Nonlinearities and Effects of Transverse Beam Size in Beam Position Monitors (revised)

The fields produced by a long beam with a given transverse charge distribution in a homogeneous vacuum chamber are studied. Signals induced by a displaced finite-size beam on electrodes of a beam position monitor (BPM) are calculated and compared to those produced by a pencil beam. The non-linearities and corrections to BPM signals due to a finite transverse beam size are calculated for an arbitrary chamber cross section. Simple analytical expressions are given for a few particular transverse distributions of the beam current in a circular or rectangular chamber. Of particular interest is a general proof that in an arbitrary homogeneous chamber the beam-size corrections vanish for any axisymmetric beam current distribution.Comment: REVTeX, 8 pages, 9 figures. Corrected Eqs. (7),(22),(25) and Figs. 2-9. Expande

Age and growth, reproduction and diet of a sublittoral population of the rock goby Gobius paganellus (Teleostei, Gobiidae)

Copyright © 2000 Kluwer Academic Publishers. Printed in the Netherlands.Basic biological information for a sublittoral population of the rock goby Gobius paganellus Linnaeus, 1758 is presented based on a 2-year study involving 1680 specimens. The length-weight relationship was given by TW = 0.0089 * TL^3,163 (where TW= total weight in g; TL= total length in mm). Age at length data were inferred by modal analysis of the monthly length-frequency distributions. The parameters of the fitted Von Bertalanffy growth equation (with seasonal component, birth date on the 1st of January) were L1 = 13.8 cm; K = 0.73 yr^-1; to = -0.22 yr; C = 0.95; W = 0.07. This growth rate is much higher than that described for northern Europe populations (where K is about 0.3 yr^-1) and is probably associated with a shorter life span. Macroscopic examination of the gonads, and analysis of the monthly values of the gonadosomatic index, indicated that reproduction occurs in winter and early spring, with a maximum in February and March, when water temperatures are lowest. Individuals become sexually mature around 6-7 cm TL, a size that can be reached in less than 1 year. By contrast, individuals of this goby in the British Isles mature in their second or third year. Stomach contents were mainly small benthic invertebrates, predominantly crustaceans

Shear band dynamics from a mesoscopic modeling of plasticity

The ubiquitous appearance of regions of localized deformation (shear bands) in different kinds of disordered materials under shear is studied in the context of a mesoscopic model of plasticity. The model may or may not include relaxational (aging) effects. In the absence of relaxational effects the model displays a monotonously increasing dependence of stress on strain-rate, and stationary shear bands do not occur. However, in start up experiments transient (although long lived) shear bands occur, that widen without bound in time. I investigate this transient effect in detail, reproducing and explaining a t^1/2 law for the thickness increase of the shear band that has been obtained in atomistic numerical simulations. Relaxation produces a negative sloped region in the stress vs. strain-rate curve that stabilizes the formation of shear bands of a well defined width, which is a function of strain-rate. Simulations at very low strain-rates reveal a non-trivial stick-slip dynamics of very thin shear bands that has relevance in the study of seismic phenomena. In addition, other non-stationary processes, such as stop-and-go, or strain-rate inversion situations display a phenomenology that matches very well the results of recent experimental studies.Comment: 10 pages, 10 figure

In vitro fermentation of juçara pulp (Euterpe edulis) by human colonic microbiota

This study was carried out to investigate the potential fermentation properties of juçara pulp, using pH-controlled anaerobic batch cultures reflective of the distal region of the human large intestine. Effects upon major groups of the microbiota were monitored over 24 h incubations by fluorescence in situ hybridisation (FISH). Short-chain fatty acids (SCFA) were measured by HPLC. Phenolic compounds, during an in vitro simulated digestion and fermentation, were also analysed. Juçara pulp can modulate the intestinal microbiota in vitro, promoting changes in the relevant microbial populations and shifts in the production of SCFA. Fermentation of juçara pulp resulted in a significant increase in numbers of bifidobacteria after a 24 h fermentation compared to a negative control. After in vitro digestion, 46% of total phenolic content still remained. This is the first study reporting the potential prebiotic effect of juçara pulp; however, human studies are necessary to prove its efficacy

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Investigation of the Enteric Pathogenic Potential of Oral Campylobacter concisus Strains Isolated from Patients with Inflammatory Bowel Disease

BACKGROUND: Campylobacter concisus, a bacterium colonizing the human oral cavity, has been shown to be associated with inflammatory bowel disease (IBD). This study investigated if patients with IBD are colonized with specific oral C. concisus strains that have potential to cause enteric diseases. METHODOLOGY: Seventy oral and enteric C. concisus isolates obtained from eight patients with IBD and six controls were examined for housekeeping genes by multilocus sequence typing (MLST), Caco2 cell invasion by gentamicin-protection-assay, protein analysis by mass spectrometry and SDS-PAGE, and morphology by scanning electron microscopy. The whole genome sequenced C. concisus strain 13826 which was isolated from an individual with bloody diarrhea was included in MLST analysis. PRINCIPAL FINDINGS: MLST analysis showed that 87.5% of individuals whose C. concisus belonged to Cluster I had inflammatory enteric diseases (six IBD and one with bloody diarrhea), which was significantly higher than that in the remaining individuals (28.6%) (P<0.05). Enteric invasive C. concisus (EICC) oral strain was detected in 50% of patients with IBD and none of the controls. All EICC strains were in Cluster 1. The C. concisus strain colonizing intestinal tissues of patient No. 1 was closely related to the oral C. concisus strain from patient No. 6 and had gene recombination with the patient's own oral C. concisus. The oral and intestinal C. concisus strains of patient No. 3 were the same strain. Some individuals were colonized with multiple oral C. concisus strains that have undergone natural recombination. CONCLUSIONS: This study provides the first evidence that patients with IBD are colonized with specific oral C. concisus strains, with some being EICC strains. C. concisus colonizing intestinal tissues of patients with IBD at least in some instances results from an endogenous colonization of the patient's oral C. concisus and that C. concisus strains undergo natural recombination

Reduced Cortisol and Metabolic Responses of Thin Ewes to an Acute Cold Challenge in Mid-Pregnancy: Implications for Animal Physiology and Welfare

Background: Low food availability leading to reductions in Body Condition Score (BCS; 0 indicates emaciation and 5 obesity) in sheep often coincides with low temperatures associated with the onset of winter in New Zealand. The ability to adapt to reductions in environmental temperature may be impaired in animals with low BCS, in particular during pregnancy when metabolic demand is higher. Here we assess whether BCS affects a pregnant animal’s ability to cope with cold challenges. Methods: Eighteen pregnant ewes with a BCS of 2.760.1 were fed to attain low (LBC: BCS2.360.1), medium (MBC: BCS3.260.2) or high BCS (HBC: BCS3.660.2). Shorn ewes were exposed to a 6-h acute cold challenge in a climate-controlled room (wet and windy conditions, 4.460.1uC) in mid-pregnancy. Blood samples were collected during the BCS change phase, acute cold challenge and recovery phase. Results: During the BCS change phase, plasma glucose and leptin concentrations declined while free fatty acids (FFA) increased in LBC compared to MBC (P,0.01, P,0.01 and P,0.05, respectively) and HBC ewes (P,0.05, P,0.01 and P,0.01, respectively). During the cold challenge, plasma cortisol concentrations were lower in LBC than MBC (P,0.05) and HBC ewes (P,0.05), and FFA and insulin concentrations were lower in LBC than HBC ewes (P,0.05 and P,0.001, respectively). Leptin concentrations declined in MBC and HBC ewes while remaining unchanged in LBC ewes (P,0.01). Glucose concentrations and internal body temperature (Tcore) increased in all treatments, although peak Tcore tended to be higher in HBC ewes (P,0.1). During the recovery phase, T4 concentrations were lower in LBC ewes (P,0.05). Conclusion: Even though all ewes were able to increase Tcore and mobilize glucose, low BCS animals had considerably reduced cortisol and metabolic responses to a cold challenge in mid-pregnancy, suggesting that their ability to adapt to cold challenges through some of the expected pathways was reduced