bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probing the Xenopus laevis inner ear transcriptome for biological function
Authors: Powers TuShun R , Virk Selene M , Trujillo-Provencio Casilda , Serrano Elba E 
Published: June 2012

Abstract

Background
The senses of hearing and balance depend upon mechanoreception, a process that originates in the inner ear and shares features across species. Amphibians have been widely used for physiological studies of mechanotransduction by sensory hair cells. In contrast, much less is known of the genetic basis of auditory and vestibular function in this class of animals. Among amphibians, the genus Xenopus is a well-characterized genetic and developmental model that offers unique opportunities for inner ear research because of the amphibian capacity for tissue and organ regeneration. For these reasons, we implemented a functional genomics approach as a means to undertake a large-scale analysis of the Xenopus laevis inner ear transcriptome through microarray analysis.

Results
Microarray analysis uncovered genes within the X. laevis inner ear transcriptome associated with inner ear function and impairment in other organisms, thereby supporting the inclusion of Xenopus in cross-species genetic studies of the inner ear. The use of gene categories (inner ear tissue; deafness; ion channels; ion transporters; transcription factors) facilitated the assignment of functional significance to probe set identifiers. We enhanced the biological relevance of our microarray data by using a variety of curation approaches to increase the annotation of the Affymetrix GeneChip® Xenopus laevis Genome array. In addition, annotation analysis revealed the prevalence of inner ear transcripts represented by probe set identifiers that lack functional characterization.

Conclusions
We identified an abundance of targets for genetic analysis of auditory and vestibular function. The orthologues to human genes with known inner ear function and the highly expressed transcripts that lack annotation are particularly interesting candidates for future analyses. We used informatics approaches to impart biologically relevant information to the Xenopus inner ear transcriptome, thereby addressing the impediment imposed by insufficient gene annotation. These findings heighten the relevance of Xenopus as a model organism for genetic investigations of inner ear organogenesis, morphogenesis, and regeneration.
An important role of interleukin-10 in counteracting excessive immune response in HT-29 cells exposed to Clostridium butyricum
Authors: Gao Quanxin , Qi Lili , Wu Tianxing , Wang Jinbo 
Published: June 2012

AbstractBackgroundClostridium butyricumhas become increasingly important in preventing and treating intestinal inflammation. In the intestine it may increase the resistance of the gut to pathogen invasion via inducing the secretion of anti-inflammatory cytokines. Interleukin 10 (IL-10) plays a central role in preventing certain inflammatory diseases by down-regulating inflammatory cascades. In a previous study, we observed that the level of IL-10 mRNA was modulated byC. butyricum. The aim of this study was to investigate whetherC. butyricumachieves its beneficial effects through IL-10.ResultsWe treated HT-29 cells with anti-IL-10 (IL-10 antibody) or siIL-10 (IL-10 small interfering RNA) to disrupt IL-10. In both cases, the effects ofC. butyricum-induced NF-κB activation and IL-8 expression were enhanced. We also found that neutralization or knockdown of IL-10 could induce apoptosis and necrosis of HT-29 cells treated withC. butyricumcompared with control cells.ConclusionsThese findings show that IL-10 serves an important role inC. butyricum-mediated immune protection, and in host recognition ofC. butyricum.
Mycobacterium fortuitum as a cause of peritoneal dialysis-associated peritonitis: case report and review of the literature
Authors: Jiang Simon H , Roberts Darren M , Dawson Andrew H , Jardine Meg 
Published: June 2012

Abstract

Background
Peritoneal dialysis-associated peritonitis (PD-peritonitis) due to Mycobacterium spp is uncommon. Non-tuberculous Mycobacterium (NTB) PD-peritonitis can present in a similar fashion to more common causes of bacterial PD-peritonitis. We describe the first reported case of multiresistant Mycobacterium fortuitum PD-peritonitis in an Australian patient.

Case presentation
A 38 year-old woman developed mild PD-peritonitis during an overseas holiday. Treatment was complicated by delayed diagnosis, requirement for special investigations, treatment with multiple antibiotics, and conversion to haemodialysis following removal of her Tenckhoff catheter.

Conclusion
This case demonstrates the diagnostic yield of pursuing further investigations in cases of initially culture-negative, problematic PD-peritonitis. A systematic review of the literature identified only 17 reports of M. fortuitum PD-peritonitis. Similar to our case, a delay in microbiological diagnosis was frequently noted and the Tenckhoff catheter was commonly removed at the time of diagnosis. The type and duration of antibiotic therapy also varied widely so the optimum treatment appears to be poorly defined.
ERLIN2 promotes breast cancer cell survival by modulating endoplasmic reticulum stress pathways
Authors: Wang Guohui , Liu Gang , Wang Xiaogang , Sethi Seema , Ali-Fehmi Rouba , Abrams Judith , Zheng Ze , Zhang Kezhong , Ethier Stephen , Yang Zeng-Quan 
Published: June 2012

Abstract

Background
Amplification of the 8p11-12 region has been found in approximately 15% of human breast cancer and is associated with poor prognosis. Previous genomic analysis has led us to identify the endoplasmic reticulum (ER) lipid raft-associated 2 (ERLIN2) gene as one of the candidate oncogenes within the 8p11-12 amplicon in human breast cancer, particularly in the luminal subtype. ERLIN2, an ER membrane protein, has recently been identified as a novel mediator of ER-associated degradation. Yet, the biological roles of ERLIN2 and molecular mechanisms by which ERLIN2 coordinates ER pathways in breast carcinogenesis remain unclear.

Methods
We established the MCF10A-ERLIN2 cell line, which stably over expresses ERLIN2 in human nontransformed mammary epithelial cells (MCF10A) using the pLenti6/V5-ERLIN2 construct. ERLIN2 over expressing cells and their respective parental cell lines were assayed for in vitro transforming phenotypes. Next, we knocked down the ERLIN2 as well as the ER stress sensor IRE1α activity in the breast cancer cell lines to characterize the biological roles and molecular basis of the ERLIN2 in carcinogenesis. Finally, immunohistochemical staining was performed to detect ERLIN2 expression in normal and cancerous human breast tissues

Results
We found that amplification of the ERLIN2 gene and over expression of the ERLIN2 protein occurs in both luminal and Her2 subtypes of breast cancer. Gain- and loss-of-function approaches demonstrated that ERLIN2 is a novel oncogenic factor associated with the ER stress response pathway. The IRE1α/XBP1 axis in the ER stress pathway modulated expression of ERLIN2 protein levels in breast cancer cells. We also showed that over expression of ERLIN2 facilitated the adaptation of breast epithelial cells to ER stress by supporting cell growth and protecting the cells from ER stress-induced cell death.

Conclusions
ERLIN2 may confer a selective growth advantage for breast cancer cells by facilitating a cytoprotective response to various cellular stresses associated with oncogenesis. The information provided here sheds new light on the mechanism of breast cancer malignancy
Snake venom toxin from vipera lebetina turanicainduces apoptosis of colon cancer cells via upregulation of ROS- and JNK-mediated death receptor expression
Authors: Park Mi Hee , Jo MiRan , Won Dohee , Song Ho Sueb , Han Sang Bae , Song Min Jong , Hong Jin Tae 
Published: June 2012

AbstractBackgroundAbundant research suggested that the cancer cells avoid destruction by the immune system through down-regulation or mutation of death receptors. Therefore, it is very important that finding the agents that increase the death receptors of cancer cells. In this study, we demonstrated that the snake venom toxin fromVipera lebetina turanicainduce the apoptosis of colon cancer cells through reactive oxygen species (ROS) and c-Jun N-terminal kinases (JNK) dependent death receptor (DR4 and DR5) expression.MethodsWe used cell viability assays, DAPI/TUNEL assays, as well as western blot for detection of apoptosis related proteins and DRs to demonstrate that snake venom toxin-induced apoptosis is DR4 and DR5 dependent. We carried out transient siRNA knockdowns of DR4 and DR5 in colon cancer cells.ResultsWe showed that snake venom toxin inhibited growth of colon cancer cells through induction of apoptosis. We also showed that the expression of DR4 and DR5 was increased by treatment of snake venom toxin. Moreover, knockdown of DR4 or DR5 reversed the effect of snake venom toxin. Snake venom toxin also induced JNK phosphorylation and ROS generation, however, pretreatment of JNK inhibitor and ROS scavenger reversed the inhibitory effect of snake venom toxin on cancer cell proliferation, and reduced the snake venom toxin-induced upregulation of DR4 and DR5 expression.ConclusionsOur results indicated that snake venom toxin could inhibit human colon cancer cell growth, and these effects may be related to ROS and JNK mediated activation of death receptor (DR4 and DR5) signals.
The heat shock protein-90 co-chaperone, Cyclophilin 40, promotes ALK-positive, anaplastic large cell lymphoma viability and its expression is regulated by the NPM-ALK oncoprotein
Authors: Pearson Joel D , Mohammed Zubair , Bacani Julinor T C , Lai Raymond , Ingham Robert J 
Published: June 2012

Abstract

Background
Anaplastic lymphoma kinase-positive, anaplastic large cell lymphoma (ALK+ ALCL) is a T cell lymphoma defined by the presence of chromosomal translocations involving the ALK tyrosine kinase gene. These translocations generate fusion proteins (e.g. NPM-ALK) with constitutive tyrosine kinase activity, which activate numerous signalling pathways important for ALK+ ALCL pathogenesis. The molecular chaperone heat shock protein-90 (Hsp90) plays a critical role in allowing NPM-ALK and other signalling proteins to function in this lymphoma. Co-chaperone proteins are important for helping Hsp90 fold proteins and for directing Hsp90 to specific clients; however the importance of co-chaperone proteins in ALK+ ALCL has not been investigated. Our preliminary findings suggested that expression of the immunophilin co-chaperone, Cyclophilin 40 (Cyp40), is up-regulated in ALK+ ALCL by JunB, a transcription factor activated by NPM-ALK signalling. In this study we examined the regulation of the immunophilin family of co-chaperones by NPM-ALK and JunB, and investigated whether the immunophilin co-chaperones promote the viability of ALK+ ALCL cell lines.

Methods
NPM-ALK and JunB were knocked-down in ALK+ ALCL cell lines with siRNA, and the effect on the expression of the three immunophilin co-chaperones: Cyp40, FK506-binding protein (FKBP) 51, and FKBP52 examined. Furthermore, the effect of knock-down of the immunophilin co-chaperones, either individually or in combination, on the viability of ALK+ ALCL cell lines and NPM-ALK levels and activity was also examined.

Results
We found that NPM-ALK promoted the transcription of Cyp40 and FKBP52, but only Cyp40 transcription was promoted by JunB. We also observed reduced viability of ALK+ ALCL cell lines treated with Cyp40 siRNA, but not with siRNAs directed against FKBP52 or FKBP51. Finally, we demonstrate that the decrease in the viability of ALK+ ALCL cell lines treated with Cyp40 siRNA does not appear to be due to a decrease in NPM-ALK levels or the ability of this oncoprotein to signal.

Conclusions
This is the first study demonstrating that the expression of immunophilin family co-chaperones is promoted by an oncogenic tyrosine kinase. Moreover, this is the first report establishing an important role for Cyp40 in lymphoma.
Epidemic features affecting the performance of outbreak detection algorithms
Authors: Kuang Jie , Yang Wei Zhong , Zhou Ding Lun , Li Zhong Jie , Lan Ya Jia 
Published: June 2012

Abstract

Background
Outbreak detection algorithms play an important role in effective automated surveillance. Although many algorithms have been designed to improve the performance of outbreak detection, few published studies have examined how epidemic features of infectious disease impact on the detection performance of algorithms. This study compared the performance of three outbreak detection algorithms stratified by epidemic features of infectious disease and examined the relationship between epidemic features and performance of outbreak detection algorithms.

Methods
Exponentially weighted moving average (EWMA), cumulative sum (CUSUM) and moving percentile method (MPM) algorithms were applied. We inserted simulated outbreaks into notifiable infectious disease data in China Infectious Disease Automated-alert and Response System (CIDARS), and compared the performance of the three algorithms with optimized parameters at a fixed false alarm rate of 5% classified by epidemic features of infectious disease. Multiple linear regression was adopted to analyse the relationship of the algorithms’ sensitivity and timeliness with the epidemic features of infectious diseases.

Results
The MPM had better detection performance than EWMA and CUSUM through all simulated outbreaks, with or without stratification by epidemic features (incubation period, baseline counts and outbreak magnitude). The epidemic features were associated with both sensitivity and timeliness. Compared with long incubation, short incubation had lower probability (β* = −0.13, P < 0.001) but needed shorter time to detect outbreaks (β* = −0.57, P < 0.001). Lower baseline counts were associated with higher probability (β* = −0.20, P < 0.001) and longer time (β* = 0.14, P < 0.001). The larger outbreak magnitude was correlated with higher probability (β* = 0.55, P < 0.001) and shorter time (β* = −0.23, P < 0.001).

Conclusions
The results of this study suggest that the MPM is a prior algorithm for outbreak detection and differences of epidemic features in detection performance should be considered in automatic surveillance practice.
A longitudinal cohort based association study between uric acid level and metabolic syndrome in Chinese Han urban male population
Authors: Zhang Qian , Zhang Chengqi , Song Xinhong , Lin Haiyan , Zhang Dongzhi , Meng Wenjia , Zhang Yongyuan , Zhu Zhenxin , Tang Fang , Liu Longjian , Yang Xiaowei , Xue Fuzhong 
Published: June 2012

Abstract

Background
It has been recently demonstrated that serum uric acid (UA) is associated with metabolic syndrome (MetS) or its related clinical indications based on cross-sectional or prospective cohort studies. Nonetheless, due to the fact that UA level constantly fluctuates from time to time even for the person, using a single measure of UA level at baseline of those studies may not be sufficient for estimating the UA-Mets association.

Methods
To further estimate this time-dependent association, we fitted a generalized estimating equation (GEE) regression model with data from a large-scale 6-year longitudinal study, which included 2222 participants aged > =25 years with an average of 3.5 repeated measures of UA per person in the Health Management Center of Shandong Provincial Hospital, Shandong, China.

Results
After adjusting for other potential confounding factors (i.e., total cholesterol, low-density lipoprotein), it was verified that time-dependent UA level was an independent risk factor for MetS (OR = 1.6920, p < 0.0001). It was found that UA level was positively associated with obesity, hypertension, and dyslipidemia, but was inversely associated with hyperglycemia.

Conclusions
Serum UA level may serve as an important risk factor of MetS. Additionally, our study suggested that UA level be an independent risk factor to obesity, hypertension and dyslipidemia, but a protective factor to hyperglycemia. These findings are concordant with results from other studies on Asian populations, and jointly provide a basis to further develop a risk assessment model for predicting MetS using UA levels and other factors in China.
Development and validation of sunlight exposure measurement questionnaire (SEM-Q) for use in adult population residing in Pakistan
Authors: Humayun Quratulain , Iqbal Romaina , Azam Iqbal , Khan Aysha Habib , Siddiqui Amna Rehana , Baig-Ansari Naila 
Published: June 2012

Abstract

Background
Vitamin D deficiency has been identified as a major public health problem worldwide. Sunlight is the main source of vitamin D and its measurement using dosimeters is expensive and difficult for use in population-based studies. Hence, the aim of this study was to develop and validate questionnaires to assess sunlight exposure in healthy individuals residing in Karachi, Pakistan.

Methods
Two questionnaires with seven important items for sunlight exposure assessment were developed. Fifty four healthy adults were enrolled based on their reported sunlight exposure (high = 17, moderate = 18, low = 19) from Aga Khan University, Karachi. Over four days, study participants were asked to wear a dosimeter between sunrise and sunset and report time spent and activities undertaken in the sun for questionnaire validation. Algorithm for item weightage was created as an average score based on ultraviolet B percentage received. Blood samples were obtained for serum vitamin D.

Results
The mean time (minutes) spent in sun over 4 days (±SD) was 69.5 (±32) for low, 83.5 (±29.7) for moderate and 329 (±115) for high exposure group. The correlation between average time (minutes) spent in sun over 4 days and mean change in absorbance of UV dosimeters for 4 days was 0.60 (p < 0.01). Correlation between average score and vitamin D levels was found to be 0.36 (p = 0.01) for short term questionnaire score, 0.43 (p = 0.01) for long term questionnaire score in summers and 0.48 (p = 0.01) in winters.

Conclusions
The sunlight exposure measurement questionnaires were valid tools for use in large epidemiological studies to quantify sunlight exposure.
Five-year monitoring of a gay-friendly voluntary counselling and testing facility in Switzerland: who got tested and why?
Authors: Gumy Cédric , Jeannin André , Balthasar Hugues , Huissoud Thérèse , Jobin Vincent , Häusermann Michael , Crevoisier Hubert , Sudre Philippe , Dubois-Arber Françoise 
Published: June 2012

Abstract

Background
An increase in new HIV cases among men who have sex with men (MSM) has been reported in Switzerland since 2001. A rapid result HIV testing for MSM through voluntary counselling and testing (VCT) facility (“Checkpoint”) was opened in Geneva in 2005. This gay-friendly facility, the first to open in Switzerland, provides testing for sexually transmitted infections (STI) and rapid result HIV testing and counselling. Our objective was to analyze Checkpoint’s activity over its first five years of activity and its ability to attract at-risk MSM.

Methods
We used routine data collected anonymously about the facility activity (number of clients, number of tests, and test results) and about the characteristics of the clientele (sociodemographic data, sexual risk behaviour, and reasons for testing) from 2005 to 2009.

Results
The yearly number of HIV tests performed increased from 249 in 2005 to 561 in 2009. The annual proportion of positive tests among tests performed varied between 2% and 3%. Among MSM clients, the median annual number of anal intercourse (AI) partners was three. Roughly 30% of all MSM clients had at least one unprotected anal intercourse (UAI) experience in the previous 12 months with a partner of different/unknown HIV status.
The main reason for testing in 2007, 2008, and 2009 was “sexual risk exposure” (~40%), followed by “routine” testing (~30%) and “condom stopping in the beginning of a new steady relationship” (~10%). Clients who came to the facility after a sexual risk exposure, compared to clients who came for "routine testing" or "condom stopping" reasons, had the highest number of AI partners in the previous 12 months, were more likely to have had UAI with a partner of different/unknown HIV status in the previous 12 months (respectively 57.3%, 12.5%, 23.5%), more likely to have had an STI diagnosed in the past (41.6%, 32.2%, 22.9%), and more likely to report recent feelings of sadness or depression (42.6%; 32.8%, 18.5%).

Conclusion
Many of Checkpoint's clients reported elevated sexual risk exposure and risk factors, and the annual proportion of new HIV cases in the facility is stable. This VCT facility attracts the intended population and appears to be a useful tool contributing to the fight against the HIV epidemic among MSM in Switzerland.
Usefulness and acceptability of a standardised orientation and mobility training for partially-sighted older adults using an identification cane
Authors: Ballemans Judith , Zijlstra GA Rixt , van Rens Ger HMB , Schouten Jan SAG , Kempen Gertrudis IJM 
Published: June 2012

Abstract

Background
Orientation and mobility (O&M) training in using an identification (ID) cane is provided to partially-sighted older adults to facilitate independent functioning and participation in the community. Recently, a protocolised standardised O&M-training in the use of the ID cane was developed in The Netherlands. The purpose of this study is to assess the usefulness and acceptability of both the standardised training and the regular training for participants and O&M-trainers in a randomised controlled trial (NCT00946062).

Methods
The standardised O&M-training consists of two structured face-to-face sessions and one telephone follow-up, in which, in addition to the regular training, self-management and behavioural change techniques are applied. Questionnaires and interviews were used to collect data on the training’s usefulness, e.g. the population reached, self-reported benefits or achievements, and acceptability, e.g. the performance of the intervention according to protocol and participants’ exposure to and engagement in the training.

Results
Data was collected from 29 O&M-trainers and 68 participants. Regarding the self-reported benefits, outcomes were comparable for the standardised training and the regular training according the trainers and participants e.g., about 85% of the participants in both groups experienced benefits of the cane and about 70% gained confidence in their capabilities. Participants were actively involved in the standardised training. Nearly 40% of the participants in the standardised training group was not exposed to the training according to protocol regarding the number of sessions scheduled and several intervention elements, such as action planning and contracting.

Conclusions
The standardised and regular O&M-training showed to be useful and mostly acceptable for the partially-sighted older adults and trainers. Yet, a concern is the deviation from the protocol of the standardised O&M-training by the O&M-trainers regarding distinguishing elements such as action planning. Overall, participants appreciated both trainings and reported benefit.