bluuebunny/crossref_metadata_2025 huggingface dataset:
Epidemiological and molecular analysis of human norovirus infections in Taiwan during 2011 and 2012
Authors: Tang Meng-Bin , Chen Chien-Hsien , Chen Shou-Chien , Chou Yu-Ching , Yu Chia-Peng
Published: July 2013

Background

The human norovirus (NV) circulates worldwide and is a major cause of epidemics, which have increased in Taiwan since 2002. NV in acute gastroenteritis (AGE) and non-acute gastroenteritis (asymptomatic) patients, including children and adults, have not been previously examined in Taiwan; therefore, we examined the epidemiology and phylogeny of NV in AGE and asymptomatic patients of all ages.

Methods

253 stool samples were collected from August 2011 to July 2012 (including 155 AGE and 98 asymptomatic samples in Taiwan) and analyzed using reverse transcription-polymerase chain reaction (RT-PCR) for NV. Primers targeting the RNA-polymerase gene were used for RT-PCR to allow DNA sequencing of Taiwan NV strains and phylogenetic analyses.

Results

NV was detected in 24 (9.5%) of 253 stool specimens using RT-PCR. NV was isolated from all age groups (1 to 86 y) and those NV-positive samples were major identified from inpatients (79.2%, 19/24). Statistical analysis showed that the NV infectious rate of AGE patients was statistically significant (P < 0.05) for age, season and water type, respectively. Phylogenetic analyses of the RdRp region sequence showed that 24 NV isolates belonged to Genogroup II Genotype 4 (GII.4). They were closely related to the epidemic strain in Taiwan in 2006, the GII.4-2006b pandemic strain in 2006, and the GII.4-New Orleans strain in 2010.

Conclusion

This study is the first to examine NV in sporadic AGE and asymptomatic patients in Taiwan. Furthermore, epidemic strains of isolated GII.4 were predominant in Taiwan during 2011 and 2012.
Reticulocyte dynamic and hemoglobin variability in hemodialysis patients treated with Darbepoetin alfa and C.E.R.A.: a randomized controlled trial
Authors: Forni Valentina , Bianchi Giorgia , Ogna Adam , Salvadé Igor , Vuistiner Philippe , Burnier Michel , Gabutti Luca
Published: July 2013

Background

In a simulation based on a pharmacokinetic model we demonstrated that increasing the erythropoiesis stimulating agents (ESAs) half-life or shortening their administration interval decreases hemoglobin variability. The benefit of reducing the administration interval was however lessened by the variability induced by more frequent dosage adjustments. The purpose of this study was to analyze the reticulocyte and hemoglobin kinetics and variability under different ESAs and administration intervals in a collective of chronic hemodialysis patients.

Methods

The study was designed as an open-label, randomized, four-period cross-over investigation, including 30 patients under chronic hemodialysis at the regional hospital of Locarno (Switzerland) in February 2010 and lasting 2 years. Four subcutaneous treatment strategies (C.E.R.A. every 4 weeks Q4W and every 2 weeks Q2W, Darbepoetin alfa Q4W and Q2W) were compared with each other. The mean square successive difference of hemoglobin, reticulocyte count and ESAs dose was used to quantify variability. We distinguished a short- and a long-term variability based respectively on the weekly and monthly successive difference.

Results

No difference was found in the mean values of biological parameters (hemoglobin, reticulocytes, and ferritin) between the 4 strategies. ESAs type did not affect hemoglobin and reticulocyte variability, but C.E.R.A induced a more sustained reticulocytes response over time and increased the risk of hemoglobin overshooting (OR 2.7, p = 0.01). Shortening the administration interval lessened the amplitude of reticulocyte count fluctuations but resulted in more frequent ESAs dose adjustments and in amplified reticulocyte and hemoglobin variability. Q2W administration interval was however more favorable in terms of ESAs dose, allowing a 38% C.E.R.A. dose reduction, and no increase of Darbepoetin alfa.

Conclusions

The reticulocyte dynamic was a more sensitive marker of time instability of the hemoglobin response under ESAs therapy. The ESAs administration interval had a greater impact on hemoglobin variability than the ESAs type. The more protracted reticulocyte response induced by C.E.R.A. could explain both, the observed higher risk of overshoot and the significant increase in efficacy when shortening its administration interval.

Trial registration

ClinicalTrials.gov: NCT01666301
An unusual case of glomerulonephritis in a patient with non-Hodgkin Mucosal Associated Lymphoid Tissue (MALT) B-cell lymphoma
Authors: Yeo See Cheng , Chuah Khoon Leong , Lee Hwei Yee , Liew Adrian
Published: July 2013

Background

Kidney involvement in non-Hodgkin lymphoma is well recognized and glomerulonephritis, when present, has been commonly reported to be associated with a membranoproliferative pattern.

Case presentation

We report a case of a 58-year-old lady with a recurrence of non-Hodgkin MALT B-cell lymphoma, presenting with acute kidney injury, nephrotic range proteinuria and a cellular urinalysis. She underwent a renal biopsy that showed a severe diffuse proliferative and exudative lupus-like glomerulonephritis, which is likely paraneoplastic in nature. We discuss the differential diagnosis and possible pathogenesis of glomerular injury in lymphoma-related proliferative glomerulonephritis.

Conclusion

Differentiating between true lupus nephritis and a paraneoplastic glomerulonephritis is important, as it would have significant implications on treatment and clinical course.
Calcified, minimally Fat-contained angiomyolipoma clinically indistinguishable from a renal cell carcinoma
Authors: Chen Chin-Li , Tang Shou-Hung , Wu Sheng-Tang , Meng En , Tsao Chih-Wei , Sun Guang-Huan , Yu Dah-Shyong , Chang Sun-Yran , Cha Tai-Lung
Published: July 2013

Background

Angiomyolipomas are benign tumors of the kidney. Typical angiomyolipomas are usually recognized by identifying fat components before any intervention. On the contrary, solid renal masses without evident fatty components but containing calcifications on the computed tomography scan are suspicious for malignancy. However, as in this rare case, rules of diagnostic imaging are of exceptions.

Case presentation

A 40-year-old man presented with left flank pain. The plain X-ray showed multiple coarse calcifications of 4.0 x 3.2 cm in diameter on the left upper quadrant abdomen. Computed tomography scan further revealed a solid renal mass and inside the mass there were calcifications. The size of the tumor was 5.6 × 5.5 × 6.3 cm. We performed a radical nephrectomy, and the histopathology showed a minimally fat-contained angiomyolipoma of multiple calcifications. The patient was free of recurrence or metastases after a follow-up period of 3 years.

Conclusion

An angiomyolipoma containing calcification is rare. An angiomyolipoma with minimal fat concomitant with calcifications is an even rarer presentation. It is very difficult to differentiate a minimal-fat angiomyolipoma with calcifications from a renal cell carcinoma preoperatively. In such a circumstance, a well-planned partial nephrectomy may be optimal for the patient, regardless of the tumor size.
Randomized comparison of vaginal self-sampling by standard vs. dry swabs for Human papillomavirus testing
Authors: Eperon Isabelle , Vassilakos Pierre , Navarria Isabelle , Menoud Pierre-Alain , Gauthier Aude , Pache Jean-Claude , Boulvain Michel , Untiet Sarah , Petignat Patrick
Published: July 2013

Background

To evaluate if human papillomavirus (HPV) self-sampling (Self-HPV) using a dry vaginal swab is a valid alternative for HPV testing.

Methods

Women attending colposcopy clinic were recruited to collect two consecutive Self-HPV samples: a Self-HPV using a dry swab (S-DRY) and a Self-HPV using a standard wet transport medium (S-WET). These samples were analyzed for HPV using real time PCR (Roche Cobas). Participants were randomized to determine the order of the tests. Questionnaires assessing preferences and acceptability for both tests were conducted. Subsequently, women were invited for colposcopic examination; a physician collected a cervical sample (physician-sampling) with a broom-type device and placed it into a liquid-based cytology medium. Specimens were then processed for the production of cytology slides and a Hybrid Capture HPV DNA test (Qiagen) was performed from the residual liquid. Biopsies were performed if indicated. Unweighted kappa statistics (к) and McNemar tests were used to measure the agreement among the sampling methods.

Results

A total of 120 women were randomized. Overall HPV prevalence was 68.7% (95% Confidence Interval (CI) 59.3–77.2) by S-WET, 54.4% (95% CI 44.8–63.9) by S-DRY and 53.8% (95% CI 43.8–63.7) by HC. Among paired samples (S-WET and S-DRY), the overall agreement was good (85.7%; 95% CI 77.8–91.6) and the κ was substantial (0.70; 95% CI 0.57-0.70). The proportion of positive type-specific HPV agreement was also good (77.3%; 95% CI 68.2-84.9). No differences in sensitivity for cervical intraepithelial neoplasia grade one (CIN1) or worse between the two Self-HPV tests were observed. Women reported the two Self-HPV tests as highly acceptable.

Conclusion

Self-HPV using dry swab transfer does not appear to compromise specimen integrity. Further study in a large screening population is needed.

Trial registration

ClinicalTrials.gov: NCT01316120
The effect of depressive symptoms on the association between radiographic osteoarthritis and knee pain: a cross-sectional study
Authors: Pereira Duarte , Severo Milton , Barros Henrique , Branco Jaime , Santos Rui A , Ramos Elisabete
Published: July 2013

Background

The progressive nature of knee osteoarthritis (OA) leads to not only to physical but also to psychosocial decline; this aspect can influence knee pain experience, manifestations and inevitably diagnostic accuracy.

To analyze the role of depressive symptoms on the association between radiographic OA and knee pain, understanding the ability of knee pain symptoms to find out individuals with radiographic OA.

Methods

Data on 663 subjects was obtained by interview using a structured questionnaire on social, demographic, behavioural and clinical data. Painful knee was assessed regarding having pain: ever, in the last year, in the last 6 months and in the last month. Using factor analysis, participants were graded using a knee pain score, with higher scores representing more symptomatology. Depressive symptoms were evaluated with the Beck Depressive Inventory (BDI), and radiographic knee OA was classified using the Kellgren Lawrence (KL) scale; those with KL ≥ 2 were considered as having radiographic OA.

Results

Knee pain was reported by 53.2% of those with radiographic KL ≥ 2 and by 33.2% of those with radiographic KL < 2. The prevalence of depressive symptoms (BDI > 14) was 19.9% among participants with radiographic KL ≥ 2 and 12.6% among those with radiographic KL < 2 (p = 0.01). The association of knee pain with radiographic knee OA was higher in higher pain scores and in participants without depressive symptoms. Among participants with BDI ≤ 14 the likelihood ratio to identify patients with radiographic knee OA increased with increased pain scores: 1.02 for score 1; 2.19 for score 2 and 7.34 when participants responded positively to all pain questions (score 3). Among participants with depressive symptoms (BDI > 14) likelihood ratios were 0.51, 1.92, 1.82, respectively. The results were similar for both genders.

Conclusions

Knee pain scores increased ability to identify participants with radiographic KL ≥ 2 in both sexes. However, the presence of depressive symptoms impairs the ability of knee pain complaints to identify patients with radiographic OA.
Antioxidant and anti-dermatophytic properties leaf and stem bark of Xylosma longifolium clos
Authors: Devi Wangkheirakpam Radhapiyari , Singh S Brojendro , Singh Chingakham B
Published: July 2013

Background

The present study was carried out to assess the phytochemical and anti-dermatophytic effect of the leaf and bark extracts ofXylosma longifoliumClos. The leaf and stem bark are used by the indigenous people of Manipur, India for treatment of skin diseases.

Methods

The leaves and stem barks ofXylosma longifoliumwere extracted using petroleum ether, chloroform and methanol respectively. The different extracts of each plant parts were tested for antioxidant activity using DPPH assay. The phenolic content was assayed using Folin-Ciocalteu colorimetric method. Each extracts was further analysed by RP-HPLC to quantify some individual flavonoid components. The anti-dermatophytic activity was evaluated both by agar diffusion method and micro wells dilution method against theMicrosporum boullardiiMTCC 6059,M. canis(MTCC 2820 and MTCC 32700),M. gypseumMTCC 2819,Trichophyton ajelloiMTCC 4878,T. rubrum(MTCC 296 and MTCC 3272).

Results

The free radical scavenging activity values were ranged from 0.7 to 1.41 mg/ml and 0.6 to 1.23 mg/ml, respectively for leaf and stem bark extracts. The amount of total phenolic contents of the extracts occurred in both leaf and bark in the range of 12 to 56.6 mg GAE/100 g and 16 to 58 mg GAE/100 g respectively. RP-HPLC analysis for flavonoids revealed the presence of two major flavonoid compounds, rutin and catechin. Kaempferol was in trace or absent. Methanol leaf extract showed significant low inhibitory effect against tested fungusTrichophyton ajelloiMTCC 4878 (0.140625 mg/ml) as the most sensitive. These finding suggest that the methanol leaf extract tested contain compounds with antimicrobial properties.

Conclusion

The results of our study may partially justify the folkloric uses on the plant studied and further provide an evidence that the leaf extract ofXylosma longifoliummight be indeed a potential sources of antimicrobial agents.
“Everyone just keeps their eyes closed and their fingers crossed”: Sexual health communication among black parents and children in Nova Scotia, Canada
Authors: Davis Antoinette N , Gahagan Jacqueline C , George Clemon
Published: July 2013

Background

Black Canadian youth remain disproportionally affected by an array of social and health issues, including sexually transmitted infections. While research exists in support of the involvement of parents as a key means to prevent or modify harmful behaviours among youth, less is known about how parent–child communication can serve as a prevention intervention strategy within Black families in Canada. This study explores sexual health communication between Black parents and youth in Nova Scotia and identifies facilitators, obstacles and issues that families face in dialoguing about sexual health.

Methods

Focus groups and in-depth interview sessions were held with a diverse sample of parents of Black youth, health and education professionals, and Black youth in Nova Scotia, as part of a larger study aimed at exploring parent–child communication on sexual health and HIV. The research team worked in partnership with and received feedback from key informants and a community advisory committee throughout the various stages of this study. All sessions were audio-taped with permission and thematic analysis was carried out on the verbatim transcripts.

Results

Six key themes emerged from the data analysis in relation to parent–child communication within Black families in Nova Scotia: 1. the gendered nature of [sexual] health communication; 2. fear and uncertainty as obstacles; 3. open and honest dialogue from an early age as a facilitator; 4. media as both a catalyst and a barrier; 5. peers as a catalyst; and 6. time constraints as an obstacle.

Conclusions

The findings of this study reveal that parent–child communication regarding sexual health promotion within Black families in Nova Scotia remains varied and is heavily affected by a myriad of intersecting determinants of health faced by Black youth and their parents. Health promotion interventions aimed at fostering and supporting parent–child communication on sexual health must simultaneously target both parents and youth and further, such efforts must engage a high level of cultural competency in order to better meet the needs of this population.
Azacytidine induces necrosis of multiple myeloma cells through oxidative stress
Authors: Tian Enbing , Tang Haiping , Xu Renhua , Liu Chongdong , Deng Haiteng , Wang Qingtao
Published: July 2013

Azacytidine is an inhibitor of DNA methyltransferase and is known to be an anti-leukemic agent to induce cancer cell apoptosis. In the present study, multiple myeloma cells were treated with azacytidine at clinically relevant concentrations to induce necrosis through oxidative stress. Necrotic myeloma cells exhibit unique characteristics, including enrichment of the cell-bound albumin and overexpression of endoplasmic reticulum (ER)- and mitochondrial-specific chaperones, which were not observed in other necrotic cells, including HUH-7, A2780, A549, and Hoc1a. Proteomic analysis shows that HSP60 is the most abundant up-regulated mitochondrial specific chaperone, and azacytidine-induced overexpression of HSP60 is confirmed by western blot analysis. In contrast, expression levels of cytosolic chaperones such as HSP90 and HSP71 were down-regulated in azacytidine-treated myeloma cells, concomitant with an increase of these chaperones in the cell culture medium, suggesting that mitochondrial chaperones and cytosolic chaperones behave differently in necrotic myeloma cells; ER- and mitochondrial-chaperones being retained, and cytosolic chaperones being released into the cell culture medium through the ruptured cell membrane. Our data suggest that HSP60 is potentially a new target for multiple myeloma chemotherapy.
Vitamin d deficiency impacts on expression of toll-like receptor-2 and cytokine profile: a pilot study
Authors: Ojaimi Samar , Skinner Narelle A , Strauss Boyd JG , Sundararajan Vijaya , Woolley Ian , Visvanathan Kumar
Published: July 2013

Background

Vitamin D is believed to play an important role outside the endocrine system in the regulation of the immune system, and in cellular proliferation and differentiation. The aim of the study was to investigate the impact of vitamin D levels on innate immunity.

Methods

Participants for this prospective, longitudinal study were recruited amongst otherwise healthy staff of a large hospital in Victoria, Australia. Those fulfilling the inclusion criteria, including a vitamin D level of <50 nmol/L, were supplemented. Using flow cytometry, expression of the innate immune receptors TLR2, TLR4 and CD86 was measured on peripheral blood mononuclear cells (PBMCs) collected prior to vitamin D treatment and then at 1 and 3 months. Additonally, PBMCs at each timepoint were stimulated with specific TLR ligands and resultant supernatants were assayed for the cytokines TNFα, IL-6, IFN-α and IP-10.

Results

In participants whose vitamin D level was >100 nmol/L post supplementation (n=11), TLR2 expression on PBMCs increased significantly, with no change noted in TLR4 or CD86 expression. Stimulation of vitamin D deficient samples with TLR ligands produced a number of proinflammatory cytokines, which were significantly reduced upon vitamin D normalisation. In patients whose levels returned to a deficient level at 3 months despite ongoing low-level supplementation, an increase in the pro-inflamamtory state returned. This suggests that vitamin D may play an important role in ensuring an appropriate baseline pro-inflammatory state.

Conclusions

This ex-vivo pilot study adds clinical evidence supporting a possibly important role for vitamin D in innate immunity. If confirmed, this unique clinical study has potentially significant implications for the treatment of a variety of inflammatory conditions, where achieving optimal vitamin D levels may help reduce inflammation.
Factors influencing the intention of women in rural Ghana to adopt postpartum family planning
Authors: Eliason Sebastian , Baiden Frank , Quansah-Asare Gloria , Graham-Hayfron Yvonne , Bonsu Derek , Phillips James , Awusabo-Asare Kofi
Published: July 2013

Background

Uptake of postpartum family planning (PPFP) remains low in sub-Saharan Africa and very little is known about how pregnant women arrive at their decisions to adopt PPFP. This information is needed to guide the development of interventions to promote PPFP.

Methods

We conducted a survey among pregnant women attending antenatal clinics in a rural district in Ghana. We used univariate and multivariate logistic regression analysis to explore how knowledge of various family planning (FP) methods, past experience with their use and the acceptability of PPFP to male partners and close relations influenced the intention of pregnant women to adopt PPFP.

Results

We interviewed 1914 pregnant women in four health facilities. About 84% considered PPFP acceptable, and 70% intended to adopt a method. The most preferred methods were injectables (31.5%), exclusive breastfeeding (16.7%), and oral contraceptive pills (14.8%). Women whose first choice of PPFP method were injectables were more likely to be women who had had past experience with its use (O.R = 2.07, 95% C.I. 1.50-2.87). Acceptability of PPFP by the pregnant woman (O.R. = 3.21, 1.64-6.26), perception of partner acceptability (O.R. = 3.20, 1.94-5.48), having had prior experience with the use of injectables (O.R. = 3.72, 2.61-5.30) were the strongest predictors of the intention to adopt PPFP. Conversely women who knew about the diaphragm (O.R. = 0.59, 0.38-0.93) and those who had past experience with IUD use (O.R. = 0.13, 0.05-0.38) were less likely to want to adopt PPFP.

Conclusions

Acceptability of PPFP to the pregnant woman, male partner approval, and past experience with the use of injectables are important factors in the PPFP decisions of women in this population. Antenatal and early postnatal care need to be adapted to take these factors into consideration.
Bridging the gap between gene expression and metabolic phenotype via kinetic models
Authors: Vital-Lopez Francisco G , Wallqvist Anders , Reifman Jaques
Published: July 2013

Background

Despite the close association between gene expression and metabolism, experimental evidence shows that gene expression levels alone cannot predict metabolic phenotypes, indicating a knowledge gap in our understanding of how these processes are connected. Here, we present a method that integrates transcriptome, fluxome, and metabolome data using kinetic models to create a mechanistic link between gene expression and metabolism.

Results

We developed a modeling framework to construct kinetic models that connect the transcriptional and metabolic responses of a cell to exogenous perturbations. The framework allowed us to avoid extensive experimental characterization, literature mining, and optimization problems by estimating most model parameters directly from fluxome and transcriptome data. We applied the framework to investigate how gene expression changes led to observed phenotypic alterations of Saccharomyces cerevisiae treated with weak organic acids (i.e., acetate, benzoate, propionate, or sorbate) and the histidine synthesis inhibitor 3-aminotriazole under steady-state conditions. We found that the transcriptional response led to alterations in yeast metabolism that mimicked measured metabolic fluxes and concentration changes. Further analyses generated mechanistic insights of how S. cerevisiae responds to these stresses. In particular, these results suggest that S. cerevisiae uses different regulation strategies for responding to these insults: regulation of two reactions accounted for most of the tolerance to the four weak organic acids, whereas the response to 3-aminotriazole was distributed among multiple reactions. Moreover, we observed that the magnitude of the gene expression changes was not directly correlated with their effect on the ability of S. cerevisiae to grow under these treatments. In addition, we identified another potential mechanism of action of 3-aminotriazole associated with the depletion of tetrahydrofolate.

Conclusions

Our simulation results show that the modeling framework provided an accurate mechanistic link between gene expression and cellular metabolism. The proposed method allowed us to integrate transcriptome, fluxome, and metabolome data to determine and interpret important features of the physiological response of yeast to stresses. Importantly, given its flexibility and robustness, our approach can be applied to investigate the transcriptional-metabolic response in other cellular systems of medical and industrial relevance.
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Authors: Bradnam Keith R , Fass Joseph N , Alexandrov Anton , Baranay Paul , Bechner Michael , Birol Inanç , Boisvert Sébastien , Chapman Jarrod A , Chapuis Guillaume , Chikhi Rayan , Chitsaz Hamidreza , Chou Wen-Chi , Corbeil Jacques , Del Fabbro Cristian , Docking T Roderick , Durbin Richard , Earl Dent , Emrich Scott , Fedotov Pavel , Fonseca Nuno A , Ganapathy Ganeshkumar , Gibbs Richard A , Gnerre Sante , Godzaridis Élénie , Goldstein Steve , Haimel Matthias , Hall Giles , Haussler David , Hiatt Joseph B , Ho Isaac Y , Howard Jason , Hunt Martin , Jackman Shaun D , Jaffe David B , Jarvis Erich D , Jiang Huaiyang , Kazakov Sergey , Kersey Paul J , Kitzman Jacob O , Knight James R , Koren Sergey , Lam Tak-Wah , Lavenier Dominique , Laviolette François , Li Yingrui , Li Zhenyu , Liu Binghang , Liu Yue , Luo Ruibang , MacCallum Iain , MacManes Matthew D , Maillet Nicolas , Melnikov Sergey , Naquin Delphine , Ning Zemin , Otto Thomas D , Paten Benedict , Paulo Octávio S , Phillippy Adam M , Pina-Martins Francisco , Place Michael , Przybylski Dariusz , Qin Xiang , Qu Carson , Ribeiro Filipe J , Richards Stephen , Rokhsar Daniel S , Ruby J Graham , Scalabrin Simone , Schatz Michael C , Schwartz David C , Sergushichev Alexey , Sharpe Ted , Shaw Timothy I , Shendure Jay , Shi Yujian , Simpson Jared T , Song Henry , Tsarev Fedor , Vezzi Francesco , Vicedomini Riccardo , Vieira Bruno M , Wang Jun , Worley Kim C , Yin Shuangye , Yiu Siu-Ming , Yuan Jianying , Zhang Guojie , Zhang Hao , Zhou Shiguo , Korf Ian F
Published: July 2013

Background

The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly.

Results

In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies.

Conclusions

Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
Trace level ammonia sensing by SWCNTs (network/film) based resistive sensor using a simple approach in sensor development and design
Authors: Mishra Prabhash , Harsh  , Islam S S
Published: July 2013

Highly stable and sensitive detection of trace level (approximately 1 ppm) of NH3 gas at room temperature is demonstrated for single wall carbon nanotube (SWCNT)-based resistive sensor. The sensor device was comprised of two planer Au electrodes deposited on carbon nanotubes (CNTs) by thermal evaporation method followed by patterning with photolithography process. For the growth of high-quality SWCNTs, multiple catalysts were deposited by co-sputtering method, and the yielded CNTs were in the diameter range of 0.8 to 1.5 nm. The CNTs were characterized by various techniques including Raman spectroscopy, field emission scanning electron microscopy, and transmission electron microscopy. As-grown SWCNTs-based resistive sensor showed an excellent variation in sensor response in the trace sensing range from 1 to 50 ppm of NH3 where the sensor response linearly increased with NH3 concentration. The sensing mechanism was attributed to the electron transfer to the SWCNTs as a result of NH3 oxidation on the nanotube surface. The sensor was found to have good sensitivity with a response time of a few minutes at room temperature. Sensor recovery posed a great problem at room temperature, and the fast and complete recovery was successfully achieved by using appropriate thermal treatment protocol.
Safety and efficacy of noninvasive ventilation in patients with blunt chest trauma: a systematic review
Authors: Duggal Abhijit , Perez Pablo , Golan Eyal , Tremblay Lorraine , Sinuff Tasnim
Published: July 2013

Introduction

This systematic review looks at the use of noninvasive ventilation (NIV), inclusive of noninvasive positive pressure ventilation (NPPV) and continuous positive pressure ventilation (CPAP), in patients with chest trauma to determine its safety and clinical efficacy in patients with blunt chest trauma who are at high risk of acute lung injury (ALI) and respiratory failure.

Methods

We searched the MEDLINE, EMBASE and Cochrane Central Register of Controlled Trials (CENTRAL) databases. Pairs of reviewers abstracted relevant clinical data and assessed the methodological quality of randomized controlled trials (RCTs) using the Cochrane domain and observational studies using the Newcastle-Ottawa Scale.

Results

Nine studies were included (three RCTs, two retrospective cohort studies and four observational studies without a comparison group). There was significant heterogeneity among the included studies regarding the severity of injuries, degree of hypoxemia and timing of enrollment. One RCT of moderate quality assessed the use of NPPV early in the disease process before the development of respiratory distress. All others evaluated the use of NPPV and CPAP in patients with blunt chest trauma after the development of respiratory distress. Overall, up to 18% of patients enrolled in the NIV group needed intubation. The duration of NIV use was highly variable, but NIV use itself was not associated with significant morbidity or mortality. Four low-quality observational studies compared NIV to invasive mechanical ventilation in patients with respiratory distress and showed decreased ICU stay (5.3 to 16 days vs 9.5 to 15 days), complications (0% to 18% vs 38% to 49%) and mortality (0% to 9% vs 6% to 50%) in the NIV group.

Conclusions

Early use of NIV in appropriately identified patients with chest trauma and without respiratory distress may prevent intubation and decrease complications and ICU length of stay. Use of NIV to prevent intubation in patients with chest trauma who have ALI associated with respiratory distress remains controversial because of the lack of good-quality data.
Five-year risk of end-stage renal disease among intensive care patients surviving dialysis-requiring acute kidney injury: a nationwide cohort study
Authors: Gammelager Henrik , Christiansen Christian Fynbo , Johansen Martin Berg , Tønnesen Else , Jespersen Bente , Sørensen Henrik Toft
Published: July 2013

Introduction

Dialysis-requiring acute kidney injury (D-AKI) is common among intensive care unit (ICU) patients. However, follow-up data on the risk of end-stage renal disease (ESRD) among these patients remain sparse. We assessed the short-term and long-term risk of ESRD after D-AKI, compared it with the risk in other ICU patients, and examined the risk within subgroups of ICU patients.

Methods

We used population-based medical registries to identify all adult patients admitted to an ICU in Denmark from 2005 through 2010, who survived for 90 days after ICU admission. D-AKI was defined as needing acute dialysis at or after ICU admission. Subsequent ESRD was defined as a need for chronic dialysis for more than 90 days or a kidney transplant. We computed the cumulative ESRD risk for patients with D-AKI and for other ICU patients, taking into account death as a competing risk, and computed hazard ratios (HRs) using a Cox model adjusted for potential confounders.

Results

We identified 107,937 patients who survived for 90 days after ICU admission. Of these, 3,062 (2.8%) had an episode of D-AKI following ICU admission. The subsequent risk of ESRD up to 180 days after ICU admission was 8.5% for patients with D-AKI, compared with 0.1% for other ICU patients. This corresponds to an adjusted HR of 105.6 (95% confidence interval (CI): 78.1 to 142.9). Among patients who survived 180 days after ICU admission without developing ESRD (n = 103,996), the 181-day to 5-year ESRD risk was 3.8% for patients with D-AKI, compared with 0.3% for other ICU patients, corresponding to an adjusted HR of 6.2 (95% CI: 4.7 to 8.1). During the latter period, the impact of AKI was most pronounced in the youngest patients, aged 15 to 49 years (adjusted HR = 12.8, 95% CI: 6.5 to 25.4) and among patients without preexisting chronic kidney disease (adjusted HR = 11.9, 95% CI: 8.5 to 16.8).

Conclusion

D-AKI is an important risk factor for ESRD for up to five years after ICU admission.
VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer
Authors: St Laurent Georges , Shtokalo Dmitry , Dong Biao , Tackett Michael R , Fan Xiaoxuan , Lazorthes Sandra , Nicolas Estelle , Sang Nianli , Triche Timothy J , McCaffrey Timothy A , Xiao Weidong , Kapranov Philipp
Published: July 2013

Background

The function of the non-coding portion of the human genome remains one of the most important questions of our time. Its vast complexity is exemplified by the recent identification of an unusual and notable component of the transcriptome - very long intergenic non-coding RNAs, termed vlincRNAs.

Results

Here we identify 2,147 vlincRNAs covering 10 percent of our genome. We show they are present not only in cancerous cells, but also in primary cells and normal human tissues, and are controlled by canonical promoters. Furthermore, vlincRNA promoters frequently originate from within endogenous retroviral sequences. Strikingly, the number of vlincRNAs expressed from endogenous retroviral promoters strongly correlates with pluripotency or the degree of malignant transformation. These results suggest a previously unknown connection between the pluripotent state and cancer via retroviral repeat-driven expression of vlincRNAs. Finally, we show that vlincRNAs can be syntenically conserved in humans and mouse and their depletion using RNAi can cause apoptosis in cancerous cells.

Conclusions

These intriguing observations suggest that vlincRNAs could create a framework that combines many existing short ESTs and lincRNAs into a landscape of very long transcripts functioning in the regulation of gene expression in the nucleus. Certain types of vlincRNAs participate at specific stages of normal development and, based on analysis of a limited set of cancerous and primary cell lines, they appear to be co-opted by cancer-associated transcriptional programs. This provides additional understanding of transcriptome regulation during the malignant state, and could lead to additional targets and options for its reversal.
GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data
Authors: Zhao Keyan , Lu Zhi-xiang , Park Juw Won , Zhou Qing , Xing Yi
Published: July 2013

To characterize the genetic variation of alternative splicing, we develop GLiMMPS, a robust statistical method for detecting splicing quantitative trait loci (sQTLs) from RNA-seq data. GLiMMPS takes into account the individual variation in sequencing coverage and the noise prevalent in RNA-seq data. Analyses of simulated and real RNA-seq datasets demonstrate that GLiMMPS outperforms competing statistical models. Quantitative RT-PCR tests of 26 randomly selected GLiMMPS sQTLs yielded a validation rate of 100%. As population-scale RNA-seq studies become increasingly affordable and popular, GLiMMPS provides a useful tool for elucidating the genetic variation of alternative splicing in humans and model organisms.
Equine tendonitis therapy using mesenchymal stem cells and platelet concentrates: a randomized controlled trial
Authors: Carvalho Armandode Mattos , Badial Peres Ramos , Álvarez Luis Emiliano Cisneros , Yamada Ana Lucia Miluzzi , Borges Alexandre Secorun , Deffune Elenice , Hussni Carlos Alberto , Garcia Alves Ana Liz
Published: July 2013

Introduction

Tendon injury is a major cause of lameness and decreased performance in athletic equines. Various therapies for tendonitis have been described; however, none of these therapies results in complete tissue regeneration, and the injury recurrence rate is high even after long recovery periods involving rest and physiotherapy.

Methods

A lesion was induced with collagenase gel in the superficial digital flexor tendon in the center portion of the metacarpal region of eight equines of mixed breed. After two weeks, the lesions of the animals in the treated and control groups were treated through the intralesional administration of mesenchymal stem cells derived from adipose tissue (adMSCs) suspended in platelet concentrate (PC) and with phosphate buffered saline (PBS), respectively. Serial ultrasound analyses were performed every two weeks. After 16 weeks of therapy, a biopsy was performed for histopathological, immunohistochemical and gene expression (type I collagen (COL1A1), type III collagen (COL3A1), tenascin-C (TNC), tenomodulin (TNMD), and scleraxis (SCX)) analyses.

Results

Differences in the ultrasound and histopathological analyses were observed between the groups. Improved results were reported in the group treated with adMSCs suspended in PC. There was no difference in the gene expression levels observed after the different treatments. The main results observed from the histopathological evaluation of the treated group were as follows: a prevention of the progression of the lesion, a greater organization of collagen fibers, and a decreased inflammatory infiltrate. A lack of progression of the lesion area and its percentage was observed in the ultrasound image, and increased blood flow was measured by Power Doppler.

Conclusions

The use of adMSCs combined with PC for the therapy of experimentally induced tendonitis prevented the progression of the tendon lesion, as observed in the ultrasound examination, and resulted in a greater organization and decreased inflammation, as observed in the histopathological evaluation. These data demonstrate the therapeutic potential of this therapy for the treatment of equine tendonitis.
Major factors of economic development of modern Russia
Authors: Басовская  , Basovskaya Elena
Published: July 2013

Tendencies and factors of change of branch structure of economy of Russia

in the period of 1999–2008 are investigated. Data of branch structure of

investments of the Russian statistics and econometric methods are used.

The regression, cluster and discriminated analysis, the factorial analysis on

the basis of model main a component are applied. Discrepancy of tendencies

of development of structure of economy is established. Major factors of

development — a factor of preindustrial development (to 33–46% of changes),

a factor of industrial development (to 18–22% of changes) and a factor of postindustrial

development (to 28–36% of changes). The established ratio of factors

of development doesn’t correspond to current trends. This discrepancy became

one of preconditions of an economic crisis and delay of growth rates of

economy during the post-crisis period. For overcoming of contradictions the

active economic policy of attraction of investments in key is necessary for postindustrial

development of branch of economy. In work are submitted data,

characterizing results of the factorial analysis that is able to afford to specify

their interpretation.
Restricting the conversion of the defense industry complex risks
Authors: Булавина  , Bulavina O. , Иваница  , Ivanitsa I.
Published: July 2013

The development of civilian products at the enterprises is the most important

factor in ensuring the stability and performance. Only the balance between fixed

and conversion production can ensure their sustainability in a competitive

distribution of the state defense order and reduction in the volume of its funding

due to the possible negative trends in the Russian economy. Proposed a system

of indicators that have the greatest impact on the value of the share of civilian

production at the enterprises of the defense-industrial complex. Proposed the

approach to determining the minimum share of civilian products, allowing the

company to operate effectively in the event of an unexpected reduction of the

size or the lack of govement orders.
Human capital and labor productivity in modern Russia
Authors: Комарова  , Komarova Anna
Published: July 2013

Performed econometric studies have shown that the main factors determining productivity in Russia were the capital-labor and the level of education of the employed population. The performance impact of the level of education of the employed population surpasses the effect of the capital. The influence of the level of education of the employed population is growing, and the effect of the capital-labor falls due to wear and tear and obsolescence of fixed assets. The main tool for increasing productivity and GDP growth in the country is to raise the level of education of the employed population. Going on 11 years of general education can help increase productivity and GDP growth of 40%. Extension of the general education up to 12–13 years of age may contribute to a further increase in labor productivity and GDP growth for another 40–80%. Lack of capital invested in fixed assets in the future may reduce efficiency of human capital employed and devalue measures to increase the level of education of the employed population. For the effective use of human capital in the future necessary investments in fixed assets.
Methods of evaluating diffusion of new technological ways
Authors: Наташкина  , Natashkina E.
Published: July 2013

This article describes concept of technological ways and global crisis as natural process of changing ways. Application triangular model effect of technological ways on economic area countries and regions of world. There are functions impact of ways and parameters of function.
Typology of old-industrial regions
Authors: Сорокина  , Sorokina Natalia
Published: July 2013

The article presents an approach to the classification of old-industrial regions, to identify and to give a general characteristic areas of this type. Asked to identify six types of old-industrial regions, each of which is designed graphical model, reflecting the specificity of the socio-economic development of the territory. Presents empirical interpretation typology on the example of old-industrial regions of the Central Federal district of Russia.
The molecular biology of selenocysteine
Authors: Gonzalez-Flores Jonathan N. , Shetty Sumangala P. , Dubey Aditi , Copeland Paul R.
Published: July 2013

Selenium is an essential trace element that is incorporated into 25 human proteins as the amino acid selenocysteine (Sec). The incorporation of this amino acid turns out to be a fascinating problem in molecular biology because Sec is encoded by a stop codon, UGA. Layered on top of the canonical translation elongation machinery is a set of factors that exist solely to incorporate this important amino acid. The mechanism by which this process occurs, put into the context of selenoprotein biology, is the focus of this review.
Plant phospholipase A: advances in molecular biology, biochemistry, and cellular function
Authors: Chen Guanqun , Greer Michael S. , Weselake Randall J.
Published: July 2013

Plant phospholipase As (PLAs) are a complex group of enzymes that catalyze the release of free fatty acids from phospholipids. Plant PLAs can be grouped into three families, PLA1, PLA2, and patatin-like PLA, that catalyze the hydrolysis of acyl groups from the sn-1 and/or sn-2 position. Each family is composed of multiple isoforms of phospholipases that differ in structural, catalytic, and physiological characteristics. In this review, recently acquired information on molecular, biochemical, and functional aspects of plant PLAs will be discussed.
Topological full groups of one-sided shifts of finite type
Authors: Matui Hiroki
Published: July 2013

We explore the topological full group

〚
G
〛

$\llbracket G\rrbracket $

of
an essentially principal étale groupoid G on a Cantor set.
When G is minimal,
we show that

〚
G
〛

$\llbracket G\rrbracket $

(and its certain normal subgroup) is a complete invariant
for the isomorphism class of the étale groupoid G.
Furthermore, when G is either almost finite or purely infinite,
the commutator subgroup

D
(
〚
G
〛
)

$D(\llbracket G\rrbracket )$

is shown to be simple.
The étale groupoid G
arising from a one-sided irreducible shift of finite type is
a typical example of a purely infinite minimal groupoid.
For such G,

〚
G
〛

$\llbracket G\rrbracket $

is thought of as a generalization of the Higman–Thompson group.
We prove that

〚
G
〛

$\llbracket G\rrbracket $

is of type F
∞,
and so in particular it is finitely presented.
This gives us a new infinite family of
finitely presented infinite simple groups.
Also, the abelianization of

〚
G
〛

$\llbracket G\rrbracket $

is calculated and described
in terms of the homology groups of G.
Weak multiplier Hopf algebras I. The main theory
Authors: Van Daele Alfons , Wang Shuanhong
Published: July 2013

A weak multiplier Hopf algebra is a pair (A, Δ) of a non-degenerate idempotent algebra A and a coproduct Δ on A. The coproduct is a coassociative homomorphism from A to the multiplier algebra M(A ⊗ A) with some natural extra properties (like the existence of a counit). Further we impose extra but natural conditions on the ranges and the kernels of the canonical maps T
1 and T
2
defined from A ⊗ A to M(A ⊗ A) by
T
1(a ⊗ b) = Δ(a)(1 ⊗ b) and
T
2(a ⊗ b) = (a ⊗ 1)Δ(b).
The first condition is about the ranges of these maps. It is assumed that there exists an idempotent element
E ∈ M(A ⊗ A) such that Δ(A)(1 ⊗ A) = E(A ⊗ A) and
(A ⊗ 1)Δ(A) = (A ⊗ A)E. This element is unique if it exists. Then it is possible to extend the coproduct in a unique way to a homomorphism
Δ˜: M(A) → M(A ⊗ A) such that Δ˜(1) = E. In the case of a multiplier Hopf algebra we have E = 1 ⊗ 1 but this is no longer assumed for weak multiplier Hopf algebras. The second condition determines the behavior of the coproduct on the legs of E. We require
(Δ ⊗ ι)(E) = (ι ⊗ Δ)(E) = (1 ⊗ E)(E ⊗ 1) = (E ⊗ 1)(1 ⊗ E).
Finally, the last condition determines the kernels of the canonical maps T
1 and T
2 in terms of this idempotent E by a very specific relation.

From these conditions we develop the theory. In particular, we construct a unique antipode satisfying the expected properties and various other data. Special attention is given to the regular case (that is when the antipode is bijective) and the case of a *-algebra (where regularity is automatic).

Weak Hopf algebras are special cases of such weak multiplier Hopf algebras. Conversely, if the underlying algebra of a (regular) weak multiplier Hopf algebra has an identity, it is a weak Hopf algebra. Also any groupoid, finite or not, yields two weak multiplier Hopf algebras in duality. We will give more and interesting examples of weak multiplier Hopf algebras in parts II and III of this series of papers.