bluuebunny/crossref_metadata_2025_split huggingface dataset:
The bacteriophage WORiC is the active phage element in wRi of Drosophila simulans and represents a conserved class of WO phages
Authors: Biliske Jennifer A , Batista Philip D , Grant Chantalle L , Harris Harriet L 
Published: November 2011

Abstract

Background
The alphaproteobacterium Wolbachia pipientis, the most common endosymbiont in eukaryotes, is found predominantly in insects including many Drosophila species. Although Wolbachia is primarily vertically transmitted, analysis of its genome provides evidence for frequent horizontal transfer, extensive recombination and numerous mobile genetic elements. The genome sequence of Wolbachia in Drosophila simulans Riverside (wRi) is available along with the integrated bacteriophages, enabling a detailed examination of phage genes and the role of these genes in the biology of Wolbachia and its host organisms. Wolbachia is widely known for its ability to modify the reproductive patterns of insects. One particular modification, cytoplasmic incompatibility, has previously been shown to be dependent on Wolbachia density and inversely related to the titer of lytic phage. The wRi genome has four phage regions, two WORiBs, one WORiA and one WORiC.

Results
In this study specific primers were designed to distinguish between these four prophage types in wRi, and quantitative PCR was used to measure the titer of bacteriophages in testes, ovaries, embryos and adult flies. In all tissues tested, WORiA and WORiB were not found to be present in excess of their integrated prophages; WORiC, however, was found to be present extrachromosomally. WORiC is undergoing extrachromosomal replication in wRi. The density of phage particles was found to be consistent in individual larvae in a laboratory population. The WORiC genome is organized in conserved blocks of genes and aligns most closely with other known lytic WO phages, WOVitA and WOCauB.

Conclusions
The results presented here suggest that WORiC is the lytic form of WO in D. simulans, is undergoing extrachromosomal replication in wRi, and belongs to a conserved family of phages in Wolbachia.
DPOFA, a Cl-/HCO3
-exchanger antagonist, stimulates fluid absorption across basolateral surface of the retinal pigment epithelium
Authors: Iserovich Pavel , Qin Qiong , Petrukhin Konstantin 
Published: November 2011

Abstract

Background
Retinal detachment is a disorder of the eye in which sensory retina separates from the retinal pigment epithelium (RPE) due to accumulation of fluid in subretinal space. Pharmacological stimulation of fluid reabsorption from subretinal space to choroid across the RPE has been suggested as a treatment strategy for retinal detachment. DPOFA, (R)-(+)-(5,6-dichloro 2,3,9,9a-tetrahydro 3-oxo-9a-propyl-1H-fluoren-7-yl)oxy]acetic acid, is an abandoned drug capable of inhibiting Cl-/HCO3
- exchanger activity. We hypothesized that DPOFA may increase fluid absorption across basolateral surface of the RPE.

Methods
Reverse transcription polymerase chain reaction (RT-PCR) analysis of mRNA for six different transporters that may act as Cl-/HCO3
- exchangers was conducted in bovine and human RPE to confirm that RPE from two species expresses the same repertoire of Cl-/HCO3
- exchanger isoforms. The degree of amino acid homology between orthologous human and bovine RPE-specific isoforms was calculated after performing protein alignments. Transport of fluid across bovine RPE-choroid explants mounted in the Ussing chamber was used to assess the ability of DPOFA to modulate fluid absorption across the RPE.

Results
Using RT-PCR we showed that three isoforms (SLC4A2, SLC4A3, and SLC26A6) are strongly expressed in human and bovine RPE preparations. Amino acid comparisons conducted for RPE-specific isoforms support the use of bovine RPE-choroid explants as an adequate experimental system for assessing fluid absorption activity for DPOFA. Our data is consistent with the fact that DPOFA stimulates fluid absorption across the RPE in bovine RPE-choroid explants.

Conclusions
DPOFA seems to stimulate transport of water across the RPE in bovine RPE-choroid explants. Additional experiments are required to establish dose-dependent effect of DPOFA on fluid absorption in the bovine RPE-choroid experimental system.
Evaluation of the role of location and distance in recruitment in respondent-driven sampling
Authors: McCreesh Nicky , Johnston Lisa G , Copas Andrew , Sonnenberg Pam , Seeley Janet , Hayes Richard J , Frost Simon DW , White Richard G 
Published: November 2011

AbstractBackgroundRespondent-driven sampling(RDS) is an increasingly widely used variant of a link tracing design for recruiting hidden populations. The role of the spatial distribution of the target population has not been robustly examined for RDS. We examine patterns of recruitment by location, and how they may have biased an RDS study findings.MethodsTotal-population data were available on a range of characteristics on a population of 2402 male household-heads from an open cohort of 25 villages in rural Uganda. The locations of households were known a-priori. An RDS survey was carried out in this population, employing current RDS methods of sampling and statistical inference.ResultsThere was little heterogeneity in the population by location. Data suggested more distant contacts were less likely to be reported, and therefore recruited, but if reported more distant contacts were as likely as closer contacts to be recruited. There was no evidence that closer proximity to a village meeting place was associated with probability of being recruited, however it was associated with a higher probability of recruiting a larger number of recruits. People living closer to an interview site were more likely to be recruited.ConclusionsHousehold location affected the overall probability of recruitment, and the probability of recruitment by a specific recruiter. Patterns of recruitment do not appear to have greatly biased estimates in this study. The observed patterns could result in bias in more geographically heterogeneous populations. Care is required in RDS studies when choosing the network size question and interview site location(s).
Dietary weight loss and exercise interventions effects on quality of life in overweight/obese postmenopausal women: a randomized controlled trial
Authors: Imayama Ikuyo , Alfano Catherine M , Kong Angela , Foster-Schubert Karen E , Bain Carolyn E , Xiao Liren , Duggan Catherine , Wang Ching-Yun , Campbell Kristin L , Blackburn George L , McTiernan Anne 
Published: November 2011

Abstract

Background
Although lifestyle interventions targeting multiple lifestyle behaviors are more effective in preventing unhealthy weight gain and chronic diseases than intervening on a single behavior, few studies have compared individual and combined effects of diet and/or exercise interventions on health-related quality of life (HRQOL). In addition, the mechanisms of how these lifestyle interventions affect HRQOL are unknown. The primary aim of this study was to examine the individual and combined effects of dietary weight loss and/or exercise interventions on HRQOL and psychosocial factors (depression, anxiety, stress, social support). The secondary aim was to investigate predictors of changes in HRQOL.

Methods
This study was a randomized controlled trial. Overweight/obese postmenopausal women were randomly assigned to 12 months of dietary weight loss (n = 118), moderate-to-vigorous aerobic exercise (225 minutes/week, n = 117), combined diet and exercise (n = 117), or control (n = 87). Demographic, health and anthropometric information, aerobic fitness, HRQOL (SF-36), stress (Perceived Stress Scale), depression [Brief Symptom Inventory (BSI)-18], anxiety (BSI-18) and social support (Medical Outcome Study Social Support Survey) were assessed at baseline and 12 months. The 12-month changes in HRQOL and psychosocial factors were compared using analysis of covariance, adjusting for baseline scores. Multiple regression was used to assess predictors of changes in HRQOL.

Results
Twelve-month changes in HRQOL and psychosocial factors differed by intervention group. The combined diet + exercise group improved 4 aspects of HRQOL (physical functioning, role-physical, vitality, and mental health), and stress (p ≤ 0.01 vs. controls). The diet group increased vitality score (p < 0.01 vs. control), while HRQOL did not change differently in the exercise group compared with controls. However, regardless of intervention group, weight loss predicted increased physical functioning, role-physical, vitality, and mental health, while increased aerobic fitness predicted improved physical functioning. Positive changes in depression, stress, and social support were independently associated with increased HRQOL, after adjusting for changes in weight and aerobic fitness.

Conclusions
A combined diet and exercise intervention has positive effects on HRQOL and psychological health, which may be greater than that from exercise or diet alone. Improvements in weight, aerobic fitness and psychosocial factors may mediate intervention effects on HRQOL.

Trial Registration
Clinical Trials, ClinicalTrials.gov register, NCT00470119
Blind recovery of k/n rate convolutional encoders in a noisy environment
Authors: Marazin Melanie , Gautier Roland , Burel Gilles 
Published: November 2011

Abstract
In order to enhance the reliability of digital transmissions, error correcting codes are used in every digital communication system. To meet the new constraints of data rate or reliability, new coding schemes are currently being developed. Therefore, digital communication systems are in perpetual evolution and it is becoming very difficult to remain compatible with all standards used. A cognitive radio system seems to provide an interesting solution to this problem: the conception of an intelligent receiver able to adapt itself to a specific transmission context. This article presents a new algorithm dedicated to the blind recognition of convolutional encoders in the general k/n rate case. After a brief recall of convolutional code and dual code properties, a new iterative method dedicated to the blind estimation of convolutional encoders in a noisy context is developed. Finally, case studies are presented to illustrate the performances of our blind identification method.
Survival of tumor cells after proton irradiation with ultra-high dose rates
Authors: Auer Susanne , Hable Volker , Greubel Christoph , Drexler Guido A , Schmid Thomas E , Belka Claus , Dollinger Günther , Friedl Anna A 
Published: November 2011

Abstract

Background
Laser acceleration of protons and heavy ions may in the future be used in radiation therapy. Laser-driven particle beams are pulsed and ultra high dose rates of >109 Gy s-1may be achieved. Here we compare the radiobiological effects of pulsed and continuous proton beams.

Methods
The ion microbeam SNAKE at the Munich tandem accelerator was used to directly compare a pulsed and a continuous 20 MeV proton beam, which delivered a dose of 3 Gy to a HeLa cell monolayer within < 1 ns or 100 ms, respectively. Investigated endpoints were G2 phase cell cycle arrest, apoptosis, and colony formation.

Results
At 10 h after pulsed irradiation, the fraction of G2 cells was significantly lower than after irradiation with the continuous beam, while all other endpoints including colony formation were not significantly different. We determined the relative biological effectiveness (RBE) for pulsed and continuous proton beams relative to x-irradiation as 0.91 ± 0.26 and 0.86 ± 0.33 (mean and SD), respectively.

Conclusions
At the dose rates investigated here, which are expected to correspond to those in radiation therapy using laser-driven particles, the RBE of the pulsed and the (conventional) continuous irradiation mode do not differ significantly.
Effects of RNA interference-mediated gene silencing of JMJD2A on human breast cancer cell line MDA-MB-231 in vitro
Authors: Li Bei-Xu , Zhang Ming-Chang , Luo Cheng-Liang , Yang Peng , Li Hui , Xu Hong-Mei , Xu Hong-Fei , Shen Yi-Wen , Xue Ai-Min , Zhao Zi-Qin 
Published: November 2011

Abstract
Previous data demonstrate that JMJD2A is a cancer-associated gene and may be involved in human breast cancer by demethylation of H3K9me3. The aim of this study was to investigate depressive effects on JMJD2A by transfection with JMJD2A-sepcific siRNA in human breast cancer cell line MDA-MB-231 and effects on cell proliferation, invasion and migration. JMJD2A-specific siRNA was chemically synthesised and transfected into human breast cancer cell line MDA-MB-231. Expression levels of JMJD2A were detected by quantitative real-time PCR and Western blot analysis. Cells proliferation was evaluated by using flow cytometric anlysis and MTT assay. The abilities of invasion and migration were evaluated by cell migration and invasion assay with Boyden chambers. The results showed that the transfection was successful and expression levels of JMJD2A mRNA and protein in siRNA group were both down-regulated. By MTT assay, the mean actual absorbance in siRNA group was significantly lower than that in blank control group (P < 0.05) and negative control group (P < 0.05). In addition, the percentage of cells in G0/G1 phase in siRNA group was significantly more than that in blank control group (P < 0.05) and negative control group (P < 0.05). Furthermore, by cell invasion and migration assay, the decreased number of migrated cells in siRNA group was observed (P < 0.05). These data imply that silencing JMJD2A gene could result in cell cycle change and proliferation inhibition, and lead to suppress tumor cell invasion and migration. It provides a new perspective in understanding the pleiotropic functions of JMJD2A and its contribution to human breast cancer.
Relationship between Dietary and Other Lifestyle Habits and Cardiometabolic Risk Factors in Men
Authors: Katano Sayuri , Nakamura Yasuyuki , Okuda Nagako , Murakami Yoshitaka , Chiba Nagako , Yoshita Katsushi , Tanaka Taichiro , Tamaki Junko , Takebayashi Toru , Okayama Akira , Miura Katsuyuki , Okamura Tomonori , Ueshima Hirotsugu ,   HIPOP-OHP Research Group
Published: November 2011

Abstract

Background
Prevalence of men with cardiometabolic risk factors (CMRF) is increasing in Japan. Few studies have comprehensively examined the relation between lifestyles and CMRF.

Methods
We examined the baseline data from 3,498 male workers ages 19 to 69 years who participated in the high-risk and population strategy for occupational health promotion (HIPOP-OHP) study at 12 large-scale companies throughout Japan. The physical activity of each participant was classified according to the International Physical Activity Questionnaire (IPAQ). Dietary intake was surveyed by a semi-quantitative Food Frequency Questionnaire. We defined four CMRF in this study as follows: 1) high blood pressure (BP): systolic BP ≥ 130 mmHg, or diastolic BP ≥ 85 mmHg, or the use of antihypertensive drugs; 2) dyslipidemia: high-density lipoprotein-cholesterol concentration < 40 mg/dl, or triglycerides concentration ≥ 150 mg/dl, or on medication for dyslipidemia; 3) impaired glucose tolerance: fasting blood sugar concentration ≥110 mg/dl; 4) obese: a body mass index ≥ 25 kg/m2.

Results
Those who had 0 to 4 CMRF accounted for 1,597 (45.7%), 1,032 (29.5%), 587 (16.8%), 236 (6.7%), and 44 (1.3%) participants, respectively, in the Poisson distribution. Poisson regression analysis revealed that independent factors that contributed to the number of CMRF were age (b = 0.020, P < 0.01), IPAQ (b = -0.091, P < 0.01), alcohol intake (ml/day) (b = 0.001, P = 0.03), percentage of protein intake (b = 0.059, P = 0.01), and total energy intake (kcal)(b = 0.0001, P < 0.01). Furthermore, alcohol intake and its frequency had differential effects.

Conclusions
Alcohol intake, percent protein and total energy intake were positively associated, whereas drinking frequency and IPAQ were inversely associated, with the number of CMRF.
Systematic Review and Meta-Analysis of Efficacy, Safety, and Tolerability Data from Randomized Controlled Trials of Drugs Used to Treat Postherpetic Neuralgia
Authors: Edelsberg John S , Lord Claudia , Oster Gerry 
Published: November 2011

Objective: To conduct a systematic review of available data from reports of randomized controlled trials on the efficacy, safety, and tolerability of drugs used to treat postherpetic neuralgia (PHN), a common type of neuropathic pain. Data Sources: The MEDLINE (1950-June 30. 2009) and EMBASE (1974-June 30, 2009) databases were used to identify source studies, in conjunction with a review of reference citations from identified published reports. Study Selection and Data Extraction: We selected all English-language reports of randomized placebo-controlled trials of the efficacy, tolerability, and safety of drugs (oral or transdermal) used for treatment in patients with PHN. Studies with treatment duration less than 4 weeks were excluded. From each identified trial, we extracted information on (1) placebo-corrected percentage reductions in pain intensity from randomization to end of active treatment; (2) relative risks of withdrawal due to lack of efficacy; (3) relative risks of various adverse events; and (4) relative risks of withdrawal due to adverse events. Data Synthesis: Twelve reports of randomized controlled trials in patients with PHN were identified, involving 8 different agents (amitriptyline, capsaicin, divalproex sodium, gabapentin, morphine, nortriptyline, pregabalin, tramadol). Most studies were small, involving fewer than 200 patients. Pain intensity was reported to have been reduced significantly with all drugs (range: 13.8% [tramadol] to 42,4% [amitriptyline]); data were pooled using techniques of meta-analysis when information was available from more than 1 trial. No clinical trial reported a significant reduction in risk of withdrawal as a result of lack of efficacy. Analysis of adverse events was greatly limited by erratic and inconsistent reporting and wide variation in sample sizes. Conclusions: While available literature establishes the efficacy of 6 drugs in treatment of PHN, it does not provide adequate guidance as to which agents are best to treat this condition, in part because of inadequate reporting of data on tolerability and safety.
Kangaroo Care: Is It for Everyone?
Authors: Neu Madalynn 
Published: November 2011

Purpose: In spite of the benefits reported for kangaroo holding, many mothers of preterm infants requiring intensive care do not choose to hold kangaroo style. The purpose of this study is to describe factors that influence mothers of healthy preterm infants to choose kangaroo holding compared to the standard care method of blanket holding.Sample: Twenty-four primiparous mothers of healthy infants born at 30–34 weeks gestational age.Design: In this naturalistic inquiry, mothers were interviewed twice: once while the infant was hospitalized and again after the infant was discharged home.Results: Mothers’ holding practices divided them into three groups: (1) kangaroo holding in hospital and home, (2) blanket holding in hospital and home, and (3) holding practice switched from hospital to home. Three themes emerged from the interview data: (1) emotional state, (2) holding environment, and (3) benefits of close contact with the infant.
Neonatal Back Transport: Perspectives from Parents of Medicaid-Insured Infants and Providers
Authors: Hanrahan Krystal , Attar Mohammad-Ali , Frohna Alice , Gates Molly , Lang Sylvia , Clark Sarah 
Published: November 2011

Purpose:To examine parents’ and health care providers’ perceptions of back transport from a tertiary care neonatal intensive care unit to a community hospital.Design:Qualitative, hypothesis-generating, cross-sectional study utilizing focus group methodology.Sample:Participants included 12 parents of back-transported infants insured by Medicaid, 6 regional NICU health care providers, and 17 community hospital special care nursery health care providers.Main Outcome Measures:Participant perceptions of factors that support or impede successful back transport.Results:Data from the focus groups were analyzed to identify five main themes: early communication about back transport, preparing parents for back transport, communication between hospitals at the time of back transport, follow-up and information exchange after back transport, and improving the back-transport experience for parents.
The ABCs of In-Situ Combustion Simulations: From Laboratory Experiments to the Field Scale
Authors: Gutiérrez D. , Moore R. G. , Ursenbach M. G. , Mehta S. A. 
Published: November 2011

Abstract
Air-injection-based recovery processes are receiving increased interest due to their high recovery potentials and applicability to a wide range of reservoirs. However, most operators require a certain level of confidence in the potential recovery from these (or any) processes prior to committing resources, which can be achieved with the use of numerical reservoir simulation.
In a previous paper (JCPT, April 2009, pp. 23–34) it was proposed that, after successful laboratory testing, analytical calculations and semi-quantitative simulation models would be used for pilot design and further optimization of the actual operation. However, the specific steps for building the field-scale simulation models were not explicitly addressed. This paper discusses a detailed workflow which could be followed to engineer an air injection project using thermal reservoir simulation.
The first step of the simulation study involves the selection of a kinetic model which could be either developed specifically for the reservoir in question or taken from public literature. Second, the oil would be characterized in terms of the same pseudo-components employed by the kinetic model and relevant PVT data would be matched to develop a fluid model for the thermal simulator. This new fluid model is used in the field-scale simulation model to history match the production history (i.e. prior to air injection) of the field. Third, relevant combustion tube tests would be history matched to validate the kinetic model and refine the thermal data that would go into the field-scale model. Finally, the results and knowledge gained from the combustion tube match(es) are applied to the field-scale model with the proper upscaling of some parameters. This simulation model would aid in selecting optimum well locations and operating strategies of the pilot. It would then be refined as the actual operation progresses to enhance its predictability and allow further optimization of the project.
Technical considerations, advantages, and limitations of each step of the workflow are discussed in detail. This paper also presents workflow variations and recommendations applicable to new and already mature air injection projects for which simulation models are being developed.