bluuebunny/crossref_metadata_2025_split huggingface dataset:
Side chain requirements for affinity and specificity in D5, an HIV-1 antibody derived from the VH1-69 germline segment
Authors: Stewart Alex , Harrison Joseph S , Regula Lauren K , Lai Jonathan R 
Published: April 2013

AbstractBackgroundAnalysis of factors contributing to high affinity antibody-protein interactions provides insight into natural antibody evolution, and guides the design of antibodies with new or enhanced function. We previously studied the interaction between antibody D5 and its target, a designed protein based on HIV-1 gp41 known as 5-Helix, as a model system [Da Silva, G. F.; Harrison, J. S.; Lai, J. R., Biochemistry, 2010, 49, 5464–5472]. Antibody D5 represents an interesting case study because it is derived from the VH1-69 germline segment; this germline segment is characterized by a hydrophobic second heavy chain complementarity determining region (HCDR2) that constitutes the major functional paratope in D5 and several antibodies derived from the same progenitor.ResultsHere we explore side chain requirements for affinity and specificity in D5 using phage display. Two D5-based libraries were prepared that contained diversity in all three light chain complementarity determining regions (LCDRs 1–3), and in the third HCDR (HCDR3). The first library allowed residues to vary among a restricted set of six amino acids (Tyr/Ala/Asp/Ser/His/Pro; D5-Lib-I). The second library was designed based on a survey of existing VH1-69 antibody structures (D5-Lib-II). Both libraries were subjected to multiple rounds of selection against 5-Helix, and individual clones characterized. We found that selectants from D5-Lib-I generally had moderate affinity and specificity, while many clones from D5-Lib-II exhibited D5-like properties. Additional analysis of the D5-Lib-II functional population revealed position-specific biases for particular amino acids, many that differed from the identity of those side chains in D5.ConclusionsTogether these results suggest that there is some permissiveness for alternative side chains in the LCDRs and HCDR3 of D5, but that replacement with a minimal set of residues is not tolerated in this scaffold for 5-Helix recognition. This work provides novel information about this high-affinity interaction involving an antibody from the VH1-69 germline segment.
High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity
Authors: Granados-Cifuentes Camila , Bellantuono Anthony J , Ridgway Tyrone , Hoegh-Guldberg Ove , Rodriguez-Lanetty Mauricio 
Published: April 2013

Abstract

Background
Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global warming. Studies to date have focused on determining genetic diversity, the sequence variability of genes in a species, as a proxy to estimate and predict the potential adaptive response of coral populations to environmental changes linked to climate changes. However, the examination of natural gene expression variation has received less attention. This variation has been implicated as an important factor in evolutionary processes, upon which natural selection can act.

Results
We acclimatized coral nubbins from six colonies of the reef-building coral Acropora millepora to a common garden in Heron Island (Great Barrier Reef, GBR) for a period of four weeks to remove any site-specific environmental effects on the physiology of the coral nubbins. By using a cDNA microarray platform, we detected a high level of gene expression variation, with 17% (488) of the unigenes differentially expressed across coral nubbins of the six colonies (jsFDR-corrected, p < 0.01). Among the main categories of biological processes found differentially expressed were transport, translation, response to stimulus, oxidation-reduction processes, and apoptosis. We found that the transcriptional profiles did not correspond to the genotype of the colony characterized using either an intron of the carbonic anhydrase gene or microsatellite loci markers.

Conclusion
Our results provide evidence of the high inter-colony variation in A. millepora at the transcriptomic level grown under a common garden and without a correspondence with genotypic identity. This finding brings to our attention the importance of taking into account natural variation between reef corals when assessing experimental gene expression differences. The high transcriptional variation detected in this study is interpreted and discussed within the context of adaptive potential and phenotypic plasticity of reef corals. Whether this variation will allow coral reefs to survive to current challenges remains unknown.
Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array
Authors: Liu Jiasen , Zhang Li , Xu Lingyang , Ren Hangxing , Lu Jian , Zhang Xiaoning , Zhang Shifang , Zhou Xinlei , Wei Caihong , Zhao Fuping , Du Lixin 
Published: April 2013

Abstract

Background
In recent years, genome-wide association studies have successfully uncovered single-nucleotide polymorphisms (SNPs) associated with complex traits such as diseases and quantitative phenotypes. These variations account for a small proportion of heritability. With the development of high throughput techniques, abundant submicroscopic structural variations have been found in organisms, of which the main variations are copy number variations (CNVs). Therefore, CNVs are increasingly recognized as an important and abundant source of genetic variation and phenotypic diversity.

Results
Analyses of CNVs in the genomes of three sheep breeds were performed using the Ovine SNP50 BeadChip array. A total of 238 CNV regions (CNVRs) were identified, including 219 losses, 13 gains, and six with both events (losses and gains), which cover 60.35 Mb of the sheep genomic sequence and correspond to 2.27% of the autosomal genome sequence. The length of the CNVRs on autosomes range from 13.66 kb to 1.30 Mb with a mean size of 253.57 kb, and 75 CNVRs events had a frequency > 3%. Among these CNVRs, 47 CNVRs identified by the PennCNV overlapped with the CNVpartition. Functional analysis indicated that most genes in the CNVRs were significantly enriched for involvement in the environmental response. Furthermore, 10 CNVRs were selected for validation and 6 CNVRs were further experimentally confirmed by qPCR. In addition, there were 57 CNVRs overlapped in our new dataset and other published ruminant CNV studies.

Conclusions
In this study, we firstly constructed a sheep CNV map based on the Ovine SNP50 array. Our results demonstrated the differences of two detection tools and integration of multiple algorithms can enhance the detection of sheep genomic structure variations. Furthermore, our findings would be of help for understanding the sheep genome and provide preliminary foundation for carrying out the CNVs association studies with economically important phenotypes of sheep in the future.
Life threatening intracerebral haemorrhage following saw- scaled viper (Echis carinatus) envenoming-authenticated case report from Sri Lanka
Authors: Fonseka Chathuranga Lakmal , Jeevagan Vijayabala , Gnanathasan Christeine Ariaranee 
Published: April 2013

Abstract

Background

Echis carinatus (Saw scaled viper {SSV}) is a venomous snake found in the parts of Middle East and Central Asia. SSV envenoming is characterized by local swelling and coagulopathy. Various bleeding manifestations are commonly seen with SSV envenoming. In contrast to other part of Asia, saw scale viper envenoming has not been reported to cause life threatening haemorrhagic manifestations in Sri Lanka.

Case presentation
We report a 19 years old healthy boy who developed massive left temporo-parietal intra cerebral haemorrhage following Echis carinatus (Saw scaled viper) bite in Sri Lanka.

Conclusion
Although subspecies of SSV in Sri Lanka is regarded as a ‘non lethal venomous snake’, the occurrence of rare potentially fatal complications such as intracerebral haemorrhage should be considered in their management. This case report is intended to bring the awareness of this fatal complication of SSV envenoming in Sri Lanka.
Transarterial chemoembolization for hepatocellular carcinoma with portal vein tumor thrombus: a meta-analysis
Authors: Xue Tong-Chun , Xie Xiao-Ying , Zhang Lan , Yin Xin , Zhang Bo-Heng , Ren Zheng-Gang 
Published: April 2013

Abstract

Background
Although transarterial chemoembolization (TACE) has been used extensively for advanced hepatocellular carcinoma (HCC) with portal vein tumor thrombus (PVTT), no consensus has been reached and an evidence base for practice is lacking. This meta-analysis evaluated the efficacy and safety of TACE for treatment of HCC with PVTT.

Methods
Ovid Medline, EMBASE, Web of Knowledge, and Cochrane library databases were searched up to August 2012 for controlled trials assessing TACE in patients with PVTT. Data concerning the study design, characteristics of trials, and outcomes were extracted. Hazard ratio (HR) and 95% confidence interval (CI) were calculated using random effects models.

Results
Eight controlled trials involving 1601 HCC patients were included. TACE significantly improved the 6-month (HR, 0.41; 95% CI: 0.32–0.53; z, 6.28; p = 0.000) and 1-year (HR, 0.44; 95% CI: 0.34–0.57; z, 6.22; p = 0.000) overall survival of patients with PVTT compared with conservative treatment. Subgroup analyses showed that TACE was significantly effective in HCC patients whether with main portal vein (MPV) obstruction or with segmental PVTT. Fatal complications were rare, even in patients with MPV obstruction. Temporary liver decompensation and postembolization syndrome occurred frequently. However, they could be treated successfully with conservative treatment.

Conclusions
TACE, as a safe treatment, has potential for incurring a survival benefit for advanced HCC with PVTT, even with MPV obstruction. Further large randomized controlled trials may be needed to confirm this result.
Possible role of Escherichia coli in propagation and perpetuation of chronic inflammation in ulcerative colitis
Authors: Pilarczyk-Zurek Magdalena , Chmielarczyk Agnieszka , Gosiewski Tomasz , Tomusiak Anna , Adamski Pawel , Zwolinska-Wcislo Malgorzata , Mach Tomasz , Heczko Piotr B , Strus Magdalena 
Published: April 2013

Abstract

Background
This study investigated a possible role of Escherichia coli in propagation and perpetuation of the chronic inflammation in ulcerative colitis (UC). The lesions of UC are located superficially on the rectal and/or colonic mucosa. It is suggested that the commensal bacteria of the digestive tract may play a role in the pathogenesis of UC. Several studies have demonstrated proliferation of E. coli in the gut of UC patients. An increase in the number of E. coli in the inflamed tissue is most probably related to the abundance of iron ions produced by the bacteria.

Methods
Colon mucosal biopsies were collected from 30 patients with acute-phase UC, both from tissues with inflammatory changes (n = 30) and unchanged tissue with no inflammatory changes (n = 30) from the same patient. Biopsies were also taken from 16 patients with irritable bowel syndrome diarrhea who comprised the control group. Quantitative and qualitative analysis of the biopsy specimens was performed using culture methods and real-time polymerase chain reaction (PCR). Genotyping of the E. coli isolates was done using pulsed-field gel electrophoresis. Multiplex PCR was used to compare the E. coli strains for the presence of genes responsible for synthesis of iron acquisition proteins: iroN, iutA, iha, ireA, chuA, and hlyA.

Results
We demonstrated that there was a significant increase in the number of E. coli at the sites of inflammation in patients with UC compared to the control group (P = 0.031). Comparative analysis of the restriction patterns of E. coli isolated from inflammatory and unchanged tissues showed that the local inflammatory changes did not promote specific E. coli strains. There was a significant difference in the frequency of the iroN gene in E. coli isolated from patients with UC as compared to the control group.

Conclusions
The increase in the numbers of E. coli in the inflammatory tissues is related to the presence of chuA and iutA genes, which facilitate iron acquisition during chronic intestinal inflammatory processes.
RETRACTED ARTICLE: Correlation of CD44v6 expression with ovarian cancer progression and recurrence
Authors: Shi Jun , Zhou Zhou , Di Wen , Li Ningli 
Published: April 2013

Abstract

Background
Previously some groups demonstrated that CD44 variant 6 (CD44v6) is correlated with progression and metastasis of ovarian cancer. However, a number of other groups failed to find such an association. Moreover, epithelial ovarian cancer is known to easily metastasize to distinct sites such as the pelvic and abdominal cavities, but the potential association of CD44v6 expression with site-specific metastasis of ovarian cancer has not been explored. This study sought to evaluate the expression of CD44 standard (CD44s) and CD44v6 in primary, metastatic and recurrent epithelial ovarian cancer to explore the potential association of CD44s and CD44v6 with tumor progression and recurrence.

Methods
Tumor specimens were procured from patients with advanced (FIGO III, G3) and recurrent ovarian serous adenocarcinoma. CD44s and CD44v6 expression in the tumor tissues was evaluated by real-time RT-PCR and Western blot. Moreover, serum soluble CD44s or CD44v6 concentrations of early stage (FIGO I, G1), advanced (FIGO III, G3) and recurrent ovarian serous adenocarcinoma patients were determined by enzyme-linked immunosorbent assays (ELISA). CD44v6 expression in a different set of tumor samples on an ovarian cancer tissue chip was evaluated by immunohistochemistry (IHC) and the correlation of CD44v6 expression with clinicopathologic features was analyzed. Finally, the effects of knockdown of CD44v6 in SKOV3 cells on cell adhesion, invasion and migration were assessed.

Results
The expression of CD44v6, but not CD44s, is up-regulated in recurrent ovarian serous cancer compared to advanced primary tumor. CD44v6 expression is also preferentially increased in the tumor at the abdominal cavity metastasis site of advanced diseases. Consistently, serum soluble CD44v6 levels of recurrent ovarian cancer were higher than those of early stage and advanced primary diseases. The IHC data demonstrate that CD44v6 expression is correlated with clinicopathologic features and tumor progression. Lastly, knockdown of CD44v6 decreases the adhesion and migration but not invasion capacities of SKOV3 cells.

Conclusions
CD44v6 expression levels are associated with epithelial ovarian cancer progression, metastasis and relapse. Moreover, serum soluble CD44v6 may be used as a potential marker for identifying tumor relapse. Finally, CD44v6 may play a role in ovarian cancer metastasis by mediating tumor cell adhesion and migration.
Sharing good NEWS across the world: developing comparable scores across 12 countries for the neighborhood environment walkability scale (NEWS)
Authors: Cerin Ester , Conway Terry L , Cain Kelli L , Kerr Jacqueline , De Bourdeaudhuij Ilse , Owen Neville , Reis Rodrigo S , Sarmiento Olga L , Hinckson Erica A , Salvo Deborah , Christiansen Lars B , MacFarlane Duncan J , Davey Rachel , Mitáš Josef , Aguinaga-Ontoso Ines , Sallis James F 
Published: April 2013

Abstract

Background
The IPEN (International Physical Activity and Environment Network) Adult project seeks to conduct pooled analyses of associations of perceived neighborhood environment, as measured by the Neighborhood Environment Walkability Scale (NEWS) and its abbreviated version (NEWS-A), with physical activity using data from 12 countries. As IPEN countries used adapted versions of the NEWS/NEWS-A, this paper aimed to develop scoring protocols that maximize cross-country comparability in responses. This information is also highly relevant to non-IPEN studies employing the NEWS/NEWS-A, which is one of the most popular measures of perceived environment globally.

Methods
The following countries participated in the IPEN Adult study: Australia, Belgium, Brazil, Colombia, Czech Republic, Denmark, Hong Kong, Mexico, New Zealand, Spain, the United Kingdom, and the United States. Participants (N = 14,305) were recruited from neighborhoods varying in walkability and socio-economic status. Countries collected data on the perceived environment using a self- or interviewer-administered version of the NEWS/NEWS-A. Confirmatory Factor Analysis (CFA) was used to derive comparable country-specific measurement models of the NEWS/NEWS-A. The level of correspondence between standard and alternative versions of the NEWS/NEWS-A factor-analyzable subscales was determined by estimating the correlations and mean standardized difference (Cohen’s d) between them using data from countries that had included items from both standard and alternative versions of the subscales.

Results
Final country-specific measurement models of the NEWS/NEWS-A provided acceptable levels of fit to the data and shared the same factorial structure with six latent factors and two single items. The correspondence between the standard and alternative versions of subscales of Land use mix – access, Infrastructure and safety for walking/cycling, and Aesthetics was high. The Brazilian version of the Traffic safety subscale was highly, while the Australian and Belgian versions were marginally, comparable to the standard version. Single-item versions of the Street connectivity subscale used in Australia and Belgium showed marginally acceptable correspondence to the standard version.

Conclusions
We have proposed country-specific modifications to the original scoring protocol of the NEWS/NEWS-A that enhance inter-country comparability. These modifications have yielded sufficiently equivalent measurement models of the NEWS/NEWS-A. Some inter-country discrepancies remain. These need to be considered when interpreting findings from different countries.
Vildagliptin in addition to metformin improves retinal blood flow and erythrocyte deformability in patients with type 2 diabetes mellitus – results from an exploratory study
Authors: Berndt-Zipfel Christine , Michelson Georg , Dworak Markus , Mitry Michael , Löffler Andrea , Pfützner Andreas , Forst Thomas 
Published: April 2013

Abstract
Numerous rheological and microvascular alterations characterize the vascular pathology in patients with type 2 diabetes mellitus (T2DM). This study investigated effects of vildagliptin in comparison to glimepiride on retinal microvascular blood flow and erythrocyte deformability in T2DM.
Fourty-four patients with T2DM on metformin monotherapy were included in this randomized, exploratory study over 24 weeks. Patients were randomized to receive either vildagliptin (50 mg twice daily) or glimepiride individually titrated up to 4 mg in addition to ongoing metformin treatment. Retinal microvascular blood flow (RBF) and the arteriolar wall to lumen ratio (WLR) were assessed using a laser doppler scanner. In addition, the erythrocyte elongation index (EI) was measured at different shear stresses using laserdiffractoscopy.
Both treatments improved glycaemic control (p < 0.05 vs. baseline; respectively). While only slight changes in RBF and the WLR could be observed during treatment with glimepiride, vildagliptin significantly increased retinal blood flow and decreased the arterial WLR (p < 0.05 vs. baseline respectively). The EI increased during both treatments over a wide range of applied shear stresses (p < 0.05 vs. baseline). An inverse correlation could be observed between improved glycaemic control (HbA1c) and EI (r = −0.524; p < 0.0001) but not with the changes in retinal microvascular measurements.
Our results suggest that vildagliptin might exert beneficial effects on retinal microvascular blood flow beyond glucose control. In contrast, the improvement in erythrocyte deformability observed in both treatment groups, seems to be a correlate of improved glycaemic control.
Blood pressure and endothelial function in healthy, pregnant women after acute and daily consumption of flavanol-rich chocolate: a pilot, randomized controlled trial
Authors: Mogollon Jaime Andres , Bujold Emmanuel , Lemieux Simone , Bourdages Mélodie , Blanchet Claudine , Bazinet Laurent , Couillard Charles , Noël Martin , Dodin Sylvie 
Published: April 2013

Abstract

Background
Several randomized clinical trials (RCTs) indicate that flavanol-rich chocolate has beneficial effects on flow-mediated dilation (FMD) and blood pressure (BP). However, no RCTs have evaluated these outcomes in pregnant women. The objective of this 2-group, parallel, double-blind RCT was to examine the effects of flavanol-rich chocolate on FMD and BP in pregnant women with normal BP.

Methods
Forty-four healthy, pregnant women were randomized to the high-flavanol (n = 23) or low-flavanol (n = 21) chocolate consumption for 12 weeks. At randomization (0, 60, 120 and 180 min after a single 40-g dose of chocolate), 6 and 12 weeks after daily 20-g chocolate intake, we evaluated plasma concentrations of flavanols and theobromine, as well as the FMD and BP.

Results
Plasma epicatechin was significantly increased (p < 0.001) 180 min after the consumption of 40-g high-flavanol chocolate compared to low-flavanol chocolate. Theobromine concentrations were significantly higher 180 min and 12 weeks after the intake of experimental chocolate or low-flavanol chocolate (p < 0.001). FMD was not different between the 2 groups at all pre-defined time periods. No other significant within-group or between-group changes were observed.

Conclusion
These results confirm the feasibility of a large-scale RCT comparing daily consumption of flavanol-rich chocolate to an equivalent placebo during pregnancy and demonstrate higher plasma epicatechin and theobromine concentration in the intervention group after acute ingestion

Trial registration
ClinicalTrials.gov Identifier: NCT01659060
Growth and optical properties of ZnO nanorod arrays on Al-doped ZnO transparent conductive film
Authors: Lin Suanzhi , Hu Hailong , Zheng Weifeng , Qu Yan , Lai Fachun 
Published: April 2013

Abstract
ZnO nanorod arrays (NRAs) on transparent conductive oxide (TCO) films have been grown by a solution-free, catalyst-free, vapor-phase synthesis method at 600°C. TCO films, Al-doped ZnO films, were deposited on quartz substrates by magnetron sputtering. In order to study the effect of the growth duration on the morphological and optical properties of NRAs, the growth duration was changed from 3 to 12 min. The results show that the electrical performance of the TCO films does not degrade after the growth of NRAs and the nanorods are highly crystalline. As the growth duration increases from 3 to 8 min, the diffuse transmittance of the samples decreases, while the total transmittance and UV emission enhance. Two possible nanorod self-attraction models were proposed to interpret the phenomena in the sample with 9-min growth duration. The sample with 8-min growth duration has the highest total transmittance of 87.0%, proper density about 75 μm−2, diameter about 26 nm, and length about 500 nm, indicating that it can be used in hybrid solar cells.
Solvability for a coupled system of fractional differential equations with impulses at resonance
Authors: Zhang Xiaozhi , Zhu Chuanxi , Wu Zhaoqi 
Published: April 2013

Abstract
In this paper, some Banach spaces are introduced. Based on these spaces and the coincidence degree theory, a 2m-point boundary value problem for a coupled system of impulsive fractional differential equations at resonance is considered, and the new criterion on existence is obtained. Finally, an example is also given to illustrate the availability of our main results.

MSC:34A08, 34B10, 34B37.