bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complex formation of EphB1/Nck/Caskin1 leads to tyrosine phosphorylation and structural changes of the Caskin1 SH3 domain
Authors: Pesti Szabolcs , Balázs Annamária , Udupa Roopesh , Szabó Beáta , Fekete Anna , Bőgel Gábor , Buday László 
Published: November 2012

Abstract

Background
Scaffold proteins have an important role in the regulation of signal propagation. These proteins do not possess any enzymatic activity but can contribute to the formation of multiprotein complexes. Although scaffold proteins are present in all cell types, the nervous system contains them in the largest amount. Caskin proteins are typically present in neuronal cells, particularly, in the synapses. However, the signaling mechanisms by which Caskin proteins are regulated are largely unknown.

Results
Here we demonstrate that EphB1 receptor tyrosine kinase can recruit Caskin1 through the adaptor protein Nck. Upon activation of the receptor kinase, the SH2 domain of Nck binds to one of its tyrosine residues, while Nck SH3 domains interact with the proline-rich domain of Caskin1. Complex formation of the receptor, adaptor and scaffold proteins results in the tyrosine phosphorylation of Caskin1 on its SH3 domain. The phosphorylation sites were identified by mass-spectrometry as tyrosines 296 and 336. To reveal the structural consequence of this phosphorylation, CD spectroscopy was performed. This measurement suggests that upon tyrosine phosphorylation the structure of the Caskin1 SH3 domain changes significantly.

Conclusion
Taken together, we propose that the scaffold protein Caskin1 can form a complex with the EphB1 tyrosine kinase via the Nck protein as a linker. Complex formation results in tyrosine phosphorylation of the Caskin1 SH3 domain. Although we were not able to identify any physiological partner of the SH3 domain so far, we could demonstrate that phosphorylation on conserved tyrosine residues results in marked changes in the structure of the SH3 domain.
Chemical vapor-deposited carbon nanofibers on carbon fabric for supercapacitor electrode applications
Authors: Gao Yang , Pandey Gaind P , Turner James , Westgate Charles R , Sammakia Bahgat 
Published: November 2012

Abstract
Entangled carbon nanofibers (CNFs) were synthesized on a flexible carbon fabric (CF) via water-assisted chemical vapor deposition at 800°C at atmospheric pressure utilizing iron (Fe) nanoparticles as catalysts, ethylene (C2H4) as the precursor gas, and argon (Ar) and hydrogen (H2) as the carrier gases. Scanning electron microscopy, transmission electron microscopy, and electron dispersive spectroscopy were employed to characterize the morphology and structure of the CNFs. It has been found that the catalyst (Fe) thickness affected the morphology of the CNFs on the CF, resulting in different capacitive behaviors of the CNF/CF electrodes. Two different Fe thicknesses (5 and 10 nm) were studied. The capacitance behaviors of the CNF/CF electrodes were evaluated by cyclic voltammetry measurements. The highest specific capacitance, approximately 140 F g−1, has been obtained in the electrode grown with the 5-nm thickness of Fe. Samples with both Fe thicknesses showed good cycling performance over 2,000 cycles.
CuInS2 quantum dot-sensitized TiO2 nanorod array photoelectrodes: synthesis and performance optimization
Authors: Zhou Zhengji , Yuan Shengjie , Fan Junqi , Hou Zeliang , Zhou Wenhui , Du Zuliang , Wu Sixin 
Published: November 2012

Abstract
CuInS2 quantum dots (QDs) were deposited onto TiO2 nanorod arrays for different cycles by using successive ionic layer adsorption and reaction (SILAR) method. The effect of SILAR cycles on the light absorption and photoelectrochemical properties of the sensitized photoelectrodes was studied. With optimization of CuInS2 SILAR cycles and introduction of In2S3 buffer layer, quantum dot-sensitized solar cells assembled with 3-μm thick TiO2 nanorod film exhibited a short-circuit current density (I
sc) of 4.51 mA cm−2, an open-circuit voltage (V
oc) of 0.56 V, a fill factor (FF) of 0.41, and a power conversion efficiency (η) of 1.06%, respectively. This study indicates that SILAR process is a very promising strategy for preparing directly anchored semiconductor QDs on TiO2 nanorod surface in a straightforward but controllable way without any complicated fabrication procedures and introduction of a linker molecule.
Photocatalytic degradation of 4-chlorophenol by UV/H2O2/NiO process in aqueous solution
Authors: Alimoradzadeh Roya , Assadi Ali , Nasseri Simin , Mehrasbi Mohammad Reza 
Published: November 2012

Abstract
The removal of 4-chlorophenol from aqueous phase continues to be an important environmental issue. In this work, the photochemical oxidation of 4-chlorophenol in aqueous solutions in a batch reactor using ultraviolet irradiation, hydrogen peroxide and nickel oxide was studied. The efficiency of the system was evaluated with respect to reaction time, pH, feed concentration of reactants, catalyst load, light intensity, and the reaction rate constant. The concentrations of 4-chlorophenol and chloride ions were determined by high performance liquid chromatography and ion chromatography, respectively. Pure nanosized nickel oxide was characterized by X-ray diffraction and scanning electron microscopy. The results showed that the optimum conditions (the complete 4-chlorophenol removal (100%) at 60 min) were obtained at a neutral pH, with 0.2 mol/L H2O2, and 0.05 g/L of nickel oxide. However, no pH effects were observed in the range of 4–10. Analytical profiles on 4-chlorophenol transformation were consistent with the best line fit of the first-order kinetics. Moreover, the degradation rate constant increased with both UV light intensity and decreasing initial concentration of 4-chlorophenol. Finally, the results of mineralization and chloride ions studies indicated that dechlorination was better accomplished but more time was required to completely mineralize 4-chlorophenol into water and carbon dioxide.
Isolation of avian influenza H5N1 virus from vaccinated commercial layer flock in Egypt
Authors: El-Zoghby Elham F , Arafa Abdel-Satar , Kilany Walid H , Aly Mona M , Abdelwhab Elsayed M , Hafez Hafez M 
Published: November 2012

Abstract

Background
Uninterrupted transmission of highly pathogenic avian influenza virus (HPAIV) H5N1 of clade 2.2.1 in Egypt since 2006 resulted in establishment of two main genetic clusters. The 2.2.1/C group where all recent human and majority of backyard origin viruses clustered together, meanwhile the majority of viruses derived from vaccinated poultry in commercial farms grouped in 2.2.1.1 clade.

Findings
In the present investigation, an HPAIV H5N1 was isolated from twenty weeks old layers chickens that were vaccinated with a homologous H5N1 vaccine at 1, 7 and 16 weeks old. At twenty weeks of age, birds showed cyanosis of comb and wattle, decrease in egg production and up to 27% mortality. Examined serum samples showed low antibody titer in HI test (Log2 3.2± 4.2). The hemagglutinin (HA) and neuraminidase (NA) genes of the isolated virus were closely related to viruses in 2.2.1/C group isolated from poultry in live bird market (LBM) and backyards or from infected people. Conspicuous mutations in the HA and NA genes including a deletion within the receptor binding domain in the HA globular head region were observed.

Conclusions
Despite repeated vaccination of layer chickens using a homologous H5N1 vaccine, infection with HPAIV H5N1 resulted in significant morbidity and mortality. In endemic countries like Egypt, rigorous control measures including enforcement of biosecurity, culling of infected birds and constant update of vaccine virus strains are highly required to prevent circulation of HPAIV H5N1 between backyard birds, commercial poultry, LBM and humans.
Transcriptome analysis of symptomatic and recovered leaves of geminivirus-infected pepper (Capsicum annuum)
Authors: Góngora-Castillo Elsa , Ibarra-Laclette Enrique , Trejo-Saavedra Diana L , Rivera-Bustamante Rafael F 
Published: November 2012

AbstractBackgroundGeminiviruses are a large and important family of plant viruses that infect a wide range of crops throughout the world. TheBegomovirusgenus contains species that are transmitted by whiteflies and are distributed worldwide causing disease on an array of horticultural crops. Symptom remission, in which newly developed leaves of systemically infected plants exhibit a reduction in symptom severity (recovery), has been observed on pepper (Capsicum annuum) plants infected withPepper golden mosaic virus(PepGMV). Previous studies have shown that transcriptional and post-transcriptional gene silencing mechanisms are involved in the reduction of viral nucleic acid concentration in recovered tissue. In this study, we employed deep transcriptome sequencing methods to assess transcriptional variation in healthy (mock), symptomatic, and recovered pepper leaves following PepGMV infection.ResultsDifferential expression analyses of the pepper leaf transcriptome from symptomatic and recovered stages revealed a total of 309 differentially expressed genes between healthy (mock) and symptomatic or recovered tissues. Computational prediction of differential expression was validated using quantitative reverse-transcription PCR confirming the robustness of our bioinformatic methods. Within the set of differentially expressed genes associated with the recovery process were genes involved in defense responses including pathogenesis-related proteins, reactive oxygen species, systemic acquired resistance, jasmonic acid biosynthesis, and ethylene signaling. No major differences were found when compared the differentially expressed genes in symptomatic and recovered tissues. On the other hand, a set of genes with novel roles in defense responses was identified including genes involved in histone modification. This latter result suggested that post-transcriptional and transcriptional gene silencing may be one of the major mechanisms involved in the recovery process. Genes orthologous to theC. annuumproteins involved in the pepper-PepGMV recovery response were identified in bothSolanum lycopersicumandSolanum tuberosumsuggesting conservation of components of the viral recovery response in the Solanaceae.ConclusionThese data provide a valuable source of information for improving our understanding of the underlying molecular mechanisms by which pepper leaves become symptomless following infection with geminiviruses. The identification of orthologs for the majority of genes differentially expressed in recovered tissues in two major solanaceous crop species provides the basis for future comparative analyses of the viral recovery process across related taxa.
Green tea powder and Lactobacillus plantarum affect gut microbiota, lipid metabolism and inflammation in high-fat fed C57BL/6J mice
Authors: Axling Ulrika , Olsson Crister , Xu Jie , Fernandez Céline , Larsson Sara , Ström Kristoffer , Ahrné Siv , Holm Cecilia , Molin Göran , Berger Karin 
Published: November 2012

Abstract

Background
Type 2 diabetes is associated with obesity, ectopic lipid accumulation and low-grade inflammation. A dysfunctional gut microbiota has been suggested to participate in the pathogenesis of the disease. Green tea is rich in polyphenols and has previously been shown to exert beneficial metabolic effects. Lactobacillus plantarum has the ability to metabolize phenolic acids. The health promoting effect of whole green tea powder as a prebiotic compound has not been thoroughly investigated previously.

Methods
C57BL/6J mice were fed a high-fat diet with or without a supplement of 4% green tea powder (GT), and offered drinking water supplemented with Lactobacillus plantarum DSM 15313 (Lp) or the combination of both (Lp + GT) for 22 weeks. Parameters related to obesity, glucose tolerance, lipid metabolism, hepatic steatosis and inflammation were examined. Small intestinal tissue and caecal content were collected for bacterial analysis.

Results
Mice in the Lp + GT group had significantly more Lactobacillus and higher diversity of bacteria in the intestine compared to both mice in the control and the GT group. Green tea strongly reduced the body fat content and hepatic triacylglycerol and cholesterol accumulation. The reduction was negatively correlated to the amount of Akkermansia and/or the total amount of bacteria in the small intestine. Markers of inflammation were reduced in the Lp + GT group compared to control. PLS analysis of correlations between the microbiota and the metabolic variables of the individual mice showed that relatively few components of the microbiota had high impact on the correlation model.

Conclusions
Green tea powder in combination with a single strain of Lactobacillus plantarum was able to promote growth of Lactobacillus in the intestine and to attenuate high fat diet-induced inflammation. In addition, a component of the microbiota, Akkermansia, correlated negatively with several metabolic parameters known to be risk factors for the development of type 2 diabetes.
Critical role of surface chemical modifications induced by length shortening on multi-walled carbon nanotubes-induced toxicity
Authors: Bussy Cyrill , Pinault Mathieu , Cambedouzou Julien , Landry Marion Julie , Jegou Pascale , Mayne-L'hermite Martine , Launois Pascale , Boczkowski Jorge , Lanone Sophie 
Published: November 2012

Abstract
Given the increasing use of carbon nanotubes (CNT) in composite materials and their possible expansion to new areas such as nanomedicine which will both lead to higher human exposure, a better understanding of their potential to cause adverse effects on human health is needed. Like other nanomaterials, the biological reactivity and toxicity of CNT were shown to depend on various physicochemical characteristics, and length has been suggested to play a critical role. We therefore designed a comprehensive study that aimed at comparing the effects on murine macrophages of two samples of multi-walled CNT (MWCNT) specifically synthesized following a similar production process (aerosol-assisted CVD), and used a soft ultrasonic treatment in water to modify the length of one of them. We showed that modification of the length of MWCNT leads, unavoidably, to accompanying structural (i.e. defects) and chemical (i.e. oxidation) modifications that affect both surface and residual catalyst iron nanoparticle content of CNT. The biological response of murine macrophages to the two different MWCNT samples was evaluated in terms of cell viability, pro-inflammatory cytokines secretion and oxidative stress. We showed that structural defects and oxidation both induced by the length reduction process are at least as responsible as the length reduction itself for the enhanced pro-inflammatory and pro-oxidative response observed with short (oxidized) compared to long (pristine) MWCNT. In conclusion, our results stress that surface properties should be considered, alongside the length, as essential parameters in CNT-induced inflammation, especially when dealing with a safe design of CNT, for application in nanomedicine for example.
Pyrosequencing of 16S rRNA genes in fecal samples reveals high diversity of hindgut microflora in horses and potential links to chronic laminitis
Authors: Steelman Samantha M , Chowdhary Bhanu P , Dowd Scot , Suchodolski Jan , Janečka Jan E 
Published: November 2012

Abstract

Background
The nutrition and health of horses is closely tied to their gastrointestinal microflora. Gut bacteria break down plant structural carbohydrates and produce volatile fatty acids, which are a major source of energy for horses. Bacterial communities are also essential for maintaining gut homeostasis and have been hypothesized to contribute to various diseases including laminitis. We performed pyrosequencing of 16S rRNA bacterial genes isolated from fecal material to characterize hindgut bacterial communities in healthy horses and those with chronic laminitis.

Results
Fecal samples were collected from 10 normal horses and 8 horses with chronic laminitis. Genomic DNA was extracted and the V4-V5 segment of the 16S rRNA gene was PCR amplified and sequenced on the 454 platform generating a mean of 2,425 reads per sample after quality trimming. The bacterial communities were dominated by Firmicutes (69.21% control, 56.72% laminitis) and Verrucomicrobia (18.13% control, 27.63% laminitis), followed by Bacteroidetes, Proteobacteria, and Spirochaetes. We observed more OTUs per individual in the laminitis group than the control group (419.6 and 355.2, respectively, P = 0.019) along with a difference in the abundance of two unassigned Clostridiales genera (P = 0.03 and P = 0.01). The most abundant bacteria were Streptococcus spp., Clostridium spp., and Treponema spp.; along with unassigned genera from Subdivision 5 of Verrucomicrobia, Ruminococcaceae, and Clostridiaceae, which together constituted ~ 80% of all OTUs. There was a high level of individual variation across all taxonomic ranks.

Conclusions
Our exploration of the equine fecal microflora revealed higher bacterial diversity in horses with chronic laminitis and identification of two Clostridiales genera that differed in abundance from control horses. There was large individual variation in bacterial communities that was not explained in our study. The core hindgut microflora was dominated by Streptococcus spp., several cellulytic genera, and a large proportion of uncharacterized OTUs that warrant further investigation regarding their function. Our data provide a foundation for future investigations of hindgut bacterial factors that may influence the development and progression of chronic laminitis.
Community member perspectives from transgender women and men who have sex with men on pre-exposure prophylaxis as an HIV prevention strategy: implications for implementation
Authors: Galindo Gabriel R. , Garrett-Walker J. J. , Hazelton Patrick , Lane Tim , Steward Wayne T. , Morin Stephen F. , Arnold Emily A. 
Published: November 2012

Abstract
Background
An international randomized clinical trial (RCT) on pre-exposure prophylaxis (PrEP) as an human immunodeficiency virus (HIV)-prevention intervention found that taken on a daily basis, PrEP was safe and effective among men who have sex with men (MSM) and male-to-female transgender women. Within the context of the HIV epidemic in the United States (US), MSM and transgender women are the most appropriate groups to target for PrEP implementation at the population level; however, their perspectives on evidenced-based biomedical research and the results of this large trial remain virtually unknown. In this study, we examined the acceptability of individual daily use of PrEP and assessed potential barriers to community uptake.

Methods
We conducted semi-structured interviews with an ethnoracially diverse sample of thirty HIV-negative and unknown status MSM (n = 24) and transgender women (n = 6) in three California metropolitan areas. Given the burden of disease among ethnoracial minorities in the US, we purposefully oversampled for these groups. Thematic coding and analysis of data was conducted utilizing an approach rooted in grounded theory.

Results
While participants expressed general interest in PrEP availability, results demonstrate: a lack of community awareness and confusion about PrEP; reservations about PrEP utilization, even when informed of efficacious RCT results; and concerns regarding equity and the manner in which a PrEP intervention could be packaged and marketed in their communities.

Conclusions
In order to effectively reduce HIV health disparities at the population level, PrEP implementation must take into account the uptake concerns of those groups who would actually access and use this biomedical intervention as a prevention strategy. Recommendations addressing these concerns are provided.
An array CGH based genomic instability index (G2I) is predictive of clinical outcome in breast cancer and reveals a subset of tumors without lymph node involvement but with poor prognosis
Authors: Bonnet Françoise , Guedj Mickael , Jones Natalie , Sfar Sana , Brouste Véronique , Elarouci Nabila , Banneau Guillaume , Orsetti Béatrice , Primois Charlotte , de Lara Christine Tunon , Debled Marc , de Mascarel Isabelle , Theillet Charles , Sévenet Nicolas , de Reynies Aurélien , MacGrogan Gaëtan , Longy Michel 
Published: November 2012

Abstract

Background
Despite entering complete remission after primary treatment, a substantial proportion of patients with early stage breast cancer will develop metastases. Prediction of such an outcome remains challenging despite the clinical use of several prognostic parameters. Several reports indicate that genomic instability, as reflected in specific chromosomal aneuploidies and variations in DNA content, influences clinical outcome but no precise definition of this parameter has yet been clearly established.

Methods
To explore the prognostic value of genomic alterations present in primary tumors, we performed a comparative genomic hybridization study on BAC arrays with a panel of breast carcinomas from 45 patients with metastatic relapse and 95 others, matched for age and axillary node involvement, without any recurrence after at least 11 years of follow-up. Array-CGH data was used to establish a two-parameter index representative of the global level of aneusomy by chromosomal arm, and of the number of breakpoints throughout the genome.

Results
Application of appropriate thresholds allowed us to distinguish three classes of tumors highly associated with metastatic relapse. This index used with the same thresholds on a published set of tumors confirms its prognostic significance with a hazard ratio of 3.24 [95CI: 1.76-5.96] p = 6.7x10-5 for the bad prognostic group with respect to the intermediate group. The high prognostic value of this genomic index is related to its ability to individualize a specific group of breast cancers, mainly luminal type and axillary node negative, showing very high genetic instability and poor outcome. Indirect transcriptomic validation was obtained on independent data sets.

Conclusion
Accurate evaluation of genetic instability in breast cancers by a genomic instability index (G2I) helps individualizing specific tumors with previously unexpected very poor prognosis.