Miracle-dz/UniFAR-FTUs huggingface dataset:
Top-down effects of a lytic bacteriophage and protozoa on bacteria in aqueous and biofilm phases

Lytic bacteriophages and protozoan predators are the major causes of bacterial mortality in natural microbial communities, which also makes them potential candidates for biological control of bacterial pathogens. However, little is known about the relative impact of bacteriophages and protozoa on the dynamics of bacterial biomass in aqueous and biofilm phases. Here, we studied the temporal and spatial dynamics of bacterial biomass in a microcosm experiment where opportunistic pathogenic bacteria Serratia marcescens was exposed to particle-feeding ciliates, surface-feeding amoebas, and lytic bacteriophages for 8 weeks, ca. 1300 generations. We found that ciliates were the most efficient enemy type in reducing bacterial biomass in the open water, but least efficient in reducing the biofilm biomass. Biofilm was rather resistant against bacterivores, but amoebae had a significant long-term negative effect on bacterial biomass both in the open-water phase and biofilm. Bacteriophages had only a minor long-term effect on bacterial biomass in open-water and biofilm phases. However, separate short-term experiments with the ancestral bacteriophages and bacteria revealed that bacteriophages crash the bacterial biomass dramatically in the open-water phase within the first 24 h. Thereafter, the bacteria evolve phage-resistance that largely prevents top-down effects. The combination of all three enemy types was most effective in reducing biofilm biomass, whereas in the open-water phase the ciliates dominated the trophic effects. Our results highlight the importance of enemy feeding mode on determining the spatial distribution and abundance of bacterial biomass. Moreover, the enemy type can be crucially important predictor of whether the rapid defense evolution can significantly affect top-down regulation of bacteria.
Near-Optimal Bayesian Ambiguity Sets for Distributionally Robust Optimization

We propose a Bayesian framework for assessing the relative strengths of data-driven ambiguity sets in distributionally robust optimization (DRO) when the underlying distribution is defined by a finite-dimensional parameter. The key idea is to measure the relative size between a candidate ambiguity set and a specific asymptotically optimal set. As the amount of data grows large, this asymptotically optimal set is the smallest convex ambiguity set that satisfies a novel Bayesian robustness guarantee that we introduce. This guarantee is defined with respect to a given class of constraints and is a Bayesian analog of more common frequentist feasibility guarantees from the DRO literature. Using this framework, we prove that many popular existing ambiguity sets are significantly larger than the asymptotically optimal set for constraints that are concave in the ambiguity. By contrast, we construct new ambiguity sets that are tractable, satisfy our Bayesian robustness guarantee, and are at most a small, constant factor larger than the asymptotically optimal set; we call these sets Bayesian near-optimal. We further prove that asymptotically, solutions to DRO models with our Bayesian near-optimal sets enjoy strong frequentist robustness properties, despite their smaller size. Finally, our framework yields guidelines for practitioners selecting between competing ambiguity set proposals in DRO. Computational evidence in portfolio allocation using real and simulated data confirms that our framework, although motivated by asymptotic analysis in a Bayesian setting, provides practical insight into the performance of various DRO models with finite data under frequentist assumptions. This paper was accepted by Yinyu Ye, optimization.
Competency assessment of primary care physicians as part of a peer review program.

OBJECTIVE To design and test a program that assesses clinical competence as a second stage in a peer review process and to determine the program's reliability. DESIGN AND SETTING A three-cohort study of Ontario primary care physicians. PARTICIPANTS Reference physicians (n = 26) randomly drawn from the Hamilton, Ontario, area; volunteer, self-referred physicians (n = 20); and physicians referred by the licensing body (n = 37) as a result of a disciplinary hearing or peer review. MAIN OUTCOME MEASURES Standardized patients, structured oral examinations, chart-stimulated recall, objective structured clinical examination, and multiple-choice examination. RESULTS Test reliability was high, ranging from 0.73 to 0.91, and all tests discriminated among subgroups. Demographic variables relating to the final category were age, Canadian or foreign graduates, and whether or not participants were certified in family medicine. CONCLUSIONS The study demonstrated the feasibility, reliability, and validity of a multicomponent examination in the peer review process.
INTRODUCING CONCEPTS OF STATISTICAL INFERENCE VIA RANDOMIZATION TESTS

For over a decade now, technology tools have been advocated to assist student understanding of statistical concepts. We have designed and used applets that simulate sampling and randomization tests as a means for introducing students to concepts of statistical inference. In this talk we present the results of our investigation on the impact of using applets for this purpose with tertiary students. The foci of our investigation include appreciating the reasoning process behind statistical significance, understanding what a p-value is, and recognizing factors that affect p-values. We present the results of small classroom experiments designed to help inform our curricular materials and manner of teaching.
Linkage-Based Analysis and Optimization of an Underactuated Planar Manipulator for In-Hand Manipulation

This paper investigates the in-hand manipulation capabilities of a compliant, underactuated planar robotic hand by treating the system as a simple, symmetric, 6-bar linkage mechanism with compliant joints. Although underactuated hands are generally not considered to be adept at dexterous tasks, we have found through past work that an underactuated manipulator can control n degrees of freedom with n actuators by leveraging the passive compliance to satisfy contact constraints on the object. Assuming the system to be quasi-static, the workspace of the underactuated mechanism is found through constraint-based energy minimization by sweeping through the set of allowable inputs. In this study, we investigate achievable workspaces by exploring the nondimensionalized design space, consisting of linkage ratio, joint stiffness ratio, transmission ratio, base linkage length, and object linkage length. The results of this study are useful in motivating the design of dexterous, underactuated manipulators, as well as to predict the achievable workspace of specific hand/object configurations.
Low concentrations of adropin are associated with endothelial dysfunction as assessed by flow-mediated dilatation in patients with metabolic syndrome

Abstract Background: In individuals with atherosclerotic risk factors, endothelial dysfunction (ED) appears as an early phase in the development of clinical symptoms. Recent studies indicate that adropin, a newly identified peptide, participates in cardiovascular health through the regulation of several metabolic events including angiogenesis and blood flow. In this study, we aimed to determine the relation of adropin with biochemical and radiologic parameters which reflect ED such as endothelial nitric oxide synthase (eNOS), endothelin 1 (ET-1), nitric oxide (NO) and flow-mediated dilatation (FMD) along with the routine biochemical measurements in patients recently diagnosed with metabolic syndrome (MetS). Methods: Fasting blood samples from 110 patients with MetS diagnosed according to the NCEP ATP III-2005 criteria were collected to measure the concentrations of adropin and other parameters including the lipid profile, insulin and glucose. Serum NOx concentrations were determined by measuring NO2 plus NO3. FMD test was performed by ultrasonography, and patients were stratified as FMD (+) or (–). Data were compared between these two subgroups and also with matching healthy controls (n=50). Biochemical data were evaluated using Student’s t or Mann-Whitney U tests. Results: Fifty-nine subjects had ED (+) and the remaining 101 subjects were ED (–). In the first group, adropin levels were significantly lower than the latter (2.13±1.05 vs. 3.41±1.63 ng/mL, respectively; p<0.001) and independently associated with FMD positivity as assessed by the logistic regression analysis. Conclusions: Low adropin level in circulation is related to ED and has a close association with FMD. Any alterations in its level may be of help in order to assess the development of ED before the occurrence of clinical symptoms in patients with metabolic syndrome.
USE OF HAPTEN-CARRIER COMPLEXES FOR BENZIMIDAZOLE PESTICIDES IMMUNOASSAYS DEVELOPMENT

In order to develop immunoassays for pesticides detection, this work describes the choice of three different haptens that present structural similarity to benzimidazole molecule, methods for coupling them with two carrier proteins in order to make them immunogenic, a protocol for immunization of laboratory rodents with hapten-carrier complexes, and the evaluation of the specific antibody responses against haptens using an in-house developed immunoassay. Three carbendazim (methyl 2-benzimidazole-carbamate) derivatives bearing different functional reactive groups (-NH2, -SH and -COOH), namely 2-(2-Aminoethyl) benzimidazole (AEB),2-Mercaptobenzimidazole (2MB) and 2-Benzimidazole propionic acid (BPA), were coupled to keyhole limpet haemocyanin (KLH) and bovine serum albumin(BSA), respectively, mixed with immuno-adjuvants, and injected four times into Balb/C mice and Wistar rats for induction of specific immune responses.All three chemicals elicited a specific but weak antibodies response upon immunization with hapten-KLH complexes followed by serological testing by indirect ELISA with hapten-BSA complexes, and showed detectabledifferences in antibody titers with regard to number of inoculations, hapten structure and animal species. Whereas the AEB-KLH complex was the strongest, the 2MB-KLH complex was the weakest immunogenic in mice. However, the best animal responders allow the application of technologies for getting monoclonal antibodies against benzimidazoles, which can then be used for immunoassays development.
In Silico Analysis of Epitope-Based Vaccine Candidates against Hepatitis B Virus Polymerase Protein

Hepatitis B virus (HBV) infection has persisted as a major public health problem due to the lack of an effective treatment for those chronically infected. Therapeutic vaccination holds promise, and targeting HBV polymerase is pivotal for viral eradication. In this research, a computational approach was employed to predict suitable HBV polymerase targeting multi-peptides for vaccine candidate selection. We then performed in-depth computational analysis to evaluate the predicted epitopes’ immunogenicity, conservation, population coverage, and toxicity. Lastly, molecular docking and MHC-peptide complex stabilization assay were utilized to determine the binding energy and affinity of epitopes to the HLA-A0201 molecule. Criteria-based analysis provided four predicted epitopes, RVTGGVFLV, VSIPWTHKV, YMDDVVLGA and HLYSHPIIL. Assay results indicated the lowest binding energy and high affinity to the HLA-A0201 molecule for epitopes VSIPWTHKV and YMDDVVLGA and epitopes RVTGGVFLV and VSIPWTHKV, respectively. Regions 307 to 320 and 377 to 387 were considered to have the highest probability to be involved in B cell epitopes. The T cell and B cell epitopes identified in this study are promising targets for an epitope-focused, peptide-based HBV vaccine, and provide insight into HBV-induced immune response.
Concrete Subjected to Varying Confinement, II: Modeling

A unique model for estimating the axial response of concrete under varying or constant levels of confinement is developed. The proposed model is empirically developed from a companion experimental study of concrete tested under linear, elastic perfectly plastic (EPP), elasto-plastic with strain hardening, and constant triaxial confinement. The axial stress-strain response is divided into three regions separated by two characteristic response levels. The model is based on the variation of the confining pressure due to the lateral dilation of the concrete. An estimate of dilation with respect to axial strain is also developed. The model is shown to provide an accurate prediction of historical experimental studies of constant confinement tests on cylinders, fiber reinforced polymer (FRP) jacketed specimens, and columns confined with conventional lateral reinforcement or FRP jacket.
Avian BMR in Marine and Non-Marine Habitats: A Test Using Shorebirds

Basal metabolic rate (BMR) is closely linked to different habitats and way of life. In birds, some studies have noted that BMR is higher in marine species compared to those inhabiting terrestrial habitats. However, the extent of such metabolic dichotomy and its underlying mechanisms are largely unknown. Migratory shorebirds (Charadriiformes) offer a particularly interesting opportunity for testing this marine–non-marine difference as they are typically divided into two broad categories in terms of their habitat occupancy outside the breeding season: ‘coastal’ and ‘inland’ shorebirds. Here, we measured BMR for 12 species of migratory shorebirds wintering in temperate inland habitats and collected additional BMR values from the literature for coastal and inland shorebirds along their migratory route to make inter- and intraspecific comparisons. We also measured the BMR of inland and coastal dunlins Calidris alpina wintering at a similar latitude to facilitate a more direct intraspecific comparison. Our interspecific analyses showed that BMR was significantly lower in inland shorebirds than in coastal shorebirds after the effects of potentially confounding climatic (latitude, temperature, solar radiation, wind conditions) and organismal (body mass, migratory status, phylogeny) factors were accounted for. This indicates that part of the variation in basal metabolism might be attributed to genotypic divergence. Intraspecific comparisons showed that the mass-specific BMR of dunlins wintering in inland freshwater habitats was 15% lower than in coastal saline habitats, suggesting that phenotypic plasticity also plays an important role in generating these metabolic differences. We propose that the absence of tidally-induced food restrictions, low salinity, and less windy microclimates associated with inland freshwater habitats may reduce the levels of energy expenditure, and hence BMR. Further research including common-garden experiments that eliminate phenotypic plasticity as a source of phenotypic variation is needed to determine to what extent these general patterns are attributable to genotypic adaptation.
STRUCTURAL CHARACTERISATION OF NOVEL Ti-Cu INTERMETALLIC COATINGS

AbstractThe structure and composition of an innovative Ti-Cu intermetallic coating has been investigated by means of metallographic examination, X-ray diffraction, glow discharge optical spectroscopy, and microhardness measurements. For this purpose, Ti-6Al-4V substrates were coated with a uniform layer of copper by an electroplating technique, then a diffusion anneal was conducted in an argon controlled atmosphere. Microstructural examination revealed that the compound coating microstructure consisted of four layers: the outer two layers are composed of various intermetallic compounds, including TiCu3 + Ti3 Al and TiCu; the third layer is the transformation product of the β phase electroplatformed at the diffusion temperature, which contains α- Ti and Ti2Cu; and the fourth layer was identified as the product of this transformation precipitated mainly at proeutectoid (α- Ti boundaries. These microstructural features reveal the two essential characteristics of the coatings, namely the continuous layers of .
The impact of opioid analgesics on the gastrointestinal tract function and the current management possibilities

Opioid-induced bowel dysfunction (OIBD) comprises gastrointestinal symptoms such as constipation, anorexia, nausea, vomiting, gastro-oesophageal reflux, delayed digestion, abdominal pain, bloating, hard stool and incomplete evacuation that significantly deteriorate patients’ quality of life and compliance. Approximately one third of patients treated with opioids do not adhere to the opioid regimen or simply quit the treatment due to OIBD. Several strategies are undertaken to prevent or treat OIBD. Traditional oral laxatives are used but their effectiveness is limited and they display adverse effects. Other possibilities comprise opioid switch or changing the administration route. New therapies target opioid receptors in the gut that seem to be the main source of OIBD. One is a combination of an opioid and opioid antagonist (oxycodone/naloxone) in prolonged-release tablets, and another is a purely peripherally acting opioid receptor antagonist (methylnaltrexone) available in subcutaneous injections. The aim of this article is to review the pathomechanism and possible treatment strategies of OIBD.
A Bayesian, Exemplar-Based Approach to Hierarchical Shape Matching

This paper presents a novel probabilistic approach to hierarchical, exemplar-based shape matching. No feature correspondence is needed among exemplars, just a suitable pairwise similarity measure. The approach uses a template tree to efficiently represent and match the variety of shape exemplars. The tree is generated offline by a bottom-up clustering approach using stochastic optimization. Online matching involves a simultaneous coarse-to-fine approach over the template tree and over the transformation parameters. The main contribution of this paper is a Bayesian model to estimate the a posteriori probability of the object class, after a certain match at a node of the tree. This model takes into account object scale and saliency and allows for a principled setting of the matching thresholds such that unpromising paths in the tree traversal process are eliminated early on. The proposed approach was tested in a variety of application domains. Here, results are presented on one of the more challenging domains: real-time pedestrian detection from a moving vehicle. A significant speed-up is obtained when comparing the proposed probabilistic matching approach with a manually tuned nonprobabilistic variant, both utilizing the same template tree structure.
Phylogeny and Immunoreactivity of Norovirus GII.P16-GII.2, Japan, Winter 2016–17

During the 2016–17 winter season in Japan, human norovirus GII.P16-GII.2 strains (2016 strains) caused large outbreaks of acute gastroenteritis. Phylogenetic analyses suggested that the 2016 strains derived from the GII.2 strains detected during 2010–12. Immunochromatography between 2016 strains and the pre-2016 GII.2 strains showed similar reactivity.
Power Analysis Attacks and Algorithmic Approaches to Their Countermeasures for Koblitz Curve Cryptosystems

Because of their shorter key sizes, cryptosystems based on elliptic curves are being increasingly used in practical applications. A special class of elliptic curves, namely, Koblitz curves, offers an additional but crucial advantage of considerably reduced processing time. In this article, power analysis attacks are applied to cryptosystems that use scalar multiplication on Koblitz curves. Both the simple and the differential power analysis attacks are considered and a number of countermeasures are suggested. While the proposed countermeasures against the simple power analysis attacks rely on making the power consumption for the elliptic curve scalar multiplication independent of the secret key, those for the differential power analysis attacks depend on randomizing the secret key prior to each execution of the scalar multiplication.
Spectral analysis of nonlinear flows

We present a technique for describing the global behaviour of complex nonlinear flows by decomposing the flow into modes determined from spectral analysis of the Koopman operator, an infinite-dimensional linear operator associated with the full nonlinear system. These modes, referred to as Koopman modes, are associated with a particular observable, and may be determined directly from data (either numerical or experimental) using a variant of a standard Arnoldi method. They have an associated temporal frequency and growth rate and may be viewed as a nonlinear generalization of global eigenmodes of a linearized system. They provide an alternative to proper orthogonal decomposition, and in the case of periodic data the Koopman modes reduce to a discrete temporal Fourier transform. The Arnoldi method used for computations is identical to the dynamic mode decomposition recently proposed by Schmid & Sesterhenn (Sixty-First Annual Meeting of the APS Division of Fluid Dynamics, 2008), so dynamic mode decomposition can be thought of as an algorithm for finding Koopman modes. We illustrate the method on an example of a jet in crossflow, and show that the method captures the dominant frequencies and elucidates the associated spatial structures.
The Influence of Drivers and Barriers on Urban Adaptation and Mitigation Plans—An Empirical Analysis of European Cities

Cities are recognised as key players in global adaptation and mitigation efforts because the majority of people live in cities. However, in Europe, which is highly urbanized and one of the most advanced regions in terms of environmental policies, there is considerable diversity in the regional distribution, ambition and scope of climate change responses. This paper explores potential factors contributing to such diversity in 200 large and medium-sized cities across 11 European countries. We statistically investigate institutional, socio-economic, environmental and vulnerability characteristics of cities as potential drivers of or barriers to the development of urban climate change plans. Our results show that factors such as membership of climate networks, population size, GDP per capita and adaptive capacity act as drivers of mitigation and adaptation plans. By contrast, factors such as the unemployment rate, warmer summers, proximity to the coast and projected exposure to future climate impacts act as barriers. We see that, overall, it is predominantly large and prosperous cities that engage in climate planning, while vulnerable cities and those at risk of severe climate impacts in the future are less active. Our analysis suggests that climate change planning in European cities is not proactive, i.e. not significantly influenced by anticipated future impacts. Instead, we found that the current adaptive capacity of a city significantly relates to climate planning. Along with the need to further explore these relations, we see a need for more economic and institutional support for smaller and less resourceful cities and those at high risk from climate change impacts in the future.