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Specialised metabolites from microbial sources are well-known for their wide range of biomedical applications, particularly as antibiotics. When mining paired genomic and metabolomic data sets for novel specialised metabolites, establishing links between Biosynthetic Gene Clusters (BGCs) and metabolites represents a promising way of finding such novel chemistry. However, due to the lack of detailed biosynthetic knowledge for the majority of predicted BGCs, and the large number of possible combinations, this is not a simple task. This problem is becoming ever more pressing with the increased availability of paired omics data sets. Current tools are not effective at identifying valid links automatically, and manual verification is a considerable bottleneck in natural product research. We demonstrate that using multiple link-scoring functions together makes it easier to prioritise true links relative to others. Based on standardising a commonly used score, we introduce a new, more effective score, and introduce a novel score using an Input-Output Kernel Regression approach. Finally, we present NPLinker, a software framework to link genomic and metabolomic data. Results are verified using publicly available data sets that include validated links. Author summary: In this article, we introduce NPLinker, a software framework to link genomic and metabolomic data, to link microbial secondary metabolites to their producing genomic regions. Two of the major approaches for such linking are analysis of the correlation between sets of strains, and analysis of predicted features of the molecules. While these methods are usually used separately, we demonstrate that they are in fact complementary, and show a way to combine them to improve their performance. We begin by demonstrating a weakness in the most common method of strain correlation analysis, and suggest an improvement. We then introduce a new feature-based analysis method which, unlike most such methods, does not directly depend on the natural product compound class. Finally, we demonstrate that the two are complementary and proceed to combine them into a single scoring function for genomic and metabolomic links, which shows improved performance over either of the individual approaches. Verification is done using curated databases of genomic and metabolomic data, as well as public data sets of microbial data including validated links. [ABSTRACT FROM AUTHOR]

We investigated the infection dynamics of 2 influenza A(H1N1) virus isolates from the swine 1A.3.3.2 (pandemic 2009) and 1C (Eurasian, avian-like) lineages. The 1C-lineage virus, A/Pavia/65/2016, although phylogenetically related to swine-origin viruses, was isolated from a human clinical case. This strain infected ferrets, a human influenza model species, and could be transmitted by direct contact and, less efficiently, by airborne exposure. Infecting ferrets and pigs (the natural host) resulted in mild or inapparent clinical signs comparable to those observed with 1A.3.3.2-lineage swine-origin viruses. Both H1N1 viruses could infect pigs and were transmitted to cohoused ferrets. Ferrets vaccinated with a human 2016–17 seasonal influenza vaccine were protected against infection with the antigenically matched 1A pandemic 2009 virus but not against the swine-lineage 1C virus. Our results reaffirm the need for continuous influenza A virus surveillance in pigs and identification of candidate human vaccine viruses. [ABSTRACT FROM AUTHOR]

The III-V nanowire quantum dots (NWQDs) monolithically grown on silicon substrates, combining the advantages of both one- and zero-dimensional materials, represent one of the most promising technologies for integrating advanced III-V photonic technologies on a silicon microelectronics platform. However, there are great challenges in the fabrication of high-quality III-V NWQDs by a bottom-up approach, that is, growth by the vapor-liquid-solid method, because of the potential contamination caused by external metal catalysts and the various types of interfacial defects introduced by self-catalyzed growth. Here, we report the defect-free self-catalyzed III-V NWQDs, GaAs quantum dots in GaAsP nanowires, on a silicon substrate with pure zinc blende structure for the first time. Well-resolved excitonic emission is observed with a narrow line width. These results pave the way toward on-chip III-V quantum information and photonic devices on silicon platform. [ABSTRACT FROM AUTHOR]

The article discusses the role of the Special Programme for Research and Training in Tropical Diseases (TDR) in improving disease prevention and control. TDR was established in 1975 to address the social and economic factors that affect the transmission and control of diseases in tropical regions. The program has focused on applied social and economic research, community participation in disease control, and the integration of human behavioral factors in program design. TDR has also played a significant role in implementing research findings into practical solutions, such as the use of insecticide-treated nets and community-directed approaches for disease control. The program has also emphasized the importance of gender research and gender-sensitive interventions in addressing tropical diseases. TDR's work has contributed to important results in disease prevention and control, and the program continues to evolve to address current challenges, including multidrug-resistant tuberculosis and the impact of climate change on vector-borne diseases. [Extracted from the article]

The article focuses on the role played by the Special Programme for Research and Training in Tropical Diseases (TDR) in social and health development. Its states that TDR was among the United Nation's programs that has provided large contribution in eliminating the barriers that limit people's access to healthcare technologies. It adds that TDR has also partnered with the African Programme for Onchocerciasis Control (APOC) to support communities developing onchocerciasis treatments.

A precise understanding of the genomic and epigenomic features of chronic lymphocytic leukemia (CLL) may benefit the study of the disease's staging and treatment. While recent reports have shed some light on these aspects, several challenges need to be addressed before translating this research into clinical practice. Thus, even the best candidate driver genes display low mutational rates compared to other tumors. This means that a large percentage of cases do not display clear tumor-driving point mutations, or show candidate driving point mutations with no obvious biochemical relationship to the more frequently mutated genes. This genomic landscape probably reflects either an unknown underlying biochemical mechanism playing a key role in CLL or multiple biochemical pathways independently driving the development of this tumor. The elucidation of either scenario will have important consequences on the clinical management of CLL. Herein, we review the recent advances in the definition of the genomic landscape of CLL and the ongoing research to characterize the underlying biochemical events that drive this disease. [ABSTRACT FROM AUTHOR]

Chronic lymphocytic leukemia (CLL) is the most frequent leukemia in adults. We have analyzed exome sequencing data from 127 individuals with CLL and Sanger sequencing data from 214 additional affected individuals, identifying recurrent somatic mutations in POT1 (encoding protection of telomeres 1) in 3.5% of the cases, with the frequency reaching 9% when only individuals without IGHV@ mutations were considered. POT1 encodes a component of the shelterin complex and is the first member of this telomeric structure found to be mutated in human cancer. Somatic mutation of POT1 primarily occurs in gene regions encoding the two oligonucleotide-/oligosaccharide-binding (OB) folds and affects key residues required to bind telomeric DNA. POT1-mutated CLL cells have numerous telomeric and chromosomal abnormalities that suggest that POT1 mutations favor the acquisition of the malignant features of CLL cells. The identification of POT1 as a new frequently mutated gene in CLL may facilitate novel approaches for the clinical management of this disease. [ABSTRACT FROM AUTHOR]

The mitochondrial quality control system is essential for the preservation and regulation of mitochondrial function. This system is formed by a complex machinery that controls and maintains protein function and regulates mitochondrial morphology through a coordinated system of continual fusion and fission events. Impairments in the mitochondrial quality control system through either mutation or deficiency in any of its components, can lead to mitochondrial dysfunction. However, the physiological consequences of these deficiencies remain unknown in most cases. Here, we briefly review the role of the OPA1-OMA1 system in mitochondrial biology, and summarize our recent report on the generation and phenotypic characterization of a model deficient in OMA1, an ATPindependent mitochondrial metalloprotease that participates in mitochondrial quality control. Interestingly, Oma1-deficient mice display an obesity phenotype, characterized by hepatic steatosis, decrease in energy expenditure and defective thermogenic regulation. In addition, our study has provided in vivo evidence of OMA1 function as a mitochondrial quality control protease, inactivating OPA1 under stress conditions and inhibiting mitochondrial fusion. Further, we have demonstrated the essential role of the OMA1-OPA1 system for brown adipose function and how this system regulates metabolic homeostasis in mice. [ABSTRACT FROM AUTHOR]

Mitochondria are dynamic subcellular organelles that convert nutrient intermediates into readily available energy equivalents. Optimal mitochondrial function is ensured by a highly evolved quality control system, coordinated by protein machinery that regulates a process of continual fusion and fission. In this work, we provide in vivo evidence that the ATP-independent metalloprotease OMA1 plays an essential role in the proteolytic inactivation of the dynamin-related GTPase OPA1 (optic atrophy 1). We also show that OMA1 deficiency causes a profound perturbation of the mitochondrial fusion-fission equilibrium that has important implications for metabolic homeostasis. Thus, ablation of OMA1 in mice results in marked transcriptional changes in genes of lipid and glucose metabolic pathways and substantial alterations in circulating blood parameters. Additionally, Oma1-mutant mice exhibit an increase in body weight due to increased adipose mass, hepatic steatosis, decreased energy expenditure and impaired thermogenenesis. These alterations are especially significant under metabolic stress conditions, indicating that an intact OMA1-OPA1 system is essential for developing the appropriate adaptive response to different metabolic stressors such as a high-fat diet or cold-shock. This study provides the first description of an unexpected role in energy metabolism for the metalloprotease OMA1 and reinforces the importance of mitochondrial quality control for normal metabolic function. [ABSTRACT FROM AUTHOR]

Diagnostic tests for active tuberculosis (TB) based on the detection of antibodies (serological tests) have been commercially available for decades, although no international guidelines have recommended their use. An estimated 1.5 million serological TB tests, mainly enzyme-linked immunosorbent assays, are performed in India alone every year, mostly in the private sector. The cost of serological tests in India is conservatively estimated at US $15 million (825 million) per year. Findings from systematic reviews on the diagnostic accuracy of serological tests for both pulmonary and extra-pulmonary TB suggest that these tests are inaccurate and imprecise. A cost-effectiveness modelling study suggests that, if used as a replacement test for sputum microscopy, serology would increase costs to the Indian TB control sector approximately 4-fold and result in fewer disability-adjusted life years averted and more false-positive diagnoses. After considering all available evidence, the World Health Organization issued a strong recommendation against the use of currently available commercial serological tests for the diagnosis of TB disease. The expanding evidence base continues to demonstrate that the harms/risks of serological tests far outweigh the benefits. Greater engagement of the private sector is needed to discontinue the use of serological tests and to replace these tests with WHO-endorsed new diagnostics in India. The recent ban on import or sale of TB serological tests by the Indian health ministry is a welcome step in the right direction. [ABSTRACT FROM AUTHOR]

Aging is a multifactorial process that affects most of the biological functions of the organism and increases susceptibility to disease and death. Recent studies with animal models of accelerated aging have unveiled some mechanisms that also operate in physiological aging. However, little is known about the role of microRNAs (miRNAs) in this process. To address this question, we have analysed miRNA levels in Zmpste24-deficient mice, a model of Hutchinson-Gilford progeria syndrome. We have found that expression of the miR-29 family of miRNAs is markedly upregulated in Zmpste24−/− progeroid mice as well as during normal aging in mouse. Functional analysis revealed that this transcriptional activation of miR-29 is triggered in response to DNA damage and occurs in a p53-dependent manner since p53−/− murine fibroblasts do not increase miR-29 expression upon doxorubicin treatment. We have also found that miR-29 represses Ppm1d phosphatase, which in turn enhances p53 activity. Based on these results, we propose the existence of a novel regulatory circuitry involving miR-29, Ppm1d and p53, which is activated in aging and in response to DNA damage. [ABSTRACT FROM AUTHOR]

Prions are largely contained within the nervous and lymphoid tissue of transmissible spongiform encephalopathy (TSE) infected animals. However, following advances in diagnostic sensitivity, PrP , a marker for prion disease, can now be located in a wide range of viscera and body fluids including muscle, saliva, blood, urine and milk, raising concerns that exposure to these materials could contribute to the spread of disease in humans and animals. Previously we demonstrated low levels of infectivity in the liver of sheep experimentally challenged with bovine spongiform encephalopathy. In this study we show that PrPSc accumulated in the liver of 89% of sheep naturally infected with scrapie and 100% of sheep challenged with BSE, at both clinical and preclinical stages of the disease. PrPSc was demonstrated in the absence of obvious inflammatory foci and was restricted to isolated resident cells, most likely Kupffer cells. [ABSTRACT FROM AUTHOR]

Background: A delay is evident between the development of new policies on TB diagnostics and their implementation at country level. The Stop TB Partnership would benefit from information from national TB program (NTP) managers on progress towards implementation of new recommendations as well as the opportunities and challenges encountered in the process. Methods and Findings: To solicit information on the introduction of new TB diagnostics at country level, questionnaires were sent out to NTP managers of high-burden TB countries and a subset of managers was interviewed. The results indicate that about 50% of high-burden TB countries are using the TB diagnostic tools newly recommended by the World Health Organization (WHO). Most NTP managers reported that new diagnostics would only be implemented when officially endorsed by the WHO. All countries have plans to adopt newly endorsed diagnostics at reference laboratory level, while approaches to optimize smear microscopy at lower levels of the health service are given less attention. NTP managers reported diverse challenges to the implementation of new diagnostics. Conclusions: More information on the obstacles and advantages of introducing new diagnostic tools should be provided to NTP managers to ensure the rational adoption of new diagnostics. A single recommendation covering the introduction of a package of diagnostic tools might be preferable to NTP managers and facilitate implementation in high-burden TB countries. [ABSTRACT FROM AUTHOR]

The article discusses the Global Technical Strategy for Malaria 2016-2030 which is adopted by the 68th World Health Assembly in May 2015 which aims to control and eliminate the human suffering caused by malaria. It outlines the three main pillars of Global Technical Strategy which is considered as a reliable way to build research capacity in public health programmes.

Madhukar Pai and colleagues discuss how systematic reviews on tuberculosis diagnostics can influence research, policy, and clinical practice. [ABSTRACT FROM AUTHOR]

Background. The purpose of the study was to evaluate the performance and feasibility of tuberculosis diagnosis by sputum microscopy after bleach sedimentation, compared with by conventional direct smear microscopy, in a setting of high prevalence of HIV. Methods. In a community-based study in Kenya (a population in which 50% of individuals with tuberculosis are infected with HIV), individuals with suspected pulmonary tuberculosis submitted 3 sputum specimens during 2 consecutive days, which were examined by blind evaluation. Ziehl-Neelsen-stained smears were made of fresh specimens and of specimens that were processed with 3.5% household bleach followed by overnight sedimentation. Two different cutoffs for acid-fast bacilli (AFB) per 100 high-power fields (HPF) were used to define a positive smear: >10 AFB/100 HPF and 1 AFB/100 HPF. Four smear-positive case definitions, based on 1 or 2 positive smears with the 1 AFB or 10 AFB cutoff, were used. Results. Of 1879 specimens from 644 patients, 363 (19.3%) and 460 (24.5%) were positive by bleach sedimentation microscopy, compared with 301 (16.0%) and 374 (19.9%) by direct smear microscopy, with use of the 10 AFB/100 HPF (P<.001) and 1 AFB/100 HPF (P<.001) cutoffs, respectively. Regardless of the case definition used, bleach sedimentation microscopy detected significantly more positive cases than did direct smear microscopy: 26.7% (172 of 644) versus 21.7% (140 of 644), respectively, with the case definition of 1 positive smear and the 1 AFB/100 HPF cutoff (P<.001), and 21.4% (138 of 644) versus 18.6% (120 of 644), respectively, with the case definition of 1 positive smear and the 10 AFB/100 HPF cutoff (P<.001). Inter- and intrareader reproducibility were favorable, with κ coefficients of 0.83 and 0.91, respectively. Bleach sedimentation was relatively inexpensive and was not time consuming. Conclusions. Bleach sedimentation microscopy is an effective, simple method to improve the yield of smear microscopy in a setting of high prevalence of HIV. Further evaluation of this method, under operational conditions, is urgently needed to determine its potential as a tool for tuberculosis control. [ABSTRACT FROM AUTHOR]

The prostate is a site of high expression of serine proteinases including members of the kallikrein-related peptidase (KLK) family, as well as other secreted and membrane-anchored serine proteinases. It has been known for some time that members of this enzyme family elicit cellular responses by acting directly on cells. More recently, it has been recognised that for serine proteinases with specificity for cleavage after arginine and lysine residues (trypsin-like or tryptic enzymes) these cellular responses are often mediated by cleavage of members of the proteinase-activated receptor (PAR) family – a four member sub-family of G protein-coupled receptors. Here, we review the expression of PARs in prostate, the ability of prostatic trypsin-like KLKs and other prostate-expressed tryptic enzymes to cleave PARs, as well as the prostate cancer-associated consequences of PAR activation. In addition, we explore the dysregulation of trypsin-like serine proteinase activity through the loss of normal inhibitory mechanisms and potential interactions between these dysregulated enzymes leading to aberrant PAR activation, intracellular signalling and cancer-promoting cellular changes. [ABSTRACT FROM AUTHOR]

Kallikrein-related peptidase 4 (KLK4) is one of the 15 members of the human KLK family and a trypsin-like, prostate cancer-associated serine protease. Signaling initiated by trypsin-like serine proteases are transduced across the plasma membrane primarily by members of the protease-activated receptor (PAR) family of G protein-coupled receptors. Here we show, using Ca2+ flux assays, that KLK4 signals via both PAR-1 and PAR-2 but not via PAR-4. Dose-response analysis over the enzyme concentration range 0.1-1000 nM indicated that KLK4-induced Ca2+ mobilization via PAR-1 is more potent than via PAR-2, whereas KLK4 displayed greater efficacy via the latter PAR. We confirmed the specificity of KLK4 signaling via PAR-2 using in vitro protease cleavage assays and anti-phospho-ERK1/2/total ERK1/2 Western blot analysis of PAR-2-overexpressing and small interfering RNA-mediated receptor knockdown cell lines. Consistently, confocal microscopy analyses indicated that KLK4 initiates loss of PAR-2 from the cell surface and receptor internalization. Immunohistochemical analysis indicated the co-expression of agonist and PAR-2 in primary prostate cancer and bone metastases, suggesting that KLK4 signaling via this receptor will have pathological relevance. These data provide insight into KLK4-mediated cell signaling and suggest that signals induced by this enzyme via PARs may be important in prostate cancer. [ABSTRACT FROM AUTHOR]

Objective: To compare the therapeutic outcomes after deep lamellar keratoplasty (DLK) and penetrating keratoplasty (PK) in patients with keratoconus.Design: Retrospective case–control study.Participants: We reviewed the clinical notes of 47 patients diagnosed clinically with keratoconus who had received DLK (26 eyes of 25 patients) or PK (25 eyes of 22 patients) at Moorfields Eye Hospital or the Royal Shrewsbury Hospital between 1994 and 2001. The patients in the 2 groups were matched for severity of their keratoconus by preoperative visual acuity.Methods: Deep lamellar keratoplasty was performed with the Melles technique in 7 eyes and the technique described by Sugita and Kondo in 19 eyes. Penetrating keratoplasty was performed with a standard technique using a Hessburg-Barron trephine. A single continuous 16-bite 10-0 nylon suture was placed and adjusted in both groups.Main outcome measures: Best-corrected visual acuity (BCVA), refractive results, surgical techniques for DLK, and complication rates were analyzed.Results: The 25 patients with keratoconus who underwent DLK had a mean age of 32.6 years and a median follow-up of 28 months. The mean age of the 22 patients who underwent PK for keratoconus was 34 years. This group was followed up for a median time of 55 months. The median final BCVA of patients in the DLK group was 6/9 and in the PK group 6/6 (no statistical significance). The median result for the final spherical equivalent power in both groups was mild myopia, although the DLK group had more myopia, and the median astigmatism was less than 5.00 diopters cylinder for both groups. Complication rates were similar for DLK and PK, although the nature of the complications varied.Conclusions: Penetrating keratoplasty is no longer an automatic choice for the surgical treatment for keratoconus; DLK seems to be a safe alternative. Best-corrected visual acuity, refractive results, and complication rates are similar after DLK and PK. Deep lamellar keratoplasty is more technically challenging but allows the risk of endothelial rejection to be avoided and may reduce the risk of late endothelial failure. [Copyright &y& Elsevier]

A case report of Stickler's syndrome associated with congenital glaucoma is presented. Stickler's syndrome is an autosomal dominant disorder characterised by progressive arthropathy, midfacial flattening, Pierre Robin anomaly or cleft palate, sensorineural hearing loss, progressive myopia, vitreoretinal degeneration, and retinal detachment. Congenital glaucoma and Stickler's syndrome are two diagnoses frequently considered in high myopia in infancy. The case report described presents a case of Stickler's syndrome in association with congenital glaucoma. This association is unusual, but important to recognise in the neonatal period. The possibility of coexistence of these clinical entities should be considered in the future. [ABSTRACT FROM AUTHOR]

The term necrotizing herpetic retinopathies encompasses a spectrum of diseases which includes cytomegalovirus (CMV) retinitis, acute retinal necrosis (ARN) and Varicella zoster retinitis (VZR).Varicella zoster retinitis is a rapidly progressive, necrotizing condition most commonly reported in patients with AIDS. A case of vitreous biopsy-proven VZR is reported in a patient with AIDS that progressed despite immune recovery on highly active antiretroviral therapy (HAART) to a viral load < 50 copies/mL and a CD4 count of 230 cells/μL This is in contrast to CMV retinitis in which maintenance therapy appears unnecessary once the CD4 count rises and the viral load falls on HAART. Patients with VZR and AIDS should therefore be monitored for reactivation of retinal disease despite HAART-induced remission. [ABSTRACT FROM AUTHOR]

A precise understanding of the genomic and epigenomic features of chronic lymphocytic leukemia (CLL) may benefit the study of the disease's staging and treatment. While recent reports have shed some light on these aspects, several challenges need to be addressed before translating this research into clinical practice. Thus, even the best candidate driver genes display low mutational rates compared to other tumors. This means that a large percentage of cases do not display clear tumor-driving point mutations, or show candidate driving point mutations with no obvious biochemical relationship to the more frequently mutated genes. This genomic landscape probably reflects either an unknown underlying biochemical mechanism playing a key role in CLL or multiple biochemical pathways independently driving the development of this tumor. The elucidation of either scenario will have important consequences on the clinical management of CLL. Herein, we review the recent advances in the definition of the genomic landscape of CLL and the ongoing research to characterize the underlying biochemical events that drive this disease. [ABSTRACT FROM AUTHOR]

Background. Ebola virus disease (EVD) in health workers (HWs) has been a major challenge during the 2014-2015 outbreak. We examined factors associated with Ebola virus exposure and mortality in HWs in Kenema District, Sierra Leone. Methods. We analyzed data from the Sierra Leone National Viral Hemorrhagic Fever Database, contact tracing records, Kenema Government Hospital (KGH) staff and Ebola Treatment Unit (ETU) rosters, and burial logs. Results. From May 2014 through January 2015, 600 cases of EVD originated in Kenema District, including 92 (15%) HWs, 66 (72%) of whom worked at KGH. Among KGH medical staff and international volunteers, 18 of 62 (29%) who worked in the ETU developed EVD, compared with 48 of 83 (58%) who worked elsewhere in the hospital. Thirteen percent of HWs with EVD reported contact with EVD patients, while 27% reported contact with other infected HWs. The number of HW EVD cases at KGH declined roughly 1 month after implementation of a new triage system at KGH and the opening of a second ETU within the district. The case fatality ratio for HWs and non-HWs with EVD was 69% and 74%, respectively. Conclusions. The cluster of HW EVD cases in Kenema District is one of the largest ever reported. Most HWs with EVD had potential virus exposure both inside and outside of hospitals. Prevention measures for HWs must address a spectrum of infection risks in both formal and informal care settings as well as in the community. [ABSTRACT FROM AUTHOR]

The article discusses research which reveals the influence of SF3B1 mutations on the natural history of chronic lymphocytic leukemia. Patients with mutations in SF3B1 had more aggressive disease versus patients without such mutations. Cox analyses suggest that the mutational status of SF3B1 had a prognostic value that was independent of clinical stage or expression of ZAP70 or CD38. There is an indication that SF3B1 mutations perhaps occur during disease development.

A letter to the editor is presented concerning problems with recognition of chartered engineers as individuals qualified to witness or verify financial documents as professionals in Great Britain.

Deleterious germline variants in CDKN2A account for around 40% of familial melanoma cases, and rare variants in CDK4, BRCA2, BAP1 and the promoter of TERT have also been linked to the disease. Here we set out to identify new high-penetrance susceptibility genes by sequencing 184 melanoma cases from 105 pedigrees recruited in the UK, The Netherlands and Australia that were negative for variants in known predisposition genes. We identified families where melanoma cosegregates with loss-of-function variants in the protection of telomeres 1 gene (POT1), with a proportion of family members presenting with an early age of onset and multiple primary tumors. We show that these variants either affect POT1 mRNA splicing or alter key residues in the highly conserved oligonucleotide/oligosaccharide-binding (OB) domains of POT1, disrupting protein-telomere binding and leading to increased telomere length. These findings suggest that POT1 variants predispose to melanoma formation via a direct effect on telomeres. [ABSTRACT FROM AUTHOR]

Abstract: Mutations of the TMPRSS6 gene, encoding the serine protease matriptase-2, lead to iron-refractory iron deficiency anemia. Matriptase-2 is a potent negative regulator of hepcidin. Based on in vitro data, it has recently been proposed that matriptase-2 decreases hepcidin synthesis by cleaving membrane hemojuvelin, a key protein of the hepcidin-regulatory pathway. However, in vivo evidence for this mechanism of action of matriptase-2 is lacking. To investigate the hemojuvelin–matriptase-2 interaction in vivo, an immunoblot assay for liver membrane hemojuvelin was optimized using hemojuvelin-mutant mice as a negative control. In wild-type mice, two hemojuvelin-specific bands of 35kDa and 20kDa were detected in mouse liver membrane fraction under reducing conditions; under non-reducing conditions, a single band of approximately 50kDa was seen. Phosphatidylinositol-specific phospholipase C treatment confirmed binding of the detected protein to the cell membrane by a glycosylphosphatidylinositol anchor, indicating that the major form of mouse liver membrane hemojuvelin is a glycosylphosphatidylinositol-bound heterodimer. Unexpectedly, comparison of liver homogenates from Tmprss6+/+ and Tmprss6−/− mice revealed significantly decreased, rather than increased, hemojuvelin heterodimer content in Tmprss6−/− mice. These data do not provide direct support for the concept that matriptase-2 cleaves membrane hemojuvelin and may indicate that, in vivo, the role of matriptase-2 in the regulation of hepcidin gene expression is more complex. [Copyright &y& Elsevier]

Introduction: Light emitting diode fluorescence microscopes have many practical advantages over conventional mercury vapour fluorescence microscopes, which would make them the preferred choice for laboratories in both low- and highresource settings, provided performance is equivalent. Methods: In a nested case-control study, we compared diagnostic accuracy and time required to read slides with the Zeiss PrimoStar iLED, LW Scientific Lumin, and a conventional fluorescence microscope (Leica DMLS). Mycobacterial culture was used as the reference standard, and subgroup analysis by specimen source and organism isolated were performed. Results: There was no difference in sensitivity or specificity between the three microscopes, and agreement was high for all comparisons and subgroups. The Lumin and the conventional fluorescence microscope were equivalent with respect to time required to read smears, but the Zeiss iLED was significantly time saving compared to both. Conclusions: Light emitting diode microscopy should be considered by all tuberculosis diagnostic laboratories, including those in high income countries, as a replacement for conventional fluorescence microscopes. Our findings provide support to the recent World Health Organization policy recommending that conventional fluorescence microscopy be replaced by light emitting diode microscopy using auramine staining in all settings where fluorescence microscopy is currently used. [ABSTRACT FROM AUTHOR]

Swine influenza A virus (swIAV) infection causes substantial economic loss and disease burden in humans and animals. The 2009 pandemic H1N1 (pH1N1) influenza A virus is now endemic in both populations. In this study, we evaluated the efficacy of different vaccines in reducing nasal shedding in pigs following pH1N1 virus challenge. We also assessed transmission from immunized and challenged pigs to naive, directly in-contact pigs. Pigs were immunized with either adjuvanted, whole inactivated virus (WIV) vaccines or virus-vectored (ChAdOx1 and MVA) vaccines expressing either the homologous or heterologous influenza A virus hemagglutinin (HA) glycoprotein, as well as an influenza virus pseudotype (S-FLU) vaccine expressing heterologous HA. Only two vaccines containing homologous HA, which also induced high hemagglutination inhibitory antibody titers, significantly reduced virus shedding in challenged animals. Nevertheless, virus transmission from challenged to naive, in-contact animals occurred in all groups, although it was delayed in groups of vaccinated animals with reduced virus shedding. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented in response to the article "EPO-mediated reduction in Hamp expression in vivo corrects iron deficiency anaemia in TMPRSS6 deficiency," by H. Peng and colleagues in the 2010 issue.

Input devices such as motor-imagery brain-computer interfaces (BCIs) are often unreliable. In theory, channel coding can be used in the human-machine loop to robustly encapsulate intention through noisy input devices but standard feedforward error correction codes cannot be practically applied. We present a practical and general probabilistic user interface for binary input devices with very high noise levels. Our approach allows any level of robustness to be achieved, regardless of noise level, where reliable feedback such as a visual display is available. In particular, we show efficient zooming interfaces based on feedback channel codes for two-class binary problems with noise levels characteristic of modalities such as motor-imagery based BCI, with accuracy <75%. We outline general principles based on separating channel, line and source coding in human-machine loop design. We develop a novel selection mechanism which can achieve arbitrarily reliable selection with a noisy two-state button. We show automatic online adaptation to changing channel statistics, and operation without precise calibration of error rates. A range of visualisations are used to construct user interfaces which implicitly code for these channels in a way that it is transparent to users. We validate our approach with a set of Monte Carlo simulations, and empirical results from a human-in-the-loop experiment showing the approach operates effectively at 50-70% of the theoretical optimum across a range of channel conditions. [ABSTRACT FROM AUTHOR]

H5N8 highly-pathogenic avian influenza viruses (HPAIVs, clade 2.3.4.4) have spread globally via migratory waterfowl. Pekin ducks infected with a UK virus (H5N8-2014) served as the donors of infection in three separate cohousing experiments to attempt onward transmission chains to sequentially introduced groups of contact ducks, chickens and turkeys. Efficient transmission occurred among ducks and turkeys up to the third contact stage, with all (100%) birds becoming infected. Introduction of an additional fourth contact group of ducks to the turkey transmission chain demonstrated retention of H5N8-2014's waterfowl-competent adaptation. However, onward transmission ceased in chickens at the second contact stage where only 13% became infected. Analysis of viral progeny at this contact stage revealed no emergent polymorphisms in the intra-species (duck) transmission chain, but both terrestrial species included changes in the polymerase and accessory genes. Typical HPAIV pathogenesis and mortality occurred in infected chickens and turkeys, contrasting with 5% mortality among ducks. [ABSTRACT FROM AUTHOR]

The membranes of the first protocells on the early Earth were likely self-assembled from fatty acids. A major challenge in understanding how protocells could have arisen and withstood changes in their environment is that fatty acid membranes are unstable in solutions containing high concentrations of salt (such as would have been prevalent in early oceans) or divalent cations (which would have been required for RNA catalysis). To test whether the inclusion of amino acids addresses this problem, we coupled direct techniques of cryoelectron microscopy and fluorescence microscopy with techniques of NMR spectroscopy, centrifuge filtration assays, and turbidity measurements. We find that a set of unmodified, prebiotic amino acids binds to prebiotic fatty acid membranes and that a subset stabilizes membranes in the presence of salt and Mg2+. Furthermore, we find that final concentrations of the amino acids need not be high to cause these effects; membrane stabilization persists after dilution as would have occurred during the rehydration of dried or partially dried pools. In addition to providing a means to stabilize protocell membranes, our results address the challenge of explaining how proteins could have become colocalized with membranes. Amino acids are the building blocks of proteins, and our results are consistent with a positive feedback loop in which amino acids bound to selfassembled fatty acid membranes, resulting in membrane stabilization and leading to more binding in turn. High local concentrations of molecular building blocks at the surface of fatty acid membranes may have aided the eventual formation of proteins. [ABSTRACT FROM AUTHOR]

Abstract Swine influenza A virus (SwIV) infection has considerable economic and animal welfare consequences and, because of the zoonotic potential, can also have public health implications. The 2009 pandemic H1N1 'swine-origin' infection is now endemic in both pigs and humans. In Europe, avian-like H1 av N1, human-like H1 hu N2, human-like swine H3N2 and, since 2009, pandemic H1N1 (pH1N1) lineage viruses and reassortants, constitute the dominant subtypes. In this study, we used a swine pH1N1 challenge virus to investigate the efficacy of whole inactivated virus vaccines homologous or heterologous to the challenge virus as well as a commercial vaccine. We found that vaccine-mediated protection was most effective when vaccine antigen and challenge virus were homologous and correlated with the specific production of neutralising antibodies and a cellular response to the challenge virus. We conclude that a conventional whole inactivated SwIV vaccine must be antigenically matched to the challenge strain to be an effective control measure. [ABSTRACT FROM AUTHOR]

The article reports on a survey on problems faced by survivors of Ebola virus disease (EVD) in Sierra Leone. It mentions that the survey revealed common complaints like musculoskeletal pain, visual problems and abdominal and epigastric pain; and was used to establish a clinic for EVD survivors in Kenema, Sierra Leone. It adds the study by researcher A. I. Qureshi and colleagues on Ebola virus disease survivors in Guinea.

Background: C-reactive protein (CRP) is an inflammatory biomarker that may identify patients at risk of infections or death. Mortality among HIV-infected persons commencing antiretroviral therapy (ART) is often attributed to tuberculosis (TB) or bloodstream infections (BSI).Methods: In two district hospitals in southern Malawi, we recruited HIV-infected adults with one or more unexplained symptoms present for at least one month (weight loss, fever or diarrhoea) and negative expectorated sputum microscopy for TB. CRP determination for 452 of 469 (96%) participants at study enrolment was analysed for associations with TB, BSI or death to 120 days post-enrolment.Results: Baseline CRP was significantly elevated among patients with confirmed or probable TB (52), BSI (50) or death (60) compared to those with no identified infection who survived at least 120 days (269). A CRP value of >10 mg/L was associated with confirmed or probable TB (adjusted odds ratio 5.7; 95% CI 2.6, 14.3; 87% sensitivity) or death by 30 days (adjusted odds ratio 9.2; 95% CI 2.2, 55.1; 88% sensitivity). CRP was independently associated with TB, BSI or death, but the prediction of these endpoints was enhanced by including haemoglobin (all outcomes), CD4 count (BSI, death) and whether ART was started (death) in logistic regression models.Conclusion: High CRP at the time of ART initiation is associated with TB, BSI and early mortality and so has potential utility for stratifying patients for intensified clinical and laboratory investigation and follow-up. They may also be considered for empirical treatment of opportunistic infections including TB. [ABSTRACT FROM AUTHOR]

BACKGROUND: Physical activity (PA) in stroke survivors is low however the ubiquitous nature of smartphone technology means smartphone-based interventions could be a feasible and cost-effective approach to increase PA. We developed STARFISH, a group behavioural change intervention delivered via a smartphone app to help increase PA. OBJECTIVE: Following the positive results of our pilot study the aim of this single-blind, Randomised Controlled Trial (RCT) is to examine the effect of the STARFISH intervention, on PA in stroke survivors, compared to usual care. METHODS: One hundred and twenty-eight community dwelling stroke survivors will be recruited, from four NHS boards in Scotland, and randomised to intervention or control groups. The interventional groups will use the STARFISH app. The control group will receive literature on PA post-stroke. Outcome measures will be taken at: baseline, four months (end of the intervention), two months post-intervention. The primary outcome will be objectively measured PA. Secondary outcome measures will be sedentary time, activity profiles, walking speed and endurance, fatigue, anxiety and depression, activities of daily living, quality of life and metabolic health-risk biomarkers. CONCLUSION: If improvements are found in the PA and health of stroke survivors then STARFISH could be deployed through app stores to allow implementation at scale. [ABSTRACT FROM AUTHOR]

Background: Smartphone sensors are underutilised in rehabilitation.Objective: To validate the step count algorithm used in the STARFISH smartphone application.Methods: Twenty-two healthy adults (8 male, 14 female) walked on a treadmill for 5 minutes at 0.44, 0.67, 0.90 and 1.33 m⋅s-1. Each wore an activPALTM and four Samsung Galaxy S3TM smartphones, with the STARFISH application running, in: 1) a belt carrycase, 2) a trouser or skirt pocket), 3a) a handbag on shoulder for females or 3b) shirt pocket for males and 4) an upper arm strap. Step counts of the STARFISH application and the activPALTM were compared at corresponding speeds and Bland-Altman statistics used to assess level of agreement (LOA).Results: The LOA between the STARFISH application and activPALTM varied across the four speeds and positions, but improved as speed increased. The LOA ranged from 105-177% at 0.44 m⋅s-1; 50-98% at 0.67 m⋅s-1; 19-67% at 0.9 m⋅s-1 and 8-53% at 1.33 m⋅s-1. The best LOAs were at 1.33 m⋅s-1 in the shirt pocket (8%) and upper arm strap (12%) positions.Conclusions: Step counts measured by the STARFISH smartphone application are valid in most body positions especially at walking speeds of 0.9 m⋅s-1 and above. [ABSTRACT FROM AUTHOR]

Background: During pulmonary tuberculosis (PTB) antibodies are generated to trehalose esters of mycolic acids which are cell wall lipids of Mycobacterium tuberculosis (Mtb). Attempts have been made to use these complex natural mixtures in serological tests for PTB diagnosis. Aim: The aim of this work was to determine whether a serological test based on a panel of defined individual trehalose esters of characteristic synthetic mycolic acids has improved diagnostic accuracy in distinguishing patients with culture positive PTB from individuals who were Mtb culture negative. Method: One hundred serum samples from well-characterized patients with presumptive tuberculosis, and diagnosed as having pulmonary smear and culture positive TB, or being culture and smear negative were evaluated by ELISA using different combinations of synthetic antigens and secondary antibodies. Using cut-off values determined from these samples, we validated this study blind in samples from a further 249 presumptive TB patients. Results: With the first 100 samples, detailed responses depended both on the precise structure of the antigen and on the secondary antibody. Using a single antigen, a sensitivity/specificity combination for smear and culture positive PTB detection of 85 and 88% respectively was achieved; this increased to 96% and 95% respectively by a statistical combination of the results with seven antigens. In the blind study a sensitivity/specificity of 87% and 83% was reached with a single antigen. With some synthetic antigens, the responses from all 349 samples were significantly better than those with the natural mixture. Combining the results for seven antigens allowed a distinction between culture positive and negative with a ROC AUC of 0.95. Conclusion: We have identified promising antigen candidates for serological assays that could be used to diagnose PTB and which could be the basis of a much-needed, simple, rapid diagnostic test that would bring care closer to communities. [ABSTRACT FROM AUTHOR]

Background: In Uzbekistan, despite stable and relatively high tuberculosis treatment success rates, relatively high rates of recurrent tuberculosis have recently been reported. Recurrent tuberculosis is when a patient who was treated for pulmonary tuberculosis and cured, later develops the disease again. This requires closer analysis to identify possible causes and recommend interventions to improve the situation. Using countrywide data, this study aimed to analyse trends in recurrent tuberculosis cases and describe their associations with socio-demographic and clinical factors. Method: Countrywide retrospective cohort study comparing recurrent tuberculosis patients with all new tuberculosis patients registered within the NTP between January 2006 and December 2010 using routinely collected data. Determinants studied were baseline characteristics and treatment outcomes. Results: Of 107,380 registered patients during the period January 2006 and December 2010, 9358 (8.7%) were recurrent cases. Between 2006 and 2008, the number of recurrent cases per annum increased from 1530 to 2081, then fell slightly thereafter from 2081 to 1888 cases. The proportion of all notified cases during this period increased from 6.5% to 9.9%. Factors associated with recurrent tuberculosis included age (35–55 years old), having smear positive pulmonary tuberculosis, residing in certain areas of Uzbekistan, having particular co-morbidities (including chronic obstructive pulmonary disease and HIV), and being unemployed, a pensioner or disabled. Recurrent tuberculosis patients also had a higher likelihood of having an unfavourable treatment outcome Conclusion: Despite signs of declining national tuberculosis notifications between 2006 and 2010, the relative proportion of recurrent cases appears to have increased. These findings, together with the identification of possible risk factors associated with recurrent tuberculosis, highlight various areas where Uzbekistan needs to focus its tuberculosis control efforts, particularly in light of the country’s rapidly emerging multi drug resistant tuberculosis epidemic. [ABSTRACT FROM AUTHOR]

Setting: Research capacity is weakest in low and middle-income countries (LMICs) where operational research is highly relevant and needed. Structured Operational Research and Training Initiative (SORT IT) courses have been developed to train participants to conduct and publish operational research and influence policy and practice. Twenty courses were completed in Asia, Africa, Europe and the South Pacific between 2009 and 2014. Objectives: In the 20 completed SORT IT courses, to assess where the research was conducted, who was trained, who became facilitators in subsequent courses and course outcomes. Design: A cohort study of completed SORT IT courses Results: There were 236 participants (41% female) including 64 nationalities who conducted research in 59 countries, mostly from Asia and Africa (mean course duration = 9.7 months). Most participants (68%) were from government health programs and non-governmental agencies. A total of 213(90%) participants completed all milestones successfully with 41(19%) becoming subsequent course facilitators, 88% of whom were from LMICs. Of 228 manuscripts submitted to scientific journals, 197(86%) were either published or in press; in 86%, the principal investigator (first author) was a LMIC national. Papers were published in 23 scientific journals (impact factor 0.5–4.4) and covered 21 disease categories (median publication time = 5.7 months). Published papers (186) had 94,794 cumulative article views/downloads. Article views/downloads for immediate open access articles were double those from closed access journals. Conclusion: The SORT IT model has been effective in training personnel to produce relevant operational research in LMICs. It merits continued commitment and support for further scale-up and development. [ABSTRACT FROM AUTHOR]

Background: A major impediment to the treatment of TB is a diagnostic process that requires multiple visits. Descriptions of patient costs associated with diagnosis use different protocols and are not comparable. Methods: We aimed to describe the direct costs incurred by adults attending TB diagnostic centres in four countries and factors associated with expenditure for diagnosis. Surveys of 2225 adults attending smear-microscopy centres in Nigeria, Nepal, Ethiopia and Yemen. Adults >18 years with cough >2 weeks were enrolled prospectively. Direct costs were quantified using structured questionnaires. Patients with costs >75th quartile were considered to have high expenditure (cases) and compared with patients with costs <75th quartile to identify factors associated with high expenditure. Results: The most significant expenses were due to clinic fees and transport. Most participants attended the centres with companions. High expenditure was associated with attending with company, residing in rural areas/other towns and illiteracy. Conclusions: The costs incurred by patients are substantial and share common patterns across countries. Removing user fees, transparent charging policies and reimbursing clinic expenses would reduce the poverty-inducing effects of direct diagnostic costs. In locations with limited resources, support could be prioritised for those most at risk of high expenditure; those who are illiterate, attend the service with company and rural residents. [ABSTRACT FROM AUTHOR]

Background: Combating the spread of drug resistant tuberculosis is a global health priority. Whole genome association studies are being applied to identify genetic determinants of resistance to anti-tuberculosis drugs. Protein structure and interaction modelling are used to understand the functional effects of putative mutations and provide insight into the molecular mechanisms leading to resistance.Methods: To investigate the potential utility of these approaches, we analysed the genomes of 144 Mycobacterium tuberculosis clinical isolates from The Special Programme for Research and Training in Tropical Diseases (TDR) collection sourced from 20 countries in four continents. A genome-wide approach was applied to 127 isolates to identify polymorphisms associated with minimum inhibitory concentrations for first-line anti-tuberculosis drugs. In addition, the effect of identified candidate mutations on protein stability and interactions was assessed quantitatively with well-established computational methods.Results: The analysis revealed that mutations in the genes rpoB (rifampicin), katG (isoniazid), inhA-promoter (isoniazid), rpsL (streptomycin) and embB (ethambutol) were responsible for the majority of resistance observed. A subset of the mutations identified in rpoB and katG were predicted to affect protein stability. Further, a strong direct correlation was observed between the minimum inhibitory concentration values and the distance of the mutated residues in the three-dimensional structures of rpoB and katG to their respective drugs binding sites.Conclusions: Using the TDR resource, we demonstrate the usefulness of whole genome association and convergent evolution approaches to detect known and potentially novel mutations associated with drug resistance. Further, protein structural modelling could provide a means of predicting the impact of polymorphisms on drug efficacy in the absence of phenotypic data. These approaches could ultimately lead to novel resistance mutations to improve the design of tuberculosis control measures, such as diagnostics, and inform patient management. [ABSTRACT FROM AUTHOR]

In public health, implementation research is done to improve access to interventions that have been shown to work but have not reached many of the people who could benefit from them. Researchers identify practical problems facing public health programmes and aim to find solutions that improve health outcomes. In operational research, routinely-collected programme data are used to uncover ways of delivering more effective, efficient and equitable health care. As implementation research can address many types of questions, many research designs may be appropriate. Existing reporting guidelines partially cover the methods used in implementation and operational research, so we ran a consultation through the World Health Organization (WHO), the Alliance for Health Policy & Systems Research (AHPSR) and the Special Programme for Research and Training in Tropical Diseases (TDR) and developed guidelines to facilitate the funding, conduct, review and publishing of such studies. Our intention is to provide a practical reference for funders, researchers, policymakers, implementers, reviewers and editors working with implementation and operational research. This is an evolving field, so we plan to monitor the use of these guidelines and develop future versions as required. [ABSTRACT FROM AUTHOR]

Background: The ChinaÂ's 1-3-7 strategy was initiated and extensively adopted in different types of counties (geographic regions) for reporting of malaria cases within 1 day, their confirmation and investigation within 3 days, and the appropriate public health response to prevent further transmission within 7 days. Assessing the level of compliance to the 1-3-7 strategy at the county level is a first step towards determining whether the surveillance and response strategy is happening according to plan. This study assessed if the time-bound targets of the 1-3-7 strategy were being sustained over time. Such information would be useful to improve implementation of the 1-3-7 strategy in China. Methods: This cross-sectional study involved country-wide programmatic data for the period January 1st 2013 to June 30th 2014. Data variables were extracted from the national malaria information system and included socio-demographic information, type of county, date of diagnosis, date of reporting, date of case investigation, case classification (indigenous, or imported, or unknown), focus investigation, date of reactive case detection (RACD), and date of indoor residual spraying (IRS). Summary statistics and proportions were used and comparisons between groups were assessed using the chi-square test. Level of significance was set at a P-value ≤ 0.05. Results: Of a total of 5,688 malaria cases from 731 counties, there were 55 (1%) indigenous cases (only in Type 1 and Type 2 counties) and 5,633 (99%) imported cases from all types of counties. There was no delay in reporting malaria cases by type of county. In terms of case investigation, 97.5% cases were investigated within 3 days with the proportion of delays (1.5%) in type 2 counties, being significantly lower than type 1 counties (4.1%). Regarding active foci, 96.4% were treated by RACD and/or IRS. Conclusions: The performance of 1-3-7 strategy was encouraging but identified some challenges that if addressed can further improve implementation. [ABSTRACT FROM AUTHOR]

Great progress has recently been achieved in the understanding of the genomic alterations driving chronic lymphocytic leukemia (CLL). Nevertheless, the specific molecular mechanisms governing chromatin remodeling in CLL are unknown. Here we report the genetic and functional characterization of somatic mutations affecting the chromatin remodeler CHD2, one of the most frequently mutated genes in CLL (5.3%) and in monoclonal B lymphocytosis (MBL, 7%), a B-cell expansion that can evolve to CLL. Most of the mutations affecting CHD2, identified by whole-exome sequencing of 456 CLL and 43 MBL patients, are either truncating or affect conserved residues in functional domains, thus supporting a putative role for CHD2 as a tumor suppressor gene. CHD2 mutants show altered nuclear distribution, and a chromodomain helicase DNA binding protein 2 (CHD2) mutant affected in its DNA-binding domain exhibits defective association with active chromatin. Clinicobiological analyses show that most CLL patients carrying CHD2 mutations also present mutated immunoglobulin heavy chain variable region genes (IGHVs), being the most frequently mutated gene in this prognostic subgroup. This is the first study providing functional evidence supporting CHD2 as a cancer driver and opens the way to further studies of the role of this chromatin remodeler in CLL. [ABSTRACT FROM AUTHOR]