bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low-Dose Penile SIVmac251 Exposure of Rhesus Macaques Infected with Adenovirus Type 5 (Ad5) and Then Immunized with a Replication-Defective Ad5-Based SIV
gag/pol/nef
Vaccine Recapitulates the Results of the Phase IIb Step Trial of a Similar HIV-1 Vaccine
Authors: Qureshi Huma , Ma Zhong-Min , Huang Ying , Hodge Gregory , Thomas Michael A. , DiPasquale Janet , DeSilva Veronique , Fritts Linda , Bett Andrew J. , Casimiro Danilo R. , Shiver John W. , Robert-Guroff Marjorie , Robertson Michael N. , McChesney Michael B. , Gilbert Peter B. , Miller Christopher J. 
Published: December 2011

ABSTRACT

The Step Trial showed that the MRKAd5 HIV-1 subtype B Gag/Pol/Nef vaccine did not protect men from HIV infection or reduce setpoint plasma viral RNA (vRNA) levels but, unexpectedly, it did modestly enhance susceptibility to HIV infection in adenovirus type 5 (Ad5)-seropositive, uncircumcised men. As part of the process to understand the results of the Step Trial, we designed a study to determine whether rhesus macaques chronically infected with a host-range mutant Ad5 (Ad5hr) and then immunized with a replication defective Ad5 SIVmac239 Gag/Pol/Nef vaccine were more resistant or susceptible to SIV infection than unimmunized rhesus macaques challenged with a series of escalating dose penile exposures to SIVmac 251. The Ad5 SIV vaccine induced CD8
+
T cell responses in 70% of the monkeys, which is similar to the proportion of humans that responded to the vaccine in the Step Trial. However, the vaccine did not protect vaccinated animals from penile SIV challenge. At the lowest SIV exposure dose (10
3
50% tissue culture infective doses), 2 of 9 Ad5-seropositive animals immunized with the Ad5 SIV vaccine became infected compared to 0 of 34 animals infected in the other animal groups (naive animals, Ad5-seropositive animals immunized with the empty Ad5 vector, Ad5-seronegative animals immunized with the Ad5 SIV vaccine, and Ad5-seronegative animals immunized with the empty Ad5 vector). Penile exposure to more concentrated virus inocula produced similar rates of infection in all animal groups. Although setpoint viral loads were unaffected in Step vaccinees, the Ad5 SIV-immunized animals had significantly lower acute-phase plasma vRNA levels compared to unimmunized animals. Thus, the results of the nonhuman primate (NHP) study described here recapitulate the lack of protection against HIV acquisition seen in the Step Trial and suggest a greater risk of infection in the Ad5-seropositive animals immunized with the Ad5 SIV vaccine. Further studies are necessary to confirm the enhancement of virus acquisition and to discern associated mechanisms.
Molecular community analysis of magnesium-rich bittern brine recovered from a Tunisian solar saltern
Authors: Baati Houda , Jarboui Raja , Gharsallah Néji , Sghir Abdelghani , Ammar Emna 
Published: December 2011

The microbial community of a magnesium-rich bittern brine saturated with NaCl (380–400 g/L) from a Tunisian solar saltern was investigated using a molecular approach based on 16S rRNA gene analysis and viability tests. The results revealed the existence of microbial flora. Viability test assessment showed that 46.4% of this flora was viable but not detectable by culturability tests. 16S rRNA genes from 49 bacterial clones and 38 archaeal clones were sequenced and phylogenetically analyzed. Eleven operational taxonomic units (OTUs) determined by the DOTUR program with 97% sequence similarity were generated for Bacteria. These OTUs were affiliated with Bacteroidetes and Gammaproteobacteria. The archaeal community composition exhibited more diversity with 38 clones, resulting in 13 OTUs affiliated with the Euryarchaeota phylum. Diversity measurement showed a more diverse archaeal than bacterial community at the saturated pond.
Identification of virulence factors in Vibrio cholerae isolated from Iraq during the 2007–2009 outbreak
Authors: Saleh Tahreer Hadi , Sabbah Majeed Arsheed , Jasem Kifah A. , Hammad Zuhair N. 
Published: December 2011

Thousands of people were infected with Vibrio cholerae during the outbreak in Iraq in 2007–2009. Vibrio cholerae was shown to be variable in its content of virulence determinants and in its antibiotic sensitivity. This study was designed to isolate and characterize clinical and environmental V. cholerae isolates and to determine antibiotic sensitivity, enzyme and toxin production, and the presence of virulence genes. Eighty clinical and five environmental bacterial isolates were collected and diagnosed by subjecting them to microscopic, biochemical, serological, and molecular analysis. The results revealed that 55% of clinical isolates belonged to the Inaba serotype, 32.5% to the Ogawa serotypes, and 12.5% to the Non-O1 serotype. All environmental V. cholerae isolates belonged to the Non-O1 serotype. All environmental isolates were sensitive to all examined antimicrobial agents, while all clinical isolates showed a high sensitivity (100%) to ampicillin, gentamicin, cephalothin, tetracycline, erythromycin, and ciprofloxacin, and a high resistance (97.5%) to co-trimoxazole, nalidixic acid, and chloramphenicol. It was found that all V. cholerae (O1) isolates were resistant to the Vibrio static O129 and all Non-O1 V. cholerae isolates were sensitive to the Vibrio static O129. All clinical and environmental isolates produced hemolysin (100%) and lecithinase (100%), while they showed various production rates of protease (90% of clinical and 60% of environmental) and lipase (50% of clinical and 20% of environmental). The ompW gene was amplified in all the clinical and environmental V. cholerae isolates, but not in other related and nonrelated bacteria. Multiplex PCR analysis showed that the toxR gene was amplified in all clinical and environmental isolates, while ctxA, ctxB, tcpA genes were amplified only in clinical (O1) isolates. This study indicates the differences in the production of some enzymes and toxins and in the content of virulence genes between clinical and environmental isolates in Iraq during the outbreak (2007–2009).
Computational prediction of microRNAs and their targets from three unicellular algae species with complete genome sequences
Authors: Huang Aiyou , Wu Xiaojie , Wang Guangce , Jia Zhaojun , He Linwen 
Published: December 2011

The genome sequences of Phaeodactylum tricornutum , Thalassiosira pseudonana , and Cyanidioschyzon merolae have provided significant evidence for the secondary endosymbiosis of diatoms in regard to the genome. Yet little about their relationships in regard to gene regulation pattern, such as microRNA (miRNA), has been reported. Using a homology search based on genomic sequences, 13, 3, and 7 predicted miRNA genes were found in genomes from P. tricornutum, T. pseudonana, and C. merolae, respectively. Of the 23 miRNA genes, 18 had homology with animal miRNAs, implying that they are ancestral miRNAs. A phylogenetic tree based on common miRNA families shared by these three unicellular algae, higher plants, and animals showed that P. tricornutum shared most miRNAs with animals. The phylogenetic tree also showed that C. merolae shared more miRNAs with plants than did the two diatoms, and the majority of its miRNAs were shared with the two diatoms. Our results were consistent with diatoms originating from a secondary endosymbiosis.
openBIS: a flexible framework for managing and analyzing complex data in biology research
Authors: Bauch Angela , Adamczyk Izabela , Buczek Piotr , Elmer Franz-Josef , Enimanev Kaloyan , Glyzewski Pawel , Kohler Manuel , Pylak Tomasz , Quandt Andreas , Ramakrishnan Chandrasekhar , Beisel Christian , Malmström Lars , Aebersold Ruedi , Rinn Bernd 
Published: December 2011

Abstract

Background
Modern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that in order to overcome the challenge of managing those large quantitative datasets and maximise the biological information extracted from them, a sound information system is required. Ease of integration with data analysis pipelines and other computational tools is a key requirement for it.

Results
We have developed openBIS, an open source software framework for constructing user-friendly, scalable and powerful information systems for data and metadata acquired in biological experiments. openBIS enables users to collect, integrate, share, publish data and to connect to data processing pipelines. This framework can be extended and has been customized for different data types acquired by a range of technologies.

Conclusions
openBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies. The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, scalability to very large data, flexibility to handle any biological data type and extensibility to the needs of any research domain.
qDTY
1.1
, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds
Authors: Vikram Prashant , Swamy BP Mallikarjuna , Dixit Shalabh , Ahmed Helal Uddin , Teresa Sta Cruz Ma , Singh Alok Kumar , Kumar Arvind 
Published: December 2011

Abstract

Background
Drought is one of the most important abiotic stresses causing drastic reductions in yield in rainfed rice environments. The suitability of grain yield (GY) under drought as a selection criterion has been reported in the past few years. Most of the quantitative trait loci (QTLs) for GY under drought in rice reported so far has been in the background of low-yielding susceptible varieties. Such QTLs have not shown a similar effect in multiple high- yielding drought-susceptible varieties, thus limiting their use in marker-assisted selection. Genetic control of GY under reproductive-stage drought stress (RS) in elite genetic backgrounds was studied in three F3:4 mapping populations derived from crosses of N22, a drought-tolerant aus cultivar, with Swarna, IR64, and MTU1010, three high-yielding popular mega-varieties, with the aim to identify QTLs for GY under RS that show a consistent effect in multiple elite genetic backgrounds. Three populations were phenotyped under RS in the dry seasons (DS) of 2009 and 2010 at IRRI. For genotyping, whole-genome scans for N22/MTU1010 and bulked segregant analysis for N22/Swarna and N22/IR64 were employed using SSR markers.

Results
A major QTL for GY under RS, qDTY

1.1
, was identified on rice chromosome 1 flanked by RM11943 and RM431 in all three populations. In combined analysis over two years, qDTY

1.1
showed an additive effect of 29.3%, 24.3%, and 16.1% of mean yield in N22/Swarna, N22/IR64, and N22/MTU1010, respectively, under RS. qDTY

1.1
also showed a positive effect on GY in non-stress (NS) situations in N22/Swarna, N22/IR64 over both years, and N22/MTU1010 in DS2009.

Conclusions
This is the first reported QTL in rice with a major and consistent effect in multiple elite genetic backgrounds under both RS and NS situations. Consistency of the QTL effect across different genetic backgrounds makes it a suitable candidate for use in marker-assisted breeding.
Rationale and study design for a randomised controlled trial to reduce sedentary time in adults at risk of type 2 diabetes mellitus: project stand (Sedentary Time ANd diabetes)
Authors: Wilmot Emma G , Davies Melanie J , Edwardson Charlotte L , Gorely Trish , Khunti Kamlesh , Nimmo Myra , Yates Thomas , Biddle Stuart JH 
Published: December 2011

Abstract

Background
The rising prevalence of Type 2 Diabetes Mellitus (T2DM) is a major public health problem. There is an urgent need for effective lifestyle interventions to prevent the development of T2DM. Sedentary behaviour (sitting time) has recently been identified as a risk factor for diabetes, often independent of the time spent in moderate-to-vigorous physical activity. Project STAND (Sedentary Time ANd Diabetes) is a study which aims to reduce sedentary behaviour in younger adults at high risk of T2DM.

Methods/Design
A reduction in sedentary time is targeted using theory driven group structured education. The STAND programme is subject to piloting and process evaluation in line with the MRC framework for complex interventions. Participants are encouraged to self-monitor and self-regulate their behaviour. The intervention is being assessed in a randomised controlled trial with 12 month follow up. Inclusion criteria are a) aged 18-40 years with a BMI in the obese range; b) 18-40 years with a BMI in the overweight range plus an additional risk factor for T2DM. Participants are randomised to the intervention (n = 89) or control (n = 89) arm. The primary outcome is a reduction in sedentary behaviour at 12 months as measured by an accelerometer (count < 100/min). Secondary outcomes include physical activity, sitting/lying time using the ActivPAL posture monitor, fasting and 2 h oral glucose tolerance test, lipids, inflammatory biomarkers, body weight, waist circumference, blood pressure, illness perceptions, and efficacy beliefs for behaviour change.

Conclusions
This is the first UK trial to address sedentary behaviour change in a population of younger adults at risk of T2DM. The results will provide a platform for the development of a range of future multidisciplinary interventions in this rapidly expanding high-risk population.

Trial registration
Current controlled trials ISRCTN08434554, MRC project 91409.
ATP synthase ecto-α-subunit: a novel therapeutic target for breast cancer
Authors: Pan Jian , Sun Li-Chao , Tao Yan-Fang , Zhou Zhuan , Du Xiao-Li , Peng Liang , Feng Xing , Wang Jian , Li Yi-Ping , Liu Ling , Wu Shui-Yan , Zhang Yan-Lan , Hu Shao-Yan , Zhao Wen-Li , Zhu Xue-Ming , Lou Guo-Liang , Ni Jian 
Published: December 2011

Abstract

Background
Treatment failure for breast cancer is frequently due to lymph node metastasis and invasion to neighboring organs. The aim of the present study was to investigate invasion- and metastasis-related genes in breast cancer cells in vitro and in vivo. Identification of new targets will facilitate the developmental pace of new techniques in screening and early diagnosis. Improved abilities to predict progression and metastasis, therapeutic response and toxicity will help to increase survival of breast cancer patients.

Methods
Differential protein expression in two breast cancer cell lines, one with high and the other with low metastatic potential, was analyzed using two-dimensional liquid phase chromatographic fractionation (Proteome Lab PF 2D system) followed by matrix-assisted laser desorption/time-of-flight mass spectrometry (MALDI-TOF/MS).

Results
Up regulation of α-subunit of ATP synthase was identified in high metastatic cells compared with low metastatic cells. Immunohistochemical analysis of 168 human breast cancer specimens on tissue microarrays revealed a high frequency of ATP synthase α-subunit expression in breast cancer (94.6%) compared to normal (21.2%) and atypical hyperplasia (23%) breast tissues. Levels of ATP synthase expression levels strongly correlated with large tumor size, poor tumor differentiation and advanced tumor stages (P < 0.05). ATP synthase α-subunit over-expression was detected on the surface of a highly invasive breast cancer cell line. An antibody against the ATP synthase α-subunit inhibited proliferation, migration and invasion in these breast cancer cells but not that of a non-tumor derived breast cell line.

Conclusions
Over-expression of ATP synthase α-subunit may be involved in the progression and metastasis of breast cancer, perhaps representing a potential biomarker for diagnosis, prognosis and a therapeutic target for breast cancer. This finding of this study will help us to better understand the molecular mechanism of tumor metastasis and to improve the screening, diagnosis, as well as prognosis and/or prediction of responses to therapy for breast cancer.
An occupancy-based and channel-aware multi-level adaptive scheme for video communications over wireless channels
Authors: Mukhtar Husameldin , Hassan Mohamed , Landolsi Taha 
Published: December 2011

Abstract
Video streaming over wireless channels is challenged with the time-varying nature of the underlying channels and the stringent requirements of video applications. In particular, video streaming has strict requirements on bandwidth, delay, and loss rate while wireless channels are dynamic and error-prone by nature. In this article, we propose a novel multilevel adaptive scheme that is designed to mitigate the challenges facing video streaming over unreliable channels. This is done while preventing potential playback discontinuities and guaranteeing a graceful degradation of the rendered video quality. Scalable video coding, adaptive modulation, and adaptive channel coding are integrated to achieve the objectives of the proposed scheme. If adaptive modulation and channel coding are not enough to guarantee the on-time delivery of decodable video frames, we adopt scalable coding. Simulation results show that the proposed adaptive scheme achieves an improvement of about 2.5 dB in the peak signal-to-noise ratio over a nonadaptive one. In addition, the proposed scheme reduces the number of starvation instances by 50 and 90% in the cases of Stop-and-Wait and Go-Back-N automatic repeat requests, respectively.
Diagnosis and management of an immature teratoma during ovarian stimulation: a case report
Authors: Douay-Hauser Nathalie , Koskas Martin , Walker Francine , Luton Dominique , Yazbeck Chadi 
Published: December 2011

Abstract

Introduction
The discovery of a mature teratoma (dermoid cyst) of the ovary during ovarian stimulation is not a rare event. Conversely, we could not find any reported cases of immature teratoma in such a situation. Clinical and ultrasound arguments for this immature form are scarcely or poorly evaluated.

Case Presentation
We describe the case of a 31-year-old Caucasian woman with primary infertility, who developed an immature teratoma during an in vitro fertilization ovarian stimulation cycle.

Conclusions
Ultrasound signs of an atypical cyst during ovarian stimulation allowed us to adopt a careful medical attitude and to adapt the required surgical oncological treatment.
Regulation of myotube formation by the actin-binding factor drebrin
Authors: Mancini Annalisa , Sirabella Dario , Zhang Weijia , Yamazaki Hiroyuki , Shirao Tomoaki , Krauss Robert S 
Published: December 2011

Abstract

Background
Myogenic differentiation involves cell-cycle arrest, activation of the muscle-specific transcriptome, and elongation, alignment and fusion of myoblasts into multinucleated myotubes. This process is controlled by promyogenic transcription factors and regulated by signaling pathways in response to extracellular cues. The p38 mitogen-activated protein kinase (p38 MAPK) pathway promotes the activity of several such transcription factors, including MyoD and MEF2, thereby controlling the muscle-specific transcription program. However, few p38-regulated genes that play a role in the regulation of myogenesis have been identified.

Methods
RNA interference (RNAi), chemical inhibition and immunofluorescence approaches were used to assess the role of drebrin in differentiation of primary mouse myoblasts and C2C12 cells.

Results
In a search for p38-regulated genes that promote myogenic differentiation, we identified Dbn1, which encodes the actin-binding protein drebrin. Drebrin is an F-actin side-binding protein that remodels actin to facilitate the change of filopodia into dendritic spines during synaptogenesis in developing neurons. Dbn1 mRNA and protein are induced during differentiation of primary mouse and C2C12 myoblasts, and induction is substantially reduced by the p38 MAPK inhibitor SB203580. Primary myoblasts and C2C12 cells depleted of drebrin by RNAi display reduced levels of myogenin and myosin heavy chain and form multinucleated myotubes very inefficiently. Treatment of myoblasts with BTP2, a small-molecule inhibitor of drebrin, produces a phenotype similar to that produced by knockdown of drebrin, and the inhibitory effects of BTP2 are rescued by expression of a mutant form of drebrin that is unable to bind BTP2. Drebrin in myoblasts is enriched in cellular projections and cell cortices and at regions of cell-cell contact, all sites where F-actin, too, was concentrated.

Conclusions
Our findings reveal that Dbn1 expression is a target of p38 MAPK signaling during myogenesis and that drebrin promotes myoblast differentiation.
Risk factors for repetition and suicide following self-harm in
older adults: multicentre cohort study
Authors: Murphy Elizabeth , Kapur Navneet , Webb Roger , Purandare Nitin , Hawton Keith , Bergen Helen , Waters Keith , Cooper Jayne 
Published: December 2011

BackgroundOlder adults have elevated suicide rates. Self-harm is the most important
risk factor for suicide. There are few population-based studies of
self-harm in older adults.AimsTo calculate self-harm rates, risk factors for repetition and rates of
suicide following self-harm in adults aged 60 years and over.MethodWe studied a prospective, population-based self-harm cohort presenting to
six general hospitals in three cities in England during 2000 to 2007.ResultsIn total 1177 older adults presented with self-harm and 12.8% repeated
self-harm within 12 months. Independent risk factors for repetition were
previous self-harm, previous psychiatric treatment and age 60–74 years.
Following self-harm, 1.5% died by suicide within 12 months. The risk of
suicide was 67 times that of older adults in the general population. Men
aged 75 years and above had the highest suicide rates.ConclusionsOlder adults presenting to hospital with self-harm are a high-risk group
for subsequent suicide, particularly older men.
Effects of a Brief Cognitive Intervention Aimed at Communicating the Negative Reinforcement Explanation for Smoking on Relevant Cognitions and Urges to Smoke
Authors: McDermott Máirtín S. , Marteau Theresa M. , Hajek Peter 
Published: December 2011

AbstractIntroduction:The aim of the current study was to assess the impact of an intervention aimed at communicating the negative reinforcement explanation for smoking, a set of ideas derived from popular self-help books, upon participants' cognitions and urges to smoke. Methods: Smokers (n = 205) undergoing standard stop-smoking treatment were randomised to receive either the experimental intervention, a brief intervention aimed at communicating the explanation or a control intervention, a video on the health risks of smoking. Outcomes were participants' acceptance of the negative reinforcement explanation for smoking, positive outcome expectations for smoking, self-efficacy and urges to smoke reported at one week post-cessation. Results: Post-cessation urges to smoke were similar in the two groups (Adjusted expt. group mean = 2.50, Control group mean = 2.75, F(1,60) = 0.98, p = .33). Other cognitive measures were also unchanged. Conclusions: The brief cognitive intervention offered as an adjunct to standard care failed to reduce urges to smoke or alter smokers' cognitions. Changing smokers' cognitions may be as challenging as changing their behaviours. Suggestions are provided for further research.