The transcriptome of equine peripheral blood mononuclear cells.

Complete transcriptomic data at high resolution are available only for a few model organisms with medical importance. The gene structures of non-model organisms are mostly computationally predicted based on comparative genomics with other species. As a result, more than half of the horse gene models are known only by projection. Experimental data supporting these gene models are scarce. Moreover, most of the annotated equine genes are single-transcript genes. Utilizing RNA sequencing (RNA-seq) the experimental validation of predicted transcriptomes has become accessible at reasonable costs. To improve the horse genome annotation we performed RNA-seq on 561 samples of peripheral blood mononuclear cells (PBMCs) derived from 85 Warmblood horses. The mapped sequencing reads were used to build a new transcriptome assembly. The new assembly revealed many alternative isoforms associated to known genes or to those predicted by the Ensembl and/or Gnomon pipelines. We also identified 7,531 transcripts not associated with any horse gene annotated in public databases. Of these, 3,280 transcripts did not have a homologous match to any sequence deposited in the NCBI EST database suggesting horse specificity. The unknown transcripts were categorized as coding and noncoding based on predicted coding potential scores. Among them 230 transcripts had high coding potential score, at least 2 exons, and an open reading frame of at least 300 nt. We experimentally validated 9 new equine coding transcripts using RT-PCR and Sanger sequencing. Our results provide valuable detailed information on many transcripts yet to be annotated in the horse genome.

Molecular Consequences of the SERPINH1/HSP47 Mutation in the Dachshund Natural Model of Osteogenesis Imperfecta.

Osteogenesis imperfecta (OI) is a heritable connective tissue disease characterized by bone fragility and increased risk of fractures. Up to now, mutations in at least 18 genes have been associated with dominant and recessive forms of OI that affect the production or post-translational processing of procollagen or alter bone homeostasis. Among those, SERPINH1 encoding heat shock protein 47 (HSP47), a chaperone exclusive for collagen folding in the ER, was identified to cause a severe form of OI in dachshunds (L326P) as well as in humans (one single case with a L78P mutation). To elucidate the disease mechanism underlying OI in the dog model, we applied a range of biochemical assays to mutant and control skin fibroblasts as well as on bone samples. These experiments revealed that type I collagen synthesized by mutant cells had decreased electrophoretic mobility. Procollagen was retained intracellularly with concomitant dilation of ER cisternae and activation of the ER stress response markers GRP78 and phospho-eIF2α, thus suggesting a defect in procollagen processing. In line with the migration shift detected on SDS-PAGE of cell culture collagen, extracts of bone collagen from the OI dog showed a similar mobility shift, and on tandem mass spectrometry, the chains were post-translationally overmodified. The bone collagen had a higher content of pyridinoline than control dog bone. We conclude that the SERPINH1 mutation in this naturally occurring model of OI impairs how HSP47 acts as a chaperone in the ER. This results in abnormal post-translational modification and cross-linking of the bone collagen.

Encapsulation of caesium-loaded Ionsiv in cement

The microporous material Ionsiv is used for 137Cs removal from aqueous nuclear waste streams. In the UK, Cs-loaded Ionsiv is classed as an intermediate-level waste; no sentencing and disposal route is yet defined for this material and it is currently held in safe interim storage on several nuclear sites. In this study, the suitability of fly ash and blast furnace slag blended cements for encapsulation of Cs-Ionsiv in a monolithic wasteform was investigated. No evidence of reaction or dissolution of the Cs-Ionsiv in the cementitious environment was found by scanning electron microscopy and X-ray diffraction. However, a small fraction (<= 1.6 wt.%) of the Cs inventory was released from the encapsulated Ionsiv during leaching experiments carried out on hydrated samples. Furthermore, it was evident that K and Na present in the cementitious pore water exchanged with Cs and H in the Ionsiv. Therefore, cement systems lower in K and Na, such as slag based cements, showed lower Cs release than the fly ash based cements.

Size parameters, size-class distribution and area-number relationship of microscopic charcoal: relevance for fire reconstruction

Charcoal analysis was conducted on sediment cores from three lakes to assess the relationship between the area and number of charcoal particles. Three charcoal-size parameters (maximum breadth, maximum length and area) were measured on sediment samples representing various vegetation types, including shrub tundra, boreal forest and temperate forest. These parameters and charcoal size-class distributions do not differ statistically between two sites where the same preparation technique (glycerine pollen slides) was used, but they differ for the same core when different techniques were applied. Results suggest that differences in charcoal size and size-class distribution are mainly caused by different preparation techniques and are not related to vegetation-type variation. At all three sites, the area and number concentrations of charcoal particles are highly correlated in standard pollen slides; 82–83% of the variability of the charcoal-area concentration can be explained by the particle-number concentration. Comparisons between predicted and measured area concentrations show that regression equations linking charcoal number and area concentrations can be used across sites as long as the same pollen-preparation technique is used. Thus it is concluded that it is unnecessary to measure charcoal areas in standard pollen slides – a time-consuming and tedious process.

Evidence for biological shaping of hair ice

An unusual ice type, called hair ice, grows on the surface of dead wood of broad-leaf trees at temperatures slightly below 0 °C. We describe this phenomenon and present physical, chemical, and biological investigations to gain insight in the properties and processes related to hair ice. Tests revealed that the biological activity of a winter-active fungus is required in the wood for enabling the growth of hair ice. We confirmed the fungus hypothesis originally suggested by Wegener (1918) by reproducing hair ice on wood samples. Treatment by heat and fungicide suppresses the formation of hair ice. Fruiting bodies of Asco- and Basidiomycota are identified on hair-ice-carrying wood. One species, Exidiopsis effusa (Ee), was present on all investigated samples. Both hair-ice-producing wood samples and those with killed fungus show essentially the same temperature variation, indicating that the heat produced by fungal metabolism is very small, that the freezing rate is not influenced by the fungus activity, and that ice segregation is the common mechanism of ice growth on the wood surface. The fungus plays the role of shaping the ice hairs and preventing them from recrystallisation. Melted hair ice indicates the presence of organic matter. Chemical analyses show a complex mixture of several thousand CHO(N,S) compounds similar to fulvic acids in dissolved organic matter (DOM). The evaluation reveals decomposed lignin as being the main constituent. Further work is needed to clarify its role in hair-ice growth and to identify the recrystallisation inhibitor.

Canakinumab in adults with steroid-refractory pyoderma gangrenosum

BACKGROUND Pyoderma gangrenosum (PG) is a rare, neutrophilic, ulcerative skin disease that is difficult to treat, especially when unresponsive to steroids. OBJECTIVES To determine whether canakinumab is an effective and safe treatment in PG. METHODS Five adult patients with clinically and histologically confirmed steroid-refractory PG were enrolled in this prospective open-label study. They received canakinumab 150 mg subcutaneously at week 0 with an optional 150 mg at week 2 in case of an inadequate response [Physician's Global Assessment (PGA) ≥ 2], and an optional 150-300 mg at week 8 depending on PGA. The primary clinical end point was clinical improvement (PGA at least -1 from baseline) and/or complete remission (PGA 0 or 1) at week 16. Real-time quantitative polymerase chain reaction was performed on skin samples to quantify cytokine mRNA levels. RESULTS Interleukin (IL)-1β and its known target genes IL6, CXCL8 and IL36A were significantly increased in lesional skin of PG. Under canakinumab therapy, four of five patients showed a decrease in target-lesion size, PGA and Dermatology Life Quality Index (DLQI), and three of five achieved complete remission. The mean diameter of target lesions decreased from 4·32 ± 2·6 cm at visit 1 to 0·78 ± 1·3 cm at visit 7 (P = 0·03). Mean DLQI decreased from 15 ± 5 at visit 1 to 8 ± 4 by visit 7 (P = 0·01). Adverse effects were reported in two patients: fatigue in one and worsening of disease at a nontarget lesion in the other. CONCLUSIONS Our data indicate that IL-1β plays a key pathogenic role in PG and canakinumab may represent a therapeutic option for steroid-refractory PG.

Occurrence of Brachyspira hyodysenteriae in multiplier pig herds in Switzerland

OBJECTIVE: This research was aimed to determine the occurrence of Brachyspira (B.) hyodysenteriae in Swiss multiplier pig herds. MATERIALS AND METHODS: In a pilot study a direct real-time polymerase chain reaction (PCR) method for B. hyodysenteriae was compared to culture followed by PCR on 106 samples from three herds. Subsequently 40 multiplier herds were epidemiologically characterized and analysed for the presence of B. hyodysenteriae using direct PCR on 1412 rectal swabs. For external validation 20 swabs obtained from two positive conventional herds were analysed. RESULTS: The comparison of direct PCR with culture followed by PCR resulted in a moderate agreement (kappa index: 0.58). In the two conventional herds, 35% of the samples (7/20) tested positive. Samples from 39 multipliers tested negative. In one multiplier herd, 25% (9/36) of the samples tested PCR positive. Risk factors in the multiplier herd may have been rodents or birds, but not pig purchase. CONCLUSION AND CLINICAL RELEVANCE: B. hyodysenteriae have been detected in a Swiss multiplier herd, which underlines the threat of potential spread by replacement pigs. Consequently, a Brachyspira monitoring programme was established for Swiss multiplier herds.

Permittivity measurements of porous matter in support of investigations of the surface and interior of 67P/Churyumov-Gerasimenko

Aims. Permittivity measurements on porous samples of volcanic origin have been performed in the 0.05-190 GHz range under laboratory conditions in support of the Rosetta mission to comet 67P/Churyumov-Gerasimenko, specifically with the MIRO radiometric experiment and CONSERT radar experiment. Methods. The samples were split into several subsamples with different size ranges covering a few mu m to 500 mu m. Bulk densities of the subsamples were estimated to be in the 800 to 1500 kg/m(3) range. The porosities were in the range of 48% to 65%. From 50 MHz to 6 GHz and at 190 GHz, permittivity has been determined with a coaxial cell and with a quasi-optical bench, respectively. Results. Without taking into account the volume-scattering effect at 190 GHz, the real part of the permittivity, normalized by the bulk density, is in the range of 2.1 to 2.6. The results suggest that the real part of the permittivity of an ice-free dust mantle covering the nucleus is in the 1.5-2.2 range at 190 GHz. From these values, a lower limit for the absorption length for the millimeter receiver of MIRO has been estimated to be between 0.6 and 2 cm, in agreement with results obtained from MIRO in September 2014. At frequencies of interest for CONSERT experiment, the real part of the permittivity of a suspected ice-free dust mantle should be below 2.2. It may be in the range of 1.2 to 1.7 for the nucleus, in agreement with first CONSERT results, taking into account a mean temperature of 110 K and different values for the dust-to-ice volumetric ratio. Estimations of contributions of the different parameters to the permittivity variation may indicate that the porosity is the main parameter.

Characterization of HFO2 Capacitors

Hafnium oxide (HfOn) is a promising dielectric for future microelectronic applications. Hf02 thin films (10-75nm) were deposited on Pt/Si02/Si substrates by pulsed DC magnetron reactive sputtering. Top electrodes of Pt were formed by e-beam evapo- ration through an aperture mask on the samples to create MIM (Metal-Insulator-Metal) capacitors. Various processing conditions (Arloz ratio, DC power and deposition rate) and post-deposition annealing conditions (time and temperature) were investigated. The structure of the Hf02 films was characterized by X-ray diffraction (XRD) and the roughness was measured by a profilometer. The electrical properties were characterized in terms of their relative permittivity (E,(T) and ~,.(f)) and leakage behavior (I-V, I-T and I- time). The electrical measurements were performed over a temperature range from -5 to 200°C. For the samples with best experimental results, the relative permittivity of HfOa was found to be -- 27 after anneal and increased by 0.027%/"C with increasing temperature over the measured temperature range. At 25"C, leakage current density was below lop8 ~ l c m ' at 1 volt. The leakage current increased with temperature above a specific threshold temperature below which the leakage current didn't change much. The leakage current increased with voltage. At voltages below lvolt, it's ohmic; at higher voltages, it follows Schottky model. The breakdown field is - 1 . 8 2 ~ lo6 Vlcm. The optical bandgap was measured with samples deposited on quartz substrates to be 5.4eV after anneal.

The Spanish translation, cultural adaptation and validation of the Powe Fatalism Inventory

Background/significance. The scarcity of reliable and valid Spanish language instruments for health related research has hindered research with the Hispanic population. Research suggests that fatalistic attitudes are related to poor cancer screening behaviors and may be one reason for low participation of Mexican-Americans in cancer screening. This problem is of major concern because Mexican-Americans constitute the largest Hispanic subgroup in the U.S.^ Purpose. The purposes of this study were: (1) To translate the Powe Fatalism Inventory, (PFI) into Spanish, and culturally adapt the instrument to the Mexican-American culture as found along the U.S.-Mexico border and (2) To test the equivalence between the Spanish translated, culturally adapted version of the PFI and the English version of the PFI to include clarity, content validity, reading level and reliability.^ Design. Descriptive, cross-sectional.^ Methods. The Spanish language translation used a translation model which incorporates a cultural adaptation process. The SPFI was administered to 175 bilingual participants residing in a midsize, U.S-Mexico border city. Data analysis included estimation of Cronbach's alpha, factor analysis, paired samples t-test comparison and multiple regression analysis using SPSS software, as well as measurement of content validity and reading level of the SPFI. ^ Findings. A reliability estimate using Cronbach's alpha coefficient was 0.81 for the SPFI compared to 0.80 for the PFI in this study. Factor Analysis extracted four factors which explained 59% of the variance. Paired t-test comparison revealed no statistically significant differences between the SPFI and PFI total or individual item scores. Content Validity Index was determined to be 1.0. Reading Level was assessed to be less than a 6th grade reading level. The correlation coefficient between the SPFI and PFI was 0.95.^ Conclusions. This study provided strong psychometric evidence that the Spanish translated, culturally adapted SPFI is an equivalent tool to the English version of the PFI in measuring cancer fatalism. This indicates that the two forms of the instrument can be used interchangeably in a single study to accommodate reading and speaking abilities of respondents. ^

A cross-sectional study of disparities in suicide ideation between Hispanic and non-Hispanic white female adolescents

Suicide is recognized as a major public health and clinical problem in the United States. One fifth of adolescents in the United States seriously consider suicide each year, and about 8% of high school students attempt suicide at least once. Hispanic ethnicity constitutes a risk factor for suicidal ideation and suicide attempts, with Hispanic females at highest risk. Nevertheless, published studies on suicidal behavior in Hispanic female adolescents are extremely limited and focus on suicidal ideation in school samples. Given the severity of the problem and the paucity of information on this topic, more research on ethnic differences in suicidal ideation in community samples of high-risk children is urgently needed. This cross-sectional study delineated differences in suicide ideation between Hispanic female adolescents and non-Hispanic white female adolescents attending a mental health clinic and examined the association of ethnicity with suicide ideation independent of other known risk factors. Data were accrued between June 2004 and December 2008 in a Harris County Mental Health and Mental Retardation Association (MHMRA) clinic. Data were limited to adolescents who were Harris County Residents between the ages of 10 to 17 years when they were admitted to the clinic. The objective of this study was to determine whether differences in socio-demographic and clinical variables play a significant role in ethnic disparities in suicide ideation. A series of logistic regressions were performed to estimate the association between ethnicity and suicide ideation after controlling for potentially confounding factors. ^ Results showed an interaction between Hispanic ethnicity and having a history of treatment: Hispanic girls having history of treatment had lower odds of having suicide ideation than Hispanic girls without such a history. After adjusting for treatment history, family problems, substance use, juvenile justice involvement, current treatment, and age, Hispanic girls had 1.86 times the odds of having suicide ideation than non Hispanic girls (OR=1.86, 95% CI=0.88-1.46). Although additional studies on community samples of high risk adolescents are needed to verify these findings, our study highlights the fact that Hispanic girls are at significantly higher risk and need to be targeted for prevention and treatment efforts. ^

YKL -40, a vascular -associated serum marker for glioblastoma, correlates with chronic activation of AKT

YKL-40 is a secreted glycoprotein that has been reported to be expressed in pathologic conditions of extracellular matrix degradation and angiogenesis, such as rheumatoid arthritis, severe osteoarthritis, primary colorectal cancer, metastatic breast cancer, and recurrent ovarian cancer (Dehn, Hogdall et al. 2003). ^ We have identified YKL-40 as a serum marker for glioblastoma multiforme (GBM) using microarray analysis from samples of GBM. We compared the gene expression profile of 19 gliomas to pooled normal brain tissue using the Incyte 10,000 gene expression array. The most differentially expressed gene in this analysis was YKL-40; it was detected in GBM samples with a range of 3 to 62-fold elevation over normal brain. Western blot analysis of glioma samples for YKL-40 protein levels revealed substantial elevation in approximately 65% of GBMs, and undetectable levels in lower-grade gliomas and normal brain tissue. ELISA analysis on serum samples of glioma patients showed that YKL-40 levels were substantially elevated in many of the GBM patients. Statistical analysis indicated that in patients with glioma, serum YKL-40 levels correlate with tumor grade and potentially tumor burden in GBM. ^ Furthermore, we found that YKL-40 expression by in-situ hybridization on a brain tumor tissue array was limited to GBM's and gliosarcomas (GSA), and that YKL-40 expression was specific to the GBM component of GSA. Additional in-situ hybridization analysis, found it to be regionally associated with tumor vasculature as well as activated AKT expression in both human and mouse GBM's. Correlation of elevated YKL-40 with phospho-AKT was confirmed by Western blot analysis on a series of glioblastoma tumors, and inhibition of PI3 Kinase signaling by addition of LY294002 also decreased secretion of YKL-40 over a 7-day period in U87 glioblastoma cell tine. Lastly, YKL-40 expression was induced in response to serum starvation and altered by interaction with specific extracellular matrix (ECM) modules. In summary, we have identified the first accurate serum marker for high-grade gliomas. Furthermore, our findings indicate that YKL-40 is a highly expressed vascular-related glycoprotein in human GBM tissue and that it is affected by the AKT signaling pathway and interaction with components of brain ECM proteins. ^

Description and chemical composition of ferromanganese deposits from Trout Lake, northern Wisconsin

Sediments were collected with Eckman and Petersen dredges from the bottom of Trout Lake, northern Wisconsin, at 221 stations. Sampling was done with a spud sampler at 32 stations, and core samples were obtained with a Jenkins and Mortimer and a Twenhofel sampler at 17 stations. The shore and offshore deposits of the shores of Trout Lake and the shores of the islands are described. Megascopic descriptions are given of the samples collected with the Eckman and Petersen dredges. Sediments on bottoms of about 10 meters or deeper are mainly gyttja, or crusts composed of mixtures of organic matter, ferric hydroxide, and some form of manganese oxide. The latter deposits are extensive. Detailed descriptions of some of the samples of sands are given, and generalizations respecting size and distribution are made. Tables showing quartiles, medians, and coefficients of sorting and skewness of the coarse sediments collected from the bottom are given in tables. Mechanical analyses of all fine sediments, mainly gyttja, were not made, as previous experience seems to have demonstrated that results have no sedimentational value. Organic matter of the gyttja was determined and also the percentages of lignin in the organic matter. Core samples are composed almost entirely of fine materials, mainly gyttja, and determinations were made on these samples in the same way as on the samples obtained with the Eckman and Petersen dredges. Studies of the core samples show that the fine sediments usually contain in excess of 90 per cent moisture and there is very little change in the moisture content from top to bottom of cores. A map shows the distribution of the iron and manganese deposits. These deposits were found to contain 10 to 20 per cent of organic matter, 11 to 16 per cent of metallic iron, and 12 to 30 per cent of metallic manganese. No stratification of any kind was found in any of the deep-water sediments of Trout Lake except in the iron and manganese crusts. Absence of stratification is considered to be due to the slow rate of deposition and the mixing of sediments by organisms which dwell in them. The data indicate that the rate of deposition in the deep waters of Trout Lake is of the order of 1 foot in 15,000 years.

Physical properties and neutron texture measuerments of deep-sea carbonates of DSDP Holes 62-463 and 62-465A

In weakly indurated, nannofossil-rich, deep-sea carbonates compressional wave velocity is up to twice as fast parallel to bedding than normal to it. It has been suggested that this anisotropy is due to alignment of calcite c-axes perpendicular to the shields of coccoliths and shield deposition parallel to bedding. This hypothesis was tested by measuring the preferred orientation (fabric) of calcite c-axes in acoustic anisotropic, calcareous DSDP sediment samples by X-ray goniometry, and it was found that the maximum c-axis concentrations are by far too low to explain the anisotropies. The X-ray method is subject to a number of uncertainties due to preparatory and technical shortcomings in weakly indurated rocks. The most serious weaknesses are: sample preparation, volume of measured sample (fraction of a mm3), beam defocusing and background intensity corrections, combination of incomplete pole figures, and necessity of recalculation of the c-axis orientations from other crystallographic directions. Goniometry using thermal neutrons overcomes most of these difficulties, but it is time consuming. We test the interferences made about velocity anisotropy by X-ray studies about the concentration of c-axes in deep-sea carbonates by employing neutron texture goniometry to eight DSDP samples comprising mostly nannofossil material. Fabric and sonic velocity were determined directly on the core specimens, thus from the same rock volume and requiring no preparation. The c-axis orientation is obtained directly from the [0006] calcite diffraction peak without corrections. The fabrics are clearly defined, but weak (1.1 to 1.86 times uniform) with the maximum about normal to bedding. They have crudely orthorhombic symmetry, but are not axisymmetric around the bedding normal. The observed c-axis intensities, although higher than determined by the X-ray method on other samples, are by far too low to explain the observed acoustic anisotropies.

(Table 1) K and Ar content, and age determination of ODP Holes 126-792E and 126-793B

Results of conventional K-Ar dating on five samples from two sites from the Izu-Bonin forearc are presented. Two samples recovered from a volcanic edifice and overlying sediments drilled on the western side of the forearc basin (Site 792) indicate a basement age of 34 Ma. This is consistent with early Oligocene biostratigraphic ages from the overlying sediments. Three samples from the basement of Hole 793B at the center of the basin are not analytically distinguishable, with a best age of 27.1 +/- 0.6 Ma. This is slightly younger than the 30-33 Ma biostratigraphic and magnetostratigraphic estimates from the overlying sediments, suggesting that alteration processes have lowered the apparent K-Ar ages. These ages suggest that syn-rift volcanism occurred in a forearc location during the middle Oligocene.