bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salarL.)
Authors: Ozerov Mikhail , Vasemägi Anti , Wennevik Vidar , Niemelä Eero , Prusov Sergey , Kent Matthew , Vähä Juha-Pekka 
Published: January 2013

AbstractBackgroundNew sequencing technologies have tremendously increased the number of known molecular markers (single nucleotide polymorphisms; SNPs) in a variety of species. Concurrently, improvements to genotyping technology have now made it possible to efficiently genotype large numbers of genome-wide distributed SNPs enabling genome wide association studies (GWAS). However, genotyping significant numbers of individuals with large number of SNPs remains prohibitively expensive for many research groups. A possible solution to this problem is to determine allele frequencies from pooled DNA samples, such ‘allelotyping’ has been presented as a cost-effective alternative to individual genotyping and has become popular in human GWAS. In this article we have tested the effectiveness of DNA pooling to obtain accurate allele frequency estimates for Atlantic salmon (Salmo salarL.) populations using an Illumina SNP-chip.ResultsIn total, 56 Atlantic salmon DNA pools from 14 populations were analyzed on an Atlantic salmon SNP-chip containing probes for 5568 SNP markers, 3928 of which were bi-allelic. We developed an efficient quality control filter which enables exclusion of loci showing high error rate and minor allele frequency (MAF) close to zero. After applying multiple quality control filters we obtained allele frequency estimates for 3631 bi-allelic loci. We observed high concordance (r> 0.99) between allele frequency estimates derived from individual genotyping and DNA pools. Our results also indicate that even relatively small DNA pools (35 individuals) can provide accurate allele frequency estimates for a given sample.ConclusionsDespite of higher level of variation associated with array replicates compared to pool construction, we suggest that both sources of variation should be taken into account. This study demonstrates that DNA pooling allows fast and high-throughput determination of allele frequencies in Atlantic salmon enabling cost-efficient identification of informative markers for discrimination of populations at various geographical scales, as well as identification of loci controlling ecologically and economically important traits.
Genetic variation and expression diversity between grain and sweet sorghum lines
Authors: Jiang Shu-Ye , Ma Zhigang , Vanitha Jeevanandam , Ramachandran Srinivasan 
Published: January 2013

Abstract

Background
Biological scientists have long sought after understanding how genes and their structural/functional changes contribute to morphological diversity. Though both grain (BT×623) and sweet (Keller) sorghum lines originated from the same species Sorghum bicolor L., they exhibit obvious phenotypic variations. However, the genome re-sequencing data revealed that they exhibited limited functional diversity in their encoding genes in a genome-wide level. The result raises the question how the obvious morphological variations between grain and sweet sorghum occurred in a relatively short evolutionary or domesticated period.

Results
We implemented an integrative approach by using computational and experimental analyses to provide a detail insight into phenotypic, genetic variation and expression diversity between BT×623 and Keller lines. We have investigated genome-wide expression divergence between BT×623 and Keller under normal and sucrose treatment. Through the data analysis, we detected more than 3,000 differentially expressed genes between these two varieties. Such expression divergence was partially contributed by differential cis-regulatory elements or DNA methylation, which was genetically determined by functionally divergent genes between these two varieties. Both tandem and segmental duplication played important roles in the genome evolution and expression divergence.

Conclusion
Substantial differences in gene expression patterns between these two varieties have been observed. Such an expression divergence is genetically determined by the divergence in genome level.
Genome-wide expression profiling of maize in response to individual and combined water and nitrogen stresses
Authors: Humbert Sabrina , Subedi Sanjeena , Cohn Jonathan , Zeng Bin , Bi Yong-Mei , Chen Xi , Zhu Tong , McNicholas Paul D , Rothstein Steven J 
Published: January 2013

AbstractBackgroundWater and nitrogen are two of the most critical inputs required to achieve the high yield potential of modern corn varieties. Under most agricultural settings however they are often scarce and costly. Fortunately, tremendous progress has been made in the past decades in terms of modeling to assist growers in the decision making process and many tools are now available to achieve more sustainable practices both environmentally and economically. Nevertheless large gaps remain between our empirical knowledge of the physiological changes observed in the field in response to nitrogen and water stresses, and our limited understanding of the molecular processes leading to those changes.ResultsThis work examines in particular the impact of simultaneous stresses on the transcriptome. In a greenhouse setting, corn plants were grown under tightly controlled nitrogen and water conditions, allowing sampling of various tissues and stress combinations. A microarray profiling experiment was performed using this material and showed that the concomitant presence of nitrogen and water limitation affects gene expression to an extent much larger than anticipated. A clustering analysis also revealed how the interaction between the two stresses shapes the patterns of gene expression over various levels of water stresses and recovery.ConclusionsOverall, this study suggests that the molecular signature of a specific combination of stresses on the transcriptome might be as unique as the impact of individual stresses, and hence underlines the difficulty to extrapolate conclusions obtained from the study of individual stress responses to more complex settings.
Enhancing the utility of Proteomics Signature Profiling (PSP) with Pathway Derived Subnets (PDSs), performance analysis and specialised ontologies
Authors: Goh Wilson Wen Bin , Fan Mengyuan , Low Hong Sang , Sergot Marek , Wong Limsoon 
Published: January 2013

Abstract

Background
Proteomics Signature Profiling (PSP) is a novel hit-rate based method that proved useful in resolving consistency and coverage issues in proteomics. As a follow-up study, several points need to be addressed: 1/ PSP’s generalisability to pathways, 2/ understanding the biological interplay between significant complexes and pathway subnets co-located on the same pathways on our liver cancer dataset, 3/ understanding PSP’s false positive rate and 4/ demonstrating that PSP works on other suitable proteomics datasets as well as expanding PSP’s analytical resolution via the use of specialised ontologies.

Results
1/ PSP performs well with Pathway-Derived Subnets (PDSs). Comparing the performance of PDSs derived from various pathway databases, we find that an integrative approach is best for optimising analytical resolution. Feature selection also confirms that significant PDSs are closely connected to the cancer phenotype.
2/ In liver cancer, correlation studies of significant PSP complexes and PDSs co-localised on the same pathways revealed an interesting relationship between the purine metabolism pathway and two other complexes involved in DNA repair. Our work suggests progression to poor stage requires additional mutations that disrupt DNA repair enzymes.
3/ False positive analysis reveals that PSP, applied on both complexes and PDSs, is powerful and precise.
4/ Via an expert-curated lipid ontology, we uncovered several interesting lipid-associated complexes that could be associated with cancer progression. Of particular interest is the HMGB1-HMGB2-HSC70-ERP60-GAPDH complex which is also involved in DNA repair. We also demonstrated generalisability of PSP using a non-small-cell lung carcinoma data set.

Conclusions
PSP is a powerful and precise technique, capable of identifying biologically coherent features. It works with biological complexes, network-predicted clusters as well as PDSs. Here, an instance of the interplay between significant PDSs and complexes, possibly significantly involved in liver cancer progression but not well understood as yet, is demonstrated. Also demonstrated is the enhancement of PSP’s analytical resolution using specialised ontologies.
Role of N-terminal protein formylation in central metabolic processes in Staphylococcus aureus
Authors: Mader Diana , Liebeke Manuel , Winstel Volker , Methling Karen , Leibig Martina , Götz Friedrich , Lalk Michael , Peschel Andreas 
Published: January 2013

Abstract

Background
Bacterial protein biosynthesis usually depends on a formylated methionyl start tRNA but Staphylococcus aureus is viable in the absence of Fmt, the tRNAMet formyl transferase. fmt mutants exhibit reduced growth rates indicating that the function of certain proteins depends on formylated N-termini but it has remained unclear, which cellular processes are abrogated by the lack of formylation.

Results
In order to elucidate how global metabolic processes are affected by the absence of formylated proteins the exometabolome of an S. aureus fmt mutant was compared with that of the parental strain and the transcription of corresponding enzymes was analyzed to identify possible regulatory changes. The mutant consumed glucose and other carbon sources slower than the wild type. While the turnover of several metabolites remained unaltered fmt inactivation led to increases pyruvate release and, concomitantly, reduced pyruvate dehydrogenase activity. In parallel, the release of the pyruvate-derived metabolites lactate, acetoin, and alanine was reduced. The anaerobic degradation of arginine was also reduced in the fmt mutant compared to the wild-type strain. Moreover, the lack of formylated proteins caused increased susceptibility to the antibiotics trimethoprim and sulamethoxazole suggesting that folic acid-dependant pathways were perturbed in the mutant.

Conclusions
These data indicate that formylated proteins are crucial for specific bacterial metabolic processes and they may help to understand why it has remained important during bacterial evolution to initiate protein biosynthesis with a formylated tRNAMet.
Evaluation of intravenous voriconazole in patients with compromised renal function
Authors: Lilly Craig M , Welch Verna L , Mayer Thomas , Ranauro Paul , Meisner Joanne , Luke David R 
Published: January 2013

Abstract

Background
Incorporation of the solubilizing excipient, sulfobutylether-β-cyclodextrin (SBECD), in the intravenous (IV) formulation of voriconazole has resulted in the recommendation that this formulation be used with caution in patients with creatinine clearances (Clcr) < 50 mL/min. This study evaluated the safety of IV voriconazole compared with two other IV antifungals not containing SBECD in patients with compromised renal function.

Methods
A total of 128 patients aged 11–93 years who had a baseline Clcr < 50 mL/min between January 1, 2007 and December 31, 2010 were identified from a database of a university-affiliated inpatient healthcare system; of these, 55 patients received caspofungin, 54 patients received fluconazole, and 19 patients received voriconazole. Changes in serum creatinine (Scr) and Clcr levels while on therapy were compared with baseline values and between groups.

Results
The groups had similar characteristics apart from the larger proportion of females that received fluconazole. Baseline Scr was higher in those receiving caspofungin, but maximal increases of Scr and decreases in Clcr were greatest for the fluconazole group. Acute kidney injury (AKI), assessed by RIFLE criteria, was more frequent in the fluconazole vs. the caspofungin group (p < 0.01); incidence of AKI in the voriconazole group was not significantly different than found in the other two groups. The infecting organism was a predictor of AKI and formulation with SBECD was not.

Conclusions
Treatment of fungal infections in patients with compromised renal function with an SBECD-containing antifungal agent was not associated with AKI in clinical practice. Since the infecting organism was associated with AKI, decision on which antifungal to use should be determined by susceptibilities to the organism and not the incorporation of SBECD in the IV formulation.
Debate around infection-dependent hemophagocytic syndrome in paediatrics
Authors: Ansuini Valentina , Rigante Donato , Esposito Susanna 
Published: January 2013

AbstractBackgroundHemophagocytic syndrome (HPS) is clinically defined as a combination of fever, liver dysfunction, coagulation abnormalities, pancytopenia, progressive macrophage proliferation throughout the reticuloendothelial system, and cytokine over-production, and may be primary or secondary to infectious, auto-immune, and tumoral diseases. The most consistent association is with viral infections but, as it is still debated whether any micro-organisms are involved in its pathogenesis, we critically appraised the literature concerning HPS and its relationship with infections.DiscussionInfection-dependent HPS has been widely observed, but there are no data concerning its incidence in children. A better understanding of the pathophysiology of HPS may clarify the interactions between the immune system and the variously implicated potential infectious agents. Epstein-Barr virus (EBV) infection has been prominently associated with HPS, with clonal proliferation and the hyperactivation of EBV-infected T cells. However, a number of other viral, bacterial, fungal, and parasitic infections have been reported in association with HPS. In the case of low-risk HPS, corticosteroids and/or intravenous immunoglobulin or cyclosporine A may be sufficient to control the biological process, but etoposide is recommended as a means of reversing infection-dependent lymphohistiocytic dysregulation in high-risk cases.SummaryHPS is a potential complication of various infections. A polymerase chain reaction search for infectious agents including EBV, cytomegalovirus andLeishmaniais recommended in clinical settings characterised by non-remitting fever, organomegaly, cytopenia and hyperferritinemia.
Rifampin-associated tubulointersititial nephritis and Fanconi syndrome presenting as hypokalemic paralysis
Authors: Min Hong Ki , Kim Eun Oh , Lee Sang Ju , Chang Yoon Kyung , Suh Kwang Sun , Yang Chul Woo , Kim Suk Young , Hwang Hyeon Seok 
Published: January 2013

Abstract

Background
Rifampin is one of the most important drugs in first-line therapies for tuberculosis. The renal toxicity of rifampin has been reported sporadically and acute tubulointerstitial nephritis (ATIN) is a frequent histological finding. We describe for the first time a case of ATIN and Fanconi syndrome presenting as hypokalemic paralysis, associated with the use of rifampin.

Case presentation
A 42-year-old man was admitted with sudden-onset lower extremity paralysis and mild renal insufficiency. He had been treated for pulmonary tuberculosis with isoniazid, rifampin, and ethambutol for 2 months. Laboratory tests revealed proteinuria, profound hypokalemia, hyperchloremic metabolic acidosis with a normal anion gap, positive urine anion gap, hypophosphatemia with hyperphosphaturia, hypouricemia with hyperuricosuria, glycosuria with normal serum glucose level, generalized aminoaciduria, and β2-microglobulinuria. A kidney biopsy revealed findings typical of ATIN and focal granular deposits of immunoglubulin A and complement 3 in the glomeruli and tubules. Electron microscopy showed epithelial foot process effacement and electron-dense deposits in the subendothelial and mesangial spaces. Cessation of rifampin resolved the patient’s clinical presentation of Fanconi syndrome, and improved his renal function and proteinuria.

Conclusion
This case demonstrates that rifampin therapy can be associated with Fanconi syndrome presenting as hypokalemic paralysis, which is a manifestation of ATIN. Kidney function and the markers of proximal tubular injury should be carefully monitored in patients receiving rifampin.
Mineral metabolism and outcomes in chronic kidney disease stage 2–4 patients
Authors: Chartsrisak Kamonwan , Vipattawat Kotcharat , Assanatham Montira , Nongnuch Arkom , Ingsathit Atiporn , Domrongkitchaiporn Somnuek , Sumethkul Vasant , Distha-Banchong Sinee 
Published: January 2013

Abstract

Background
Marked hyperphosphatemia, hyperparathyroidism and 25-hydroxyvitamin D deficiency are associated with mortality in dialysis patients. Such data in chronic kidney disease stage 2–4 population are limited. It has been suggested that high-normal serum phosphate predicts worse renal and patient outcomes. The data regarding parathyroid hormone and outcomes in this population is limited. The present study examined mineral metabolism and its association with the development of end-stage renal disease and mortality in stage 2–4 chronic kidney disease patients.

Methods
This is a prospective cohort study that included 466 non-dialysis chronic kidney disease stage 2–4 patients. Mineral parameters were obtained at the time of enrollment and the patients were followed prospectively for 25 (1–44) months or until they reached the endpoints of end-stage renal disease or mortality.

Results
Hyperparathyroidism and 25-hydroxyvitamin D deficiency began to occur in the early stages of chronic kidney disease, whereas significant hyperphosphatemia only developed in the later stages. High-normal and mildly elevated serum phosphate (>4.2 mg/dL) predicted the composite outcome of end-stage renal disease or mortality after adjustments for cardiovascular risk factors, chronic kidney disease stage and other mineral parameters. Parathyroid hormone levels above the upper limit of normal (>65 pg/mL) predicted the future development of end-stage renal disease and the composite outcome of end-stage renal disease or mortality after adjustments. 25-hydroxyvitamin D deficiency (<15 ng/mL) was also associated with worse outcomes.

Conclusions
In chronic kidney disease, hyperparathyroidism developed prior to significant hyperphosphatemia confirming the presence phosphate retention early in the course of chronic kidney disease. High-normal serum phosphate and mildly elevated parathyroid hormone levels predicted worse renal and patient outcomes. This data emphasizes the need for early intervention in the care of chronic kidney disease stage 2–4 patients.
The risk of upper gastrointestinal bleeding in patients treated with hemodialysis: a population-based cohort study
Authors: Kuo Chien-Chun , Kuo Hsin-Wei , Lee I-Ming , Lee Chien-Te , Yang Chun-Yuh 
Published: January 2013

AbstractBackgroundThere are no prior studies that have estimated the risk of upper gastrointestinal bleeding (UGIB) among the dialysis population relative to the general population. The aim of this study was to examine the risk of UGIB among end-stage renal disease (ESRD) patients during a 6-year period following their initiation of hemodialysis (HD) therapy in Taiwan- a country with the highest incidence of ESRD in the world, using general population as an external comparison group.MethodsData were obtained from the Taiwan National health Insurance Research Database. In total, 796 patients who were beginning HD between 1999 and 2003 were recruited as the study cohort and 3,184 patients matched for age and sex were included as comparison cohort. Multivariate Cox proportional hazard regression models were used to adjust for confounding and to compare the 6-year UGIB-free survival rate between these two cohorts.ResultsThe incidence rate of UGIB (42.01 per 1000 person-year) was significantly higher in the HD cohort than in the control cohort (27.39 per 1000 person-years). After adjusting for potential confounders, the adjusted hazard ratios for UGIB during the 6-year follow-up periods for HD patients was 1.27 (95% CI=1.03-1.57) compared to patients in the comparison cohort.ConclusionsWe conclude that HD patients were at an increased risk for UGIB compared with the general population.
Prevention and management of excessive gestational weight gain: a survey of overweight and obese pregnant women
Authors: Leslie W S , Gibson A , Hankey C R 
Published: January 2013

Abstract

Background
Excessive gestational weight gain is associated with adverse infant, childhood and maternal outcomes and research to develop interventions to address this issue is ongoing. The views of women on gestational weight gain and the resources they would consider helpful in addressing this are however largely unknown. This survey aimed to determine the views of newly pregnant women, living in areas of social disadvantage, on 1) their current body weight and potential gestational weight gain and 2) the resources or interventions they would consider helpful in preventing excessive gestational weight gain.

Methods
A convenience sample of overweight and obese pregnant women living in Fife, UK, were invited to complete a short anonymised questionnaire at their 12 week booking visit.

Results
428 women, BMI>25 kg/m2, completed the questionnaire. Fifty-four per cent of respondents were obese (231) and 62% were living in areas of mild to moderate deprivation. Over three-quarters of participants felt dissatisfied with their current weight (81%). The majority of women (60%) expressed some concern about potential weight gain. Thirty-nine percent were unconcerned about weight gain during their pregnancy, including 34 women (19%) who reported having retained weight gained in earlier pregnancies. Amongst those concerned about weight gain advice on physical activity (41%) and access to sports/leisure facilities were favoured resources (36%). Fewer women (12%) felt that group sessions on healthy eating or attending a clinic for individualised advice (14%) would be helpful. “Getting time off work” was the most frequently cited barrier (48%) to uptake of resources other than leaflets.

Conclusions
These data suggest a lack of awareness amongst overweight and obese women regarding excessive gestational weight gain. Monitoring of gestational weight gain, and approaches for its management, should be formally integrated into routine antenatal care. Barriers to the uptake of resources to address weight gain are numerous and must be considered in the design of future interventions and services.