Temperature dependence of the energy and broadening parameter of the fundamental band gap of GaSb and Ga1-xInxAsySb1-y/GaSb (0.07 <= x <= 0.22, 0.05 <= y <= 0.19) quaternary alloys using infrared photoreflectance

We have measured the temperature dependence of the energy [E-0(T)] and broadening parameter [Gamma (0)(T)] of the fundamental gap for GaSb and four samples of Ga1-xInxAsySb1-y (lattice matched to GaSb) using infrared photoreflectance. The parameters that describe the temperature variation of the energy (including thermal-expansion effects) were evaluated using both the semiempirical Vashni relation as well as an equation that incorporates the Bose-Einstein occupation factor. The behavior of Gamma (0)(T) was described by a Bose-Einstein-type equation.6224166001660

A Survey on Gaussian Processes for Earth-Observation Data Analysis: A Comprehensive Investigation

Gaussian processes (GPs) have experienced tremendous success in biogeophysical parameter retrieval in the last few years. GPs constitute a solid Bayesian framework to consistently formulate many function approximation problems. This article reviews the main theoretical GP developments in the field, considering new algorithms that respect signal and noise characteristics, extract knowledge via automatic relevance kernels to yield feature rankings automatically, and allow applicability of associated uncertainty intervals to transport GP models in space and time that can be used to uncover causal relations between variables and can encode physically meaningful prior knowledge via radiative transfer model (RTM) emulation. The important issue of computational efficiency will also be addressed. These developments are illustrated in the field of geosciences and remote sensing at local and global scales through a set of illustrative examples. In particular, important problems for land, ocean, and atmosphere monitoring are considered, from accurately estimating oceanic chlorophyll content and pigments to retrieving vegetation properties from multi- and hyperspectral sensors as well as estimating atmospheric parameters (e.g., temperature, moisture, and ozone) from infrared sounders

Leprosy Associated with Atypical Cutaneous Leishmaniasis in Nicaragua and Honduras

In Central America, few cases of leprosy have been reported, but the disease may be unrecognized. Diagnosis is based on clinical criteria and histology. Preliminary field work in Nicaragua and Honduras found patients, including many children, with skin lesions clinically suggestive of atypical cutaneous leishmaniasis or indeterminate leprosy. Histology could not distinguish these diseases although acid-fast organisms were visible in a few biopsies. Lesions healed after standard antimicrobial therapy for leprosy. In the present study, patients, family members, and other community members were skin-tested and provided nasal swabs and blood samples. Biopsies were taken from a subgroup of patients with clinical signs of infection. Two laboratories analyzed samples, using local in-house techniques. Mycobacterium leprae, Leishmania spp. and Leishmania infantum were detected using polymerase chain reactions. Mycobacterium leprae DNA was detected in blood samples and nasal swabs, including some cases where leprosy was not clinically suspected. Leishmania spp. were also detected in blood and nasal swabs. Most biopsies contained Leishmania DNA and coinfection of Leishmania spp. with M. leprae occurred in 33% of cases. Mycobacterium leprae DNA was also detected and sequenced from Nicaraguan and Honduran environmental samples. In conclusion, leprosy and leishmaniasis are present in both regions, and leprosy appears to be widespread. The nature of any relationship between these two pathogens and the epidemiology of these infections need to be elucidated

Improved genome editing in human cell lines using the CRISPR method

The Cas9/CRISPR system has become a popular choice for genome editing. In this system, binding of a single guide (sg) RNA to a cognate genomic sequence enables the Cas9 nuclease to induce a double-strand break at that locus. This break is next repaired by an error-prone mechanism, leading to mutation and gene disruption. In this study we describe a range of refinements of the method, including stable cell lines expressing Cas9, and a PCR based protocol for the generation of the sgRNA. We also describe a simple methodology that allows both elimination of Cas9 from cells after gene disruption and re-introduction of the disrupted gene. This advance enables easy assessment of the off target effects associated with gene disruption, as well as phenotype-based structure-function analysis. In our study, we used the Fan1 DNA repair gene as control in these experiments. Cas9/CRISPR-mediated Fan1 disruption occurred at frequencies of around 29%, and resulted in the anticipated spectrum of genotoxin hypersensitivity, which was rescued by re-introduction of Fan1

Field Evaluation of the Cepheid GeneXpert Chlamydia trachomatis assay for Detection of Infection in a Trachoma Endemic Community in Tanzania.

\ud \ud To determine the sensitivity, specificity, and field utility of the Cepheid GeneXpert Chlamydia trachomatis (CT) Assay (GeneXpert) for ocular chlamydia infection compared to Roche Amplicor CT assay (Amplicor). In a trachoma-endemic community in Kongwa Tanzania, 144 children ages 0 to 9 were surveyed to assess clinical trachoma and had two ocular swabs taken. One swab was processed at Johns Hopkins University, Baltimore MD, using Amplicor, (Roche Molecular Diagnostics) and the other swab was processed at a field station in Kongwa using the GeneXpert Chlamydia trachomatis/Neisseria gonorrhoeae assay (Cepheid). The sensitivity and specificity of GeneXpert was compared to the Amplicor assay. Of the 144 swabs taken the prevalence of follicular trachoma by clinical exam was 43.7%, and by evidence of infection according to Amplicor was 28.5%. A total of 17 specimens (11.8%) could not be processed by GeneXpert in the field due to lack of sample volume, other specimen issues or electricity failure. The sensitivity of GeneXpert when compared to Amplicor was 100% and the specificity was 95%. The GeneXpert test identified more positives in individuals with clinical trachoma than Amplicor, 55% versus 52%. The GeneXpert test for C. trachomatis performed with high sensitivity and specificity and demonstrated excellent promise as a field test for trachoma control.\u

Molecular Characterization of Growth Hormone-producing Tumors in the GC Rat Model of Acromegaly

D.A.C. was supported by the Nicolás Monardes program of the Andalusian Ministry of Health (C-0015-2014) and by a grant from the Andalusian Ministry of Science and Innovation (CTS-7478). A.S-M and A.L.C were supported by grants from the ISCIII-Subdirección General de Evaluación y Fomento de la Investigación co-funded with Fondos FEDER (PI12/0143 and PI13/02043, respectively) and the Andalusian Regional Government (CTS-444) and a grant from Pfizer Spain. R.L.C. was supported by a grant from Andalusian Ministry of Health (PI0302-2012). R.M.L. was supported by grants from Proyecto de Investigación en Salud (FIS) PI13- 00651 (funded by Instituto de Salud Carlos III), CTS-1406, PI-0639-2012, BIO-0139 (funded by Junta de Andalucía) and by Ayuda Merck Serono 2013. J. P. C. was funded by a grant (BFU2013-43282-R) from Ministerio de Economía y Competitividad. CIBER is an initiative of Instituto de Salud Carlos III, Ministerio de Sanidad, Servicios Sociales e Igualdad, Spain. J.F.M.R. is supported by the “Sara Borrell” program from the Instituto de Salud Carlos III. R.M. Luque and J.P. Castaño have received grants and lecture fees from Ipsen and Novartis. E. Venegas-Moreno and A. Soto-Moreno received grants and lecture fees from Ipsen, Novartis and Pfizer. A. Leal-Cerro received grants from Novartis and Pfizer. David Cano received a grant from Novartis

Dengue Virus Inhibits Immune Responses in Aedes aegypti Cells

The ability of many viruses to manipulate the host antiviral immune response often results in complex host-pathogen interactions. In order to study the interaction of dengue virus (DENV) with the Aedes aegypti immune response, we have characterized the DENV infection-responsive transcriptome of the immune-competent A. aegypti cell line Aag2. As in mosquitoes, DENV infection transcriptionally activated the cell line Toll pathway and a variety of cellular physiological systems. Most notably, however, DENV infection down-regulated the expression levels of numerous immune signaling molecules and antimicrobial peptides (AMPs). Functional assays showed that transcriptional induction of AMPs from the Toll and IMD pathways in response to bacterial challenge is impaired in DENV-infected cells. In addition, Escherichia coli, a Gram-negative bacteria species, grew better when co-cultured with DENV-infected cells than with uninfected cells, suggesting a decreased production of AMPs from the IMD pathway in virus-infected cells. Pre-stimulation of the cell line with Gram-positive bacteria prior to DENV infection had no effect on DENV titers, while pre-stimulation with Gram-negative bacteria resulted in an increase in DENV titers. These results indicate that DENV is capable of actively suppressing immune responses in the cells it infects, a phenomenon that may have important consequences for virus transmission and insect physiology

An fMRI Investigation of Preparatory Set in the Human Cerebral Cortex and Superior Colliculus for Pro- and Anti-Saccades

Previous studies have identified several cortical regions that show larger BOLD responses during preparation and execution of anti-saccades than pro-saccades. We confirmed this finding with a greater BOLD response for anti-saccades than pro-saccades during the preparation phase in the FEF, IPS and DLPFC and in the FEF and IPS in the execution phase. We then applied multi-voxel pattern analysis (MVPA) to establish whether different neural populations are involved in the two types of saccade. Pro-saccades and anti-saccades were reliably decoded during saccade execution in all three cortical regions (FEF, DLPFC and IPS) and in IPS during saccade preparation. This indicates neural specialization, for programming the desired response depending on the task rule, in these regions. In a further study tailored for imaging the superior colliculus in the midbrain a similar magnitude BOLD response was observed for pro-saccades and anti-saccades and the two saccade types could not be decoded with MVPA. This was the case both for activity related to the preparation phase and also for that elicited during the execution phase. We conclude that separate cortical neural populations are involved in the task-specific programming of a saccade while in contrast, the SC has a role in response preparation but may be less involved in high-level, task-specific aspects of the control of saccades

Incidence and drug treatment of emotional distress after cancer diagnosis : a matched primary care case-control study

Notes This work is published under the standard license to publish agreement. After 12 months the work will become freely available and the license terms will switch to a Creative Commons Attribution-NonCommercial-Share Alike 3.0 Unported License.Peer reviewedPublisher PD

Recombination and positive selection identified in complete genome sequences of Japanese encephalitis virus

The mosquito-borne Japanese encephalitis virus (JEV) causes encephalitis in man but not in pigs. Complete genomes of a human, mosquito and pig isolate from outbreaks in 1982 and 1985 in Thailand were sequenced with the aim of identifying determinants of virulence that may explain the differences in outcomes of JEV infection between pigs and man. Phylogenetic analysis revealed that five of these isolates belonged to genotype I, but the 1982 mosquito isolate belonged to genotype III. There was no evidence of recombination among the Thai isolates, but there were phylogenetic signals suggestive of recombination in a 1994 Korean isolate (K94P05). Two sites of the genome under positive selection were identified: codons 996 and 2296 (amino acids 175 of the non-structural protein NS1 and 24 of NS4B, respectively). A structurally significant substitution was seen at NS4B position 24 of the human isolate compared with the mosquito and pig isolates from the 1985 outbreak in Thailand. The potential importance of the two sites in the evolution and ecology of JEV merits further investigation