The IMGT/HLA database Robinson, James; Waller, Matthew J.; Fail, Sylvie C. ...
Nucleic acids research,
01/2009, Letnik:
37, Številka:
suppl-1
Journal Article
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It is 10 years since the IMGT/HLA database was released, providing the HLA community with a searchable repository of highly curated HLA sequences. The HLA complex is located within the 6p21.3 region ...of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and are highly polymorphic. The naming of these HLA genes and alleles, and their quality control is the responsibility of the WHO Nomenclature Committee for Factors of the HLA System. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute, we are able to provide public access to this data through the website http://www.ebi.ac.uk/imgt/hla/. The first release contained 964 sequences, the most recent release 3300 sequences, with around 450 new sequences been added each year. The tools provided on the website have been updated to allow more complex alignments, which include genomic sequence data, as well as the development of tools for probe and primer design and the inclusion of data from the HLA Dictionary. Regular updates to the website ensure that new and confirmatory sequences are dispersed to the HLA community, and the wider research and clinical communities.
There are no minimally invasive diagnostic metrics for acute kidney transplant rejection (AR), especially in the setting of the common confounding diagnosis, acute dysfunction with no rejection ...(ADNR). Thus, though kidney transplant biopsies remain the gold standard, they are invasive, have substantial risks, sampling error issues and significant costs and are not suitable for serial monitoring. Global gene expression profiles of 148 peripheral blood samples from transplant patients with excellent function and normal histology (TX; n = 46), AR (n = 63) and ADNR (n = 39), from two independent cohorts were analyzed with DNA microarrays. We applied a new normalization tool, frozen robust multi‐array analysis, particularly suitable for clinical diagnostics, multiple prediction tools to discover, refine and validate robust molecular classifiers and we tested a novel one‐by‐one analysis strategy to model the real clinical application of this test. Multiple three‐way classifier tools identified 200 highest value probesets with sensitivity, specificity, positive predictive value, negative predictive value and area under the curve for the validation cohort ranging from 82% to 100%, 76% to 95%, 76% to 95%, 79% to 100%, 84% to 100% and 0.817 to 0.968, respectively. We conclude that peripheral blood gene expression profiling can be used as a minimally invasive tool to accurately reveal TX, AR and ADNR in the setting of acute kidney transplant dysfunction.
This study of kidney transplantation describes a three‐way classifier based on global gene expression profiling of peripheral blood and the blood signatures of patients with excellent functioning grafts that can be used in the setting of acute kidney transplant dysfunction to accurately distinguish between biopsy‐proven acute rejection and acute dysfunction with no rejection.
We present the discovery of the second binary with a Roche lobe-filling hot subdwarf transferring mass to a white dwarf (WD) companion. This 56 minute binary was discovered using data from the Zwicky ...Transient Facility. Spectroscopic observations reveal an He-sdOB star with an effective temperature of Teff = 33,700 1000 K and a surface gravity of log(g) = 5.54 0.11. The GTC+HiPERCAM light curve is dominated by the ellipsoidal deformation of the He-sdOB star and shows an eclipse of the He-sdOB by an accretion disk as well as a weak eclipse of the WD. We infer a He-sdOB mass of MsdOB = 0.41 0.04 M and a WD mass of MWD = 0.68 0.05 M . The weak eclipses imply a WD blackbody temperature of 63,000 10,000 K and a radius RWD = 0.0148 0.0020 R as expected for a WD of such high temperature. The He-sdOB star is likely undergoing hydrogen shell burning and will continue transferring mass for 1 Myr at a rate of 10−9 M yr−1, which is consistent with the high WD temperature. The hot subdwarf will then turn into a WD and the system will merge in 30 Myr. We suggest that Galactic reddening could bias discoveries toward preferentially finding Roche lobe-filling systems during the short-lived shell-burning phase. Studies using reddening-corrected samples should reveal a large population of helium core-burning hot subdwarfs with Teff 25,000 K in binaries of 60-90 minutes with WDs. Though not yet in contact, these binaries would eventually come into contact through gravitational-wave emission and explode as a subluminous thermonuclear supernova or evolve into a massive single WD.
Metagenomic sequencing is a promising approach for identifying and characterizing organisms and their functional characteristics in complex, polymicrobial infections, such as airway infections in ...people with cystic fibrosis. These analyses are often hampered, however, by overwhelming quantities of human DNA, yielding only a small proportion of microbial reads for analysis. In addition, many abundant microbes in respiratory samples can produce large quantities of extracellular bacterial DNA originating either from biofilms or dead cells. We describe a method for simultaneously depleting DNA from intact human cells and extracellular DNA (human and bacterial) in sputum, using selective lysis of eukaryotic cells and endonuclease digestion. We show that this method increases microbial sequencing depth and, consequently, both the number of taxa detected and coverage of individual genes such as those involved in antibiotic resistance. This finding underscores the substantial impact of DNA from sources other than live bacteria in microbiological analyses of complex, chronic infection specimens.
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•Human and extracellular bacterial DNA can bias metagenomic sequencing•Hypotonic lysis, endonuclease digestion limit human and extracellular bacterial DNA•Reducing extracellular DNA optimizes metagenomic sequencing of viable bacterial cells•Increased microbial sequencing coverage improves detection of important genes
Nelson et al. describe a method for reducing both human cellular DNA and extracellular DNA (human and bacterial) in a complex respiratory sample using hypotonic lysis and endonuclease digestion. This method increases effective microbial sequencing depth and minimizes bias introduced into subsequent phylogenetic analysis by bacterial extracellular DNA.
The production and release of hematopoietic growth factors from bone marrow stromas established in vitro from patients with aplastic anemia is normal or increased. Addition of hematopoietic growth ...factors to aplastic anemia bone marrow cells results in only modest increases in colony growth, with the exception of granulocyte colony-stimulating factor (G-CSF), which corrects their impaired cloning efficiency to normal. Most clinical data on the use of hematopoietic growth factors in aplastic anemia have derived from uncontrolled and small single-arm studies or case reports. Sustained trilineage hematologic responses have not been observed when hematopoietic growth factors have been used alone or in combination. Serious side effects have been reported for most of the hematopoietic growth factors in patients with aplastic anemia, with the exception of G-CSF. There is a major concern that they may further increase the risk of clonal disorders such as myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Hematopoietic growth factors should not be used alone in newly diagnosed patients as specific treatment for aplastic anemia, and their use in combination with immunosuppressive therapy should be confined to multicenter, prospective randomized studies.
Epirubicin (4'-epidoxorubicin), a diastereoisomer of doxorubicin, has established activity in the treatment of many cancer types sensitive to doxorubicin. Its activity in other tumor targets such as ...melanoma, head and neck cancer, and recurrent colorectal cancer has been less well defined. Three concurrent phase II studies examined the efficacy and toxicity of epirubicin (90 mg/m2 given intravenously at 3-week intervals) in the treatment of 71 patients with the aforementioned cancers. Of 66 eligible patients who were assessable for response, one patient (with colorectal cancer) achieved a complete response and three patients (with head and neck cancer) achieved partial responses. The response rate in patients with head and neck cancer was 18% (95% confidence interval, 4-43%). Myelosuppression, alopecia, and nausea were the most frequent toxicities. Two patients died of neutropenic sepsis and grade IV leukopenia occurred in six patients (8%). Grade III toxicities were as follows: leukopenia (17%), anemia (10%), alopecia (8%), fever (1%), thrombocytopenia (1%). Grade I or II cardiac toxicity was noted in four patients at cumulative doses ranging between 375 mg/m2 to 1,283 mg/m2. Epirubicin is ineffective as a single agent at this dose and schedule in the treatment of patients with melanoma and colorectal cancer. In head and neck cancer, a modest response rate encourages further exploration of epirubicin and related anthracyclines in combination regimens.
Background Although hepatic metastasectomy is well established for colorectal and neuroendocrine cancer, the approach to hepatic metastases from other sites is not well defined. We sought to examine ...the management of noncolorectal non-neuroendocrine liver metastases. Study Design A retrospective review from 4 major liver centers identified patients who underwent liver resection for noncolorectal non-neuroendocrine metastases between 1990 and 2009. The Kaplan-Meier method was used to analyze survival, and Cox regression models were used to examine prognostic variables. Results There were 420 patients available for analysis. Breast cancer (n = 115; 27%) was the most common primary malignancy, followed by sarcoma (n = 98; 23%), and genitourinary cancers (n = 92; 22%). Crude postoperative morbidity and mortality rates were 20% and 2%, respectively. Overall median survival was 49 months, and 1, 3, and 5-year Kaplan-Meier survival rates were 73%, 50%, and 31%. Survival was not significantly different between the various primary tumor types. Recurrent disease was found after hepatectomy in 66% of patients. In multivariable models, lymphovascular invasion (p = 0.05) and metastases ≥5 cm (p = 0.04) were independent predictors of poorer survival. Median survival was shorter for resections performed between 1990 and 1999 (n = 101, 32 months) when compared with resections between 2000 and 2009 (n = 319, 66 months; p = 0.003). Conclusions Hepatic metastasectomy for noncolorectal non-neuroendocrine cancers is safe and feasible in selected patients. Lymphovascular invasion and metastases ≥5 cm were found to be associated with poorer survival. Patients undergoing metastasectomy in more recent years appear to be surviving longer, however, the reasons for this are not conclusively determined.
role of protein in weight loss and maintenance Leidy, Heather J; Clifton, Peter M; Astrup, Arne ...
The American journal of clinical nutrition,
06/2015, Letnik:
101, Številka:
6
Journal Article
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Over the past 20 y, higher-protein diets have been touted as a successful strategy to prevent or treat obesity through improvements in body weight management. These improvements are thought to be ...due, in part, to modulations in energy metabolism, appetite, and energy intake. Recent evidence also supports higher-protein diets for improvements in cardiometabolic risk factors. This article provides an overview of the literature that explores the mechanisms of action after acute protein consumption and the clinical health outcomes after consumption of long-term, higher-protein diets. Several meta-analyses of shorter-term, tightly controlled feeding studies showed greater weight loss, fat mass loss, and preservation of lean mass after higher-protein energy-restriction diets than after lower-protein energy-restriction diets. Reductions in triglycerides, blood pressure, and waist circumference were also reported. In addition, a review of the acute feeding trials confirms a modest satiety effect, including greater perceived fullness and elevated satiety hormones after higher-protein meals but does not support an effect on energy intake at the next eating occasion. Although shorter-term, tightly controlled feeding studies consistently identified benefits with increased protein consumption, longer-term studies produced limited and conflicting findings; nevertheless, a recent meta-analysis showed persistent benefits of a higher-protein weight-loss diet on body weight and fat mass. Dietary compliance appears to be the primary contributor to the discrepant findings because improvements in weight management were detected in those who adhered to the prescribed higher-protein regimen, whereas those who did not adhere to the diet had no marked improvements. Collectively, these data suggest that higher-protein diets that contain between 1.2 and 1.6 g protein · kg ⁻¹ · d ⁻¹ and potentially include meal-specific protein quantities of at least ∼25–30 g protein/meal provide improvements in appetite, body weight management, cardiometabolic risk factors, or all of these health outcomes; however, further strategies to increase dietary compliance with long-term dietary interventions are warranted.
Traditionally malaria epidemiology has focused on factors such as parasite rates and vector dynamics without specific reference to disease. There are limited comprehensive data on malaria as a ...life-threatening event in African children. We have identified, through hospital surveillance, 581 episodes of severe malaria in residents of a defined area on the Kenya coast over a period of 3 years. This represents an absolute minimum risk of developing severe malaria by the fifth birthday of 1 in 15. The presentation of severe malaria showed marked seasonality, but the timing and magnitude of these fluctuations varied considerably between years. A satellite navigational system was used to define the exact location of the home of each severe malaria case. Space-time clustering of severe malaria was evident in this community. Seasonal peaks in incidence of severe malaria may comprise discrete mini-epidemics. In contrast, parasite rates in the community varied little during the course of the surveillance. The monitoring of disease, as opposed to parasitization, in children may result in more effective targeting of intervention resources.
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