bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disconnect between discourse and behavior regarding concurrent sexual partnerships and condom use: findings from a qualitative study among youth in Malawi
Authors: Romero Stacy L. , Ellis Amy A. , Gurman Tilly A. 
Published: December 2012

The practice of concurrent sexual partnerships (CP) is posited to be a contributor to the elevated risk of HIV transmission among youth in Malawi. The lens through which Malawian youth conceptualize the practices of CP and condom use has yet to be fully explored. The current study – a secondary data analysis of semi-structured in-depth interviews ( n = 19) with Malawian youth aged 18 to 22 years – addresses this gap. Participants were interviewed about their sexual relationships and behavior, as well as their perceptions and knowledge regarding condom use and CP. In order to ensure that youth engaged in CP were oversampled, the recruitment process asked potential respondents to self-identify whether they currently participated in CP. Of the total sample ( n = 19), 13 self-identified as currently engaging in CP. Data were analyzed using a grounded theory approach. This qualitative study highlights a disconnect between the high level of knowledge youth exhibit about HIV prevention methods and their actual reported condom use and CP behaviors. While some youth claimed to use condoms, their discourse demonstrated fluidity in that use changed over time, or interest in changing behavior was expressed, or was inconsistent between partnerships. The disconnect between knowledge of the consequences of risky sexual behavior and actual behavior was most evident among inconsistent condom users engaged in CP. This finding indicates knowledge alone has a limited role in the adoption of lower risk behaviors such as condom use and reduction of CP among youth. Moreover, findings from this study can inform HIV prevention programs operating in Malawi and the sub-Saharan Africa region by enabling them to provide tailored, more persuasive health promotion and prevention messaging. (Global Health Promotion, 2012; 19(4): 20–28)
Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data
Authors: Zhou Ao , Breese Marcus R , Hao Yangyang , Edenberg Howard J , Li Lang , Skaar Todd C , Liu Yunlong 
Published: December 2012

Abstract

Background
Alternative splicing increases proteome diversity by expressing multiple gene isoforms that often differ in function. Identifying alternative splicing events from RNA-seq experiments is important for understanding the diversity of transcripts and for investigating the regulation of splicing.

Results
We developed Alt Event Finder, a tool for identifying novel splicing events by using transcript annotation derived from genome-guided construction tools, such as Cufflinks and Scripture. With a proper combination of alignment and transcript reconstruction tools, Alt Event Finder is capable of identifying novel splicing events in the human genome. We further applied Alt Event Finder on a set of RNA-seq data from rat liver tissues, and identified dozens of novel cassette exon events whose splicing patterns changed after extensive alcohol exposure.

Conclusions
Alt Event Finder is capable of identifying de novo splicing events from data-driven transcript annotation, and is a useful tool for studying splicing regulation.
Differential combinatorial regulatory network analysis related to venous metastasis of hepatocellular carcinoma
Authors: Zeng Lingyao , Yu Jian , Huang Tao , Jia Huliang , Dong Qiongzhu , He Fei , Yuan Weilan , Qin Lunxiu , Li Yixue , Xie Lu 
Published: December 2012

AbstractBackgroundHepatocellular carcinoma (HCC) is one of the most fatal cancers in the world, and metastasis is a significant cause to the high mortality in patients with HCC. However, the molecular mechanism behind HCC metastasis is not fully understood. Study of regulatory networks may help investigate HCC metastasis in the way of systems biology profiling.MethodsBy utilizing both sequence information and parallel microRNA(miRNA) and mRNA expression data on the same cohort of HBV related HCC patients without or with venous metastasis, we constructed combinatorial regulatory networks of non-metastatic and metastatic HCC which contain transcription factor(TF) regulation and miRNA regulation. Differential regulation patterns, classifying marker modules, and key regulatory miRNAs were analyzed by comparing non-metastatic and metastatic networks.ResultsGlobally TFs accounted for the main part of regulation while miRNAs for the minor part of regulation. However miRNAs displayed a more active role in the metastatic network than in the non-metastatic one. Seventeen differential regulatory modules discriminative of the metastatic status were identified as cumulative-module classifier, which could also distinguish survival time. MiR-16, miR-30a, Let-7e and miR-204 were identified as key miRNA regulators contributed to HCC metastasis.ConclusionIn this work we demonstrated an integrative approach to conduct differential combinatorial regulatory network analysis in the specific context venous metastasis of HBV-HCC. Our results proposed possible transcriptional regulatory patterns underlying the different metastatic subgroups of HCC. The workflow in this study can be applied in similar context of cancer research and could also be extended to other clinical topics.
Genomic sequence analysis and characterization of Sneathia amnii sp. nov
Authors: Harwich Michael D , Serrano Myrna G , Fettweis Jennifer M , Alves João MP , Reimers Mark A ,   Vaginal Microbiome Consortium (additional members), Buck Gregory A , Jefferson Kimberly K 
Published: December 2012

Abstract

Background
Bacteria of the genus Sneathia are emerging as potential pathogens of the female reproductive tract. Species of Sneathia, which were formerly grouped with Leptotrichia, can be part of the normal microbiota of the genitourinary tracts of men and women, but they are also associated with a variety of clinical conditions including bacterial vaginosis, preeclampsia, preterm labor, spontaneous abortion, post-partum bacteremia and other invasive infections. Sneathia species also exhibit a significant correlation with sexually transmitted diseases and cervical cancer. Because Sneathia species are fastidious and rarely cultured successfully in vitro; and the genomes of members of the genus had until now not been characterized, very little is known about the physiology or the virulence of these organisms.

Results
Here, we describe a novel species, Sneathia amnii sp. nov, which closely resembles bacteria previously designated "Leptotrichia amnionii". As part of the Vaginal Human Microbiome Project at VCU, a vaginal isolate of S. amnii sp. nov. was identified, successfully cultured and bacteriologically cloned. The biochemical characteristics and virulence properties of the organism were examined in vitro, and the genome of the organism was sequenced, annotated and analyzed. The analysis revealed a reduced circular genome of ~1.34 Mbp, containing ~1,282 protein-coding genes. Metabolic reconstruction of the bacterium reflected its biochemical phenotype, and several genes potentially associated with pathogenicity were identified.

Conclusions
Bacteria with complex growth requirements frequently remain poorly characterized and, as a consequence, their roles in health and disease are unclear. Elucidation of the physiology and identification of genes putatively involved in the metabolism and virulence of S. amnii may lead to a better understanding of the role of this potential pathogen in bacterial vaginosis, preterm birth, and other issues associated with vaginal and reproductive health.
Risk factors and clinical phenotypes of Beijing genotype strains in tuberculosis patients in China
Authors: Pang Yu , Song Yuanyuan , Xia Hui , Zhou Yang , Zhao Bing , Zhao Yanlin 
Published: December 2012

Abstract

Background
Beijing genotype strains are the most predominant strains in China. The aim of this study was to explore risk factors and clinical phenotypes associated with infection with Beijing genotype strains among tuberculosis patients in China.

Methods
Using data and strains derived from the first Chinese national drug resistance base-line survey, we performed a statistical analysis of the relationship between different genotypes, demographic characteristics and clinical phenotypes.

Result
Of patients infected with the 3634 strains for which detailed information was available, we found that people in young age groups [aged under 25 years, OR (95% CI): 1.30(1.03-1.62)], urban people [OR (95% CI): 1.18 (0.47-0.94)], or of Hui ethnicity [OR (95% CI): 1.96 (1.10-3.50)] or those needing retreatment [OR (95% CI): 1.22 (1.03-1.43)] were more likely to be infected with Beijing genotype strains compared with patients who were rural, or of Han ethnicity or those with new TB cases. In contrast, Uyghur [OR (95% CI): 0.45 (0.30-0.67)], or Zhuang ethnicities [OR (95% CI): 0.30 (0.19-0.48)], presented lower than average risk in infections with the Beijing genotype strain. In addition, a higher proportion of patients with hemoptysis [OR (95% CI): 0.81 (0.69-0.94)] and chest pain [OR (95% CI): 0.79 (0.69-0.91)] were infected with non-Beijing genotype strains than with Beijing genotype strains.

Conclusions
In China, young age group, urban people, Hui ethnicity and the earlier treated patients are all high risk factors for infection with Beijing genotype strains, while Uyghur and Zhuang ethnicity are lower than average risk factors for infection. The high rate of chest symptoms occurring in non-Beijing genotype infected patients indicates that more attention should be paid to basic research on non-Beijing genotype strains.
Severe falciparum malaria with dengue coinfection complicated by rhabdomyolysis and acute kidney injury: an unusual case with myoglobinemia, myoglobinuria but normal serum creatine kinase
Authors: Yong Kok Pin , Tan Ban Hock , Low Chian Yong 
Published: December 2012

Abstract

Background
Acute kidney injury (AKI) is a complication of severe malaria, and rhabdomyolysis with myoglobinuria is an uncommon cause. We report an unusual case of severe falciparum malaria with dengue coinfection complicated by AKI due to myoglobinemia and myoglobinuria while maintaining a normal creatine kinase (CK).

Case presentation
A 49-year old Indonesian man presented with fever, chills, and rigors with generalized myalgia and was diagnosed with falciparum malaria based on a positive blood smear. This was complicated by rhabdomyolysis with raised serum and urine myoglobin but normal CK. Despite rapid clearance of the parasitemia with intravenous artesunate and aggressive hydration maintaining good urine output, his myoglobinuria and acidosis worsened, progressing to uremia requiring renal replacement therapy. High-flux hemodiafiltration effectively cleared his serum and urine myoglobin with recovery of renal function. Further evaluation revealed evidence of dengue coinfection and past infection with murine typhus.

Conclusion
In patients with severe falciparum malaria, the absence of raised CK alone does not exclude a diagnosis of rhabdomyolysis. Raised serum and urine myoglobin levels could lead to AKI and should be monitored. In the event of myoglobin-induced AKI requiring dialysis, clinicians may consider using high-flux hemodiafiltration instead of conventional hemodialysis for more effective myoglobin removal. In Southeast Asia, potential endemic coinfections that can also cause or worsen rhabdomyolysis, such as dengue, rickettsiosis and leptospirosis, should be considered.
Up-regulated expression of l-caldesmon associated with malignancy of colorectal cancer
Authors: Kim Kyung-Hee , Yeo Seung-Gu , Kim Won Ki , Kim Dae Yong , Yeo Hyun Yang , Hong Jun Pyu , Chang Hee Jin , Park Ji Won , Kim Sun Young , Kim Byung Chang , Yoo Byong Chul 
Published: December 2012

Abstract

Background
Caldesmon (CaD), a major actin-associated protein, is found in smooth muscle and non-muscle cells. Smooth muscle caldesmon, h-CaD, is a multifunctional protein, and non-muscle cell caldesmon, l-CaD, plays a role in cytoskeletal architecture and dynamics. h-CaD is thought to be an useful marker for smooth muscle tumors, but the role(s) of l-CaD has not been examined in tumors.

Methods
Primary colon cancer and liver metastasis tissues were obtained from colon cancer patients. Prior to chemoradiotherapy (CRT), normal and cancerous tissues were obtained from rectal cancer patients. Whole-tissue protein extracts were analyzed by 2-DE-based proteomics. Expression and phosphorylation level of main cellular signaling proteins were determined by western blot analysis. Cell proliferation after CaD siRNA transfection was monitored by MTT assay.

Results
The expression level of l-CaD was significantly increased in primary colon cancer and liver metastasis tissues compared to the level in the corresponding normal tissues. In cancerous tissues obtained from the patients showing poor response to CRT (Dworak grade 4), the expression of l-CaD was increased compared to that of good response group (Dworak grade 1). In line with, l-CaD positive human colon cancer cell lines were more resistant to 5-fluorouracil (5-FU) and radiation treatment compared to l-CaD negative cell lines. Artificial suppression of l-CaD increased susceptibility of colon cancer cells to 5-FU, and caused an increase of p21 and c-PARP, and a decrease of NF-kB and p-mTOR expression.

Conclusion
Up-regulated expression of l-CaD may have a role for increasing metastatic property and decreasing CRT susceptibility in colorectal cancer cells.
Epidermal growth factor receptor (EGFR) mutations and expression in squamous cell carcinoma of the esophagus in central Asia
Authors: Abedi-Ardekani Behnoush , Dar Nazir Ahmad , Mir Mohammad Muzaffar , Zargar Showkat Ahmad , Lone M Muqbool , Martel-Planche Ghyslaine , Villar Stéphanie , Mounawar Mounia , Saidi Farrokh , Malekzadeh Reza , Hainaut Pierre 
Published: December 2012

Abstract

Background
Esophageal squamous cell carcinoma (ESCC) shows geographic variations in incidence, with high incidences (>50/105 person-years) in central Asia, including North Eastern Iran (Golestan) and Northern India (Kashmir). In contrast to Western countries, smoking does not appear to be a significant risk factor for ESCC in central Asia. In lung adenocarcinoma, activating mutations in the gene encoding epidermal growth factor receptor (EGFR) are frequent in tumors of never smokers of Asian origin, predicting therapeutic sensitivity to Egfr-targeting drugs.

Methods
In this study 152 cases of histologically confirmed ESCC from Iran (Tehran and Golestan Province) and North India (Kashmir Valley) have been analyzed for EGFR mutation by direct sequencing of exons 18–21. Egfr protein expression was evaluated by immunohistochemistry in 34 samples from Tehran and HER2 mutations were analyzed in 54 cases from Kashmir.

Results
A total of 14 (9.2%) EGFR variations were detected, including seven variations in exons. Among those, four (2.6%) were already documented in lung cancers, two were reported as polymorphisms and one was a potentially new activating mutation. All but one variation in introns were previously identified as polymorphisms. Over-expression of Egfr was detected in 22/34 (65%) of tested cases whereas no HER2 mutation was found in 54 cases from Kashmir.

Conclusion
Overall, EGFR mutations appear to be a rare event in ESCC in high incidence areas of central Asia, although a very small proportion of cases may harbor mutations predicting sensitivity to anti-Egfr drugs.
Unique immunologic patterns in fibromyalgia
Authors: Behm Frederick G , Gavin Igor M , Karpenko Oleksiy , Lindgren Valerie , Gaitonde Sujata , Gashkoff Peter A , Gillis Bruce S 
Published: December 2012

AbstractBackgroundFibromyalgia (FM) is a clinical syndrome characterized by chronic pain and allodynia. The diagnosis of FM has been one of exclusion as a test to confirm the diagnosis is lacking. Recent data highlight the role of the immune system in FM. Aberrant expressions of immune mediators, such as cytokines, have been linked to the pathogenesis and traits of FM. We therefore determined whether cytokine production by immune cells is altered in FM patients by comparing the cellular responses to mitogenic activators of stimulated blood mononuclear cells of a large number of patients with FM to those of healthy matched individuals.MethodsPlasma and peripheral blood mononuclear cells (PBMC) were collected from 110 patients with the clinical diagnosis of FM and 91 healthy donors. Parallel samples of PBMC were cultured overnight in medium alone or in the presence of mitogenic activators; PHA or PMA in combination with ionomycin. The cytokine concentrations of IFN-γ, IL-5, IL-6, IL-8, IL-10, MIP-1β , MCP-1, and MIP1-α in plasma as well as in cultured supernatants were determined using a multiplex immunoassay using bead array technology.ResultsCytokine levels of stimulated PBMC cultures of healthy control subjects were significantly increased as compared to matched non-stimulated PBMC cultures. In contrast, the concentrations of most cytokines were lower in stimulated samples from patients with FM compared to controls. The decreases of cytokine concentrations in patients samples ranged from 1.5-fold for MIP-1β to 10.2-fold for IL-6 in PHA challenges. In PMA challenges, we observed 1.8 to 4-fold decreases in the concentrations of cytokines in patient samples.ConclusionThe cytokine responses to mitogenic activators of PBMC isolated from patients with FM were significantly lower than those of healthy individuals, implying that cell-mediated immunity is impaired in FM patients. This novel cytokine assay reveals unique and valuable immunologic traits, which, when combined with clinical patterns, can offer a diagnostic methodology in FM.
Interferon-γ-induced activation of Signal Transducer and Activator of Transcription 1 (STAT1) up-regulates the tumor suppressing microRNA-29 family in melanoma cells
Authors: Schmitt Martina J , Philippidou Demetra , Reinsbach Susanne E , Margue Christiane , Wienecke-Baldacchino Anke , Nashan Dorothee , Behrmann Iris , Kreis Stephanie 
Published: December 2012

Abstract

Background
The type-II-cytokine IFN-γ is a pivotal player in innate immune responses but also assumes functions in controlling tumor cell growth by orchestrating cellular responses against neoplastic cells. The role of IFN-γ in melanoma is not fully understood: it is a well-known growth inhibitor of melanoma cells in vitro. On the other hand, IFN-γ may also facilitate melanoma progression. While interferon-regulated genes encoding proteins have been intensively studied since decades, the contribution of miRNAs to effects mediated by interferons is an emerging area of research.
We recently described a distinct and dynamic regulation of a whole panel of microRNAs (miRNAs) after IFN-γ-stimulation. The aim of this study was to analyze the transcriptional regulation of miR-29 family members in detail, identify potential interesting target genes and thus further elucidate a potential signaling pathway IFN-γ → Jak→ P-STAT1 → miR-29 → miR-29 target genes and its implication for melanoma growth.

Results
Here we show that IFN-γ induces STAT1-dependently a profound up-regulation of the miR-29 primary cluster pri-29a~b-1 in melanoma cell lines. Furthermore, expression levels of pri-29a~b-1 and mature miR-29a and miR-29b were elevated while the pri-29b-2~c cluster was almost undetectable. We observed an inverse correlation between miR-29a/b expression and the proliferation rate of various melanoma cell lines. This finding could be corroborated in cells transfected with either miR-29 mimics or inhibitors. The IFN-γ-induced G1-arrest of melanoma cells involves down-regulation of CDK6, which we proved to be a direct target of miR-29 in these cells. Compared to nevi and normal skin, and metastatic melanoma samples, miR-29a and miR-29b levels were found strikingly elevated in certain patient samples derived from primary melanoma.

Conclusions
Our findings reveal that the miR-29a/b1 cluster is to be included in the group of IFN- and STAT-regulated genes. The up-regulated miR-29 family members may act as effectors of cytokine signalling in melanoma and other cancer cells as well as in the immune system.
Do major life events influence physical activity among older adults: the Longitudinal Aging Study Amsterdam
Authors: Koeneman Margot A , Chinapaw Mai JM , Verheijden Marieke W , van Tilburg Theo G , Visser Marjolein , Deeg Dorly JH , Hopman-Rock Marijke 
Published: December 2012

Abstract

Background
Major life events are associated with a change in daily routine and could thus also affect habitual levels of physical activity. Major life events remain largely unexplored as determinants of older adults’ participation in physical activity and sports. This study focused on two major life events, widowhood and retirement, and asked whether these major life events were associated with moderate to vigorous physical activity (MVPA) and sports participation.

Methods
Data from the first (1992–93) and second (1995–96) wave of the Longitudinal Aging Study Amsterdam (LASA), a prospective cohort study among Dutch adults aged 55 and older, were used. Change in marital status and employment status between baseline and follow-up was assessed by self-report. Time spent in MVPA (min/d) and sports participation (yes/no) was calculated based on the LASA Physical Activity Questionnaire. The association of retirement and widowhood with MVPA and sports participation was assessed in separate multivariate linear and logistic regression analyses, respectively.

Results
Widowhood - N=136 versus 1324 stable married- was not associated with MVPA (B= 3.5 [95%CI:-57.9;64.9]) or sports participation (OR= 0.8 [95%CI:0.5;1.3]). Retired participants (N= 65) significantly increased their time spent in MVPA (B= 32.5 [95%CI:17.8;47.1]) compared to participants who continued to be employed (N= 121), but not their sports participation. Age was a significant effect modifier (B= 7.5 [90%CI:-1.1;13.8]), indicating a greater increase in MVPA in older retirees.

Discussion
Our results suggest that the associations found varied by the two major life events under investigation. MVPA increased after retirement, but no association with widowhood was seen.
Self-assembled silver nanoislands formed on glass surface via out-diffusion for multiple usages in SERS applications
Authors: Zhurikhina Valentina V , Brunkov Pavel N , Melehin Vladimir G , Kaplas Tommi , Svirko Yuri , Rutckaia Victoria V , Lipovskii Andrey A 
Published: December 2012

Abstract
We demonstrate that silver nanoisland film self-assembled on the surface of silver-containing glass in the course of thermal processing in hydrogen is capable to detect 10−7 M concentration of rhodamine 6G in water using surface enhanced Raman spectroscopy (SERS) technique. The film can be multiply restored on the same glass substrate via annealing of the glass in hydrogen. We showed that the film can be self-assembled after as much as ten circles of the substrate cleaning followed by annealing. The proposed technique of the silver nanoisland film formation enables multiple usage of the same glass substrate in SERS experiments.