Miracle-dz/UniFAR-FTUs huggingface dataset:
Extended models for nosocomial infection: parameter estimation and model selection

Abstract We consider extensions to previous models for patient level nosocomial infection in several ways, provide a specification of the likelihoods for these new models, specify new update steps required for stochastic integration, and provide programs that implement these methods to obtain parameter estimates and model choice statistics. Previous susceptible-infected models are extended to allow for a latent period between initial exposure to the pathogen and the patient becoming themselves infectious, and the possibility of decolonization. We allow for multiple facilities, such as acute care hospitals or long-term care facilities and nursing homes, and for multiple units or wards within a facility. Patient transfers between units and facilities are tracked and accounted for in the models so that direct importation of a colonized individual from one facility or unit to another might be inferred. We allow for constant transmission rates, rates that depend on the number of colonized individuals in a unit or facility, or rates that depend on the proportion of colonized individuals. Statistical analysis is done in a Bayesian framework using Markov chain Monte Carlo methods to obtain a sample of parameter values from their joint posterior distribution. Cross validation, deviance information criterion and widely applicable information criterion approaches to model choice fit very naturally into this framework and we have implemented all three. We illustrate our methods by considering model selection issues and parameter estimation for data on methicilin-resistant Staphylococcus aureus surveillance tests over 1 year at a Veterans Administration hospital comprising seven wards.
Localization of a Bacterial Group II Intron-Encoded Protein in Eukaryotic Nuclear Splicing-Related Cell Compartments

Some bacterial group II introns are widely used for genetic engineering in bacteria, because they can be reprogrammed to insert into the desired DNA target sites. There is considerable interest in developing this group II intron gene targeting technology for use in eukaryotes, but nuclear genomes present several obstacles to the use of this approach. The nuclear genomes of eukaryotes do not contain group II introns, but these introns are thought to have been the progenitors of nuclear spliceosomal introns. We investigated the expression and subcellular localization of the bacterial RmInt1 group II intron-encoded protein (IEP) in Arabidopsis thaliana protoplasts. Following the expression of translational fusions of the wild-type protein and several mutant variants with EGFP, the full-length IEP was found exclusively in the nucleolus, whereas the maturase domain alone targeted EGFP to nuclear speckles. The distribution of the bacterial RmInt1 IEP in plant cell protoplasts suggests that the compartmentalization of eukaryotic cells into nucleus and cytoplasm does not prevent group II introns from invading the host genome. Furthermore, the trafficking of the IEP between the nucleolus and the speckles upon maturase inactivation is consistent with the hypothesis that the spliceosomal machinery evolved from group II introns.
Affiliative social tuning reduces the activation of prejudice

Past research on affiliative social tuning has shown that individuals who experience affiliative motivation toward another person come to exhibit implicit prejudice consistent with the apparent beliefs of that person. The present research seeks to elucidate the mechanism by which such malleability occurs. Is it interpersonally cued cognitive control, consistent with dual-process models of prejudice regulation, or a contextual change in automatic associations, consistent with shared reality theory? QUAD modeling of participants’ responses revealed that affiliative social tuning of implicit prejudice was solely a function of changing associations (Studies 1–3). Furthermore, instructions to try to inhibit prejudice within a particular interpersonal context did not yield implicit attitude change (Study 2).
Predictive Factors for Sustained Virological Response after Treatment with Pegylated Interferon α-2a and Ribavirin in Patients Infected with HCV Genotypes 2 and 3

Background Previous trials have often defined genotype 2 and 3 patients as an “easy to treat” group and guidelines recommend similar management. Aims The present study looks for differences between the two genotypes and analyzes predictive factors for SVR. Methods Prospective, community-based cohort study involving 421 physicians throughout Germany. The analysis includes 2,347 patients with untreated chronic HCV genotype 2 (n = 391) and 3 (n = 1,956) infection treated with PEG-IFN α-2a plus ribavirin between August 2007 and July 2012. Results When compared with genotype 2 patients, those with genotype 3 were younger, had a shorter duration of infection, lower values of total cholesterol, LDL cholesterol and BMI, a higher frequency of drug use as infection mode and male gender (p<0.0001, respectively), and a higher APRI score (p<0.005). SVR was higher in genotype 2 when compared with genotype 3 (64.7% vs. 56.9%, p = 0.004). By multivariate analysis of genotype 2 patients, low baseline γ -GT and RVR predicted SVR. In genotype 3 age ≤45 years, cholesterol>130 mg/dl, a low APRI score, and a γ-GT ≥3-times ULN, RVR, and RBV starting dose were associated with SVR by multivariate analysis. Conclusions The present study corroborates that liver fibrosis is more pronounced in genotype 3 vs. 2. SVR is higher in genotype 2 versus genotype 3 partly because of follow-up problems in genotype 3 patients, in particular in those infected by drug use. Thus, subgroups of genotype 3 patients have adherence problems and need special attention also because they often have significant liver fibrosis. Trial Registration Verband Forschender Arzneimittelhersteller e.V. , Berlin, Germany ML21645 ClinicalTrials.gov NCT02106156
Patient-Related Benefits for Adults with Cochlear Implantation: A Multicultural Longitudinal Observational Study

Objectives: To assess subjectively perceived, real-world benefits longitudinally for unilateral cochlear implant (CI) recipients in a multinational population treated routinely. To identify possible predictors of self-reported benefits. Design: This was a prospective, multicenter, repeated-measures study. Self-assessment of performance at preimplantation and postimplantation at 1, 2, and 3 years using standardized, validated, local language versions of the Speech, Spatial, and Qualities of Hearing Scale (SSQ), and the Health Utilities Index Mark 3 (HUI3) was performed. Outcomes were analyzed using a longitudinal mixed-effects model incorporating country effect. Patient demographics were explored for associations with change over time. Subjects: Two hundred ninety-one routinely treated, unilateral CI recipients, aged 13-81 years, from 9 clinics across 4 countries. Results: Highly significant improvements were observed for all outcome measures (p < 0.0001). Postimplantation, mean outcome scores remained stable beyond 1 year, with notable individual variability. A significant association for one or more outcomes with preimplantation contralateral hearing aid use, telephone use, age at implantation, implantation side, preimplantation comorbidities, dizziness, and tinnitus was observed (p < 0.004). Conclusions: Longitudinal benefits of CI treatment can be measured using clinically standardized self-assessment tools to provide a holistic view of patient-related benefits in routine clinical practice for aggregated data from multinational populations. Self-reported outcomes can provide medical-based evidence regarding CI treatment to support decision-making by health service providers.
Assessing ECG signal quality indices to discriminate ECGs with artefacts from pathologically different arrhythmic ECGs

False and non-actionable alarms in critical care can be reduced by developing algorithms which assess the trueness of an arrhythmia alarm from a bedside monitor. Computational approaches that automatically identify artefacts in ECG signals are an important branch of physiological signal processing which tries to address this issue. Signal quality indices (SQIs) derived considering differences between artefacts which occur in ECG signals and normal QRS morphology have the potential to discriminate pathologically different arrhythmic ECG segments as artefacts. Using ECG signals from the PhysioNet/Computing in Cardiology Challenge 2015 training set, we studied previously reported ECG SQIs in the scientific literature to differentiate ECG segments with artefacts from arrhythmic ECG segments. We found that the ability of SQIs to discriminate between ECG artefacts and arrhythmic ECG varies based on arrhythmia type since the pathology of each arrhythmic ECG waveform is different. Therefore, to reduce the risk of SQIs classifying arrhythmic events as noise it is important to validate and test SQIs with databases that include arrhythmias. Arrhythmia specific SQIs may also minimize the risk of misclassifying arrhythmic events as noise.
Differential Effects of Declining Rates in a Per Diem Payment System.

The paper demonstrates differential effects of a prospective payment system with declining per diem rates, dependent on the percentiles of length of stay. The analysis uses dynamic panel data estimates and a recent nationwide administrative database for major diagnostic categories in 1068 Japanese hospitals in 2006-2012 to show that average length of stay significantly increases for hospitals in percentiles 0-25 of the pre-reform length of stay and significantly decreases for hospitals in percentiles 51-100. The decline of the average length of stay is larger for hospitals in higher percentiles of the length of stay. Hospitals in percentiles 51-100 significantly increase their rate of nonemergency/unanticipated readmissions within 42 days after discharge. The decline in the length of total episode of treatment is smaller for hospitals in percentiles 0-25. The findings are robust in terms of the choice of a cohort of hospitals joining the reform. The paper discusses applicability of 'best practice' rate-setting to help improve the performance of hospitals in the lowest quartile of average length of stay. Copyright © 2015 John Wiley & Sons, Ltd.
Breastfeeding beyond infancy: a concept analysis.

AIM To report an analysis of the concept of breastfeeding beyond infancy. BACKGROUND The World Health Organization and Health Canada recommends breastfeeding is sustained until 2 years old and beyond. However, little is known about breastfeeding a child beyond 12 months old. Breastfeeding beyond infancy is defined as any breastfeeding over the age of 12 months with no parameters placed on who initiates the weaning process. DESIGN Rodger's framework of concept analysis was used to organize and guide data analysis. DATA SOURCES A historical, systematic search of the literature up until 2014 was conducted using the search terms: breastfeeding OR breast feeding OR breast-feeding AND sustained, extended, prolonged, long-term and duration. METHODS Literature was selected according to whether breastfeeding beyond 12 months old was described or analysed. All study designs and observational, descriptive and opinion papers were included in the initial screenings. RESULTS Four characteristics were chosen as essential attributes of breastfeeding beyond infancy: health benefits, maternal profiles, parenting style and experiences. Consequences included stigma and secrecy. Additionally, the role of the nurse in supporting breastfeeding beyond infancy was explored. CONCLUSIONS The practice of breastfeeding beyond infancy is entrenched in parenting beliefs that serve to address the child's needs by fostering an intimate and attached relationship between the mother and child. Many women conceal their breastfeeding behaviour to protect themselves from unsolicited judgement and comments. Nurses are well-served to understand, support and promote the practice of breastfeeding beyond infancy to ensure the bio-psycho-social health of their clients.
Association of Nonoxidized Parathyroid Hormone with Cardiovascular and Kidney Disease Outcomes in Chronic Kidney Disease.

BACKGROUND AND OBJECTIVES In patients with CKD, elevated plasma parathyroid hormone (PTH) levels are associated with greater cardiovascular morbidity and mortality. However, the reference method for PTH measurement is disputed. It has been argued that measurement of nonoxidized PTH better reflects biologically active PTH than measurements with conventional assays. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS PTH and nonoxidized PTH levels were measured at study baseline in 535 patients with CKD with an eGFR range between 89 and 15 ml/min per 1.73 m2. Patients were followed over 5.1 years for the occurrence of acute heart failure, atherosclerotic events, CKD progression (doubling of serum creatinine or initiation of RRT), or all-cause death. RESULTS Atherosclerotic events, acute heart failure, CKD progression, and deaths from any cause occurred in 116, 58, 73, and 85 patients, respectively. In Kaplan-Meier analyses, patients at the highest PTH and nonoxidized-PTH tertile (79-543 and 12-172 pg/ml, respectively) showed a higher rate of atherosclerotic events, acute heart failure, CKD progression, and death from any cause. After adjustment for eGFR and albuminuria, nonoxidized PTH was no longer associated with atherosclerotic events (hazard ratio third versus first tertile, 1.04 [95% confidence intervals, 0.62-1.75]), acute heart failure (hazard ratio third versus first tertile, 1.24 [95% confidence intervals, 0.59-2.62]), CKD progression (hazard ratio third versus first tertile, 0.93 [95% confidence intervals, 0.46-1.90]), and death from any cause (hazard ratio third versus first tertile, 1.23 [95% confidence intervals, 0.66-2.31]), and PTH lost its association with atherosclerotic events (hazard ratio third versus first tertile, 0.80 [95% confidence intervals, 0.46-1.38]) and CKD progression (hazard ratio third versus first tertile, 0.99 [95% confidence intervals, 0.46-2.10]), although it remained associated with acute heart failure (hazard ratio third versus first tertile, 2.76 [95% confidence intervals, 1.11-6.89]) and all-cause death (hazard ratio third versus first tertile, 2.35 [95% confidence intervals, 1.13-4.89]). After further adjustment for cardiovascular and kidney risk factors, PTH remained associated with all-cause death (hazard ratio third versus first tertile, 2.79 [95% confidence intervals, 1.32-5.89]), but with no other end point. CONCLUSIONS In a cohort of patients with CKD, PTH was associated with all-cause mortality; there was no association of nonoxidized PTH with any of the clinical outcomes examined.
A Comparison of Markov–Functional and Market Models

The LIBOR Markov–functional model is an efficient arbitrage–free pricing model suitable for callable interest rate derivatives. We demonstrate that the one–dimensional LIBOR Markov–functional model and the separable one–factor LIBOR market model are very similar. Consequently, the intuition behind the familiar SDE formulation of the LIBOR market model may be applied to the LIBOR Markov–functional model. The application of a drift approximation to a separable one–factor LIBOR market model results in an approximating model driven by a one–dimensional Markov process, permitting efficient implementation. For a given parameterization of the driving process, the distributional structures of this model and the corresponding Markov–functional model are found to be numerically virtually indistinguishable for short–maturity tenor structures over a wide variety of market conditions, and both are very similar to the market model. A theoretical uniqueness result shows that any accurate approximation to a separable market model that reduces to a function of the driving process is effectively an approximation to the analogous Markov–functional model. Therefore, the conclusions reached in this article are not restricted to the particular choice of driving process. Minor differences are observed for longer maturities; nevertheless the models remain qualitatively similar. These differences do not have a large impact on Bermudan swaption prices. Under stress testing, the LIBOR Markov–functional and separable LIBOR market models continue to exhibit similar behavior, and Bermudan prices under these models remain comparable. However, the drift approximation model now appears to admit arbitrage that is practically significant. In this situation, the authors argue the Markov–functional model is a more appropriate choice for pricing.
Aggressive Deep Driving: Combining Convolutional Neural Networks and Model Predictive Control

We present a framework for vision-based model predictive control (MPC) for the task of aggressive, high-speed autonomous driving. Our approach uses deep convolutional neural networks to predict cost functions from input video which are directly suitable for online trajectory optimization with MPC. We demonstrate the method in a high speed autonomous driving scenario, where we use a single monocular camera and a deep convolutional neural network to predict a cost map of the track in front of the vehicle. Results are demonstrated on a 1:5 scale autonomous vehicle given the task of high speed, aggressive driving.
An MRI Study on Volumetric Changes in the Brain of Female Adolescents with Autism

Bu calisma bazi goruntu isleme tekniklerini bir arada kullanan bir yaklasimla bilinen beyin hastaliklarindan biri olan Otizm hastaligini beyin hacmindeki bolgesel farkliliklardan tespit etmeyi hedeflemektedir. Goruntuler, 17 yasinda 5 otistik kadin ergen hastadan ve 10 kisiden olusan kadin saglikli kontrol grubundan (17 ± 1 yasinda) olusmaktadir. Bu goruntuler 1,5 mm3 cift eko, hizli spin eko kesitlerden olusup Manyetik Rezonans Goruntu tarayicilarindan elde edilmistir. Kesitler gri cevher ve beyaz cevher olarak ayrilmistir. Global esikleme, adaptif esikleme gibi bazi goruntu isleme teknikleri ve k-means algoritmasi beyin dokusuna ait volumetrik veriyi hesaplamak icin birlikte kullanilmistir. Bagimsiz iki grup olan otistik ve kontrol grubu arasindaki farki karsilastirmak icin istatistiksel t-testi metodu ile analizi yapilmistir. Onceden yapilmis olan yapisal norolojik goruntuleme calismalari gozden gecirilmis; bu calismalar gri cevher, beyaz cevher ve tum beyin volumlerini ortaya cikarmada kullanilmistir. Literatur, otistik insanlar arasinda her bir yas grubu icin farkli sonuclar oldugunu gostermektedir. Sonuclar kontrol grubu ve otistik kadin ergenler arasinda tum beyin hacminde onemli bir buyukluk farkinin var olmadigini, fakat 17 yasinda kadin ergenlerde daha buyuk beyaz cevher hacminin saptandigini gostermektedir
Laughing in the Face of Fear (of Disease Detection): Using Humor to Promote Cancer Self-Examination Behavior

ABSTRACT This research examines the possible benefit of using humor to reduce anxiety associated with performing cancer self-examination behaviors. In Study 1, 187 undergraduates read a humorous public service announcement (PSA) script promoting either breast or testicular self-exams. Results suggest that perception of humor reduced anxiety about self-exams, which, in turn, related to more positive self-exam attitudes. Simultaneously, humor perception associated with greater message processing motivation, which, in turn, associated with more supportive self-exam attitudes. Self-exam attitudes also positively associated with self-exam intentions. These results were largely replicated in Study 2. Further, self-exam intentions predicted self-exam behavior 1 week later. However, consistent with past research, the humorous and serious messages did not generate differences in subsequent self-exam behavior, though the intention–behavior relationship was stronger and significant for those exposed to the humorous versus the serious messages. In light of these findings, and given that humor has the advantage of attracting and holding attention in real message environments, the use of carefully constructed humor appeals may be a viable message strategy to promote health detection behaviors.
Development of an unbiased, semi‐automated approach for classifying plasma cell immunophenotype following multicolor flow cytometry of bone marrow aspirates

Despite increased usage of multiparameter flow cytometry (MFC) to assess diagnosis, prognosis, and therapeutic efficacy (minimal residual disease, MRD) in plasma cell neoplasms (PCNs), standardization of methodology and data analysis is suboptimal. We investigated the utility of using the mean and median fluorescence intensities (FI) obtained from MFC to objectively describe parameters that distinguish plasma cell (PC) phenotypes.
Preschool Achievement Scales for Maximum Sensitivity to Learning Growth

An initial study examined multiple dimensions of preschool competency (cognitive, social, approaches to learning, and physical/motor) using both variable-oriented and person-oriented approaches, with a Head Start sample (McWayne, Fantuzzo & McDermott, 2004). Variableoriented analyses yielded three higher order classroom competency dimensions: 1) General Classroom Competence, 2) Specific Approaches to Learning, and 3) Interpersonal Classroom Behavior Problems. Hierarchical setwise regressions demonstrated that the first two of these dimensions related uniquely to an indicator of early school success (Meisels, Marsden, Wiske & Henderson, 1997). Person-oriented analyses then examined patterns of these three dimensions among children in the sample. This approach revealed seven profiles of child competence, which were then grouped into three sets: children at-risk for later learning difficulties, children demonstrating academic competence, or children who overlapped these two groups (McWayne, Fantuzzo & McDermott, 2004).
Distinct opioid circuits determine the palatability and the desirability of rewarding events

It generally is assumed that a common neural substrate mediates both the palatability and the reward value of nutritive events. However, recent evidence suggests this assumption may not be true. Whereas opioid circuitry in both the nucleus accumbens and ventral pallidum has been reported to mediate taste-reactivity responses to palatable events, the assignment of reward or inventive value to goal-directed actions has been found to involve the basolateral amygdala. Here we found that, in rats, the neural processes mediating palatability and incentive value are indeed dissociable. Naloxone infused into either the ventral pallidum or nucleus accumbens shell blocked the increase in sucrose palatability induced by an increase in food deprivation without affecting the performance of sucrose-related actions. Conversely, naloxone infused into the basolateral amygdala blocked food deprivation-induced changes in sucrose-related actions without affecting sucrose palatability. This double dissociation of opioid-mediated changes in palatability and incentive value suggests that the role of endogenous opioids in reward processing does not depend on a single neural circuit. Rather, changes in palatability and in the incentive value assigned to rewarding events seem to be mediated by distinct neural processes.