bluuebunny/crossref_metadata_2025_split huggingface dataset:
Therapeutic efficacy and safety of botulinum toxin type A in trigeminal neuralgia: a systematic review
Authors: Hu Yong , Guan Xiaofei , Fan Lin , Li Mu , Liao Yiteng , Nie Zhiyu , Jin Lingjing 
Published: August 2013

Abstract
Trigeminal neuralgia is a common disorder caused mainly by compression of the trigeminal nerve root by an overlying blood vessel. Pharmacotherapy and surgery are ineffective or unsuitable in many patients. Therefore, other therapeutic modalities have been tried, including injection of botulinum toxin type A (BTX-A). This study aims to systematically review the therapeutic efficacy and safety of BTX-A in trigeminal neuralgia. PubMed, EMBASE, Cochrane Library Clinical Trials and Web of Science from January 1966 to March 2013 were searched with the terms of “botulinum toxin” AND “trigeminal neuralgia”, and references of related articles were traced. Data on the efficacy and safety of BTX-A in this disorder were extracted and analyzed by at least 2 reviewers. Data for individual studies were reported, and pooled data were analyzed if appropriate. Five prospective studies and one double-blind, randomized, placebo-controlled study were identified. Response was achieved in approximately 70-100% of patients, and the mean pain intensity and frequency were reduced by approximately 60-100% at 4 weeks after treatment in most studies. Major adverse events were not reported. Available studies show BTX-A may be effective in treatment of trigeminal neuralgia. However, well-designed randomized, controlled, double-blinded trial is still lacking. Future BTX-A treatment studies on optimal dose, duration of the therapeutic efficacy, common AEs, and the time and indications for repeat injection would be promising.
A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments
Authors: Esnaola Mikel , Puig Pedro , Gonzalez David , Castelo Robert , Gonzalez Juan R 
Published: August 2013

AbstractBackgroundHigh-throughput RNA sequencing (RNA-seq) offers unprecedented power to capture the real dynamics of gene expression. Experimental designs with extensive biological replication present a unique opportunity to exploit this feature and distinguish expression profiles with higher resolution. RNA-seq data analysis methods so far have been mostly applied to data sets with few replicates and their default settings try to provide the best performance under this constraint. These methods are based on two well-known count data distributions: the Poisson and the negative binomial. The way to properly calibrate them with large RNA-seq data sets is not trivial for the non-expert bioinformatics user.ResultsHere we show that expression profiles produced by extensively-replicated RNA-seq experiments lead to a rich diversity of count data distributions beyond the Poisson and the negative binomial, such as Poisson-Inverse Gaussian or Pólya-Aeppli, which can be captured by a more general family of count data distributions called the Poisson-Tweedie. The flexibility of the Poisson-Tweedie family enables a direct fitting of emerging features of large expression profiles, such as heavy-tails or zero-inflation, without the need to alter a single configuration parameter. We provide a software package for R called implementing a new test for differential expression based on the Poisson-Tweedie family. Using simulations on synthetic and real RNA-seq data we show that yieldsP-values that are equally or more accurate than competing methods under different configuration parameters. By surveying the tiny fraction of sex-specific gene expression changes in human lymphoblastoid cell lines, we also show that accurately detects differentially expressed genes in a real large RNA-seq data set with improved performance and reproducibility over the previously compared methodologies. Finally, we compared the results with those obtained from microarrays in order to check for reproducibility.ConclusionsRNA-seq data with many replicates leads to a handful of count data distributions which can be accurately estimated with the statistical model illustrated in this paper. This method provides a better fit to the underlying biological variability; this may be critical when comparing groups of RNA-seq samples with markedly different count data distributions. The package forms part of the Bioconductor project and it is available for download athttp://www.bioconductor.org.
A multiple-alignment based primer design algorithm for genetically highly variable DNA targets
Authors: Brodin Johanna , Krishnamoorthy Mohan , Athreya Gayathri , Fischer Will , Hraber Peter , Gleasner Cheryl , Green Lance , Korber Bette , Leitner Thomas 
Published: August 2013

Abstract

Background
Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to population diversity and primer localization in relatively conserved regions, in addition to recognized constraints typically considered in primer design.

Results
Design constraints include degenerate sites to maximize population coverage, matching of melting temperatures, optimizing de novo sequence length, finding optimal bio-barcodes to allow efficient downstream analyses, and minimizing risk of dimerization. To facilitate primer design addressing these and other constraints, we created a novel computer program (PrimerDesign) that automates this complex procedure. We show its powers and limitations and give examples of successful designs for the analysis of HIV-1 populations.

Conclusions
PrimerDesign is useful for researchers who want to design DNA primers and probes for analyzing highly variable DNA populations. It can be used to design primers for PCR, RT-PCR, Sanger sequencing, next-generation sequencing, and other experimental protocols targeting highly variable DNA samples.
Insights into the European rabbit (Oryctolagus cuniculus) innate immune system: genetic diversity of the toll-like receptor 3 (TLR3) in wild populations and domestic breeds
Authors: Abrantes Joana , Areal Helena , Esteves Pedro J 
Published: August 2013

Abstract

Background
Toll-like receptors (TLRs) belong to the innate immune system and are a major class of pattern recognition receptors representing the first line of the innate immune response. The TLR molecule is structurally composed by an ectodomain that contains leucine rich repeats (LRRs) that interact with pathogen associated molecular patterns (PAMPs), a transmembrane domain and a conserved cytoplasmic domain designated TIR (Toll-IL1 receptor) that is responsible for the intracellular signaling. TLR3 has been associated with the direct recognition of double-stranded viral RNA resulting from viral replication, while TLR7 and TLR8 target single-stranded viral RNA. In the European rabbit (Oryctolagus cuniculus), TLR7 and TLR8 were reported to be absent and pseudogenised, respectively, making TLR3 the only available TLR for the recognition of viral RNA. Thus, the levels of diversity of TLR3 were evaluated in the European rabbit by analysing different genetic backgrounds and exposure to pathogen pressures.

Results
We detected 41 single nucleotide polymorphisms (SNPs) in the coding sequence of TLR3. The highest diversity was observed in the wild populations of Iberian Peninsula, between 22–33 polymorphic positions. In the French population, 18 SNPs were observed and only 4 polymorphic positions were detected in the domestic breeds. 14 non-synonymous substitutions were observed, most of them in the LRR molecules. The remaining were scattered across the transmembrane and TIR domains.

Conclusion
The study of TLR3 in European rabbit populations might be relevant to understand the interplay between RNA viruses and innate immunity. Wild rabbit populations presented more diversity than domestic breeds and other mammals previously studied. This might be linked to the absence of population bottlenecks during their evolution and to the almost inexistence of man-mediated selection. The observed variability might have also been potentiated by the contact of the wild populations with various pathogens. The study of these patterns of variability might reveal scenarios of host-pathogen interaction and identify TLR3 polymorphisms’ that arose due to viral pathogens affecting wild populations.
Novel bioinformatics strategies for prediction of directional sequence changes in influenza virus genomes and for surveillance of potentially hazardous strains
Authors: Iwasaki Yuki , Abe Takashi , Wada Yoshiko , Wada Kennosuke , Ikemura Toshimichi 
Published: August 2013

Abstract

Background
With the remarkable increase of microbial and viral sequence data obtained from high-throughput DNA sequencers, novel tools are needed for comprehensive analysis of the big sequence data. We have developed “Batch-Learning Self-Organizing Map (BLSOM)” which can characterize very many, even millions of, genomic sequences on one plane. Influenza virus is one of zoonotic viruses and shows clear host tropism. Important issues for bioinformatics studies of influenza viruses are prediction of genomic sequence changes in the near future and surveillance of potentially hazardous strains.

Methods
To characterize sequence changes in influenza virus genomes after invasion into humans from other animal hosts, we applied BLSOMs to analyses of mono-, di-, tri-, and tetranucleotide compositions in all genome sequences of influenza A and B viruses and found clear host-dependent clustering (self-organization) of the sequences.

Results
Viruses isolated from humans and birds differed in mononucleotide composition from each other. In addition, host-dependent oligonucleotide compositions that could not be explained with the host-dependent mononucleotide composition were revealed by oligonucleotide BLSOMs. Retrospective time-dependent directional changes of mono- and oligonucleotide compositions, which were visualized for human strains on BLSOMs, could provide predictive information about sequence changes in newly invaded viruses from other animal hosts (e.g. the swine-derived pandemic H1N1/09).

Conclusions
Basing on the host-dependent oligonucleotide composition, we proposed a strategy for prediction of directional changes of virus sequences and for surveillance of potentially hazardous strains when introduced into human populations from non-human sources. Millions of genomic sequences from infectious microbes and viruses have become available because of their medical and social importance, and BLSOM can characterize the big data and support efficient knowledge discovery.
Lack of significant association between mutations of KCNJ10 or FOXI1 and SLC26A4 mutations in pendred syndrome/enlarged vestibular aqueducts
Authors: Landa Priya , Differ Ann-Marie , Rajput Kaukab , Jenkins Lucy , Bitner-Glindzicz Maria 
Published: August 2013

Abstract

Background
Pendred syndrome is a common autosomal recessive disorder causing deafness. Features include sensorineural hearing impairment, goitre, enlarged vestibular aqueducts (EVA) and occasionally Mondini dysplasia. Hearing impairment and EVA may occur in the absence of goitre or thyroid dyshormonogensis in a condition known as non-syndromic EVA. A significant number of patients with Pendred syndrome and non-syndromic EVA show only one mutation in SLC26A4. Two genes, KCNJ10, encoding an inwardly rectifying potassium channel and FOXI1, a transcriptional factor gene, are thought to play a role in the disease phenotypes.

Methods
Using Polymerase Chain Reaction and Sanger sequencing, sixty-eight patients with monoallelic mutations of SLC26A4 were tested for mutations in KCNJ10 and FOXI1.

Results
Two variants were observed in the KCNJ10 gene, p.Arg271Cys in three patients and p.Arg18Gln in one patient; only one variant, p.Arg123Trp was observed in the FOXI1 gene in a single patient. Both p.Arg271Cys and p.Arg18Gln are likely to be polymorphisms as judged by their frequency in the general population.

Conclusion
Therefore we found no evidence for a significant association between mutations of KCNJ10 and FOXI1 with SLC26A4. It was also observed that the variant, p.Arg271Cys in KCNJ10, previously thought to have a protective effect against seizure susceptibility, was found in a patient with Pendred syndrome with co-existing epilepsy.
Sister chromatid cohesion defects are associated with chromosome instability in Hodgkin lymphoma cells
Authors: Sajesh Babu V , Lichtensztejn Zelda , McManus Kirk J 
Published: August 2013

Abstract

Background
Chromosome instability manifests as an abnormal chromosome complement and is a pathogenic event in cancer. Although a correlation between abnormal chromosome numbers and cancer exist, the underlying mechanisms that cause chromosome instability are poorly understood. Recent data suggests that aberrant sister chromatid cohesion causes chromosome instability and thus contributes to the development of cancer. Cohesion normally functions by tethering nascently synthesized chromatids together to prevent premature segregation and thus chromosome instability. Although the prevalence of aberrant cohesion has been reported for some solid tumors, its prevalence within liquid tumors is unknown. Consequently, the current study was undertaken to evaluate aberrant cohesion within Hodgkin lymphoma, a lymphoid malignancy that frequently exhibits chromosome instability.

Methods
Using established cytogenetic techniques, the prevalence of chromosome instability and aberrant cohesion was examined within mitotic spreads generated from five commonly employed Hodgkin lymphoma cell lines (L-1236, KM-H2, L-428, L-540 and HDLM-2) and a lymphocyte control. Indirect immunofluorescence and Western blot analyses were performed to evaluate the localization and expression of six critical proteins involved in the regulation of sister chromatid cohesion.

Results
We first confirmed that all five Hodgkin lymphoma cell lines exhibited chromosome instability relative to the lymphocyte control. We then determined that each Hodgkin lymphoma cell line exhibited cohesion defects that were subsequently classified into mild, moderate or severe categories. Surprisingly, ~50% of the mitotic spreads generated from L-540 and HDLM-2 harbored cohesion defects. To gain mechanistic insight into the underlying cause of the aberrant cohesion we examined the localization and expression of six critical proteins involved in cohesion. Although all proteins produced the expected nuclear localization pattern, striking differences in RAD21 expression was observed: RAD21 expression was lowest in L-540 and highest within HDLM-2.

Conclusion
We conclude that aberrant cohesion is a common feature of all five Hodgkin lymphoma cell lines evaluated. We further conclude that aberrant RAD21 expression is a strong candidate to underlie aberrant cohesion, chromosome instability and contribute to the development of the disease. Our findings support a growing body of evidence suggesting that cohesion defects and aberrant RAD21 expression are pathogenic events that contribute to tumor development.
IGF-1 receptor and IGF binding protein-3 might predict prognosis of patients with resectable pancreatic cancer
Authors: Hirakawa Toshiki , Yashiro Masakazu , Murata Akihiro , Hirata Keiichiro , Kimura Kenjiro , Amano Ryosuke , Yamada Nobuya , Nakata Bunzo , Hirakawa Kosei 
Published: August 2013

Abstract

Background
The present study aimed to elucidate the clinicopathologic role of insulin-like growth factor-1 receptor (IGF1R) and IGF binding protein-3 (IGFBP3) in patients with pancreatic cancer. The function of IGFBP3 is controversial, because both inhibition and facilitation of the action of IGF as well as IGF-independent effects have been reported. In this study, IGF1R and IGFBP3 expression was examined, and their potential roles as prognostic markers in patients with pancreatic cancer were evaluated.

Methods
Clinicopathological features of 122 patients with curatively resected pancreatic cancer were retrospectively reviewed, and expression of IGF1R and IGFBP3 was immunohistochemically analyzed.

Results
Expression of IGF1R and IGFBP3 was observed in 50 (41.0%) and 37 (30.3%) patients, respectively. IGF1R expression was significantly associated with histological grade (p = 0.037). IGFBP3 expression had a significant association with tumor location (p = 0.023), and a significant inverse association with venous invasion (p = 0.037). Tumors with IGF1R-positive and IGFBP3-negative expression (n = 32) were significantly frequently Stage II and III (p = 0.011). The prognosis for IGF1R positive patients was significantly poorer than that for IGF1R negative patients (p = 0.0181). IGFBP3 protein expression did not correlate significantly with patient survival. The subset of patients with both positive IGF1R and negative IGFBP3 had worse overall survival (8.8 months versus 12.6 months, respectively, p < 0.001).

Conclusion
IGF1R signaling might be associated with tumor aggressiveness, and IGFBP3 might show antiproliferative effects in pancreatic cancer. Both high IGF1R expression and low IGFBP3 expression represent useful prognostic markers for patients with curatively resected pancreatic cancer.
Effect of glycemic control on soluble RAGE and oxidative stress in type 2 diabetic patients
Authors: Motawi Tarek MK , Abou-Seif Mohamed A , Bader Ahmed MA , Mahmoud Mohamed O 
Published: August 2013

Abstract

Background
The interaction of advanced glycation end products (AGEs) and its receptor (RAGE) has played an important role in the pathogenesis of diabetes and its complications. A soluble form of RAGE (sRAGE) has been reported as a decoy receptor for AGEs. Oxidative stress is demonstrated in pathological condition such as atherosclerosis and diabetes mellitus. It has been suggested to be involved in the pathogenesis of both macro- and microvascular complications. This study was designed to evaluate the effect of glycemic control on sRAGE and oxidative stress markers in type 2 diabetic patients.

Methods
Seventy patients with type 2 diabetes and 20 healthy subjects were recruited into the study. Blood glutathione (GSH) and plasma total nitric oxide (NOx) levels were measured using commercially available colorimetric kits, blood superoxide dismutase (SOD) activity was measured by the method of Marklund and Marklund, and plasma C-peptide, oxidized LDL (ox-LDL), sRAGE, and VCAM-1 levels were measured using competitive ELISA kits.

Results
Plasma sRAGE levels were significantly lower (p < 0.05) while VCAM-1 levels were significantly higher (p < 0.05) in poorly controlled diabetic patients compared with healthy control. Blood GSH levels were significantly lower in diabetic patients compared with healthy control (p < 0.05). Plasma C-peptide, NOx, ox-LDL levels, and SOD activity were not significantly different in diabetic patients compared with healthy control. Plasma levels of sRAGE were negatively associated with circulating VCAM-1 levels in diabetic patients.

Conclusion
Poor glycemic control decreases plasma sRAGE and increases VCAM-1 levels while good glycemic control improves these abnormalities which provides benefit to diabetic patients.
Disrupting the CXCL12/CXCR4 axis disturbs the characteristics of glioblastoma stem-like cells of rat RG2 glioblastoma
Authors: Lee Chin-Cheng , Lai Jin-Huei , Hueng Dueng-Yang , Ma Hsin-I , Chung Yuan- Chiang , Sun Ya-yun , Tsai Yih-Ju , Wu Wen-Ben , Chen Chih-Li 
Published: August 2013

Abstract

Background
Glioblastoma stem-like cells (GSC) have been shown to promote tumor growth, tumor-associated neovascularization, therapeutic resistance, and metastasis. CXCR4 receptors have been found involved in the proliferation, metastasis, angiogenesis, and drug-resistant characteristics of glioblastoma. However, the role of CXCR4 in modulating the stem-like cell properties of rat glioblastoma remains ambiguous.

Methods
To explore the role of the CXCL12/CXCR4 axis in maintaining rat GSC properties, we disrupted the CXCR4 signaling by using small hairpin interfering RNA (shRNA). To investigate the role of the CXCL12/CXCR4 axis in maintaining rat GSC properties, we used a spheroid formation assay to assess the stem cell self-renewal properties. A western blot analysis and PCR arrays were used to examine the genes involved in proliferation, self-renewal, and cancer drug resistance. Finally, DNA content and flow cytometry, an immunohistochemical analysis, and methylcellulose colony formation, in vitro invasive and intracranial injection xenograft assays were employed to examine the disruptive effect of CXCR4 on the characteristics of GSCs of the RG2 cell line.

Results
Disrupting CXCR4 inhibited the proliferation of RG2 cells both in vitro and in vivo. The spheroid formation assay indicated that CXCR4 was vital for the self-renewal of RG2 GSCs. Disrupting the CXCL12/CXCR4 pathway also reduced the expression of GSC cell markers, including Nestin, ABCG2, and musashi (Msi), and the expression of genes involved in regulating stem cell properties, including Oct4, Nanog, maternal embryonic leucine zipper kinase (MELK), MGMT, VEGF, MMP2, and MMP9.

Conclusion
The chemokine receptor CXCR4 is crucial for maintaining the self-renewal, proliferation, therapeutic resistance, and angiogenesis of GSCs of rat RG2 glioblastoma.
Fate of TLR-1/TLR-2 agonist functionalised pDNA nanoparticles upon deposition at the human bronchial epithelium in vitro
Authors: Heuking Simon , Rothen-Rutishauser Barbara , Raemy David Olivier , Gehr Peter , Borchard Gerrit 
Published: August 2013

AbstractBackgroundPlasmid DNA vaccination is a promising approach, but studies in non-human primates and humans failed to achieve protective immunity. To optimise this technology further with focus on pulmonary administration, we developed and evaluated an adjuvant-equipped DNA carrier system based on the biopolymer chitosan. In more detail, the uptake and accompanying immune response of adjuvantPam3Cys(Toll-like receptor-1/2 agonist) decorated chitosan DNA nanoparticles (NP) were explored by using a three-dimensional (3D) cell culture model of the human epithelial barrier.Pam3Cysfunctionalised and non-functionalised chitosan DNA NP were sprayed by a microsprayer onto the surface of 3D cell cultures and uptake of NP by epithelial and immune cells (blood monocyte-derived dendritic cells (MDDC) and macrophages (MDM)) was visualised by confocal laser scanning microscopy. In addition, immune activation by TLR pathway was monitored by analysis of interleukin-8 and tumor necrosis factor-α secretions (ELISA).ResultsAt first, a high uptake rate into antigen-presenting cells (MDDC: 16-17%; MDM: 68–75%) was obtained. Although no significant difference in uptake patterns was observed forPam3Cysadjuvant functionalised and non-functionalised DNA NP, ELISA of interleukin-8 and tumor necrosis factor-α demonstrated clearly thatPam3Cysfunctionalisation elicited an overall higher immune response with the ranking ofPam3Cyschitosan DNA NP > chitosan DNA NP = DNA unloaded chitosan NP > control (culture medium).ConclusionsChitosan-based DNA delivery enables uptake into abluminal MDDC, which are the most immune competent cells in the human lung for the induction of antigen-specific immunity. In addition,Pam3Cysadjuvant functionalisation of chitosan DNA NP enhances significantly an environment favoring recruitment of immune cells together with a Th1 associated (cellular) immune response due to elevated IL-8 and TNF-α levels. The latter renders this DNA delivery approach attractive for potential DNA vaccination against intracellular pathogens in the lung (e.g.,Mycobacterium tuberculosisor influenza virus).