The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

tion’, implying that most patients ‘should’ receive a particular action. In contrast, level 2 guidelines are essentially ‘suggestions’ and are deemed to be ‘weak’ or discretionary, recognising that management decisions may vary in different clinical contexts. Each recommendation was further graded from A to D by the quality of evidence underpinning them, with grade A referring to a high quality of evidence whilst grade D recognised a ‘very low’ evidence base. The overall strength and quality of the supporting evidence is summarised in table 1 . The guidelines focused on 4 key domains: (1) AKI definition, (2) prevention and treatment of AKI, (3) contrastinduced AKI (CI-AKI) and (4) dialysis interventions for the treatment of AKI. The full summary of clinical practice statements is available at www.kdigo.org, but a few key recommendation statements will be highlighted here.

/pdf/kdigo-clinical-practice-guidelines-for-acute-kidney-injury-27tybolw7l.pdf

KDIGO clinical practice guidelines for acute kidney injury.

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

/pdf/integrative-analysis-of-111-reference-human-epigenomes-4bavnjaon6.pdf

Integrative analysis of 111 reference human epigenomes

Acute kidney injury (AKI) is a complex disorder for which currently there is no accepted definition. Having a uniform standard for diagnosing and classifying AKI would enhance our ability to manage these patients. Future clinical and translational research in AKI will require collaborative networks of investigators drawn from various disciplines, dissemination of information via multidisciplinary joint conferences and publications, and improved translation of knowledge from pre-clinical research. We describe an initiative to develop uniform standards for defining and classifying AKI and to establish a forum for multidisciplinary interaction to improve care for patients with or at risk for AKI. Members representing key societies in critical care and nephrology along with additional experts in adult and pediatric AKI participated in a two day conference in Amsterdam, The Netherlands, in September 2005 and were assigned to one of three workgroups. Each group's discussions formed the basis for draft recommendations that were later refined and improved during discussion with the larger group. Dissenting opinions were also noted. The final draft recommendations were circulated to all participants and subsequently agreed upon as the consensus recommendations for this report. Participating societies endorsed the recommendations and agreed to help disseminate the results. The term AKI is proposed to represent the entire spectrum of acute renal failure. Diagnostic criteria for AKI are proposed based on acute alterations in serum creatinine or urine output. A staging system for AKI which reflects quantitative changes in serum creatinine and urine output has been developed. We describe the formation of a multidisciplinary collaborative network focused on AKI. We have proposed uniform standards for diagnosing and classifying AKI which will need to be validated in future studies. The Acute Kidney Injury Network offers a mechanism for proceeding with efforts to improve patient outcomes.

Acute Kidney Injury Network: report of an initiative to improve outcomes in acute kidney injury

Advances in immunosuppressive treatment and supportive care over the past few decades have led to improved clinical outcomes in patients with severe lupus nephritis. The management of severe proliferative lupus nephritis can be divided into an initial induction phase followed by a prolonged maintenance phase. Combined use of corticosteroid and cyclophosphamide has been the standard induction therapy, although a significant proportion of patients develop treatment-related complications such as infection and gonadal failure. While there is general agreement on the immunosuppressive regimen for induction treatment, there is marked variation with regard to maintenance immunosuppressive regimens. The latter is consequent to a paucity of data, since a big sample size and prolonged follow-up is required for clinical studies that investigate maintenance treatment, in view of the marked heterogeneity in patient characteristics and individual differences in the propensity for relapse. Nevertheless, there is accumulating evidence that a combination of corticosteroid and mycophenolate mofetil can be adopted as effective and well-tolerated treatment both for induction and for long-term maintenance in lupus nephritis. Favourable long-term prognosis can be ensured provided that effective treatment can be instituted early, before irreversible renal parenchymal damage is established.

Mycophenolate mofetil as treatment for lupus nephritis

BacWound: Chronic non-A, non-B hepatitis is a major cause of liver disease in renal transplant recipients. Methods: One hundred eighty-five renal ailograft recipients, including 151 who had been prospectively followed up for 24 months, were studied to determine the prevalence and course of hepatitis C virus (HCV) infection. Antibody to HCV (anti-HCV) was measured by enzyme immunoassay, and HCV RNA was measured by nested polymerase chain reaction assay. Results: Twenty-three (12.4%) patients were positive for anti-HCV and/or HCV RNA: 19 (10.3%) were anti-HCV positive; and HCV RNA was detected in 18 (94.7%) anti-HCV-positive and 4 (2.4%) anti-HCV-negative patients. Markers of HCV infection persisted in all HCVpositive patients over the 2-year period. Most HCV-positlve patients acquired HCV infection before or at the time of transplantation. The incidence of new infection after transplantation was 0.45% per patient-year. Anti-HCV and/or HCV RNA was detected in 75% of patients wlth biochemical chronic non-A, non-B hepatitis, but transaminase levels were persistently normal in 30.4% of HCV-positive individuals. Conc/usions: HCV infection is common among renal transplant recipients. Testing for HCV RNA is important because some patients might not produce anti-HCV. Transaminase levels cannot be used as a surrogate marker of HCV infection in these patients.

https://www.gastrojournal.org/article/0016-5085(93)91023-B/pdf

A Prospective Study of Transplant Recipients Hepatitis C Virus Infection Among Renal

Renal artery thromboembolism is a rare event in native kidneys and has never been reported to occur in allograft kidney. We report a case of allograft kidney infarction secondary to embohsation from t

Delayed Recurrent Thromboembolism of the Allograft Kidney

Late onset-lymphocele after renal transplantation

PAN is a rare entity in the Chinese population (1). It is characterized pathologically by systemic necrotizing vasculitis on median-sized vessels. Renal involvement from aneurysm formation is common, but perinephric bleeding, especially bilateral, is unusual. Prompt diagnosis and treatment is critically important in controlling bleeding, salvaging renal function and arresting progression of the vasculitic process. Morbidity and mortality are frequently owed to uncontrolled sepsis and bleeding. We report a patient with classical PAN, which was complicated by perinephric hematoma and acute renal failure. Despite the initial well being of the patient, massive gastrointestinal bleeding supervened, which eventually triggered a series of fatal complications.

Perinephric hematoma and massive gastrointestinal hemorrhage (GIB) complicating polyarteritis nodosa (PAN).

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