Thermalization, Error-Correction, and Memory Lifetime for Ising Anyon Systems

We consider two-dimensional lattice models that support Ising anyonic excitations and are coupled to a thermal bath. We propose a phenomenological model for the resulting short-time dynamics that includes pair-creation, hopping, braiding, and fusion of anyons. By explicitly constructing topological quantum error-correcting codes for this class of system, we use our thermalization model to estimate the lifetime of the quantum information stored in the encoded spaces. To decode and correct errors in these codes, we adapt several existing topological decoders to the non-Abelian setting. We perform large-scale numerical simulations of these two-dimensional Ising anyon systems and find that the thresholds of these models range between 13% to 25%. To our knowledge, these are the first numerical threshold estimates for quantum codes without explicit additive structure.Comment: 34 pages, 9 figures; v2 matches the journal version and corrects a misstatement about the detailed balance condition of our Metropolis simulations. All conclusions from v1 are unaffected by this correctio

Effect of water, sanitation, and hygiene on the prevention of trachoma: a systematic review and meta-analysis.

BACKGROUND: Trachoma is the world's leading cause of infectious blindness. The World Health Organization (WHO) has endorsed the SAFE strategy in order to eliminate blindness due to trachoma by 2020 through "surgery," "antibiotics," "facial cleanliness," and "environmental improvement." While the S and A components have been widely implemented, evidence and specific targets are lacking for the F and E components, of which water, sanitation, and hygiene (WASH) are critical elements. Data on the impact of WASH on trachoma are needed to support policy and program recommendations. Our objective was to systematically review the literature and conduct meta-analyses where possible to report the effects of WASH conditions on trachoma and identify research gaps. METHODS AND FINDINGS: We systematically searched PubMed, Embase, ISI Web of Knowledge, MedCarib, Lilacs, REPIDISCA, DESASTRES, and African Index Medicus databases through October 27, 2013 with no restrictions on language or year of publication. Studies were eligible for inclusion if they reported a measure of the effect of WASH on trachoma, either active disease indicated by observed signs of trachomatous inflammation or Chlamydia trachomatis infection diagnosed using PCR. We identified 86 studies that reported a measure of the effect of WASH on trachoma. To evaluate study quality, we developed a set of criteria derived from the GRADE methodology. Publication bias was assessed using funnel plots. If three or more studies reported measures of effect for a comparable WASH exposure and trachoma outcome, we conducted a random-effects meta-analysis. We conducted 15 meta-analyses for specific exposure-outcome pairs. Access to sanitation was associated with lower trachoma as measured by the presence of trachomatous inflammation-follicular or trachomatous inflammation-intense (TF/TI) (odds ratio [OR] 0.85, 95% CI 0.75-0.95) and C. trachomatis infection (OR 0.67, 95% CI 0.55-0.78). Having a clean face was significantly associated with reduced odds of TF/TI (OR 0.42, 95% CI 0.32-0.52), as were facial cleanliness indicators lack of ocular discharge (OR 0.42, 95% CI 0.23-0.61) and lack of nasal discharge (OR 0.62, 95% CI 0.52-0.72). Facial cleanliness indicators were also associated with reduced odds of C. trachomatis infection: lack of ocular discharge (OR 0.40, 95% CI 0.31-0.49) and lack of nasal discharge (OR 0.56, 95% CI 0.37-0.76). Other hygiene factors found to be significantly associated with reduced TF/TI included face washing at least once daily (OR 0.76, 95% CI 0.57-0.96), face washing at least twice daily (OR 0.85, 95% CI 0.80-0.90), soap use (OR 0.76, 95% CI 0.59-0.93), towel use (OR 0.65, 95% CI 0.53-0.78), and daily bathing practices (OR 0.76, 95% CI 0.53-0.99). Living within 1 km of a water source was not found to be significantly associated with TF/TI or C. trachomatis infection, and the use of sanitation facilities was not found to be significantly associated with TF/TI. CONCLUSIONS: We found strong evidence to support F and E components of the SAFE strategy. Though limitations included moderate to high heterogenity, low study quality, and the lack of standard definitions, these findings support the importance of WASH in trachoma elimination strategies and the need for the development of standardized approaches to measuring WASH in trachoma control programs

A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist

The overarching trend in mitochondrial genome evolution is functional streamlining coupled with gene loss; therefore, gene acquisition by mitochondria is considered to be exceedingly rare. Selfish elements in the form of self-splicing introns occur in many organellar genomes, but the wider diversity of selfish elements, and how they persist in the DNA of organelles, has not been explored. In the mitochondrial genome of a marine heterotrophic katablepharid protist, we identify a functional type II restriction modification (RM) system originating from a horizontal gene transfer (HGT) event involving bacteria related to flavobacteria. This RM system consists of an HpaII-like endonuclease and a cognate cytosine methyltransferase (CM). We demonstrate that these proteins are functional by heterologous expression in both bacterial and eukaryotic cells. These results suggest that a mitochondrial-encoded RM system can function as a toxin-antitoxin selfish element and that such elements could be co-opted by eukaryotic genomes to drive biased organellar inheritance.Peer reviewe

Vorinostat Eliminates Multicellular Resistance of Mesothelioma 3D Spheroids via Restoration of Noxa Expression

When grown in 3D cultures as spheroids, mesothelioma cells acquire a multicellular resistance to apoptosis that resembles that of solid tumors. We have previously found that resistance to the proteasome inhibitor bortezomib in 3D can be explained by a lack of upregulation of Noxa, the pro-apoptotic BH3 sensitizer that acts via displacement of the Bak/Bax-activator BH3-only protein, Bim. We hypothesized that the histone deacetylase inhibitor vorinostat might reverse this block to Noxa upregulation in 3D. Indeed, we found that vorinostat effectively restored upregulation of Noxa protein and message and abolished multicellular resistance to bortezomib in the 3D spheroids. The ability of vorinostat to reverse resistance was ablated by knockdown of Noxa or Bim, confirming the essential role of the Noxa/Bim axis in the response to vorinostat. Addition of vorinostat similarly increased the apoptotic response to bortezomib in another 3D model, the tumor fragment spheroid, which is grown from human mesothelioma ex vivo. In addition to its benefit when used with bortezomib, vorinostat also enhanced the response to cisplatin plus pemetrexed, as shown in both 3D models. Our results using clinically relevant 3D models show that the manipulation of the core apoptotic repertoire may improve the chemosensitivity of mesothelioma. Whereas neither vorinostat nor bortezomib alone has been clinically effective in mesothelioma, vorinostat may undermine chemoresistance to bortezomib and to other therapies thereby providing a rationale for combinatorial strategies

Relationships Between Self-Reported Smoking, Household Environmental Tobacco Smoke Exposure and Depressive Symptoms in a Pregnant Minority Population

This study sought to examine relationships between depressive symptoms and prenatal smoking and/or household environmental tobacco smoke exposure (HHETSE) among urban minority women. We analyzed private, audio computer-assisted self interview data from a clinic-based sample of 929 minority pregnant women in Washington, DC. Depressive symptoms were assessed via the Beck Depression Inventory Fast Screen. HH-ETSE, current smoking, and former smoking were assessed via self-report. Depression levels and demographic characteristics were compared: (1) among nonsmokers, for those reporting HH-ETSE versus no HH-ETSE; and (2) among smokers, for those reporting current smoking (in last 7 days) versus former smokers. Measures associated with HH-ETSE/current smoking in bivariate analysis at P\0.20 were included in adjusted logistic regression models. HH-ETSE, as a possible indicator of a social smoking network, was assessed as a mediator for the relationship between depression and current smoking. Results: Non-smokers reporting moderate-to-severe depressive symptoms showed significantly higher adjusted odds of prenatal HH-ETSE (AOR 2.5, 95% CI [1.2, 5.2]). Smokers reporting moderate-to-severe or mild depressive symptoms showed significantly higher adjusted odds of current smoking (AOR 1.9, 95% CI [1.1, 3.5] and AOR 1.8, 95% CI [1.1, 3.1], respectively). Among smokers, HH-ETSE was a significant mediator for the association between moderate-to-severe symptoms and current smoking. In conclusion, health care providers should be aware that depressed urban minority women are at risk of continued smoking/HH-ETSE during pregnancy. Interventions designed to encourage behavior change should include screening for depression, and build skills so that women are better able to address the social environment

Epidemiology of Neonatal Acute Respiratory Distress Syndrome:Prospective, Multicenter, International Cohort Study

OBJECTIVES: Age-specific definitions for acute respiratory distress syndrome (ARDS) are available, including a specific definition for neonates (the "Montreux definition"). The epidemiology of neonatal ARDS is unknown. The objective of this study was to describe the epidemiology, clinical course, treatment, and outcomes of neonatal ARDS. DESIGN: Prospective, international, observational, cohort study. SETTING: Fifteen academic neonatal ICUs. PATIENTS: Consecutive sample of neonates of any gestational age admitted to participating sites who met the neonatal ARDS Montreux definition criteria. MEASUREMENTS AND MAIN RESULTS: Neonatal ARDS was classified as direct or indirect, infectious or noninfectious, and perinatal (≤ 72 hr after birth) or late in onset. Primary outcomes were: 1) survival at 30 days from diagnosis, 2) inhospital survival, and 3) extracorporeal membrane oxygenation (ECMO)-free survival at 30 days from diagnosis. Secondary outcomes included respiratory complications and common neonatal extrapulmonary morbidities. A total of 239 neonates met criteria for the diagnosis of neonatal ARDS. The median prevalence was 1.5% of neonatal ICU admissions with male/female ratio of 1.5. Respiratory treatments were similar across gestational ages. Direct neonatal ARDS (51.5% of neonates) was more common in term neonates and the perinatal period. Indirect neonatal ARDS was often triggered by an infection and was more common in preterm neonates. Thirty-day, inhospital, and 30-day ECMO-free survival were 83.3%, 76.2%, and 79.5%, respectively. Direct neonatal ARDS was associated with better survival outcomes than indirect neonatal ARDS. Direct and noninfectious neonatal ARDS were associated with the poorest respiratory outcomes at 36 and 40 weeks' postmenstrual age. Gestational age was not associated with any primary outcome on multivariate analyses. CONCLUSIONS: Prevalence and survival of neonatal ARDS are similar to those of pediatric ARDS. The neonatal ARDS subtypes used in the current definition may be associated with distinct clinical outcomes and a different distribution for term and preterm neonates

Fence management and time since pack formation influence African wild dog escapes from protected areas in South Africa

In human-dominated and highly fragmented landscapes, keeping wildlife within reserve boundaries is vital for conservation success. In South Africa, fences are a widely employed conservation management tool for protected areas and are successful in mitigating human-wildlife conflict. However, fences are permeable, and predators are able to cross through reserve fences. African wild dogs (Lycaon pictus) often leave fenced boundaries, resulting in high capture and translocation costs. Moreover, when wild dog packs (up to 30 individuals) leave fenced reserves they enter human-dominated landscapes where they face strong persecution and livestock predation incurs high costs. The factors driving packs to leave managed reserves are poorly understood, thus, to effectively manage wild dogs in fenced systems, it is important to understand why they leave reserve boundaries. There are several hypotheses as to why wild dogs cross through reserve fences, including inter- and intra-specific competition, social behaviour, management, prey density and environmental variability. Using a long-term dataset comprising 32 resident packs across five reserves, we investigated the relative strength of these hypotheses on the probability of wild dogs exiting a fenced reserve. During the 14-year study period, we recorded 154 exit events. We found that the interaction of fence integrity and time since pack formation were the primary factors affecting the probability of a pack leaving a reserve. When fence integrity was poor, escape probability decreased with pack age likely due to the exploratory behaviour of new packs. When fence integrity was average, escape probability increased with pack age likely due to the fitness benefits of holding larger and more exclusive territories as packs age. When fence integrity was good, the probability of a pack escaping was very low (only 1% occurrence). The implications of this research suggest that the primary management consideration for reducing wild dog escapes from fenced reserves should be maintaining adequate reserve-wide fence integrity, rather than focusing on social structure or drivers of inter- and intra-specific competition

Harvest strategy evaluation to optimise the sustainability and value of the Queensland scallop fishery. Queensland scallop fishery - FRDC Project No 2006/024 Final Report

Objective 1. Measure spatial and temporal trawl frequency of scallop grounds using VMS data. This will provide a relative measure of how often individual undersized scallops are caught and put through a tumbler 2. Estimate discard mortality and growth rates for saucer scallops using cage experiments. 3. Evaluate the current management measures, in particular the seasonal closure, rotational closure and seasonally varying minimum legal sizes using stock assessment and management modeling models. Recommend optimal range of management measures to ensure long-term viability and value of the Scallop fishery based on a formal management strategy evaluation. Outcomes acheived to date: 1. Improved understanding of the survival rates of discarded sub-legal scallops; 2. Preliminary von Bertalanffy growth parameters using data from tagged-and-released scallops; 3. Changing trends in vessels and fishing gear used in the Queensland scallop fishery and their effect on scallop catch rates over time using standardised catch rates quantified; 4. Increases in fishing power of vessels operating in the Queensland scallop fishery quantified; 5. Trawl intensity mapped and quantified for all Scallop Replenishment Areas; 6. Harvest Strategy Evaluations completed

Cancer testis antigen and interleukin expression correlates with survival in small bowel neuroendocrine tumors

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