Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Extraction Method Affects the Detection of a Fungal Pathogen in Formalin-Fixed Specimens Using qPCR

Museum collections provide indispensable repositories for obtaining information about the historical presence of disease in wildlife populations. The pathogenic amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has played a significant role in global amphibian declines, and examining preserved specimens for Bd can improve our understanding of its emergence and spread. Quantitative PCR (qPCR) enables Bd detection with minimal disturbance to amphibian skin and is significantly more sensitive to detecting Bd than histology; therefore, developing effective qPCR methodologies for detecting Bd DNA in formalin-fixed specimens can provide an efficient and effective approach to examining historical Bd emergence and prevalence. Techniques for detecting Bd in museum specimens have not been evaluated for their effectiveness in control specimens that mimic the conditions of animals most likely to be encountered in museums, including those with low pathogen loads. We used American bullfrogs (Lithobates catesbeianus) of known infection status to evaluate the success of qPCR to detect Bd in formalin-fixed specimens after three years of ethanol storage. Our objectives were to compare the most commonly used DNA extraction method for Bd (PrepMan, PM) to Macherey-Nagel DNA FFPE (MN), test optimizations for Bd detection with PM, and provide recommendations for maximizing Bd detection. We found that successful detection is relatively high (80–90%) when Bd loads before formalin fixation are high, regardless of the extraction method used; however, at lower infection levels, detection probabilities were significantly reduced. The MN DNA extraction method increased Bd detection by as much as 50% at moderate infection levels. Our results indicate that, for animals characterized by lower pathogen loads (i.e., those most commonly encountered in museum collections), current methods may underestimate the proportion of Bd-infected amphibians. Those extracting DNA from archived museum specimens should ensure that the techniques they are using are known to provide high-quality throughput DNA for later analysis.
RICH: Automatically Protecting Against Integer-Based Vulnerabilities

We present the design and implementation of RICH (Run-time Integer CHecking), a tool for efficiently detecting integer-based attacks against C programs at run time. C integer bugs, a popular avenue of attack and frequent programming error [1–15], occur when a variable value goes out of the range of the machine word used to materialize it, e.g. when assigning a large 32-bit int to a 16-bit short. We show that safe and unsafe integer operations in C can be captured by well-known sub-typing theory. The RICH compiler extension compiles C programs to object code that monitors its own execution to detect integer-based attacks. We implemented RICH as an extension to the GCC compiler and tested it on several network servers and UNIX utilities. Despite the ubiquity of integer operations, the performance overhead of RICH is very low, averaging about 5%. RICH found two new integer bugs and caught all but one of the previously known bugs we tested. These results show that RICH is a useful and lightweight software testing tool and run-time defense mechanism. RICH may generate false positives when programmers use integer overflows deliberately, and it can miss some integer bugs because it does not model certain C features.
Exhaust Pressure Waves in Diesel Engines and the Impacts on Aftertreatment Sprays

iv DEDICATION . v ACKNOWLEDGEMENTS . vi LIST OF TABLES . x LIST OF FIGURES . xi LIST OF SYMBOLS AND ABBREVIATIONS . xiii CHAPTER 1 INTRODUCTION . 1 1.1 Research background . 1 1.1.1 Diesel particulate filter (DPF) . 4 1.1.2 Selective catalytic reduction (SCR) . 5 1.1.3 Lean NOx trap (LNT) . 5 1.2 Aftertreatment injection . 6 1.3 Pressure waves in engine intake and exhaust systems . 7 1.3. 1 Non-linear gas dynamic method . 9 1.3. 2 Linear acoustic method . 10 1.3. 3 Hybrid methods . 11 1.3. 4 Properties of pressure wave in an engine system . 12 1.4 Interactions between pressure wave actions and liquid dosing sprays . 12 1.5 Objective of the thesis . 14 1.6 Structure of the thesis . 14 CHAPTER 2 EXPERIMENTAL SETUP AND SIMULATION METHOD . 16 2.1 Test setup of a Ford Puma engine . 16
Assessing the Impact of a Novel Smartphone Application Compared With Standard Follow-Up on Mobility of Patients With Knee Osteoarthritis Following Treatment With Hylan G-F 20: A Randomized Controlled Trial

Background Osteoarthritis (OA) is a leading cause of disability in the United States. Although no disease-modifying therapies exist, patients with knee OA who increase walking may reduce risk of functional limitations. Objective The objective of the study is to evaluate the impact of a mobile app (OA GO) plus wearable activity monitor/pedometer (Jawbone UP 24) used for 90 days on the mobility of patients with knee OA treated with hylan G-F 20. Methods Patients with knee OA aged 30 to 80 years who were eligible to receive hylan G-F 20 and were familiar with smartphone technology were enrolled in this randomized, multicenter, open-label study. Patients who had a body mass index above 35 kg/m2 were excluded. All patients received a single 6-mL injection of hylan G-F 20 and wore the Jawbone monitor. The patients were then randomized 1:1 to Jawbone and OA GO (Group A; n=107) with visible feedback (unblinded) or Jawbone only (Group B; n=104) with no visible feedback (blinded). The primary endpoint was mean change from baseline in steps per day at day 90 between Groups A and B. Results Baseline characteristics were similar between groups. There were significant differences between the increases in least squares (LS) mean number of steps per day (1199 vs 467, P=.03) and the mean percentage change (35.8% vs 11.5%, P=.02) from baseline in favor of Group A over Group B. There was a greater reduction in pain from baseline during the 6-minute walk test in Group A versus Group B. (LS mean change: −55.3 vs −33.8, P=.007). Most patients (65.4%) and surveys of physicians (67.3%) reported they would be likely or very likely to use/recommend the devices. Patient Activity Measure-13 scores improved from baseline (LS mean change for Groups A and B: 5.0 vs 6.9), with no significant differences between groups. The occurrence of adverse events was similar in the 2 groups. Conclusions Use of a novel smartphone app in conjunction with a wearable activity monitor provided additional improvement on mobility parameters such as steps per day and pain with walking in the 6-minute walk test in patients with knee OA who were treated with hylan G-F 20. Results also highlight the amenability of patients and physicians to using mobile health technology in the treatment of OA and suggest further study is warranted.
Volume changes during preparation of mouse embryonic tissue for scanning electron microscopy

This paper describes the results of experiments in which the volume changes in mouse embryo limb samples were followed more or less continuously after fixation through dehydration and critical point drying, with in some instances data relating to post critical point drying shrinkage. 14 and 15 day p. c. mouse embryos were fixed in 3 % glutaraldehyde in cacodylate buffer and stored in this fixative until use. Single specimens were studied using a Quantimet image analysing computer to record the changes in projected area of the unmounted specimens as they were passed through the usual series of reagents according to various commonly used dehydration schedules. The area changes were converted to volume changes for the purposes of presentation in this paper. The Quantimet system could not be used to follow volume changes in the CPD bomb so that most experiments detail the volume in the intermediate fluid before CPD and the size of the specimen immediately after it was removed from the CPD bomb. A few experiments were conducted in which the specimens were measured whilst they were in the CPD bomb. The measurements relating to dehydration and CPD procedures were compared with measurements of air dried and freeze dried specimens. All three drying methods cause considerable shrinkage: freeze drying to 85 % of the glutaraldehyde fixed tissue volume; critical point drying to 41% (after 24 h); and air drying from a volatile solvent to about 18% of the fixed tissue volume. Air drying from water caused a shrinkage to about 12% of the original volume. There was no significant difference between the various commonly used CPD schedules or between GA only and GA + Os O4 fixed tissue. CPD via cellosolve and CO2 caused substantially more shrinkage than other methods. Dimensional changes during specimen preparation are probably associated with changes in shape and in relative relationships between organelles, cells and tissues having different compositions. This should be borne in mind by all those interpreting scanning electron micrographs of dried animal soft tissue specimens.
Extracting Realistic User Behavior Models

Workloads play a central role in assessing software qualities, like performance and privacy. They are characterized by intensity and user behavior patterns. Combining multiple intensities and behaviors are used to create workload profiles which, among others, sevaluate software design, predict of system utilization. The central challenge for workload profiles is their fit to real workloads and in particular the match to specific behaviors. This is especially relevant for understanding and identifying specific user groups and support workload composition by operators. In this paper, we address the identification of such realistic user behaviors by utilizing domain specific attributes, report on our evaluation of the fitness of behavior clustering approaches, and discuss our setup to evaluate further clustering approaches.
Rheumatoid arthritis patients with continued low disease activity have similar outcomes over 10 years, regardless of initial therapy

Objectives To compare 10-year disease outcomes of RA patients who have continuous low disease activity and are on MTX with or without initial combination therapy with infliximab or prednisone and SSZ. Methods Recent-onset RA patients from the Behandel Strategieen (BeSt) (Dutch acronym for Treatment Strategies) study with 10 years of follow-up were analysed. Treatment was tightly controlled, targeted at DAS ⩽ 2.4. The selected patients had low disease activity from 6 months until 10 years and therefore did not intensify treatment. Patients were grouped into those receiving MTX monotherapy and those receiving initial combination therapy. Between-group differences over time were compared, using (generalized) linear mixed model analyses, for the outcomes DAS, HAQ, ESR, visual analogue scale patient global health, percentage of patients in (drug-free) remission and percentage of patients with Sharp/van der Heijde score progression ⩾5. Results At 10 years, 28/247 (11%) patients on MTX monotherapy (some tapered to drug free) had continued DAS ⩽ 2.4 compared with 68/261 (26%) patients on combination therapy (all tapered to monotherapy or drug free). No between-group differences in continuous responders were found over time, except for a higher percentage of patients in drug-free remission after MTX monotherapy. Significant group-time interactions were found for DAS, ESR and visual analogue scale patient global health, but the results seem clinically negligible. Conclusion More patients achieved continuous low disease activity on initial prednisone or infliximab combination therapy than on initial MTX monotherapy, but there appeared to be no additional benefits. Regardless of induction therapy, patients with continuous low disease activity have similar long-term outcomes, with only a higher proportion of patients in drug-free remission after MTX monotherapy.
Online cancer communities as informatics intervention for social support: conceptualization, characterization, and impact

Objectives: The Internet and social media are revolutionizing how social support is exchanged and perceived, making online health communities (OHCs) one of the most exciting research areas in health informatics. This paper aims to provide a framework for organizing research of OHCs and help identify questions to explore for future informatics research. Based on the framework, we conceptualize OHCs from a social support standpoint and identify variables of interest in characterizing community members. For the sake of this tutorial, we focus our review on online cancer communities. Target audience: The primary target audience is informaticists interested in understanding ways to characterize OHCs, their members, and the impact of participation, and in creating tools to facilitate outcome research of OHCs. OHC designers and moderators are also among the target audience for this tutorial. Scope: The tutorial provides an informatics point of view of online cancer communities, with social support as their leading element. We conceptualize OHCs according to 3 major variables: type of support, source of support, and setting in which the support is exchanged. We summarize current research and synthesize the findings for 2 primary research questions on online cancer communities: (1) the impact of using online social support on an individual's health, and (2) the characteristics of the community, its members, and their interactions. We discuss ways in which future research in informatics in social support and OHCs can ultimately benefit patients.
Life experiences of instability and sexual risk behaviors among high-risk adolescent females.

CONTEXT Understanding the interplay of multiple contexts of adolescents' sexual risk behaviors is essential to helping them avoid pregnancy and STDs. Although a body of research has identified multiple individual- and family-level variables associated with adolescents' sexual risk behaviors, relatively few studies have examined relationships between these behaviors and latent indicators of unstable, chaotic environments. METHODS In 2007-2008, a sample of 241 sexually active adolescent females who were at high risk for pregnancy and STDs were recruited through two school-based clinics and two community clinics in Minneapolis and St. Paul. Confirmatory factor analysis was used with baseline data to specify latent constructs of individual risk and family disengagement. Structural equation models examined longitudinal relationships between baseline measures of these constructs and sexual risk behaviors assessed six months later. RESULTS The latent construct of individual risk encompassed substance use, violence perpetration, violence victimization and having witnessed violence; that of family disengagement included family disconnection, poor family communication and perceived lack of safety at home. Baseline level of individual risk was positively associated with number of male sex partners six months later (path coefficient, 0.2); it was not associated with consistent condom use at follow-up. Level of family disengagement was negatively associated with condom use consistency six months later (-0.3), but was not associated with number of male sex partners. CONCLUSIONS To meet the health needs of vulnerable adolescents, health systems should incorporate coordinated and interdisciplinary services that acknowledge adolescents' relevant familial and social contexts.
Influence of Maturation Degree of Arbutus (Arbutus unedo L.) Fruits in Spirit Composition and Quality

The strawberry tree (Arbutus unedo L.) is a small tree or shrub from botanical Ericaceae family that grows spontaneously nearby the Mediterranean basin and produce edible red fruits. A traditional processed fruit application, in Mediterranean countries, is the production of a spirit (known as aguardente de medronho, in Portugal) obtained from the fermented fruit. The main objective of our study was to contribute to the knowledge about the influence of the degree of maturation of fruits in the volatile composition and quality of arbutus spirit. The major volatiles in the three distillates fractions (head, heart and tail) obtained from fermentation of two different fruit maturation levels were quantified by GC-FID analysis and ANOVA one-way was performed. Additionally, the total antioxidant capacity and total phenolic compounds of both arbutus fruit spirits were determined, by ABTS and Folin-Ciocalteau method, respectively. The methanol concentration is higher (1022.39 g/hL a.a.) in the spirit made from fruits with highest total soluble solids, which is a value above the legal limit (1000 g/hL a.a.). Overall, our study emphasizes, for the first time, the influence of maturation degree of arbutus fruits in the spirit volatile composition and quality. Keywords—Arbutus fruit, maturation, quality, spirit.
Zone Pricing in Retail Oligopoly

We quantify the welfare effects of zone pricing, or setting common prices across distinct markets, in retail oligopoly. Although monopolists can only increase profits by price discriminating, this need not be true when firms face competition. With novel data covering the retail home-improvement industry, we find that Home Depot would benefit from finer pricing but that Lowe’s would prefer coarser pricing. Zone pricing softens competition in markets where firms compete, but it shields consumers from higher prices in rural markets, where firms might otherwise exercise market power. Overall, zone pricing produces higher consumer surplus than finer price discrimination does. (JEL D43, L13, L81, M31, R32)
New thrombolytic strategy providing neuroprotection in experimental ischemic stroke: MMP10 alone or in combination with tissue-type plasminogen activator

Aims Early reperfusion with tissue-type plasminogen activator (tPA) is an effective therapeutic strategy to treat acute ischemic stroke, but only 1/3 of tPA-treated patients recover and are free from disability. tPA has also shown neurotoxicity in experimental models of cerebral ischemia. Considering that MMP-10 improves stroke injury, we have examined the therapeutic and protective effect of MMP10 and tPA/MMP10 as clot-dissolving and neuroprotective agent in an experimental model of ischemic stroke and studied in vitro the molecular pathways involved in MMP10-mediated effects. Methods and results Cerebral ischemia was induced by the local injection of thrombin into the middle cerebral artery followed by reperfusion with MMP10 (6.5 µg/kg) and tPA (10 mg/kg) alone or in combination with MMP10. Cell cultures were also performed to determine the effect of MMP10 and tPA/MMP10 on brain endothelial cells and neurons. tPA/MMP10 significantly reduced the infarct size in the ischemic stroke model compared with tPA alone (P < 0.05). In vitro, MMP10 reduced the tPA-promoted endothelial ionic permeability, preserved the expression of claudin-5 and decreased ERK1/2 activation. Moreover, combination of tPA/MMP10 prevented tPA-mediated neuronal excitotoxicity and calcium influx. These effects were reversed by blocking MMP10 activity with a monoclonal antibody. Conclusion These results show that MMP10, either alone or in combination with tPA, might represent a new strategy for thrombolysis in ischemic stroke, providing higher protection against cerebrovascular damage.
Involvement of Residents Does Not Increase Postoperative Complications After Open Reduction Internal Fixation of Ankle Fractures: An Analysis of 3251 Cases

ABSTRACT Ankle fractures are common injuries frequently treated by foot and ankle surgeons. Therefore, it has become a core competency for orthopedic residency training. Surgical educators must balance the task of training residents with optimizing patient outcomes and minimizing morbidity and mortality. The present study aimed to determine the effect of resident involvement on the 30‐day postoperative complication rates after open reduction and internal fixation of ankle fractures. A second objective of the present study was to determine the independent risk factors for complications after this procedure. We identified patients in the American College of Surgeons National Surgical Quality Improvement Program database who had undergone open reduction internal fixation for ankle fractures from 2005 to 2012. Propensity score matching was used to help account for a potential selection bias. We performed univariate and multivariate analyses to identify the independent risk factors associated with short‐term postoperative complications. A total of 3251 open reduction internal fixation procedures for ankle fractures were identified, of which 959 (29.4%) had resident involvement. Univariate (2.82% versus 4.54%; p = .024) and multivariate (odds ratio 0.71; p = .75) analyses demonstrated that resident involvement did not increase short‐term complication rates. The independent risk factors for complications after open reduction internal fixation of ankle fractures included insulin‐dependent diabetes, increasing age, higher American Society of Anesthesiologists score, and longer operative times.
Development and Usability Testing of a Computer-Tailored Decision Support Tool for Lung Cancer Screening: Study Protocol

Background Awareness of lung cancer screening remains low in the screening-eligible population, and when patients visit their clinician never having heard of lung cancer screening, engaging in shared decision making to arrive at an informed decision can be a challenge. Therefore, methods to effectively support both patients and clinicians to engage in these important discussions are essential. To facilitate shared decision making about lung cancer screening, effective methods to prepare patients to have these important discussions with their clinician are needed. Objective Our objective is to develop a computer-tailored decision support tool that meets the certification criteria of the International Patient Decision Aid Standards instrument version 4.0 that will support shared decision making in lung cancer screening decisions. Methods Using a 3-phase process, we will develop and test a prototype of a computer-tailored decision support tool in a sample of lung cancer screening-eligible individuals. In phase I, we assembled a community advisory board comprising 10 screening-eligible individuals to develop the prototype. In phase II, we recruited a sample of 13 screening-eligible individuals to test the prototype for usability, acceptability, and satisfaction. In phase III, we are conducting a pilot randomized controlled trial (RCT) with 60 screening-eligible participants who have never been screened for lung cancer. Outcomes tested include lung cancer and screening knowledge, lung cancer screening health beliefs (perceived risk, perceived benefits, perceived barriers, and self-efficacy), perception of being prepared to engage in a patient-clinician discussion about lung cancer screening, occurrence of a patient-clinician discussion about lung cancer screening, and stage of adoption for lung cancer screening. Results Phases I and II are complete. Phase III is underway. As of July 15, 2017, 60 participants have been enrolled into the study, and have completed the baseline survey, intervention, and first follow-up survey. We expect to have results by December 31, 2017 and to have data analysis completed by March 1, 2018. Conclusions Results from usability testing indicate that the computer-tailored decision support tool is easy to use, is helpful, and provides a satisfactory experience for the user. At the conclusion of phase III (pilot RCT), we will have preliminary effect sizes to inform a future fully powered RCT on changes in (1) knowledge about lung cancer and screening, (2) perceived risk of lung cancer, (3) perceived benefits of lung cancer screening, (4) perceived barriers to lung cancer screening, (5) self-efficacy for lung cancer screening, and (6) perceptions of being adequately prepared to engage in a discussion with their clinician about lung cancer screening.