Exploring Neutral Hydrogen and Galaxy Evolution with the SKA

One of the key science drivers for the development of the SKA is to observe the neutral hydrogen, HI, in galaxies as a means to probe galaxy evolution across a range of environments over cosmic time. Over the past decade, much progress has been made in theoretical simulations and observations of HI in galaxies. However, recent HI surveys on both single dish radio telescopes and interferometers, while providing detailed information on global HI properties, the dark matter distribution in galaxies, as well as insight into the relationship between star formation and the interstellar medium, have been limited to the local universe. Ongoing and upcoming HI surveys on SKA pathfinder instruments will extend these measurements beyond the local universe to intermediate redshifts with long observing programmes. We present here an overview of the HI science which will be possible with the increased capabilities of the SKA and which will build upon the expected increase in knowledge of HI in and around galaxies obtained with the SKA pathfinder surveys. With the SKA1 the greatest improvement over our current measurements is the capability to image galaxies at reasonable linear resolution and good column density sensitivity to much higher redshifts (0.2 < z < 1.7). So one will not only be able to increase the number of detections to study the evolution of the HI mass function, but also have the sensitivity and resolution to study inflows and outflows to and from galaxies and the kinematics of the gas within and around galaxies as a function of environment and cosmic time out to previously unexplored depths. The increased sensitivity of SKA2 will allow us to image Milky Way-size galaxies out to redshifts of z=1 and will provide the data required for a comprehensive picture of the HI content of galaxies back to z~2 when the cosmic star formation rate density was at its peak.Comment: 25 pages, 5 figures, 3 tables. Contribution to the conference 'Advancing Astrophysics with the Square Kilometre Array', June 8-13, 2014, Giardini Naxos, Ital

Bacterial diversity in the intestinal tract of the funguscultivating termite Macrotermes michaelseni (Sjöstedt)

Microorganisms in the intestinal tracts of termites play a crucial role in the nutritional physiology of termites. The bacterial diversity in the fungus-cultivating Macrotermes michaelseni was examined usingboth molecular and culture dependent methods. Total DNA was extracted from the gut of the termite and 16S rRNA genes were amplified using bacterial specific primers. Representatives from forty-one (41) RFLP patterns from a total of one hundred and two (102) clones were sequenced. Most of the clones were affiliated with 3 main groups of the domain Bacteria: Cytophaga-Flexibacter-Bacteriodes(73), Proteobacteria (13), and the low G+C content Gram-positive bacteria (9). Two RFLPs related to planctomycetes, but deeper branching than known members of the phylum, were detected. In addition, 1 and 2 RFLPs represented the spirochetes and TM7-OP11 groups, respectively. In studies using culture dependent techniques, most of the isolates obtained belonged to the Gram-positive bacteriawith a high G+C content. However, only one of the clones represented Gram-positive bacteria with High G+C content. These results show a high bacterial diversity in the intestinal microbiota of M. michaelseni, which continues to escape cultivation. As is the case in other termites many of the clones represent previously uncultured bacteria. The fact that most of the clones clustered with clones from Macrotermes gilvus provides further support for the hypothesis that microorganisms in intestinal tracts of termites have co-evolved with their hosts

Experimental study of Pomeron

A Pomeron phenomenon remains a mystery. A short review of the experimental situation in diffractive physics and an account of some spectacular manifestations of the Pomeron are given.Comment: 17 pages, 7 Figs, LATEX. Talk given at the conference "From the smallest to largest distances", ITEP, Moscow, 24-26 May 2001. Changes: Fig.2 replace

Automated detection and delineation of lymph nodes in haematoxylin & eosin stained digitised slides

Treatment of patients with oesophageal and gastric cancer (OeGC) is guided by disease stage, patient performance status and preferences. Lymph node (LN) status is one of the strongest prognostic factors for OeGC patients. However, survival varies between patients with the same disease stage and LN status. We recently showed that LN size from patients with OeGC might also have prognostic value, thus making delineations of LNs essential for size estimation and the extraction of other imaging biomarkers. We hypothesized that a machine learning workflow is able to: (1) find digital H&E stained slides containing LNs, (2) create a scoring system providing degrees of certainty for the results, and (3) delineate LNs in those images. To train and validate the pipeline, we used 1695 H&E slides from the OE02 trial. The dataset was divided into training (80%) and validation (20%). The model was tested on an external dataset of 826 H&E slides from the OE05 trial. U-Net architecture was used to generate prediction maps from which predefined features were extracted. These features were subsequently used to train an XGBoost model to determine if a region truly contained a LN. With our innovative method, the balanced accuracies of the LN detection were 0.93 on the validation dataset (0.83 on the test dataset) compared to 0.81 (0.81) on the validation (test) datasets when using the standard method of thresholding U-Net predictions to arrive at a binary mask. Our method allowed for the creation of an “uncertain” category, and partly limited false-positive predictions on the external dataset. The mean Dice score was 0.73 (0.60) per-image and 0.66 (0.48) per-LN for the validation (test) datasets. Our pipeline detects images with LNs more accurately than conventional methods, and high-throughput delineation of LNs can facilitate future LN content analyses of large datasets

Automated detection and delineation of lymph nodes in haematoxylin & eosin stained digitised slides.

Treatment of patients with oesophageal and gastric cancer (OeGC) is guided by disease stage, patient performance status and preferences. Lymph node (LN) status is one of the strongest prognostic factors for OeGC patients. However, survival varies between patients with the same disease stage and LN status. We recently showed that LN size from patients with OeGC might also have prognostic value, thus making delineations of LNs essential for size estimation and the extraction of other imaging biomarkers. We hypothesized that a machine learning workflow is able to: (1) find digital H&E stained slides containing LNs, (2) create a scoring system providing degrees of certainty for the results, and (3) delineate LNs in those images. To train and validate the pipeline, we used 1695 H&E slides from the OE02 trial. The dataset was divided into training (80%) and validation (20%). The model was tested on an external dataset of 826 H&E slides from the OE05 trial. U-Net architecture was used to generate prediction maps from which predefined features were extracted. These features were subsequently used to train an XGBoost model to determine if a region truly contained a LN. With our innovative method, the balanced accuracies of the LN detection were 0.93 on the validation dataset (0.83 on the test dataset) compared to 0.81 (0.81) on the validation (test) datasets when using the standard method of thresholding U-Net predictions to arrive at a binary mask. Our method allowed for the creation of an "uncertain" category, and partly limited false-positive predictions on the external dataset. The mean Dice score was 0.73 (0.60) per-image and 0.66 (0.48) per-LN for the validation (test) datasets. Our pipeline detects images with LNs more accurately than conventional methods, and high-throughput delineation of LNs can facilitate future LN content analyses of large datasets

How Informed Is the Decision About Breast Reconstruction After Mastectomy?: A Prospective, Cross-sectional Study

to assess how informed patients are about breast reconstruction, and how involved they are in decision making

Lymph node response to chemoradiotherapy in oesophageal cancer patients: relationship with radiotherapy fields

Background The presence of lymph node metastasis (LNmets) is a poor prognostic factor in oesophageal cancer (OeC) patients treated with neoadjuvant chemoradiotherapy (nCRT) followed by surgery. Tumour regression grade (TRG) in LNmets has been suggested as a predictor for survival. The aim of this study was to investigate whether TRG in LNmets is related to their location within the radiotherapy (RT) field. Methods Histopathological TRG was retrospectively classified in 2565 lymph nodes (LNs) from 117 OeC patients treated with nCRT and surgery as: (A) no tumour, no signs of regression; (B) tumour without regression; (C) viable tumour and regression; and (D) complete response. Multivariate survival analysis was used to investigate the relationship between LN location within the RT field, pathological TRG of the LN and TRG of the primary tumour. Results In 63 (54%) patients, viable tumour cells or signs of regression were seen in 264 (10.2%) LNs which were classified as TRG-B (n = 56), C (n = 104) or D (n = 104) LNs. 73% of B, C and D LNs were located within the RT field. There was a trend towards a relationship between LN response and anatomical LN location with respect to the RT field (p = 0.052). Multivariate analysis showed that only the presence of LNmets within the RT field with TRG-B is related to poor overall survival. Conclusion Patients have the best survival if all LNmets show tumour regression, even if LNmets are located outside the RT field. Response in LNmets to nCRT is heterogeneous which warrants further studies to better understand underlying mechanisms

Epidemiology of HIV Infection in Large Urban Areas in the United States

Background: While the U.S. HIV epidemic continues to be primarily concentrated in urban area, local epidemiologic profiles may differ and require different approaches in prevention and treatment efforts. We describe the epidemiology of HIV in large urban areas with the highest HIV burden. Methods/Principal Findings: We used data from national HIV surveillance for 12 metropolitan statistical areas (MSAs) to determine disparities in HIV diagnoses and prevalence and changes over time. Overall, 0.3 % to 1 % of the MSA populations were living with HIV at the end of 2007. In each MSA, prevalence was.1 % among blacks; prevalence was.2 % in Miami, New York, and Baltimore. Among Hispanics, prevalence was.1 % in New York and Philadelphia. The relative percentage differences in 2007 HIV diagnosis rates, compared to whites, ranged from 239 (San Francisco) to 1239 (Baltimore) for blacks and from 15 (Miami) to 413 (Philadelphia) for Hispanics. The epidemic remains concentrated, with more than 50 % of HIV diagnoses in 2007 attributed to male-to-male sexual contact in 7 of the 12 MSAs; heterosexual transmission surpassed or equaled male-to-male sexual transmission in Baltimore, Philadelphia, and Washington, DC. Yet in several MSAs, including Baltimore and Washington, DC, AIDS diagnoses increased among men-who-have sex with men in recent years. Conclusions/Significance: These data are useful to identify local drivers of the epidemic and to tailor public health effort

Impact of Tube Bundle Placement on the Thermal Charging of a Latent Heat Storage Unit

The melting process of a multi-tube’s thermal energy storage system in the existence of free convection effects is a non-linear and important problem. The placement of heated tubes could change the convective thermal circulation. In the present study, the impact of the position of seven heat exchanger tubes was systematically investigated. The energy charging process was numerically studied utilizing liquid fraction and stored energy with exhaustive temperature outlines. The tubes of heat transfer fluid were presumed in the unit with different locations. The unit’s heat transfer behavior was assessed by studying the liquid fraction graphs, streamlines, and isotherm contours. Each of the design factors was divided into four levels. To better investigate the design space for the accounted five variables and four levels, an L16 orthogonal table was considered. Changing the location of tubes could change the melting rate by 28%. The best melting rate was 94% after four hours of charging. It was found that the tubes with close distance could overheat each other and reduce the total heat transfer. The study of isotherms and streamlines showed the general circulation of natural convection flows at the final stage of melting was the most crucial factor in the melting of top regions of the unit and reduces the charging time. Thus, particular attention to the tubes’ placement should be made so that the phase change material could be quickly melted at both ends of a unit.</jats:p