• D<sup>2</sup>P<sup>2</sup>: Database of disordered protein predictions

      Oates, ME; Romero, P; Ishida, T; Ghalwash, M; Mizianty, MJ; Xue, B; Dosztányi, Z; Uversky, VN; Obradovic, Z; Kurgan, L; Dunker, AK; Gough, J (2013-01-01)
      We present the Database of Disordered Protein Prediction (D 2P2), available at http://d2p2.pro (including website source code). A battery of disorder predictors and their variants, VL-XT, VSL2b, PrDOS, PV2, Espritz and IUPred, were run on all protein sequences from 1765 complete proteomes (to be updated as more genomes are completed). Integrated with these results are all of the predicted (mostly structured) SCOP domains using the SUPERFAMILY predictor. These disorder/structure annotations together enable comparison of the disorder predictors with each other and examination of the overlap between disordered predictions and SCOP domains on a large scale. D2P2 will increase our understanding of the interplay between disorder and structure, the genomic distribution of disorder, and its evolutionary history. The parsed data are made available in a unified format for download as flat files or SQL tables either by genome, by predictor, or for the complete set. An interactive website provides a graphical view of each protein annotated with the SCOP domains and disordered regions from all predictors overlaid (or shown as a consensus). There are statistics and tools for browsing and comparing genomes and their disorder within the context of their position on the tree of life. © The Author(s) 2012.
    • Daily Snacking Occasions and Weight Status Among US Children Aged 1 to 5 Years

      Kachurak, A; Davey, A; Bailey, RL; Fisher, JO (2018-06-01)
      © 2018 The Authors. Obesity published by Wiley Periodicals, Inc. on behalf of The Obesity Society (TOS). Objective: To characterize associations of snacking frequency with weight status among US children aged 1 to 5 years. Methods: Participants were children (n = 4,669) aged 1 to 5 years in the 2005 to 2014 National Health and Nutrition Examination Survey (NHANES). Snacking was assessed by two 24-hour dietary recalls using definitions that considered “snack” occasions as well as other foods/beverages consumed between meals. Overweight/obesity (OW/OB) was defined using percentile cutoffs: ≥ 97.7th weight-for-length (< 2 years) cutoff and the ≥ 85th BMI-for-age (≥ 2 years) cutoff. Linear/logistic regressions evaluated snacking based on daily occasions and relative to current recommendations (two to three snacks per day). Results: During 2005 to 2014, US children aged 1 to 5 years consumed, on average, two to three snacks daily. Children with normal weight in both age groups tended to snack less frequently than children with OW/OB when considering all foods/beverages eaten between meals (P < 0.01-0.12). Across most snacking definitions, children < 2 years who snacked more frequently than recommended had greater odds of having OW/OB (P < 0.01-0.12) and consumed greater daily snack energy than those who snacked within recommendations (all P < 0.01). Recommendations did not clearly delineate weight status among children aged 2 to 5 years. Conclusions: Snacking frequency and weight are positively associated among US children 1 to 5 years old, with most consistent associations seen among children < 2 years old and when considering all foods/beverages consumed between meals.
    • Data Analytics and Modeling for Appointment No-show in Community Health Centers

      Mohammadi, I; Wu, H; Turkcan, A; Toscos, T; Doebbeling, BN; Wu, Huanmei|0000-0003-0346-6044 (2018-11-01)
      © The Author(s) 2018. Objectives: Using predictive modeling techniques, we developed and compared appointment no-show prediction models to better understand appointment adherence in underserved populations. Methods and Materials: We collected electronic health record (EHR) data and appointment data including patient, provider and clinical visit characteristics over a 3-year period. All patient data came from an urban system of community health centers (CHCs) with 10 facilities. We sought to identify critical variables through logistic regression, artificial neural network, and naïve Bayes classifier models to predict missed appointments. We used 10-fold cross-validation to assess the models’ ability to identify patients missing their appointments. Results: Following data preprocessing and cleaning, the final dataset included 73811 unique appointments with 12,392 missed appointments. Predictors of missed appointments versus attended appointments included lead time (time between scheduling and the appointment), patient prior missed appointments, cell phone ownership, tobacco use and the number of days since last appointment. Models had a relatively high area under the curve for all 3 models (e.g., 0.86 for naïve Bayes classifier). Discussion: Patient appointment adherence varies across clinics within a healthcare system. Data analytics results demonstrate the value of existing clinical and operational data to address important operational and management issues. Conclusion: EHR data including patient and scheduling information predicted the missed appointments of underserved populations in urban CHCs. Our application of predictive modeling techniques helped prioritize the design and implementation of interventions that may improve efficiency in community health centers for more timely access to care. CHCs would benefit from investing in the technical resources needed to make these data readily available as a means to inform important operational and policy questions.
    • Datasets for evolutionary comparative genomics

      Liberles, DA; Liberles, David A|0000-0003-3487-8826 (2005-09-05)
      Many decisions about genome sequencing projects are directed by perceived gaps in the tree of life, or towards model organisms. With the goal of a better understanding of biology through the lens of evolution, however, there are additional genomes that are worth sequencing. One such rationale for whole-genome sequencing is discussed here, along with other important strategies for understanding the phenotypic divergence of species. © 2005 BioMed Central Ltd.
    • Debunking Intellectual Property Myths: Cross Cultural Experiments on Perceptions of Property

      Mandel, Gregory N.; Olson, Kristina R.; Fast, Anne A. (2020)
      For decades, the prevailing view in the United States and many Western countries has been that China does not appropriately respect intellectual property rights. These beliefs lie at the heart of President Donald Trump’s current trade war with China. Despite substantial geopolitical debate over differences between American an d Chinese attitudes towards intellectual property rights, and despite the critical effects that such attitudes have on international economic markets and the function of intellectual property systems, empirical evidence of these attitudes is largely lacking. This Article presents original experimental survey research that explores cross cross-cultural differences between American and Chinese attitudes towards intellectual property rights, personal property rights, and real property rights. The results of the studies are somewhat counterintuitive. First, Chinese participants are found to have more consistent preferences towards different types of property rights than Americans. In a series of vignettes designed to test attitudes towards patented subject matter, copyrighted subject matter, tangible personal property, and real property, Chinese responses were more consistent and less context driven. Second, Americans do identify a preference for stronger intellectual property rights than Chinese, but only where infringement is committed by a private party for private benefit. Where infringement is conducted for public benefit, whether by a private or a governmental entity, Chinese and Americans tend to have the same attitudes towards intellectual property rights. Third , Americans display a lower regard for intellectual property rights than for tangible property rights in most contexts, a differential that is not echoed in Chinese responses. The distinctions that Americans draw based on the use to which property is put, and between intellectual property and tangible property, is not consistent with United States law. Our experiments reveal that the ongoing debates over Chinese attitudes towards intellectual property rights miss the mark in certain regards. Chinese and American preferences for property rights are more similar than most have assumed, and the manners in which they differ are inconsistent with most proffered theories. These results provide important lessons for the future of international intellectual property rights relations, discourse, and enforcement.
    • Decreased Nocturnal Awakenings in Young Adults Performing Bikram Yoga: A Low-Constraint Home Sleep Monitoring Study

      Kudesia, Ravi S; Bianchi, Matt T; Kudesia, Ravi S.|0000-0003-0561-8857 (2012-04-12)
      <jats:p>This pilot study evaluated the impact of Bikram Yoga on subjective and objective sleep parameters. We compared subjective (diary) and objective (headband sleep monitor) sleep measures on yoga versus nonyoga days during a 14-day period. Subjects () were not constrained regarding yoga-practice days, other exercise, caffeine, alcohol, or naps. These activities did not segregate by choice of yoga days. Standard sleep metrics were unaffected by yoga, including sleep latency, total sleep time, and percentage of time spent in rapid eye movement (REM), light non-REM, deep non-REM, or wake after sleep onset (WASO). Consistent with prior work, transition probability analysis was a more sensitive index of sleep architecture changes than standard metrics. Specifically, Bikram Yoga was associated with significantly faster return to sleep after nocturnal awakenings. We conclude that objective home sleep monitoring is feasible in a low-constraint, real-world study design. Further studies on patients with insomnia will determine whether the results generalize or not.</jats:p>
    • Deep-water chemosynthetic ecosystem research during the census of marine life decade and beyond: A proposed deep-ocean road map

      German, CR; Ramirez-Llodra, E; Baker, MC; Tyler, PA; Baco-Taylor, A; Boetius, A; Bright, M; de Siqueira, LC; Cordes, EE; Desbruyères, D; Dubilier, N; Fisher, CR; Fujiwara, Y; Gaill, F; Gebruk, A; Juniper, K; Levin, LA; Lokabharathi, PA; Metaxas, A; Rowden, AA; Santos, RS; Shank, TM; Smith, CR; Van Dover, CL; Young, CM; Warén, A; Cordes, Erik|0000-0002-6989-2348 (2011-01-01)
      The ChEss project of the Census of Marine Life (2002-2010) helped foster internationally-coordinated studies worldwide focusing on exploration for, and characterization of new deep-sea chemosynthetic ecosystem sites. This work has advanced our understanding of the nature and factors controlling the biogeography and biodiversity of these ecosystems in four geographic locations: the Atlantic Equatorial Belt (AEB), the New Zealand region, the Arctic and Antarctic and the SE Pacific off Chile. In the AEB, major discoveries include hydrothermal seeps on the Costa Rica margin, deepest vents found on the Mid-Cayman Rise and the hottest vents found on the Southern Mid-Atlantic Ridge. It was also shown that the major fracture zones on the MAR do not create barriers for the dispersal but may act as trans-Atlantic conduits for larvae. In New Zealand, investigations of a newly found large cold-seep area suggest that this region may be a new biogeographic province. In the Arctic, the newly discovered sites on the Mohns Ridge (71°N) showed extensive mats of sulfur-oxidisng bacteria, but only one gastropod potentially bears chemosynthetic symbionts, while cold seeps on the Haakon Mossby Mud Volcano (72°N) are dominated by siboglinid worms. In the Antarctic region, the first hydrothermal vents south of the Polar Front were located and biological results indicate that they may represent a new biogeographic province. The recent exploration of the South Pacific region has provided evidence for a sediment hosted hydrothermal source near a methane-rich cold-seep area. Based on our 8 years of investigations of deep-water chemosynthetic ecosystems worldwide, we suggest highest priorities for future research: (i) continued exploration of the deep-ocean ridge-crest; (ii) increased focus on anthropogenic impacts; (iii) concerted effort to coordinate a major investigation of the deep South Pacific Ocean - the largest contiguous habitat for life within Earth's biosphere, but also the world's least investigated deep-ocean basin. © 2011 German et al.
    • Defining a conceptual topography of word concreteness: Clustering properties of emotion, sensation, and magnitude among 750 english words

      Troche, J; Crutch, SJ; Reilly, J (2017-10-11)
      © 2017 Troche, Crutch and Reilly. Cognitive science has a longstanding interest in the ways that people acquire and use abstract vs. concrete words (e.g., truth vs. piano). One dominant theory holds that abstract and concrete words are subserved by two parallel semantic systems. We recently proposed an alternative account of abstract-concrete word representation premised upon a unitary, high dimensional semantic space wherein word meaning is nested. We hypothesize that a range of cognitive and perceptual dimensions (e.g., emotion, time, space, color, size, visual form) bound this space, forming a conceptual topography. Here we report a normative study where we examined the clustering properties of a sample of English words (N = 750) spanning a spectrum of concreteness in a continuous manner from highly abstract to highly concrete. Participants (N = 328) rated each target word on a range of 14 cognitive dimensions (e.g., color, emotion, valence, polarity, motion, space). The dimensions reduced to three factors: Endogenous factor, Exogenous factor, and Magnitude factor. Concepts were plotted in a unified, multimodal space with concrete and abstract concepts along a continuous continuum. We discuss theoretical implications and practical applications of this dataset.
    • Deletion of morpholino binding sites (DeMOBS) to assess specificity of morphant phenotypes

      Cunningham, CMP; Bellipanni, G; Habas, R; Balciunas, D (2020-12-01)
      © 2020, The Author(s). Two complimentary approaches are widely used to study gene function in zebrafish: induction of genetic mutations, usually using targeted nucleases such as CRISPR/Cas9, and suppression of gene expression, typically using Morpholino oligomers. Neither method is perfect. Morpholinos (MOs) sometimes produce off-target or toxicity-related effects that can be mistaken for true phenotypes. Conversely, genetic mutants can be subject to compensation, or may fail to yield a null phenotype due to leakiness (e.g. use of cryptic splice sites or downstream AUGs). When discrepancy between mutant and morpholino-induced (morphant) phenotypes is observed, experimental validation of such phenotypes becomes very labor intensive. We have developed a simple genetic method to differentiate between genuine morphant phenotypes and those produced due to off-target effects. We speculated that indels within 5′ untranslated regions would be unlikely to have a significant negative effect on gene expression. Mutations induced within a MO target site would result in a Morpholino-refractive allele thus suppressing true MO phenotypes whilst non-specific phenotypes would remain. We tested this hypothesis on one gene with an exclusively zygotic function, tbx5a, and one gene with strong maternal effect, ctnnb2. We found that indels within the Morpholino binding site are indeed able to suppress both zygotic and maternal morphant phenotypes. We also observed that the ability of such indels to suppress morpholino phenotypes does depend on the size and the location of the deletion. Nonetheless, mutating the morpholino binding sites in both maternal and zygotic genes can ascertain the specificity of morphant phenotypes.
    • Delineation of tumor migration paths by using a bayesian biogeographic approach

      Chroni, A; Vu, T; Miura, S; Kumar, S; Kumar, Sudhir|0000-0002-9918-8212 (2019-12-01)
      © 2019 by the authors. Licensee MDPI, Basel, Switzerland. Understanding tumor progression and metastatic potential are important in cancer biology. Metastasis is the migration and colonization of clones in secondary tissues. Here, we posit that clone migration events between tumors resemble the dispersal of individuals between distinct geographic regions. This similarity makes Bayesian biogeographic analysis suitable for inferring cancer cell migration paths. We evaluated the accuracy of a Bayesian biogeography method (BBM) in inferring metastatic patterns and compared it with the accuracy of a parsimony-based approach (metastatic and clonal history integrative analysis, MACHINA) that has been specifically developed to infer clone migration patterns among tumors. We used computer-simulated datasets in which simple to complex migration patterns were modeled. BBM and MACHINA were effective in reliably reconstructing simple migration patterns from primary tumors to metastases. However, both of them exhibited a limited ability to accurately infer complex migration paths that involve the migration of clones from one metastatic tumor to another and from metastasis to the primary tumor. Therefore, advanced computational methods are still needed for the biologically realistic tracing of migration paths and to assess the relative preponderance of different types of seeding and reseeding events during cancer progression in patients.
    • Density Visualization Pipeline: A Tool for Cellular and Network Density Visualization and Analysis

      Grein, S; Qi, G; Queisser, G (2020-06-26)
      © Copyright © 2020 Grein, Qi and Queisser. Neuron classification is an important component in analyzing network structure and quantifying the effect of neuron topology on signal processing. Current quantification and classification approaches rely on morphology projection onto lower-dimensional spaces. In this paper a 3D visualization and quantification tool is presented. The Density Visualization Pipeline (DVP) computes, visualizes and quantifies the density distribution, i.e., the “mass” of interneurons. We use the DVP to characterize and classify a set of GABAergic interneurons. Classification of GABAergic interneurons is of crucial importance to understand on the one hand their various functions and on the other hand their ubiquitous appearance in the neocortex. 3D density map visualization and projection to the one-dimensional x, y, z subspaces show a clear distinction between the studied cells, based on these metrics. The DVP can be coupled to computational studies of the behavior of neurons and networks, in which network topology information is derived from DVP information. The DVP reads common neuromorphological file formats, e.g., Neurolucida XML files, NeuroMorpho.org SWC files and plain ASCII files. Full 3D visualization and projections of the density to 1D and 2D manifolds are supported by the DVP. All routines are embedded within the visual programming IDE VRL-Studio for Java which allows the definition and rapid modification of analysis workflows.
    • Depletion of the RNA binding protein HNRNPD impairs homologous recombination by inhibiting DNA-end resection and inducing R-loop accumulation

      Alfano, L; Caporaso, A; Altieri, A; Dell'Aquila, M; Landi, C; Bini, L; Pentimalli, F; Giordano, A; Giordano, Antonio|0000-0002-5959-016X (2019-01-01)
      © The Author(s) 2019. DNA double strand break (DSB) repair through homologous recombination (HR) is crucial to maintain genome stability. DSB resection generates a single strand DNA intermediate, which is crucial for the HR process. We used a synthetic DNA structure, mimicking a resection intermediate, as a bait to identify proteins involved in this process. Among these, LC/MS analysis identified the RNA binding protein, HNRNPD. We found that HNRNPD binds chromatin, although this binding occurred independently of DNA damage. However, upon damage, HNRNPD re-localized to γH2Ax foci and its silencing impaired CHK1 S345 phosphorylation and the DNA end resection process. Indeed, HNRNPD silencing reduced: the ssDNA fraction upon camptothecin treatment; AsiSI-induced DSB resection; and RPA32 S4/8 phosphorylation. CRISPR/Cas9-mediated HNRNPD knockout impaired in vitro DNA resection and sensitized cells to camptothecin and olaparib treatment. We found that HNRNPD interacts with the heterogeneous nuclear ribonucleoprotein SAF-A previously associated with DNA damage repair. HNRNPD depletion resulted in an increased amount of RNA:DNA hybrids upon DNA damage. Both the expression of RNase H1 and RNA pol II inhibition recovered the ability to phosphorylate RPA32 S4/8 in HNRNPD knockout cells upon DNA damage, suggesting that RNA:DNA hybrid resolution likely rescues the defective DNA damage response of HNRNPD-depleted cells.
    • Design of the Endobronchial Valve for Emphysema Palliation Trial (VENT): a non-surgical method of lung volume reduction

      VENT Study Group (2007-07-03)
      Background: Lung volume reduction surgery is effective at improving lung function, quality of life, and mortality in carefully selected individuals with advanced emphysema. Recently, less invasive bronchoscopic approaches have been designed to utilize these principles while avoiding the associated perioperative risks. The Endobronchial Valve for Emphysema PalliatioN Trial (VENT) posits that occlusion of a single pulmonary lobe through bronchoscopically placed Zephyr® endobronchial valves will effect significant improvements in lung function and exercise tolerance with an acceptable risk profile in advanced emphysema. Methods: The trial design posted on Clinical trials.gov, on August 10, 2005 proposed an enrollment of 270 subjects. Inclusion criteria included: diagnosis of emphysema with forced expiratory volume in one second (FEV1) < 45% of predicted, hyperinflation (total lung capacity measured by body plethysmography > 100%; residual volume > 150% predicted), and heterogeneous emphysema defined using a quantitative chest computed tomography algorithm. Following standardized pulmonary rehabilitation, patients were randomized 2:1 to receive unilateral lobar placement of endobronchial valves plus optimal medical management or optimal medical management alone. The co-primary endpoint was the mean percent change in FEV1 and six minute walk distance at 180 days. Secondary end-points included mean percent change in St. George's Respiratory Questionnaire score and the mean absolute changes in the maximal work load measured by cycle ergometry, dyspnea (mMRC) score, and total oxygen use per day. Per patient response rates in clinically significant improvement/maintenance of FEV1 and six minute walk distance and technical success rates of valve placement were recorded. Apriori response predictors based on quantitative CT and lung physiology were defined. Conclusion: If endobronchial valves improve FEV1 and health status with an acceptable safety profile in advanced emphysema, they would offer a novel intervention for this progressive and debilitating disease. Trial Registration: ClinicalTrials.gov: NCT00129584.
    • Designing Bespoke Transitional Justice: A Pluralist Process Approach

      Ramji-Nogales, Jaya (2010)
      Although many scholars agree that contemporary transitional justice mechanisms are flawed, a comprehensive and unified alternative approach to accountability for mass violence has yet to be propounded. Like many international lawyers, transitional justice theorists have focused their assessment efforts on the successes and failures of established institutions. This Article argues that before we can measure whether transitional justice is working, we must begin with a theory of what it is trying to achieve. Once we have a coherent theory, we must use it ex ante, to design effective transitional justice mechanisms, not just to assess their effectiveness ex post. Drawing on several scholarly methods, I posit that effective transitional justice mechanisms are ones that successfully reconstruct social norms opposing mass violence. Because norm generation is an inherently communal and contingent social process, transitional justice ought to be primarily locally controlled and always precisely tailored to particular events and societies. In a word, it must be bespoke. This Article seeks to replace a universalist vision of transitional justice-imposition of a uniform set of substantive valueswith a pluralist approach to transitional justice-reconciliation of competing value frames through an inclusive process.
    • Designing cost-efficient randomized trials by using flexible recruitment strategies

      Yu, M; Wu, J; Burns, DS; Carpenter, JS (2012-11-30)
      Background: Sample size planning for clinical trials is usually based on detecting a target effect size of an intervention or treatment. Explicit incorporation of costs into such planning is considered in this article in the situation where effects of an intervention or treatment may depend on (interact with) baseline severity of the targeted symptom or disease. Because much larger sample sizes are usually required to establish such an interaction effect, investigators frequently conduct studies to establish a marginal effect of the intervention for individuals with a certain level of baseline severity. Methods. We conduct a rigorous investigation on how to determine optimum baseline symptom or disease severity inclusion criteria so that the most cost-efficient design can be used. By using a regression model with an interaction term of treatment by symptom severity, power functions were derived for various levels of baseline symptom severity. Computer algorithms and mathematical optimization were used to determine the most cost-efficient research designs assuming either single- or dual-stage screening procedures. Results: In the scenarios we considered, impressive cost savings can be achieved by informed selection of baseline symptom severity via the inclusion criteria. Further cost-savings can be achieved if a two stage screening procedure is used and there are some known, relatively inexpensively collected, pre-screening information. The amount of total cost savings are shown to depend on the ratio of the screening and intervention costs. In our investigation, we assumed that: 1) the cost of approaching available subjects for screening is constant, and 2) all variables are normally distributed. There is a need to carry out further investigations with more relaxed assumptions (e.g., skewed data distribution). Conclusions: As cost becomes a more and more prominent issue in modern clinical trials, cost-saving strategies will become more and more important. Strategies, such as the ones we propose here, can help to minimize costs while maximizing knowledge generation. © 2012 Yu et al.; licensee BioMed Central Ltd.
    • Design–functionality relationships for adhesion/ growth-regulatory galectins

      Ludwig, AK; Michalak, M; Xiao, Q; Gilles, U; Medrano, FJ; Ma, H; FitzGerald, FG; Hasley, WD; Melendez-Davila, A; Liu, M; Rahimi, K; Kostina, NY; Rodriguez-Emmenegger, C; Möller, M; Lindner, I; Kaltner, H; Cudic, M; Reusch, D; Kopitz, J; Romero, A; Oscarson, S; Klein, ML; Gabius, HJ; Percec, V (2019-02-19)
      © 2019 National Academy of Sciences. All Rights Reserved. Glycan-lectin recognition is assumed to elicit its broad range of (patho)physiological functions via a combination of specific contact formation with generation of complexes of distinct signal-triggering topology on biomembranes. Faced with the challenge to understand why evolution has led to three particular modes of modular architecture for adhesion/growth-regulatory galectins in vertebrates, here we introduce protein engineering to enable design switches. The impact of changes is measured in assays on cell growth and on bridging fully synthetic nanovesicles (glycodendrimersomes) with a chemically programmable surface. Using the example of homodimeric galectin-1 and monomeric galectin-3, the mutual design conversion caused qualitative differences, i.e., from bridging effector to antagonist/from antagonist to growth inhibitor and vice versa. In addition to attaining proof-of-principle evidence for the hypothesis that chimera-type galectin-3 design makes functional antagonism possible, we underscore the value of versatile surface programming with a derivative of the pan-galectin ligand lactose. Aggregation assays with N,N′-diacetyllactosamine establishing a parasite-like surface signature revealed marked selectivity among the family of galectins and bridging potency of homodimers. These findings provide fundamental insights into design-functionality relationships of galectins. Moreover, our strategy generates the tools to identify biofunctional lattice formation on biomembranes and galectin-reagents with therapeutic potential.
    • Detecting individual sites subject to episodic diversifying selection

      Murrell, B; Wertheim, JO; Moola, S; Weighill, T; Scheffler, K; Kosakovsky Pond, SL; Pond, Sergei L. Kosakovsky|0000-0003-4817-4029 (2012-07-01)
      The imprint of natural selection on protein coding genes is often difficult to identify because selection is frequently transient or episodic, i.e. it affects only a subset of lineages. Existing computational techniques, which are designed to identify sites subject to pervasive selection, may fail to recognize sites where selection is episodic: a large proportion of positively selected sites. We present a mixed effects model of evolution (MEME) that is capable of identifying instances of both episodic and pervasive positive selection at the level of an individual site. Using empirical and simulated data, we demonstrate the superior performance of MEME over older models under a broad range of scenarios. We find that episodic selection is widespread and conclude that the number of sites experiencing positive selection may have been vastly underestimated. © 2012 Murrell et al.
    • Detection of Anti- Leptospira IgM Antibody in Serum Samples of Suspected Patients Visiting National Public Health Laboratory, Teku, Kathmandu

      Dahal, KP; Sharma, S; Sherchand, JB; Upadhyay, BP; Bhatta, DR; Dahal, Khila|0000-0002-5543-846X (2016-01-01)
      © 2016 Krishna Prasad Dahal et al. Leptospirosis is a globally distributed zoonosis with varied clinical outcomes and multiorgan involvement in humans. In this study conducted from July 2011 to December 2011, 178 serum samples from patients suspected of leptospirosis were tested by Panbio IgM ELISA at National Public Health Laboratory, Kathmandu, out of which 51 (28.65%) were positive for anti-Leptospira IgM antibody. Leptospirosis was more common in people in their 2nd and 3rd decades of their life which together comprised 56.86% of the total positive cases. Most of those tested positive were farmers followed by students and housewives. Both animal contact and water contact seemed to play significant roles in disease transmission. Symptoms were vague with the most common being fever, headache, myalgia, abdominal pain, vomiting, jaundice, and diarrhoea. Life style heavily dominated by agronomical and farming activities in Nepal is conducive to leptospirosis transmission. Leptospirosis seems to be a significant public health problem in Nepal but is underestimated. In resource poor countries like Nepal where laboratories performing MAT or maintaining cultures are rarely available, serological test like ELISA could well depict the scenario of the disease prevalence.
    • Detection of Myoglobin with an Open-Cavity-Based Label-Free Photonic Crystal Biosensor

      Zhang, Bailin; Tamez-Vela, Juan Manuel; Solis, Steven; Bustamante, Gilbert; Peterson, Ralph; Rahman, Shafiqur; Morales, Andres; Tang, Liang; Ye, Jing Yong (2013-06-02)
      <jats:p>The label-free detection of one of the cardiac biomarkers, myoglobin, using a photonic-crystal-based biosensor in a total-internal-reflection configuration (PC-TIR) is presented in this paper. The PC-TIR sensor possesses a unique open optical microcavity that allows for several key advantages in biomolecular assays. In contrast to a conventional closed microcavity, the open configuration allows easy functionalization of the sensing surface for rapid biomolecular binding assays. Moreover, the properties of PC structures make it easy to be designed and engineered for operating at any optical wavelength. Through fine design of the photonic crystal structure, biochemical modification of the sensor surface, and integration with a microfluidic system, we have demonstrated that the detection sensitivity of the sensor for myoglobin has reached the clinically significant concentration range, enabling potential usage of this biosensor for diagnosis of acute myocardial infarction. The real-time response of the sensor to the myoglobin binding may potentially provide point-of-care monitoring of patients and treatment effects.</jats:p>
    • Developing a community-based genetic nomenclature for anole lizards

      Kusumi, K; Kulathinal, RJ; Abzhanov, A; Boissinot, S; Crawford, NG; Faircloth, BC; Glenn, TC; Janes, DE; Losos, JB; Menke, DB; Poe, S; Sanger, TJ; Schneider, CJ; Stapley, J; Wade, J; Wilson-Rawls, J; Kulathinal, Rob|0000-0003-1907-2744 (2011-11-11)
      Background: Comparative studies of amniotes have been hindered by a dearth of reptilian molecular sequences. With the genomic assembly of the green anole, Anolis carolinensis available, non-avian reptilian genes can now be compared to mammalian, avian, and amphibian homologs. Furthermore, with more than 350 extant species in the genus Anolis, anoles are an unparalleled example of tetrapod genetic diversity and divergence. As an important ecological, genetic and now genomic reference, it is imperative to develop a standardized Anolis gene nomenclature alongside associated vocabularies and other useful metrics.Results: Here we report the formation of the Anolis Gene Nomenclature Committee (AGNC) and propose a standardized evolutionary characterization code that will help researchers to define gene orthology and paralogy with tetrapod homologs, provide a system for naming novel genes in Anolis and other reptiles, furnish abbreviations to facilitate comparative studies among the Anolis species and related iguanid squamates, and classify the geographical origins of Anolis subpopulations.Conclusions: This report has been generated in close consultation with members of the Anolis and genomic research communities, and using public database resources including NCBI and Ensembl. Updates will continue to be regularly posted to new research community websites such as lizardbase. We anticipate that this standardized gene nomenclature will facilitate the accessibility of reptilian sequences for comparative studies among tetrapods and will further serve as a template for other communities in their sequencing and annotation initiatives. © 2011 Kusumi et al; licensee BioMed Central Ltd.