bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancers Are Major Targets for Murine Leukemia Virus Vector Integration
Authors: De Ravin Suk See , Su Ling , Theobald Narda , Choi Uimook , Macpherson Janet L. , Poidinger Michael , Symonds Geoff , Pond Susan M. , Ferris Andrea L. , Hughes Stephen H. , Malech Harry L. , Wu Xiaolin 
Published: February 2014

ABSTRACT

Retroviral vectors have been used in successful gene therapies. However, in some patients, insertional mutagenesis led to leukemia or myelodysplasia. Both the strong promoter/enhancer elements in the long terminal repeats (LTRs) of murine leukemia virus (MLV)-based vectors and the vector-specific integration site preferences played an important role in these adverse clinical events. MLV integration is known to prefer regions in or near transcription start sites (TSS). Recently, BET family proteins were shown to be the major cellular proteins responsible for targeting MLV integration. Although MLV integration sites are significantly enriched at TSS, only a small fraction of the MLV integration sites (<15%) occur in this region. To resolve this apparent discrepancy, we created a high-resolution genome-wide integration map of more than one million integration sites from CD34
+
hematopoietic stem cells transduced with a clinically relevant MLV-based vector. The integration sites form ∼60,000 tight clusters. These clusters comprise ∼1.9% of the genome. The vast majority (87%) of the integration sites are located within histone H3K4me1 islands, a hallmark of enhancers. The majority of these clusters also have H3K27ac histone modifications, which mark active enhancers. The enhancers of some oncogenes, including LMO2, are highly preferred targets for integration without
in vivo
selection.

IMPORTANCE
We show that active enhancer regions are the major targets for MLV integration; this means that MLV preferentially integrates in regions that are favorable for viral gene expression in a variety of cell types. The results provide insights for MLV integration target site selection and also explain the high risk of insertional mutagenesis that is associated with gene therapy trials using MLV vectors.
H6 Influenza Viruses Pose a Potential Threat to Human Health
Authors: Wang Guojun , Deng Guohua , Shi Jianzhong , Luo Weiyu , Zhang Guoquan , Zhang Qianyi , Liu Liling , Jiang Yongping , Li Chengjun , Sriwilaijaroen Nongluk , Hiramatsu Hiroaki , Suzuki Yasuo , Kawaoka Yoshihiro , Chen Hualan 
Published: February 2014

ABSTRACT
Influenza viruses of the H6 subtype have been isolated from wild and domestic aquatic and terrestrial avian species throughout the world since their first detection in a turkey in Massachusetts in 1965. Since 1997, H6 viruses with different neuraminidase (NA) subtypes have been detected frequently in the live poultry markets of southern China. Although sequence information has been gathered over the last few years, the H6 viruses have not been fully biologically characterized. To investigate the potential risk posed by H6 viruses to humans, here we assessed the receptor-binding preference, replication, and transmissibility in mammals of a series of H6 viruses isolated from live poultry markets in southern China from 2008 to 2011. Among the 257 H6 strains tested, 87 viruses recognized the human type receptor. Genome sequence analysis of 38 representative H6 viruses revealed 30 different genotypes, indicating that these viruses are actively circulating and reassorting in nature. Thirty-seven of 38 viruses tested in mice replicated efficiently in the lungs and some caused mild disease; none, however, were lethal. We also tested the direct contact transmission of 10 H6 viruses in guinea pigs and found that 5 viruses did not transmit to the contact animals, 3 viruses transmitted to one of the three contact animals, and 2 viruses transmitted to all three contact animals. Our study demonstrates that the H6 avian influenza viruses pose a clear threat to human health and emphasizes the need for continued surveillance and evaluation of the H6 influenza viruses circulating in nature.

IMPORTANCE
Avian influenza viruses continue to present a challenge to human health. Research and pandemic preparedness have largely focused on the H5 and H7 subtype influenza viruses in recent years. Influenza viruses of the H6 subtype have been isolated from wild and domestic aquatic and terrestrial avian species throughout the world since their first detection in the United States in 1965. Since 1997, H6 viruses have been detected frequently in the live poultry markets of southern China; however, the biological characterization of these viruses is very limited. Here, we assessed the receptor-binding preference, replication, and transmissibility in mammals of a series of H6 viruses isolated from live poultry markets in southern China and found that 34% of the viruses are able to bind human type receptors and that some of them are able to transmit efficiently to contact animals. Our study demonstrates that the H6 viruses pose a clear threat to human health.
Mechanism of Action and Capsid-Stabilizing Properties of VHHs with an
In Vitro
Antipolioviral Activity
Authors: Schotte Lise , Strauss Mike , Thys Bert , Halewyck Hadewych , Filman David J. , Bostina Mihnea , Hogle James M. , Rombaut Bart 
Published: February 2014

ABSTRACT

Previously, we reported on the
in vitro
antiviral activity of single-domain antibody fragments (VHHs) directed against poliovirus type 1. Five VHHs were found to neutralize poliovirus type 1 in an
in vitro
setting and showed 50% effective concentrations (EC
50
s) in the nanomolar range. In the present study, we further investigated the mechanism of action of these VHHs. All five VHHs interfere at multiple levels of the viral replication cycle, as they interfere both with attachment of the virus to cells and with viral uncoating. The latter effect is consistent with their ability to stabilize the poliovirus capsid, as observed in a ThermoFluor thermal shift assay, in which the virus is gradually heated and the temperature causing 50% of the RNA to be released from the capsid is determined, either in the presence or in the absence of the VHHs. The VHH-capsid interactions were also seen to induce aggregation of the virus-VHH complexes. However, this observation cannot yet be linked to their mechanism of action. Cryo-electron microscopy (cryo-EM) reconstructions of two VHHs in complex with poliovirus type 1 show no conformational changes of the capsid to explain this aggregation. On the other hand, these reconstructions do show that the binding sites of VHHs PVSP6A and PVSP29F overlap the binding site for the poliovirus receptor (CD155/PVR) and span interfaces that are altered during receptor-induced conformational changes associated with cell entry. This may explain the interference at the level of cell attachment of the virus as well as their effect on uncoating.

IMPORTANCE
The study describes the mechanism of neutralization and the capsid-stabilizing activity of five single-domain antibody fragments (VHHs) that have an
in vitro
neutralizing activity against poliovirus type 1. The results show that the VHHs interfere at multiple levels of the viral replication cycle (cell attachment and viral uncoating). These mechanisms are possibly shared by some conventional antibodies and may therefore provide some insight into the natural immune responses. Since the binding sites of two VHHs studied by cryo-EM are very similar to that of the receptor, the VHHs can be used as probes to study the authentic virus-cell interaction. The structures and conclusions in this study are original and raise interesting findings regarding virus-receptor interactions and the order of key events early in infection.
Relative Roles of GM1 Ganglioside,
N
-Acylneuraminic Acids, and α2β1 Integrin in Mediating Rotavirus Infection
Authors: Fleming Fiona E. , Böhm Raphael , Dang Vi T. , Holloway Gavan , Haselhorst Thomas , Madge Paul D. , Deveryshetty Jaigeeth , Yu Xing , Blanchard Helen , von Itzstein Mark , Coulson Barbara S. 
Published: February 2014

ABSTRACT

N
-acetyl- and
N
-glycolylneuraminic acids (Sia) and α2β1 integrin are frequently used by rotaviruses as cellular receptors through recognition by virion spike protein VP4. The VP4 subunit VP8*, derived from Wa rotavirus, binds the internal
N
-acetylneuraminic acid on ganglioside GM1. Wa infection is increased by enhanced internal Sia access following terminal Sia removal from main glycan chains with sialidase. The GM1 ligand cholera toxin B (CTB) reduces Wa infectivity. Here, we found sialidase treatment increased cellular GM1 availability and the infectivity of several other human (including RV-3) and animal rotaviruses, typically rendering them susceptible to methyl α-
d
-
N
-acetylneuraminide treatment, but did not alter α2β1 usage. CTB reduced the infectivity of these viruses. Aceramido-GM1 inhibited Wa and RV-3 infectivity in untreated and sialidase-treated cells, and GM1 supplementation increased their infectivity, demonstrating the importance of GM1 for infection. Wa recognition of α2β1 and internal Sia were at least partially independent. Rotavirus usage of GM1 was mapped to VP4 using virus reassortants, and RV-3 VP8* bound aceramido-GM1 by saturation transfer difference nuclear magnetic resonance (STD NMR). Most rotaviruses recognizing terminal Sia did not use GM1, including RRV. RRV VP8* interacted minimally with aceramido-GM1 by STD NMR. Unusually, TFR-41 rotavirus infectivity depended upon terminal Sia and GM1. Competition of CTB, Sia, and/or aceramido-GM1 with cell binding by VP8* from representative rotaviruses showed that rotavirus Sia and GM1 preferences resulted from VP8*-cell binding. Our major finding is that infection by human rotaviruses of commonly occurring VP4 serotypes involves VP8* binding to cell surface GM1 glycan, typically including the internal
N
-acetylneuraminic acid.

IMPORTANCE
Rotaviruses, the major cause of severe infantile gastroenteritis, recognize cell surface receptors through virus spike protein VP4. Several animal rotaviruses are known to bind sialic acids at the termini of main carbohydrate chains. Conversely, only a single human rotavirus is known to bind sialic acid. Interestingly, VP4 of this rotavirus bound to sialic acid that forms a branch on the main carbohydrate chain of the GM1 ganglioside. Here, we use several techniques to demonstrate that other human rotaviruses exhibit similar GM1 usage properties. Furthermore, binding by VP4 to cell surface GM1, involving branched sialic acid recognition, is shown to facilitate infection. In contrast, most animal rotaviruses that bind terminal sialic acids did not utilize GM1 for VP4 cell binding or infection. These studies support a significant role for GM1 in mediating host cell invasion by human rotaviruses.
Effect of a 6-month vegan low-carbohydrate (‘Eco-Atkins’) diet on cardiovascular risk factors and body weight in hyperlipidaemic adults: a randomised controlled trial
Authors: Jenkins David J A , Wong Julia M W , Kendall Cyril W C , Esfahani Amin , Ng Vivian W Y , Leong Tracy C K , Faulkner Dorothea A , Vidgen Ed , Paul Gregory , Mukherjea Ratna , Krul Elaine S , Singer William 
Published: February 2014

ObjectiveLow-carbohydrate diets may be useful for weight loss. Diets high in vegetable proteins and oils may reduce the risk of coronary heart disease. The main objective was to determine the longer term effect of a diet that was both low-carbohydrate and plant-based on weight loss and low-density lipoprotein cholesterol (LDL-C).Design, setting, participantsA parallel design study of 39 overweight hyperlipidaemic men and postmenopausal women conducted at a Canadian university-affiliated hospital nutrition research centre from April 2005 to November 2006.InterventionParticipants were advised to consume either a low-carbohydrate vegan diet or a high-carbohydrate lacto-ovo vegetarian diet for 6 months after completing 1-month metabolic (all foods provided) versions of these diets. The prescribed macronutrient intakes for the low-carbohydrate and high-carbohydrate diets were: 26% and 58% of energy from carbohydrate, 31% and 16% from protein and 43% and 25% from fat, respectively.Primary outcomeChange in body weight.Results23 participants (50% test, 68% control) completed the 6-month ad libitum study. The approximate 4 kg weight loss on the metabolic study was increased to −6.9 kg on low-carbohydrate and −5.8 kg on high-carbohydrate 6-month ad libitum treatments (treatment difference (95% CI) −1.1 kg (−2.1 to 0.0), p=0.047). The relative LDL-C and triglyceride reductions were also greater on the low-carbohydrate treatment (treatment difference (95% CI) −0.49 mmol/L (−0.70 to −0.28), p<0.001 and −0.34 mmol/L (−0.57 to −0.11), p=0.005, respectively), as were the total cholesterol:HDL-C and apolipoprotein B:A1 ratios (−0.57 (−0.83, −0.32), p<0.001 and −0.05 (−0.09, −0.02), p=0.003, respectively).ConclusionsA self-selected low-carbohydrate vegan diet, containing increased protein and fat from gluten and soy products, nuts and vegetable oils, had lipid lowering advantages over a high-carbohydrate, low-fat weight loss diet, thus improving heart disease risk factors.Trial Registrationclinicaltrials.gov (http://www.clinicaltrials.gov/), #NCT00256516.
Guidelines: is bigger better? A review of SIGN guidelines
Authors: Baird A Gordon , Lawrence James R 
Published: February 2014

ObjectivesTo quantify and analyse the quality of evidence that is presented in national guidelines.SettingLevels of evidence used in all the current valid recommendations in the Scottish Intercollegiate Guideline Network (SIGN) guidelines were reviewed and statistically analysed.Outcome measuresThe proportion of level D evidence used in each guideline and a statistical analysis.MethodData were collected from published guidelines available online to the public. SIGN methodology entails a professional group selected by a national organisation to develop each of these guidelines. Statistical analysis of the relationship between the number of guideline recommendations and the quality of evidence used in its recommendations was performed.ResultThe proportion of level D evidence increases with the number of recommendations made. This correlation is significant with Kendall's τ=0.22 (approximate 95% CI 0.008 to 0.45), p = 0.04; and Spearman ρ=0.22 (approximate 95% CI 0.02 to 0.57), p=0.04.ConclusionsPractice guidelines should be brief and based on scientific evidence. Paradoxically the longest guidelines have the highest proportion of recommendations based on the lowest level of evidence. Guideline developers should be more aware of the need for brevity and a stricter application of evidence-based principles could achieve this. The findings support calls for a review of how evidence is used and presented in guidelines.
Additive influence of genetic predisposition and conventional risk factors in the incidence of coronary heart disease: a population-based study in Greece
Authors: Yiannakouris Nikos , Katsoulis Michail , Trichopoulou Antonia , Ordovas Jose M , Trichopoulos Dimitrios 
Published: February 2014

ObjectivesAn additive genetic risk score (GRS) for coronary heart disease (CHD) has previously been associated with incident CHD in the population-based Greek European Prospective Investigation into Cancer and nutrition (EPIC) cohort. In this study, we explore GRS-‘environment’ joint actions on CHD for several conventional cardiovascular risk factors (ConvRFs), including smoking, hypertension, type-2 diabetes mellitus (T2DM), body mass index (BMI), physical activity and adherence to the Mediterranean diet.DesignA case–control study.SettingThe general Greek population of the EPIC study.Participants and outcome measures477 patients with medically confirmed incident CHD and 1271 controls participated in this study. We estimated the ORs for CHD by dividing participants at higher or lower GRS and, alternatively, at higher or lower ConvRF, and calculated the relative excess risk due to interaction (RERI) as a measure of deviation from additivity.ResultsThe joint presence of higher GRS and higher risk ConvRF was in all instances associated with an increased risk of CHD, compared with the joint presence of lower GRS and lower risk ConvRF. The OR (95% CI) was 1.7 (1.2 to 2.4) for smoking, 2.7 (1.9 to 3.8) for hypertension, 4.1 (2.8 to 6.1) for T2DM, 1.9 (1.4 to 2.5) for lower physical activity, 2.0 (1.3 to 3.2) for high BMI and 1.5 (1.1 to 2.1) for poor adherence to the Mediterranean diet. In all instances, RERI values were fairly small and not statistically significant, suggesting that the GRS and the ConvRFs do not have effects beyond additivity.ConclusionsGenetic predisposition to CHD, operationalised through a multilocus GRS, and ConvRFs have essentially additive effects on CHD risk.
Team-training in healthcare: a narrative synthesis of the literature
Authors: Weaver Sallie J , Dy Sydney M , Rosen Michael A 
Published: February 2014

BackgroundPatients are safer and receive higher quality care when providers work as a highly effective team. Investment in optimising healthcare teamwork has swelled in the last 10 years. Consequently, evidence regarding the effectiveness for these interventions has also grown rapidly. We provide an updated review concerning the current state of team-training science and practice in acute care settings.MethodsA PubMed search for review articles examining team-training interventions in acute care settings published between 2000 and 2012 was conducted. Following identification of relevant reviews with searches terminating in 2008 and 2010, PubMed and PSNet were searched for additional primary studies published in 2011 and 2012. Primary outcomes included patient outcomes and quality indices. Secondary outcomes included teamwork behaviours, knowledge and attitudes.ResultsBoth simulation and classroom-based team-training interventions can improve teamwork processes (eg, communication, coordination and cooperation), and implementation has been associated with improvements in patient safety outcomes. Thirteen studies published between 2011 and 2012 reported statistically significant changes in teamwork behaviours, processes or emergent states and 10 reported significant improvement in clinical care processes or patient outcomes, including mortality and morbidity. Effects were reported across a range of clinical contexts. Larger effect sizes were reported for bundled team-training interventions that included tools and organisational changes to support sustainment and transfer of teamwork competencies into daily practice.ConclusionsOverall, moderate-to-high-quality evidence suggests team-training can positively impact healthcare team processes and patient outcomes. Additionally, toolkits are available to support intervention development and implementation. Evidence suggests bundled team-training interventions and implementation strategies that embed effective teamwork as a foundation for other improvement efforts may offer greatest impact on patient outcomes.
Improving waiting time and operational clinic flow in a tertiary diabetes center
Authors: Ho Emily Tse Lin 
Published: February 2014

AbstractThe Singapore General Hospital Diabetes Centre (DBC) is a multidisciplinary specialist outpatient clinic which aims to provide an integrated one-stop service for diabetes. As with many tertiary academic centre clinics, DBC encounters an expanding patient load, greater patient expectations and increasingly complicated patients who require services from a multitude of health providers. Such rising demands amidst limited resources cause inefficiencies and long waiting times to consultation. This result in low patient satisfaction and an unpleasant clinic experience. A multidisciplinary team was formed to reduce the waiting time at DBC and improve communication and work processes of staff.Addressing wait-times is complicated as multiple stakeholders and operational processes are involved and interlinked. By systematically breaking down processes and identifying problem areas, targeted changes were implemented. This included a revised model of appointment scheduling, a patient reminder system, more effective communication sheets and work reassignments.The primary aim of this project was to improve the patient turn-around time (duration a patient spends at the centre for a visit). There was no documented improvement in turn-around time after project implementation ( 108.23 minutes versus 106.6 minutes) but other secondary aims were achieved. These included an increase in the percentage of patients seen by the doctor within 60 minutes from 80% to 84%, a reduction in wait-time for payment and reappointment at the cashier by 36.6% and a reduction in non-attendances of new cases to the clinic from 30.2% to 21.3%. Staff satisfaction and communication were greatly improved. To aid sustainability, personalized reports of individual doctor’s waiting times and workload were produced quarterly and tracked.As this is a first step quality improvement project, efforts to track, examine and further improve turn-around times are on-going. Future initiatives are directed at time-efficient appointment scheduling between care providers for same day appointments, a reactive SMS system for reminders and reappointments and optimization of processes and manpower allocation for clinics.
Discerning magmatic flow patterns in shallow-level basaltic dykes from the NE rift zone of Tenerife, Spain, using the Anisotropy of Magnetic Susceptibility (AMS) technique
Authors: Delcamp A. , Petronis M. S. , Troll V. R. 
Published: February 2014

Abstract
The anisotropy of magnetic susceptibility (AMS) technique is a rapid petrophysical method used to infer magma flow directions within dykes as well as other igneous intrusions. Samples for AMS study were collected from dykes along the upper part of the NE Rift Zone (NERZ) of Tenerife, Canary Islands, Spain. Of the analysed dykes, 28 have interpretable normal magnetic fabrics. These 28 dykes are therefore suitable to assess the magma flow direction using the imbrication of the magnetic foliation plane from paired dyke margins and/or the overall trend and plunge of the magnetic lineations. AMS fabrics show downwards and upwards flow that could be related to flank and summit eruptions. Overall, however, the direction and sense of magma flow does not follow a specific trend across the NERZ, suggesting that the dykes are supplied by local shallow-level reservoir(s) underneath the ridge or are responding to variations in the local stress field across the axis of the rift zone. The variability of the AMS fabrics suggests a rather complicated propagation mode of magma within the dykes of the NERZ, contrasting with the common assumption of uniform magma propagation within rift zones. Our data therefore support the notion that magma propagation beneath active volcanic systems is inherently more complex than simple subvertical flow from source to final emplacement level, which bears on volcanic hazards worldwide.