VersaCount: customizable manual tally software for cell counting

<p>Abstract</p> <p>Background</p> <p>The manual counting of cells by microscopy is a commonly used technique across biological disciplines. Traditionally, hand tally counters have been used to track event counts. Although this method is adequate, there are a number of inefficiencies which arise when managing large numbers of samples or large sample sizes.</p> <p>Results</p> <p>We describe software that mimics a traditional multi-register tally counter. Full customizability allows operation on any computer with minimal hardware requirements. The efficiency of counting large numbers of samples and/or large sample sizes is improved through the use of a "multi-count" register that allows single keystrokes to correspond to multiple events. Automatically updated multi-parameter values are implemented as user-specified equations, reducing errors and time required for manual calculations. The user interface was optimized for use with a touch screen and numeric keypad, eliminating the need for a full keyboard and mouse.</p> <p>Conclusions</p> <p>Our software provides an inexpensive, flexible, and productivity-enhancing alternative to manual hand tally counters.</p

Perfect Fluid Quantum Anisotropic Universe: Merits and Challenges

The present paper deals with quantization of perfect fluid anisotropic cosmological models. Bianchi type V and IX models are discussed following Schutz's method of expressing fluid velocities in terms of six potentials. The wave functions are found for several examples of equations of state. In one case a complete wave packet could be formed analytically. The initial singularity of a zero proper volume can be avoided in this case, but it is plagued by the usual problem of non-unitarity of anisotropic quantum cosmological models. It is seen that a particular operator ordering alleviates this problem.Comment: 13 pages, 4 figures; Accepted for publication in Gen Relativ Gravi

Argument for the need of investigation of the relationship between body fatness and experimental pain sensitivity.

In this communication, we argue about the need for an extensive investigation of the relationship between body fatness and fat distribution and experimental pain to explore the factors that might contribute to the increased prevalence of pain conditions in obese individuals

Designing an automated clinical decision support system to match clinical practice guidelines for opioid therapy for chronic pain

Abstract Background Opioid prescribing for chronic pain is common and controversial, but recommended clinical practices are followed inconsistently in many clinical settings. Strategies for increasing adherence to clinical practice guideline recommendations are needed to increase effectiveness and reduce negative consequences of opioid prescribing in chronic pain patients. Methods Here we describe the process and outcomes of a project to operationalize the 2003 VA/DOD Clinical Practice Guideline for Opioid Therapy for Chronic Non-Cancer Pain into a computerized decision support system (DSS) to encourage good opioid prescribing practices during primary care visits. We based the DSS on the existing ATHENA-DSS. We used an iterative process of design, testing, and revision of the DSS by a diverse team including guideline authors, medical informatics experts, clinical content experts, and end-users to convert the written clinical practice guideline into a computable algorithm to generate patient-specific recommendations for care based upon existing information in the electronic medical record (EMR), and a set of clinical tools. Results The iterative revision process identified numerous and varied problems with the initially designed system despite diverse expert participation in the design process. The process of operationalizing the guideline identified areas in which the guideline was vague, left decisions to clinical judgment, or required clarification of detail to insure safe clinical implementation. The revisions led to workable solutions to problems, defined the limits of the DSS and its utility in clinical practice, improved integration into clinical workflow, and improved the clarity and accuracy of system recommendations and tools. Conclusions Use of this iterative process led to development of a multifunctional DSS that met the approval of the clinical practice guideline authors, content experts, and clinicians involved in testing. The process and experiences described provide a model for development of other DSSs that translate written guidelines into actionable, real-time clinical recommendations.http://deepblue.lib.umich.edu/bitstream/2027.42/78267/1/1748-5908-5-26.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78267/2/1748-5908-5-26.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/78267/3/1748-5908-5-26-S3.TIFFhttp://deepblue.lib.umich.edu/bitstream/2027.42/78267/4/1748-5908-5-26-S2.TIFFhttp://deepblue.lib.umich.edu/bitstream/2027.42/78267/5/1748-5908-5-26-S1.TIFFPeer Reviewe

Interactions between downslope flows and a developing cold-air pool

A numerical model has been used to characterize the development of a region of enhanced cooling in an alpine valley with a width of order (Formula presented.) km, under decoupled stable conditions. The region of enhanced cooling develops largely as a region of relatively dry air which partitions the valley atmosphere dynamics into two volumes, with airflow partially trapped within the valley by a developing elevated inversion. Complex interactions between the region of enhanced cooling and the downslope flows are quantified. The cooling within the region of enhanced cooling and the elevated inversion is almost equally partitioned between radiative and dynamic effects. By the end of the simulation, the different valley atmospheric regions approach a state of thermal equilibrium with one another, though this cannot be said of the valley atmosphere and its external environment.Peer reviewe

Pollutant dispersion in a developing valley cold-air pool

Pollutants are trapped and accumulate within cold-air pools, thereby affecting air quality. A numerical model is used to quantify the role of cold-air-pooling processes in the dispersion of air pollution in a developing cold-air pool within an alpine valley under decoupled stable conditions. Results indicate that the negatively buoyant downslope flows transport and mix pollutants into the valley to depths that depend on the temperature deficit of the flow and the ambient temperature structure inside the valley. Along the slopes, pollutants are generally entrained above the cold-air pool and detrained within the cold-air pool, largely above the ground-based inversion layer. The ability of the cold-air pool to dilute pollutants is quantified. The analysis shows that the downslope flows fill the valley with air from above, which is then largely trapped within the cold-air pool, and that dilution depends on where the pollutants are emitted with respect to the positions of the top of the ground-based inversion layer and cold-air pool, and on the slope wind speeds. Over the lower part of the slopes, the cold-air-pool-averaged concentrations are proportional to the slope wind speeds where the pollutants are emitted, and diminish as the cold-air pool deepens. Pollutants emitted within the ground-based inversion layer are largely trapped there. Pollutants emitted farther up the slopes detrain within the cold-air pool above the ground-based inversion layer, although some fraction, increasing with distance from the top of the slopes, penetrates into the ground-based inversion layer.Peer reviewe

A Cross-Sectional Survey on Knowledge and Perceptions of Health Risks Associated with Arsenic and Mercury Contamination from Artisanal Gold mining in Tanzania.

An estimated 0.5 to 1.5 million informal miners, of whom 30-50% are women, rely on artisanal mining for their livelihood in Tanzania. Mercury, used in the processing gold ore, and arsenic, which is a constituent of some ores, are common occupational exposures that frequently result in widespread environmental contamination. Frequently, the mining activities are conducted haphazardly without regard for environmental, occupational, or community exposure. The primary objective of this study was to assess community risk knowledge and perception of potential mercury and arsenic toxicity and/or exposure from artisanal gold mining in Rwamagasa in northwestern Tanzania. A cross-sectional survey of respondents in five sub-villages in the Rwamagasa Village located in Geita District in northwestern Tanzania near Lake Victoria was conducted. This area has a history of artisanal gold mining and many of the population continue to work as miners. Using a clustered random selection approach for recruitment, a total of 160 individuals over 18 years of age completed a structured interview. The interviews revealed wide variations in knowledge and risk perceptions concerning mercury and arsenic exposure, with 40.6% (n=65) and 89.4% (n=143) not aware of the health effects of mercury and arsenic exposure respectively. Males were significantly more knowledgeable (n=59, 36.9%) than females (n=36, 22.5%) with regard to mercury (x²=3.99, p<0.05). An individual's occupation category was associated with level of knowledge (x²=22.82, p=<0.001). Individuals involved in mining (n=63, 73.2%) were more knowledgeable about the negative health effects of mercury than individuals in other occupations. Of the few individuals (n=17, 10.6%) who knew about arsenic toxicity, the majority (n=10, 58.8%) were miners. The knowledge of individuals living in Rwamagasa, Tanzania, an area with a history of artisanal gold mining, varied widely with regard to the health hazards of mercury and arsenic. In these communities there was limited awareness of the threats to health associated with exposure to mercury and arsenic. This lack of knowledge, combined with minimal environmental monitoring and controlled waste management practices, highlights the need for health education, surveillance, and policy changes

Bayesian Fit of Exclusive b→sℓˉℓb \to s \bar\ell\ell Decays: The Standard Model Operator Basis

We perform a model-independent fit of the short-distance couplings $C_{7,9,10}$ within the Standard Model set of $b\to s\gamma$ and $b\to s\bar\ell\ell$ operators. Our analysis of $B \to K^* \gamma$, $B \to K^{(*)} \bar\ell\ell$ and $B_s \to \bar\mu\mu$ decays is the first to harness the full power of the Bayesian approach: all major sources of theory uncertainty explicitly enter as nuisance parameters. Exploiting the latest measurements, the fit reveals a flipped-sign solution in addition to a Standard-Model-like solution for the couplings $C_i$. Each solution contains about half of the posterior probability, and both have nearly equal goodness of fit. The Standard Model prediction is close to the best-fit point. No New Physics contributions are necessary to describe the current data. Benefitting from the improved posterior knowledge of the nuisance parameters, we predict ranges for currently unmeasured, optimized observables in the angular distributions of $B\to K^*(\to K\pi)\,\bar\ell\ell$.Comment: 42 pages, 8 figures; v2: Using new lattice input for f_Bs, considering Bs-mixing effects in BR[B_s->ll]. Main results and conclusion unchanged, matches journal versio

A Systematic Mapping Approach of 16q12.2/FTO and BMI in More Than 20,000 African Americans Narrows in on the Underlying Functional Variation: Results from the Population Architecture using Genomics and Epidemiology (PAGE) Study

Genetic variants in intron 1 of the fat mass- and obesity-associated (FTO) gene have been consistently associated with body mass index (BMI) in Europeans. However, follow-up studies in African Americans (AA) have shown no support for some of the most consistently BMI-associated FTO index single nucleotide polymorphisms (SNPs). This is most likely explained by different race-specific linkage disequilibrium (LD) patterns and lower correlation overall in AA, which provides the opportunity to fine-map this region and narrow in on the functional variant. To comprehensively explore the 16q12.2/FTO locus and to search for second independent signals in the broader region, we fine-mapped a 646-kb region, encompassing the large FTO gene and the flanking gene RPGRIP1L by investigating a total of 3,756 variants (1,529 genotyped and 2,227 imputed variants) in 20,488 AAs across five studies. We observed associations between BMI and variants in the known FTO intron 1 locus: the SNP with the most significant p-value, rs56137030 (8.3×10-6) had not been highlighted in previous studies. While rs56137030was correlated at r2>0.5 with 103 SNPs in Europeans (including the GWAS index SNPs), this number was reduced to 28 SNPs in AA. Among rs56137030 and the 28 correlated SNPs, six were located within candidate intronic regulatory elements, including rs1421085, for which we predicted allele-specific binding affinity for the transcription factor CUX1, which has recently been implicated in the regulation of FTO. We did not find strong evidence for a second independent signal in the broader region. In summary, this large fine-mapping study in AA has substantially reduced the number of common alleles that are likely to be functional candidates of the known FTO locus. Importantly our study demonstrated that comprehensive fine-mapping in AA provides a powerful approach to narrow in on the functional candidate(s) underlying the initial GWAS findings in European populations

Preventable hospital admissions among the homeless in California: A retrospective analysis of care for ambulatory care sensitive conditions

Background Limited research exists that investigates hospital admissions for ambulatory care sensitive conditions (ACSCs) among the homeless, who frequently lack a usual source of care. This study profiled ACSC admissions for homeless patients. Methods Bivariate analyses and logistic regression were completed to investigate ACSC and non-ACSC admissions among homeless patients using the 2010 California State Inpatient Database. Results Homeless patients admitted for an ACSC were mostly male, non-Hispanic white, and on average 49.9 years old. In the predictive model, the odds of an ACSC admission among homeless patients increased when they were black, admitted to the emergency department or transferred from another health facility. Having Medicare was associated with a decreased odds of an ACSC admission. Conclusions Specific characteristics are associated with a greater likelihood of an ACSC admission. Research should examine how these characteristics contribute to ACSC hospitalizations and findings should be linked to programs designed to serve as a safety-net for homeless patients to reduce hospitalizations