A comparison of analysis techniques for extracting resonance parameters from lattice Monte Carlo data

Different methods for extracting resonance parameters from Euclidean lattice field theory are tested. Monte Carlo simulations of the O(4) non-linear sigma model are used to generate energy spectra in a range of different volumes both below and above the inelastic threshold. The applicability of the analysis methods in the elastic region is compared. Problems which arise in the inelastic region are also emphasised.Comment: 17 pages, 20 figures; clarification and minor corrections added, to appear in PR

Rapid creation and quantitative monitoring of high coverage shRNA libraries.

Short hairpin RNA libraries are limited by low efficacy of many shRNAs and by off-target effects, which give rise to false negatives and false positives, respectively. Here we present a strategy for rapidly creating expanded shRNA pools (approximately 30 shRNAs per gene) that are analyzed by deep sequencing (EXPAND). This approach enables identification of multiple effective target-specific shRNAs from a complex pool, allowing a rigorous statistical evaluation of true hits

Association of the SULT1A1 R213H polymorphism with colorectal cancer

1. Sulphotransferases are a superfamily of enzymes involved in both detoxification and bioactivation of endogenous and exogenous compounds. The arylsulphotransferase SULT1A1 has been implicated in a decreased activity and thermostability when the wild-type arginine at position 213 of the coding sequence is substituted by a histidine. SULT1A1 is the isoform primarily associated with the conversion of dietary N -OH arylamines to DNA binding adducts and is therefore of interest to determine whether this polymorphism is linked to colorectal cancer. 2. Genotyping, using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis, was performed using DNA samples of healthy control subjects (n = 402) and patients with histologically proven colorectal cancer (n = 383). Both control and test populations possessed similar frequencies for the mutant allele (32.1 and 31%, respectively; P = 0.935). Results were not altered when age and gender were considered as potential confounders in a logistic regression analysis. 3. Examination of the sulphonating ability of the two allozymes with respect to the substrates p -nitrophenol and paracetamol showed that the affinity and rate of sulphonation was unaffected by substitution of arginine to histidine at position 213 of the amino acid sequence. 4. From this study, we conclude that the SULT1A1 R213H polymorphism is not linked with colorectal cancer in this elderly Australian population

Electrospun Fibrinogen-Polydioxanone Composite Matrix: Potential for In Situ Urologic Tissue Engineering

Our objective is to demonstrate an electrospun fibrinogen-PDO (polydioxanone) composite scaffold will retain the superior cellular interaction of fibrinogen while producing a product with the functional strength needed for direct implantation. Fibrinogen-PDO composite scaffolds were electrospun with PDO ratios of 0% (pure fibrinogen), 10%, 20%, 30%, 40%, 50% and 100% (pure PDO) and disinfected using standard methods. Scaffolds were seeded with human BSM (bladder smooth muscle cells) and incubated with twice weekly media changes. Samples were removed at 7, 14 and 21 days for evaluation by collagen assay, scanning electron microscopy and histology. Cell seeding and culture demonstrated human BSM readily migrate throughout and remodel electrospun fibrinogen-PDO composite scaffolds with deposition of native collagen. Cell migration and collagen deposition increased with increasing fibrinogen concentration while scaffold integrity increased with increasing PDO concentration. Electrospun fibrinogen-PDO composite structures promote rapid cellular in-growth by human BSM while maintaining structural integrity. The fibrinogen to PDO ratio can be adjusted to achieve the desired properties required for a specific tissue engineering application. Our ultimate objective is to utilize this innovative biomaterial technology to produce an acellular, bioresorbable product that enables in situ tissue regeneration. While there is still much work to be done, these initial findings indicate fibrinogen-PDO composite scaffolds deserve further investigation

Hydrothermal fluid circulation through the sediment of Crater Lake, Oregon: Pore water and heat flow constraints

We present evidence for pore water flow through the sediment of Crater Lake, Oregon based on systematic variations in pore water chemical compositions and thermal gradients. Pore water was extracted from sediment by centrifugation and diffusive exchange using a gravity corer deployed from a surface vessel and a box corer and peepers deployed from the submersible Deep Rover in a known geologic context. Depth profiles of sediment temperature were measured using two probes deployed from the submersible. One probe was connected to the submersible whereas the other was self‐contained and deployed for 7 days. On the basis of measured and calculated depth profiles of pore water Na, Ca, Mg, K, Li, and temperature, we show that pore water upwells in zones of focused upflow at speeds of meters to hundreds of meters per year. These zones of focused flow are patchy and usually cover several square meters to hundreds of square meters and are marked by iron‐manganese‐rich crusts, bacterial mats, and saline pools. In contrast, most of the lake floor consists of sediment derived from the caldera walls and has a low heat flow with pore water velocities of millimeters per year. The chemical composition of the pore water that upwells through the sampled section of the sediment column differs from core to core. This difference results from mixing a hydrothermal fluid in igneous basement below the lake with lake water before the final ascent through the sediment column. Elemental ratios of this thermally and chemically altered fluid in basement match those calculated based on mass balance considerations. Calculation of mass balance and geothermometry constrain the temperature in basement and ultimately the power output, which is about 30 MW. This power output is in agreement with two other estimates that were calculated using temperature data from the water column and measurements of sediment heat flow

The ethnicity attainment gap among medical and biomedical science students: a qualitative study.

Background Black, Asian and Minority Ethnic (BAME) medical students and professionals frequently underachieve when compared with their White counterparts not only in the United Kingdom, but across the globe. There is no consensus for the definitive causes of this attainment gap, but suggestions contributing towards it include: increased feelings of isolation as a member of a minority culture or religion; a poorer higher education (HE) experience compared with White counterparts; and stereotype threat, whereby students underperform in exams from the stresses of fearing confirming to a negative-stereotype. Methods The aim of this study was to gather qualitative data on HE experiences of medical and biomedical science students to explore factors contributing to the attainment gap. Audio-recorded, semi-structured interviews and a novel approach for this research area of ethnically-homogenous student-led focus groups, were held with students and staff at a healthcare-based university in London, where lower attainment, slower rates of degree completion and lower levels of satisfaction with HE experience were identified in BAME students compared with White students. Thematic analysis was used to manage, summarize and analyse the data. Results Forty-one students and eight staff members were interviewed or took part in focus groups. The student data were best explained by two main themes: social factors and stereotyping, whilst staff data were also best explained by two main themes: social factors and student and staff behaviour. Social factors suggested ethnically-defined social networks and the informal transfer of knowledge impacted academic performance, isolating minority groups from useful academic information. BAME students may also be at a further disadvantage, being unable to attend social and academic functions for cultural or family reasons. Black students also mentioned changing their behaviour to combat negative stereotypes in a variety of contexts. Conclusions This study suggests that forms of discrimination, whether conscious or unconscious, may be negatively impacting the abilities of BAME students both in examinations and in coursework choice. It highlights the importance of social networks for the transfer of academic knowledge and the impact ethnicity may have on their formation, with issues around segregation and the sharing of information outside defined groups

Toward Uniform Implementation Of Parametric Map Digital Imaging And Communication In Medicine Standard In Multisite Quantitative Diffusion Imaging Studies

This paper reports on results of a multisite collaborative project launched by the MRI subgroup of Quantitative Imaging Network to assess current capability and provide future guidelines for generating a standard parametric diffusion map Digital Imaging and Communication in Medicine (DICOM) in clinical trials that utilize quantitative diffusion-weighted imaging (DWI). Participating sites used a multivendor DWI DICOM dataset of a single phantom to generate parametric maps (PMs) of the apparent diffusion coefficient (ADC) based on two models. The results were evaluated for numerical consistency among models and true phantom ADC values, as well as for consistency of metadata with attributes required by the DICOM standards. This analysis identified missing metadata descriptive of the sources for detected numerical discrepancies among ADC models. Instead of the DICOM PM object, all sites stored ADC maps as DICOM MR objects, generally lacking designated attributes and coded terms for quantitative DWI modeling. Source-image reference, model parameters, ADC units and scale, deemed important for numerical consistency, were either missing or stored using nonstandard conventions. Guided by the identified limitations, the DICOM PM standard has been amended to include coded terms for the relevant diffusion models. Open-source software has been developed to support conversion of site-specific formats into the standard representation

UBC-Nepal Expedition: An experimental overview of the 2016 University of British Columbia Scientific Expedition to Nepal Himalaya

The University of British Columbia Nepal Expedition took place over several months in the fall of 2016 and was comprised of an international team of 37 researchers. This paper describes the objectives, study characteristics, organization and management of this expedition, and presents novel blood gas data during acclimatization in both lowlanders and Sherpa. An overview and framework for the forthcoming publications is provided. The expedition conducted 17 major studies with two principal goals—to identify physiological differences in: 1) acclimatization; and 2) responses to sustained high-altitude exposure between lowland natives and people of Tibetan descent. We performed observational cohort studies of human responses to progressive hypobaric hypoxia (during ascent), and to sustained exposure to 5050 m over 3 weeks comparing lowlander adults (n = 30) with Sherpa adults (n = 24). Sherpa were tested both with (n = 12) and without (n = 12) descent to Kathmandu. Data collected from lowlander children (n = 30) in Canada were compared with those collected from Sherpa children (n = 57; 3400–3900m). Studies were conducted in Canada (344m) and the following locations in Nepal: Kathmandu (1400m), Namche Bazaar (3440m), Kunde Hospital (3480m), Pheriche (4371m) and the Ev-K2-CNR Research Pyramid Laboratory (5050m). The core studies focused on the mechanisms of cerebral blood flow regulation, the role of iron in cardiopulmonary regulation, pulmonary pressures, intra-ocular pressures, cardiac function, neuromuscular fatigue and function, blood volume regulation, autonomic control, and micro and macro vascular function. A total of 335 study sessions were conducted over three weeks at 5050m. In addition to an overview of this expedition and arterial blood gas data from Sherpa, suggestions for scientists aiming to perform field-based altitude research are also presented. Together, these findings will contribute to our understanding of human acclimatization and adaptation to the stress of residence at high-altitude

A pilot study of the King LT supralaryngeal airway use in a rural Iowa EMS system

Introduction In 2003, the King Laryngeal Tube (LT) received FDA approval for US sales. Prehospital systems in urban setting have begun evaluating and adopting the LT for clinical airway management. However, it is not routinely approved by State EMS Boards for use by all prehospita