WOODSTOCC: Extracting Latent Parallelism from a DNA Sequence Aligner on a GPU

An exponential increase in the speed of DNA sequencing over the past decade has driven demand for fast, space-efficient algorithms to process the resultant data. The first step in processing is alignment of many short DNA sequences, or reads, against a large reference sequence. This work presents WOODSTOCC, an implementation of short-read alignment designed for Graphics Processing Unit (GPU) architectures. WOODSTOCC translates a novel CPU implementation of gapped short-read alignment, which has guaranteed optimal and complete results, to the GPU. Our implementation combines an irregular trie search with dynamic programming to expose regularly structured parallelism. We first describe this implementation, then discuss its port to the GPU. WOODSTOCC’s GPU port exploits three generally useful techniques for extracting regular parallelism from irregular computations: dynamic thread mapping with a worklist, kernel stage decoupling, and kernel slicing. We discuss the performance impact of these techniques and suggest further opportunities for improvement

Fast spin exchange between two distant quantum dots

The Heisenberg exchange interaction between neighboring quantum dots allows precise voltage control over spin dynamics, due to the ability to precisely control the overlap of orbital wavefunctions by gate electrodes. This allows the study of fundamental electronic phenomena and finds applications in quantum information processing. Although spin-based quantum circuits based on short-range exchange interactions are possible, the development of scalable, longer-range coupling schemes constitutes a critical challenge within the spin-qubit community. Approaches based on capacitative coupling and cavity-mediated interactions effectively couple spin qubits to the charge degree of freedom, making them susceptible to electrically-induced decoherence. The alternative is to extend the range of the Heisenberg exchange interaction by means of a quantum mediator. Here, we show that a multielectron quantum dot with 50-100 electrons serves as an excellent mediator, preserving speed and coherence of the resulting spin-spin coupling while providing several functionalities that are of practical importance. These include speed (mediated two-qubit rates up to several gigahertz), distance (of order of a micrometer), voltage control, possibility of sweet spot operation (reducing susceptibility to charge noise), and reversal of the interaction sign (useful for dynamical decoupling from noise).Comment: 6 pages including 4 figures, plus 8 supplementary pages including 5 supplementary figure

Effect of a mobile app intervention on vegetable consumption in overweight adults: a randomized controlled trial.

BACKGROUND: Mobile applications (apps) have been heralded as transformative tools to deliver behavioral health interventions at scale, but few have been tested in rigorous randomized controlled trials. We tested the effect of a mobile app to increase vegetable consumption among overweight adults attempting weight loss maintenance. METHODS: Overweight adults (n=135) aged 18-50 years with BMI=28-40 kg/m2 near Stanford, CA were recruited from an ongoing 12-month weight loss trial (parent trial) and randomly assigned to either the stand-alone, theory-based Vegethon mobile app (enabling goal setting, self-monitoring, and feedback and using "process motivators" including fun, surprise, choice, control, social comparison, and competition) or a wait-listed control condition. The primary outcome was daily vegetables servings, measured by an adapted Harvard food frequency questionnaire (FFQ) 8 weeks post-randomization. Daily vegetable servings from 24-hour dietary recalls, administered by trained, certified, and blinded interviewers 5 weeks post-randomization, was included as a secondary outcome. All analyses were conducted according to principles of intention-to-treat. RESULTS: Daily vegetable consumption was significantly greater in the intervention versus control condition for both measures (adjusted mean difference: 2.0 servings; 95% CI: 0.1, 3.8, p=0.04 for FFQ; and 1.0 servings; 95% CI: 0.2, 1.9; p=0.02 for 24-hour recalls). Baseline vegetable consumption was a significant moderator of intervention effects (p=0.002) in which effects increased as baseline consumption increased. CONCLUSIONS: These results demonstrate the efficacy of a mobile app to increase vegetable consumption among overweight adults. Theory-based mobile interventions may present a low-cost, scalable, and effective approach to improving dietary behaviors and preventing associated chronic diseases. TRIAL REGISTRATION: ClinicalTrials.gov NCT01826591. Registered 27 March 2013

Embryotoxic Effects of Three Natural Occurring \u3cem\u3eVeratrum\u3c/em\u3e Alkaloids and One Synthetic Analog using In Vitro Produced Bovine Embryos

Three natural occurring plant toxins from Veratrum californicum and one related synthetic analog were screened for embryotoxicity using in vitro bovine embryo production techniques. Bovine oocytes were aspirated from ovaries collected from a local abattoir and embryos were generated through in vitro maturation (IVM) and in vitro culture (IVC) procedures. The three natural steroidal alkaloids, cyclopamine, jervine and veratramine and the synthetic steroidal derivative of cyclopamine, cyclopamine-4-en-3-one, were added to IVM and IVC media at 12 μM. Oocytes were exposed to the toxins during maturation (IVM) and pre-implantation embryo during culture (IVC). Cleavage rates and embryo growth (morula and blastocyst production) and development through the hatched blastocyst stage were evaluated. Cyclopamine and cyclopamine-4-en-3-one inhibited cleavage rates and embryo growth and development of morulae and blastocysts in culture. Oocytes that were exposed to cyclopamine and cyclopamine-4-en-3-one during IVM only showed reduced cleavage rates and resulted in lower numbers of embryos that developed to the morula, blastocyst, and hatched blastocyst stages. The effects of these steroidal alkaloids on the oocyte during IVM and on the embryo during all stages of development up to and including the hatched blastocyst stage, demonstrates a dramatic cytotoxic effect on oocytes maturation and early pre-implantation embryos. This research also suggests that the Hedgehog signaling pathway may play a role in the maturing oocyte as well as the pre-implantation embryo. These in vitro fertilization techniques provide an economical, rapid through put and effective method to screen natural toxins, especially suspected reproductive toxins for cytotoxicity

Comparison of Sheep and Goats to the Acute Toxic Effects of Foothill Death Camas

Death camas (Zigadenus spp) is a perennial forb found throughout the western United States, which is known to kill both sheep and cattle. In a previous study, goats appeared to be somewhat resistant to the adverse effects of death camas. Therefore, the objective of this study was to directly compare the susceptibility of goats and sheep to the acute toxic effects of death camas. Sheep and goats were dosed at 0.5, 1.0, 2.0, 4.0, and 6.0 g death camas per kg BW. The data presented in this manuscript suggest that goats are more susceptible to death camas than sheep. There were no differences in the serum concentrations of zygadenine in sheep versus goats. There was a difference between goats and sheep in the severity of observed clinical signs of poisoning. This is highlighted by the fact that five goats from the two highest doses died, whereas none of the sheep died. Consequently, when grazing goats in death camas infested pastures as much caution, if not more, should be taken than one would with sheep. Additionally, the data presented in the study suggests that goats can be used as a small ruminant model to study the toxic effects of death camas

Interferon-alpha/beta deficiency greatly exacerbates arthritogenic disease in mice infected with wild-type chikungunya virus but not with the cell culture-adapted live-attenuated 181/25 vaccine candidate

AbstractIn humans, chikungunya virus (CHIKV) infection causes fever, rash, and acute and persisting polyarthralgia/arthritis associated with joint swelling. We report a new CHIKV disease model in adult mice that distinguishes the wild-type CHIKV-LR strain from the live-attenuated vaccine strain (CHIKV-181/25). Although eight-week old normal mice inoculated in the hind footpad developed no hind limb swelling with either virus, CHIKV-LR replicated in musculoskeletal tissues and caused detectable inflammation. In mice deficient in STAT1-dependent interferon (IFN) responses, CHIKV-LR caused significant swelling of the inoculated and contralateral limbs and dramatic inflammatory lesions, while CHIKV-181/25 vaccine and another arthritogenic alphavirus, Sindbis, failed to induce swelling. IFN responses suppressed CHIKV-LR and CHIKV-181/25 replication equally in dendritic cells in vitro whereas macrophages were refractory to infection independently of STAT1-mediated IFN responses. Glycosaminoglycan (GAG) binding may be a CHIKV vaccine attenuation mechanism as CHIKV-LR infectivity was not dependent upon GAG, while CHIKV-181/25 was highly dependent

Shadow Libraries and You: Sci-Hub Usage and the Future of ILL

The paper "pirating" site Sci-Hub is used all over the world. Is Sci-Hub download traffic affecting usage of interlibrary loan? We use two independent methods to uncover any relationships. What is it about the most requested articles from Sci-Hub that causes users to obtain their research articles via extra-legal means? This paper attempts to answer these questions and more

PbTi1-xPdxO3: A New Room-temperature Magnetoelectric Multiferroic Device Material

There have been a large number of papers on bismuth ferrite (BiFeO3) over the past few years, trying to exploit its room-temperature magnetoelectric multiferroic properties. Although these are attractive, BiFeO3 is not the ideal multiferroic, due to weak magnetization and the difficulty in limiting leakage currents. Thus there is an ongoing search for alternatives, including such materials as gallium ferrite (GaFeO3). In the present work we report a comprehensive study of the perovskite PbTi1-xPdxO3 with 0 < x < 0.3. Our study includes dielectric, impedance and magnetization measurements, conductivity analysis and study of crystallographic phases present in the samples with special attention paid to minor phases, identified as PdO, PbPdO2, and Pd3Pb. The work is remarkable in two ways: Pd is difficult to substitute into ABO3 perovskite oxides (where it might be useful for catalysis), and Pd is magnetic under only unusual conditions (under strain or internal electric fields). The new material, as a PZT derivative, is expected to have much stronger piezoelectric properties than BiFeO3

The dog as an animal model for bladder and urethral urothelial carcinoma: comparative epidemiology and histology

Despite the recent approval of several novel agents for patients with metastatic urothelial carcinoma (UC), survival in this setting remains poor. As such, continued investigation into novel therapeutic options remains warranted. Pre clinical development of novel treatments requires an animal model that accurately simulates the disease in humans. The aim of the present study was to evaluate the dog as an animal model for human UC. A total of 260 cases of spontaneous, untreated canine primary urethral and urinary bladder UC, were epide¬miologically and histologically assessed and classified based on the current 2016 World Health Organization (WHO) tumor classification system. Canine data was compared with human data available from scientific literature. The mean age of dogs diagnosed with UC was 10.22 years (range, 4 15 years), which is equivalent to 60 70 human years. The results revealed a high association between UC diagnosis with the female sex [odds ratio (OR) 3.51; 95% confidence interval (CI) 2.57 4.79; P<0.001], surgical neutering (OR 4.57; 95% CI 1.87 11.12; P<0.001) and breed (OR 15.11 for Scottish terriers; 95% CI 8.99 25.41; P<0.001). Based on the 2016 WHO tumor (T), node and metastasis staging system, the primary tumors were characterized as T1 (38%), T2a (28%), T2b (13%) and T3 (22%). Non papillary, flat subgross tumor growth was strongly associated with muscle invasion (OR 31.00; P<0.001). Irrespective of subgross growth pattern, all assessable tumors were invading beyond the basement membrane compatible with infiltrating UC. Conventional, not further classifiable infiltrating UC was the most common type of tumor (90%), followed by UC with divergent, squamous and/or glandular differentiation (6%). Seven out of the 260 (2.8%) cases were classified as non urothelial based on their histological morphology. These cases included 5 (2%) squamous cell carci¬nomas, 1 (0.4%) adenocarcinoma and 1 (0.4%) neuroendocrine tumor. The 2 most striking common features of canine and human UC included high sex predilection and histological tumor appearance. The results support the suitability of the dog as an animal model for UC and confirm that dogs also spontaneously develop rare UC subtypes and bladder tumors, including plasmacytoid UC and neuroendocrine tumor, which are herein described for the first time in a non experimental animal species

Iterative development of Vegethon: a theory-based mobile app intervention to increase vegetable consumption.

BACKGROUND: Mobile technology may serve as a cost-effective and scalable tool for delivering behavioral nutrition interventions. This research sought to iteratively develop a theory-driven mobile app, Vegethon, to increase vegetable consumption. METHODS: Development of Vegethon followed phases outlined by the IDEAS framework: 1) empathize with users (qualitative interviews, n = 18); 2) specify target behavior; 3) ground in behavioral theory; 4) ideate implementation strategies; 5) prototype potential products; 6) gather user feedback (qualitative interviews, n = 14; questionnaire, n = 41); 7) build minimum viable product; and 8) pilot potential efficacy and usability (pilot RCT, n = 17). Findings from each phase informed subsequent phases. The target population that informed intervention development was 18-50 years of age, had BMIs of 28-40 kg/m(2), and lived in the geographical area surrounding Stanford University. A full description of the final version of Vegethon is included in the paper. RESULTS: Qualitative findings that shaped initial intervention conception were: participants' interests in accountability without judgment; their desire for simple and efficient dietary self-monitoring; and the importance of planning meals in advance. Qualitative findings identified during intervention refinement were the need for a focus on vegetable self-monitoring; inclusion of vegetable challenges; simplification of features; advice and inspiration for eating vegetables; reminder notifications; and peer comparison. Pilot RCT findings suggested the initial efficacy, acceptance, and feasibility of the intervention. The final version of Vegethon enabled easy self-monitoring of vegetable consumption and included a range of features designed to engage the user (e.g., surprise challenges; leaderboard; weekly reports). Vegethon was coded for its inclusion of 18 behavior change techniques (BCTs) (e.g., goal setting; feedback; social comparison; prompts/cues; framing/reframing; identity). CONCLUSIONS: Vegethon is a theory-based, user-informed mobile intervention that was systematically developed using the IDEAS framework. Vegethon targets increased vegetable consumption among overweight adults and is currently being evaluated in a randomized controlled efficacy trial. TRIAL REGISTRATION: Clinical Trials.gov: NCT01826591