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

Development of FTK architecture: a fast hardware track trigger for the ATLAS detector

The Fast Tracker (FTK) is a proposed upgrade to the ATLAS trigger system that will operate at full Level-1 output rates and provide high quality tracks reconstructed over the entire detector by the start of processing in Level-2. FTK solves the combinatorial challenge inherent to tracking by exploiting the massive parallelism of Associative Memories (AM) that can compare inner detector hits to millions of pre-calculated patterns simultaneously. The tracking problem within matched patterns is further simplified by using pre-computed linearized fitting constants and leveraging fast DSP's in modern commercial FPGA's. Overall, FTK is able to compute the helix parameters for all tracks in an event and apply quality cuts in approximately one millisecond. By employing a pipelined architecture, FTK is able to continuously operate at Level-1 rates without deadtime. The system design is defined and studied using ATLAS full simulation. Reconstruction quality is evaluated for single muon events with zero pileup, as well as WH events at the LHC design luminosity. FTK results are compared with the tracking capability of an offline algorithm.Comment: To be published in the proceedings of DPF-2009, Detroit, MI, July 2009, eConf C09072

Finding Web-Based Anxiety Interventions on the World Wide Web: A Scoping Review

BACKGROUND: One relatively new and increasingly popular approach of increasing access to treatment is Web-based intervention programs. The advantage of Web-based approaches is the accessibility, affordability, and anonymity of potentially evidence-based treatment. Despite much research evidence on the effectiveness of Web-based interventions for anxiety found in the literature, little is known about what is publically available for potential consumers on the Web. OBJECTIVE: Our aim was to explore what a consumer searching the Web for Web-based intervention options for anxiety-related issues might find. The objectives were to identify currently publically available Web-based intervention programs for anxiety and to synthesize and review these in terms of (1) website characteristics such as credibility and accessibility; (2) intervention program characteristics such as intervention focus, design, and presentation modes; (3) therapeutic elements employed; and (4) published evidence of efficacy. METHODS: Web keyword searches were carried out on three major search engines (Google, Bing, and Yahoo-UK platforms). For each search, the first 25 hyperlinks were screened for eligible programs. Included were programs that were designed for anxiety symptoms, currently publically accessible on the Web, had an online component, a structured treatment plan, and were available in English. Data were extracted for website characteristics, program characteristics, therapeutic characteristics, as well as empirical evidence. Programs were also evaluated using a 16-point rating tool. RESULTS: The search resulted in 34 programs that were eligible for review. A wide variety of programs for anxiety, including specific anxiety disorders, and anxiety in combination with stress, depression, or anger were identified and based predominantly on cognitive behavioral therapy techniques. The majority of websites were rated as credible, secure, and free of advertisement. The majority required users to register and/or to pay a program access fee. Half of the programs offered some form of paid therapist or professional support. Programs varied in treatment length and number of modules and employed a variety of presentation modes. Relatively few programs had published research evidence of the intervention's efficacy. CONCLUSIONS: This review represents a snapshot of available Web-based intervention programs for anxiety that could be found by consumers in March 2015. The consumer is confronted with a diversity of programs, which makes it difficult to identify an appropriate program. Limited reports and existence of empirical evidence for efficacy make it even more challenging to identify credible and reliable programs. This highlights the need for consistent guidelines and standards on developing, providing, and evaluating Web-based interventions and platforms with reliable up-to-date information for professionals and consumers about the characteristics, quality, and accessibility of Web-based interventions

A New Scintillator Tile/Fiber Preshower Detector for the CDF Central Calorimeter

A detector designed to measure early particle showers has been installed in front of the central CDF calorimeter at the Tevatron. This new preshower detector is based on scintillator tiles coupled to wavelength-shifting fibers read out by multi-anode photomultipliers and has a total of 3,072 readout channels. The replacement of the old gas detector was required due to an expected increase in instantaneous luminosity of the Tevatron collider in the next few years. Calorimeter coverage, jet energy resolution, and electron and photon identification are among the expected improvements. The final detector design, together with the R&D studies that led to the choice of scintillator and fiber, mechanical assembly, and quality control are presented. The detector was installed in the fall 2004 Tevatron shutdown and started collecting colliding beam data by the end of the same year. First measurements indicate a light yield of 12 photoelectrons/MIP, a more than two-fold increase over the design goals.Comment: 5 pages, 10 figures (changes are minor; this is the final version published in IEEE-Trans.Nucl.Sci.

The Evolution of FTK, a Real-Time Tracker for Hadron Collider Experiments

We describe the architecture evolution of the highly-parallel dedicated processor FTK, which is driven by the simulation of LHC events at high luminosity (1034 cm-2 s-1). FTK is able to provide precise on-line track reconstruction for future hadronic collider experiments. The processor, organized in a two-tiered pipelined architecture, execute very fast algorithms based on the use of a large bank of pre-stored patterns of trajectory points (first tier) in combination with full resolution track fitting to refine pattern recognition and to determine off-line quality track parameters. We describe here how the high luminosity simulation results have produced a new organization of the hardware inside the FTK processor core.Comment: 11th ICATPP conferenc

Simulation of hanging file experiments with CALOR89

This note presents the comparison of CALOR89 simulation with the ``hanging file`` test measurements conducted at Fermilab during the period of Sep 91--Jan 92. The purpose of this study is to benchmark CALOR89 code against the experimental data to enhance its reliability and predictive power. Seven hanging file configurations were simulated. The measured values of e/{pi} ratio (the ratio of electron to pion signal at the same energy), hadronic and electromagnetic resolutions were compared with the simulations. The depth profiles of the hadronic and electromagnetic showers are also compared

Genomic and protein structural maps of adaptive evolution of human influenza a virus to increased virulence in the mouse

Adaptive evolution is characterized by positive and parallel, or repeated selection of mutations. Mouse adaptation of influenza A virus (IAV) produces virulent mutants that demonstrate positive and parallel evolution of mutations in the hemagglutinin (HA) receptor and non-structural protein 1 (NS1) interferon antagonist genes. We now present a genomic analysis of all 11 genes of 39 mouse adapted IAV variants from 10 replicate adaptation experiments. Mutations were mapped on the primary and structural maps of each protein and specific mutations were validated with respect to virulence, replication, and RNA polymerase activity. Mouse adapted (MA) variants obtained after 12 or 20-21 serial infections acquired on average 5.8 and 7.9 nonsynonymous mutations per genome of 11 genes, respectively. Among a total of 115 nonsynonymous mutations, 51 demonstrated properties of natural selection including 27 parallel mutations. The greatest degree of parallel evolution occurred in the HA receptor and ribonucleocapsid components, polymerase subunits (PB1, PB2, PA) and NP. Mutations occurred in host nuclear trafficking factor binding sites as well as sites of virus-virus protein subunit interaction for NP, NS1, HA and NA proteins. Adaptive regions included cap binding and endonuclease domains in the PB2 and PA polymerase subunits. Four mutations in NS1 resulted in loss of binding to the host cleavage and polyadenylation specificity factor (CPSF30) suggesting that a reduction in inhibition of host gene expression was being selected. The most prevalent mutations in PB2 and NP were shown to increase virulence but differed in their ability to enhance replication and demonstrated epistatic effects. Several positively selected RNA polymerase mutations demonstrated increased virulence associated with >300% enhanced polymerase activity. Adaptive mutations that control host range and virulence were identified by their repeated selection to comprise a defined model for studying IAV evolution to increased virulence in the mouse

Evaluation of the efficacy and safety of sarilumab combination therapy in patients with rheumatoid arthritis with inadequate response to conventional disease-modifying antirheumatic drugs or tumour necrosis factor α inhibitors: Systematic literature review and network meta-analyses

Objective To compare efficacy and safety of subcutaneous sarilumab 200 mg and 150 mg every 2 weeks plus conventional synthetic disease-modifying antirheumatic drugs (+csDMARDs) versus other targeted DMARDs+csDMARDs and placebo+csDMARDs, in inadequate responders to csDMARDs (csDMARD-IR) or tumour necrosis factor α inhibitors (TNFi-IR). Methods Systematic literature review and network meta-analyses (NMA) conducted on 24 week efficacy and safety outcomes: Health Assessment Questionnaire Disability Index, modified total sharp score (mTSS, including 52 weeks), American College of Rheumatology (ACR) 20/50/70, European League Against Rheumatism Disease Activity Score 28-joint count erythrocyte sedimentation rate (DAS28)<2.6; serious infections/serious adverse events (including 52 weeks). Results 53 trials were selected for NMA. csDMARD-IR: Sarilumab 200 mg+csDMARDs and 150 mg+csDMARDs were superior versus placebo+csDMARDs on all outcomes. Against most targeted DMARDs, sarilumab 200 mg showed no statistically significant differences, except superiority to baricitinib 2 mg, tofacitinib and certolizumab on 24 week mTSS. Sarilumab 150 mg was similar to all targeted DMARDs. TNFi-IR: Sarilumab 200 mg was similar to abatacept, golimumab, tocilizumab 4 mg and 8 mg/kg intravenously and rituximab on ACR20/50/70, superior to baricitinib 2 mg on ACR50 and DAS28<2.6 and to abatacept, golimumab, tocilizumab 4 mg/kg intravenously and rituximab on DAS28<2.6. Sarilumab 150 mg was similar to targeted DMARDs but superior to baricitinib 2 mg and rituximab on DAS28<2.6 and inferior to tocilizumab 8 mg on ACR20 and DAS28<2.6. Serious adverse events, including serious infections, appeared similar for sarilumab versus comparators. Conclusions Results suggest that in csDMARD-IR and TNFi-IR (a smaller network), sarilumab+csDMARD had superior efficacy and similar safety versus placebo+csDMARDs and at least similar efficacy and safety versus other targeted DMARDs+csDMARDs