , Klimša Ladislav , Olejníček Jiří , Remeš Zdeněk , Jirka Ivan , Janíček Petr , Bedel‐Pereira Eléna , Kopeček Jaromir , Mistrík Jan , Mortet Vincent 
Published: June 2015

The addition of CO2 into the process gas has a significant impact on the quality and the incorporation of boron in CVD diamond layers. In this report we study the effect of CO2 addition in the gas phase on the properties of boron doped nano‐crystalline diamond (BNCD) layers grown at low substrate temperatures (450–500 °C) using a microwave linear antenna plasma‐enhanced chemical vapour deposition apparatus (MW‐LA‐PECVD). Experimental results show an increase in the layers' conductivity with a reduction in CO2 concentration, which is consistent with the variation in the atomic boron emission line intensity measured by optical emission spectroscopy (OES). At CO2 concentrations close to zero, we observed the formation of a smooth, transparent and highly resistive layer on unseeded substrates. This layer has been identified as silicon carbide (SiC) by transmission electron microscopy and X‐ray photoelectron microscopy. The presence of silicon in the plasma is confirmed by OES and it is attributed to quartz tube etching. In this specific deposition condition, diamond growth is in competition with SiC growth, which affects the diamond layer properties.SEM image of layer growth on a silicon substrate at low CO2 concentration on unseeded area (left) with a smooth, highly resistive and transparent SiC layer and seeded area (right) with a boron doped nano‐crystalline diamond layer.
Iterative image reconstruction for limited‐angle inverse helical cone‐beam computed tomography
Authors: Yu Wei , Zeng Li 
Published: June 2015

SummaryHelical trajectory satisfying the condition of exact reconstruction, has been widely utilized in the commercial computed tomography (CT). While limited by the scanning environment in some practical applications, the conventional helical cone‐beam CT imaging is hard to complete, thus, developing an imaging system suited for long‐object may be valuable. Three‐dimensional C‐arm CT is an innovative imaging technique which has been greatly concerned. Since there is a high degree of freedom of C‐arm, more flexible image acquisition trajectories for 3D imaging can be achieved. In this work, a fast iterative reconstruction algorithm based on total variation minimization is developed for a trajectory of limited‐angle inverse helical cone‐beam CT, which can be applied to detect long‐object without slip‐ring technology. The experimental results show that the developed algorithm can yield reconstructed images of low noise level and high image quality. SCANNING 38:4–13, 2016. © 2015 Wiley Periodicals, Inc.
Pretreatment of Mesenchymal Stem Cells Manipulates Their Vasculoprotective Potential While Not Altering Their Homing Within the Injured Gut
Authors: Kavanagh Dean P.J. , Suresh Shankar , Newsome Philip N. , Frampton Jon , Kalia Neena 
Published: June 2015

Abstract
Mesenchymal stem cells (MSCs) have shown therapeutic promise in many experimental and clinical models of inflammation. However, a commonly reported feature of MSC transplantation is poor homing to injured tissues. Previously, we have shown that pretreatment with cytokines/chemical factors enhances hematopoietic SC adhesion within intestinal microvasculature following ischemia-reperfusion (IR) injury. Using intravital microscopy, the ability of similar pretreatment strategies to enhance the recruitment of murine MSCs to murine intestinal microvasculature following IR injury was investigated. Primary MSCs were isolated from bone marrow and selected on the basis of platelet-derived growth factor receptor-α and SC antigen-1 positivity (PDGFRα+/Sca-1+). MSC recruitment was similar in IR injured gut mucosa when compared with sham operated controls, with limited cell adhesion observed. MSCs appeared contorted in microvessels, suggesting physical entrapment. Although not recruited specifically by injury, MSC administration significantly reduced neutrophil recruitment and improved tissue perfusion in the severely injured jejunum. Vasculoprotective effects were not demonstrated in the lesser injured ileum. Pretreatment of MSCs with tumor necrosis factor (TNF)-α, CXCL12, interferon (IFN)-γ, or hydrogen peroxide did not enhance their intestinal recruitment. In fact, TNFα and IFNγ removed the previous therapeutic ability of transplanted MSCs to reduce neutrophil infiltration and improve perfusion in the jejunum. We provide direct evidence that MSCs can rapidly limit leukocyte recruitment and improve tissue perfusion following intestinal IR injury. However, this study also highlights complexities associated with strategies to improve MSC therapeutic efficacy. Future studies using cytokine/chemical pretreatments to enhance MSC recruitment/function require careful consideration and validation to ensure therapeutic function is not impeded. Stem Cells 2015;33:2785–2797
Bioactive Structure of Membrane Lipids and Natural Products Elucidated by a Chemistry‐Based Approach
Authors: Murata Michio , Sugiyama Shigeru , Matsuoka Shigeru , Matsumori Nobuaki 
Published: June 2015

AbstractDetermining the bioactive structure of membrane lipids is a new concept, which aims to examine the functions of lipids with respect to their three‐dimensional structures. As lipids are dynamic by nature, their “structure” does not refer solely to a static picture but also to the local and global motions of the lipid molecules. We consider that interactions with lipids, which are completely defined by their structures, are controlled by the chemical, functional, and conformational matching between lipids and between lipid and protein. In this review, we describe recent advances in understanding the bioactive structures of membrane lipids bound to proteins and related molecules, including some of our recent results. By examining recent works on lipid‐raft‐related molecules, lipid–protein interactions, and membrane‐active natural products, we discuss current perspectives on membrane structural biology.
Mindsets matter: Implications for branding research and practice
Authors: John Deborah Roedder , Park Ji Kyung 
Published: June 2015

AbstractImplicit theories provide an important framework to help understand consumer behavior. In this article, we focus on applications within the context of branding research and practice. First, we explore application areas of relevance to branding practitioners, such as brand advertising and positioning, brand extensions, brand architecture, and brand dilution. We situate propositions forwarded by Murphy and Dweck into traditional areas of branding research to discuss their importance to branding and suggest extensions of these ideas. Second, we consider application areas of personal relevance to consumers. We discuss how mindsets can affect the benefits consumers derive from using brands, such as self‐enhancement, self‐threat recovery, and overcoming difficult challenges in their lives.
Exploring women's fear of childbirth in a high maternal mortality setting on the Arabian Peninsula
Authors: Kempe Annica , Theorell Töres , Alwazer Fatoom Noor-Aldin , Taher Samera Abdullah , Christensson Kyllike 
Published: June 2015

Background.Few studies from low-income countries have addressed women's fear of childbirth (FOC) although likely to affect women during both pregnancy and childbirth. The aim of this study was to explore FOC in a high maternal mortality setting in the Arab region, Yemen.Methods.A multi-stage (stratified–purposive–random) sampling process was used. We interviewed 220 women with childbirth experience in urban/rural Yemen. Answers to the question ‘Were you afraid of giving birth?’ were analyzed using qualitative content analysis.Results.Women perceived childbirth as a place of danger. Fear of death and childbirth complications stemming from previous traumatic childbirth and traumatic experience in the community was rampant. Husbands’ and in-laws’ disappointment in a girl infant constituted a strong sociocultural component of FOC. Women's perception of living in tension ‘between worlds’ of tradition and modernity reinforced fear of institutional childbirth. Women without FOC gave reasons of faith, social belonging and trust in either traditional or modern childbirth practice, past positive experience of childbirth and the desire for social status associated with children.Conclusions.The numerous maternal and infant deaths have a strong impact on women's FOC. Antenatal care has an important role in reducing fear including that of institutional childbirth and in strengthening a couple in welcoming a female infant. Staff should be sensitized to the fears of both husband and wife and women be allowed support during childbirth. Within the scope of the Millennium Development Goals and strengthening of reproductive mental health programs, FOC urgently needs to be addressed.
COMPANIES AND THEIR FUNDAMENTAL RIGHTS: A COMPARATIVE PERSPECTIVE
Authors: Oliver Peter 
Published: June 2015

AbstractThis article explores the case law of the European Court of Human Rights, the European Court of Justice and the US Supreme Court on the fundamental rights of commercial companies. The rights considered include property, the privilege against self-incrimination, freedom of speech, double jeopardy, the right to make political donations, and the freedom of religion. The article highlights the dangers of taking the fundamental rights of companies too far, as has recently occurred in the US; and it advocates a cautious and coordinated approach to this delicate issue, which has become increasingly important on both sides of the Atlantic.
The Participation of theAmicus CuriaeInstitution in Human Rights Litigation in Botswana and South Africa: A Tale of Two Jurisdictions
Authors: Jonas Obonye 
Published: June 2015

AbstractIt has become a standard feature of litigation foramicito appear before courts, acting as the vindicator of rights for the politically powerless and marginalized. Their appearance has thus contributed to the promotion and protection of human rights before municipal courts and international tribunals. They have done this through the submission of briefs that seek to broaden perspectives of cases and by advancing innovative legal and factual viewpoints, thus assisting the courts in reaching appropriate conclusions. In Botswana,amicus curiaeparticipation is still at a nascent stage. This is largely due to inflexible rules of standing and the general lack of knowledge of the potential usefulness of the institution by the judiciary. This article argues that, to enhanceamicusparticipation in litigation, thereby enhancing the epistemological quality of its public law jurisprudence, Botswana must pay close attention to the practices and experiences of South Africa whereamicusparticipation has resulted in the phenomenal growth of constitutional jurisprudence.
Bonus-Driven Repurchases
Authors: Cheng Yingmei , Harford Jarrad , Zhang Tianming (Tim) 
Published: June 2015

AbstractUsing a large hand-collected database of chief executive officer (CEO) bonus structures, we find that when a CEO’s bonus is directly tied to earnings per share (EPS), his company is more likely to conduct a buyback. This effect is especially pronounced when a company’s EPS is right below the threshold for a bonus award. Share repurchasing increases the probability the CEO receives a bonus and the magnitude of that bonus, but only when bonus pay is EPS based. Bonus-driven repurchasing firms do not exhibit positive long-run abnormal returns.
Multistate outbreak of listeriosis caused by imported cheese and evidence of cross-contamination of other cheeses, USA, 2012
Authors: HEIMAN K. E. , GARALDE V. B. , GRONOSTAJ M. , JACKSON K. A. , BEAM S. , JOSEPH L. , SAUPE A. , RICOTTA E. , WAECHTER H. , WELLMAN A. , ADAMS-CAMERON M. , RAY G. , FIELDS A. , CHEN Y. , DATTA A. , BURALL L. , SABOL A. , KUCEROVA Z. , TREES E. , METZ M. , LEBLANC P. , LANCE S. , GRIFFIN P. M. , TAUXE R. V. , SILK B. J. 
Published: June 2015

SUMMARYListeria monocytogenesis a foodborne pathogen that can cause bacteraemia, meningitis, and complications during pregnancy. In July 2012, molecular subtyping identified indistinguishableL. monocytogenesisolates from six patients and two samples of different cut and repackaged cheeses. A multistate outbreak investigation was initiated. Initial analyses identified an association between eating soft cheese and outbreak-related illness (odds ratio 17·3, 95% confidence interval 2·0–825·7) but no common brand. Cheese inventory data from locations where patients bought cheese and an additional location where repackaged cheese yielded the outbreak strain were compared to identify cheeses for microbiological sampling. Intact packages of imported ricotta salata yielded the outbreak strain. Fourteen jurisdictions reported 22 cases from March–October 2012, including four deaths and a fetal loss. Six patients ultimately reported eating ricotta salata; another reported eating cheese likely cut with equipment also used for contaminated ricotta salata, and nine more reported eating other cheeses that might also have been cross-contaminated. An FDA import alert and US and international recalls followed. Epidemiology-directed microbiological testing of suspect cheeses helped identify the outbreak source. Cross-contamination of cheese highlights the importance of using validated disinfectant protocols and routine cleaning and sanitizing after cutting each block or wheel.
The impact of heptavalent pneumococcal conjugate vaccine on the incidence of childhood community-acquired pneumonia and bacteriologically confirmed pneumococcal pneumonia in Japan
Authors: NAITO S. , TANAKA J. , NAGASHIMA K. , CHANG B. , HISHIKI H. , TAKAHASHI Y. , OIKAWA J. , NAGASAWA K. , SHIMOJO N. , ISHIWADA N. 
Published: June 2015

SUMMARYHeptavalent pneumococcal conjugate vaccine (PCV7) was introduced to Japan in 2010. We investigated the impact of PCV7 on childhood community-acquired pneumonia (CAP) and pneumococcal pneumonia (PP). Children aged <5 years living in Chiba city, Japan, who were admitted to hospitals were enrolled to estimate the incidence of CAP based on the mid-year population. PP was determined by the presence ofStreptococcus pneumoniaein cultured blood and/or sputum samples of CAP patients. The incidence of CAP andS. pneumoniaeisolated from PP patients was compared before (April 2008–March 2009) and after (April 2012–March 2013) the introduction of PCV7 immunization. The annual incidence of CAP was reduced [incidence rate ratio 0·81, 95% confidence interval (CI) 0·73–0·90]. When comparing post-vaccine with pre-vaccine periods, the odds ratio for PP incidence was 0·60 (95% CI 0·39–0·93,P= 0·024). PCV7-covered serotypes markedly decreased (66·6% in pre-vaccinevs. 15·6% in post-vaccine,P< 0·01), and serotypes 6C, 15A, 15C and 19A increased. Multidrug-resistant international clones in the pre-vaccine period (Spain6B-2/ST90, Taiwan19F-14/ST236) decreased, while Sweden15A-25/ST63 was the dominant clone in the post-vaccine period. A significant reduction in the incidence of both CAP hospitalizations and culture-confirmed PP of vaccine serotypes was observed at 2 years after PCV7 vaccination.
The importance of stories in understanding people’s relationship to food: narrative inquiry methodology has much to offer the public health nutrition researcher and practitioner
Authors: O’Kane Gabrielle , Pamphilon Barbara 
Published: June 2015

AbstractObjectiveDespite the usefulness of quantitative research, qualitative research methodologies are equally needed to allow researchers to better understand the important social and environmental factors affecting food choice and eating habits. The present paper contributes insights from narrative inquiry, a well-established qualitative methodology, to a food-related doctoral research study. The connections between food shoppers and the producer, family, friends and others in the food system, between eaters and the earth, and how these connections affect people’s meaning-making of food and pathways to food citizenship, were explored in the research.DesignThe research used narrative inquiry methodology and focus groups for data collection.SettingFive different food-ways in the Canberra region of Australia were selected for the present research; that is, community gardens, community-supported agriculture, farmers’ markets, fresh food markets and supermarkets.SubjectsFifty-two people voluntarily attended eight focus groups with four to nine participants in each.ResultsFrom a practical perspective, the present paper offers a guide to the way in which narrative inquiry has been applied to one research project. The paper describes the application of narrative inquiry methodology, revealing the important place of narratives in generating new knowledge. The paper further outlines how phased narrative analysis can lead to a defensible and rigorous interpretive framework grounded in the data generated from people’s stories and meaning-making.ConclusionsWe argue that individual, social and system change will not be possible without further rigorous qualitative studies to inform and complement the empirical basis of public health nutrition practice.