Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of Hierarchical Bayesian Models for Overdispersed Count Data using DIC and Bayes' Factors

Summary When replicate count data are overdispersed, it is common practice to incorporate this extra‐Poisson variability by including latent parameters at the observation level. For example, the negative binomial and Poisson‐lognormal (PLN) models are obtained by using gamma and lognormal latent parameters, respectively. Several recent publications have employed the deviance information criterion (DIC) to choose between these two models, with the deviance defined using the Poisson likelihood that is obtained from conditioning on these latent parameters. The results herein show that this use of DIC is inappropriate. Instead, DIC was seen to perform well if calculated using likelihood that was marginalized at the group level by integrating out the observation‐level latent parameters. This group‐level marginalization is explicit in the case of the negative binomial, but requires numerical integration for the PLN model. Similarly, DIC performed well to judge whether zero inflation was required when calculated using the group‐marginalized form of the zero‐inflated likelihood. In the context of comparing multilevel hierarchical models, the top‐level DIC was obtained using likelihood that was further marginalized by additional integration over the group‐level latent parameters, and the marginal densities of the models were calculated for the purpose of providing Bayes' factors. The computational viability and interpretability of these different measures is considered.
Graft‐versus‐host disease and survival after ABO‐incompatible allogeneic bone marrow transplantation: a single‐centre experience

The effect of ABO‐incompatibility on graft versus host disease (GVHD) and survival was evaluated in 173 consecutive patients receiving allogeneic bone marrow transplantation (BMT). Thirty‐four percent of the patients developed GVHD and univariate analysis suggested a higher incidence of GVHD in minor ABO‐incompatibility than in ABO‐identity (14/30, 47% versus 37/112, 33%; P = 0·02). However, using logistic regression adjusted for potential confounders, the GVHD risk did not differ significantly. During a mean follow‐up time of 59 months, the mortality was 37% and survival was significantly dependent on ABO‐compatibility (P = 0·004). In particular, patients with bidirectional ABO‐incompatibility had an excess mortality rate (RR, 7·6; 95% CI, 2·5–23·2; P = 0·0004). Taken together, these results suggest that ABO‐incompatibility may represent a risk factor in allogeneic BMT.
Evaluation of a New Rapid Quantitative D-dimer Assay in Patients with Clinically Suspected Deep Vein Thrombosis

Summary The sensitivity and specificity for deep vein thrombosis (DVT) of a new rapid, quantitative and precise (total imprecision < 10%) D-dimer assay suitable for individual measurements (VIDAS D-DIMER, bio-Merieux, France) were evaluated in a consecutive series of 103 in- and out-patients submitted to serial compression ultrasonography (C-US) for the clinical suspicion of DVT (n = 66) or of DVT recurrence (n = 37) and symptoms lasting from 1 to 15 days. DVT was found in 22 patients at baseline testing and no patient with an initially negative C-US developed vein incompressibility at follow up. The time elapsed from the onset of symptoms was negatively associated with D-dimer levels both in patients with and in those without DVT. In the entire series of patients, the sensitivity of a positive D-dimer test (≥1.0 Μg/ml) for the presence of DVT was 96% (21/22 patients, 95% confidence interval 75-100%) with a specificity of 75% (64-84%), a negative predictive value of 98% (90-100%), a positive predictive value of 51% (35-67%), and an overall accuracy of 80% (70-87%). A normal D-dimer value (0.22 Μg/ml) was observed in one patient with DVT and symptoms lasting from 15 days. The approach of withholding C-US testing in patients with symptoms lasting from less than 11 days and D-dimer levels below the cut-off value was compared to serial C-US testing alone in a cost-effectiveness analysis subdividing the 66 patients with a first episode according to their clinical pretest probability of DVT. Thrombosis was detected in 6.7% of the patients in the low probability group (n = 15), 16.7% of the patients in the moderate probability group (n = 24), 51.9% of the patients in the high probability group (n = 27) and 8.1% of patients with suspected DVT recurrence. Calculated cost-savings for each DVT diagnosed ranged from 5% in the high pretest probability group to 55% in the low pretest probability group and to 77% in patients with suspected DVT recurrence. The safety of avoiding C-US testing in symptomatic patients with a negative D-dimer test should be evaluated in clinical management studies.
Common mechanisms underlying refractive error identified in functional analysis of gene lists from genome-wide association study results in 2 European British cohorts.

IMPORTANCE To date, relatively few genes responsible for a fraction of heritability have been identified by means of large genetic association studies of refractive error. OBJECTIVE To explore the genetic mechanisms that lead to refractive error in the general population. DESIGN, SETTING, AND PARTICIPANTS Genome-wide association studies were carried out in 2 British population-based independent cohorts (N = 5928 participants) to identify genes moderately associated with refractive error. MAIN OUTCOMES AND MEASURES Enrichment analyses were used to identify sets of genes overrepresented in both cohorts. Enriched groups of genes were compared between both participating cohorts as a further measure against random noise. RESULTS Groups of genes enriched at highly significant statistical levels were remarkably consistent in both cohorts. In particular, these results indicated that plasma membrane (P = 7.64 × 10⁻³⁰), cell-cell adhesion (P = 2.42 × 10⁻¹⁸), synaptic transmission (P = 2.70 × 10⁻¹⁴), calcium ion binding (P = 3.55 × 10⁻¹⁵), and cation channel activity (P = 2.77 × 10⁻¹⁴) were significantly overrepresented in relation to refractive error. CONCLUSIONS AND RELEVANCE These findings provide evidence that development of refractive error in the general population is related to the intensity of photosignal transduced from the retina, which may have implications for future interventions to minimize this disorder. Pathways connected to the procession of the nerve impulse are major mechanisms involved in the development of refractive error in populations of European origin.
Performance Management and the New Workplace Tyranny : A Report for the Scottish Trades Union Congress

The Scottish Trades Union Congress (STUC) Annual Conference of 2009, held in Perth, unanimously passed a resolution on Performance Management, proposed by the Communication Workers Union and seconded by Unite the Union (Finance Services Sector). The resolution acknowledged that Performance Management was now commonplace in public and private sector organisations, a central element in Human Resource Management (HRM) policy and practice. Rather than being adopted as a means to encourage employees to improve their performance, the resolution suggested that Performance Management was all too often being used ‘to pressurise workers into producing more, drive down wages and create quotas for underperformers and manage workers out of their jobs’. Indeed, Performance Management processes were ‘a particularly brutal method of making workers behave and react to company imposed standards’. Workers who failed to measure up to strict Performance Management templates were being readily discarded, it was contended. A key aspect of the resolution and, indeed, of the conference debate it stimulated, was the possible consequence that workers subjected to such exigencies might suffer mental health problems. Negative effects might be reflected in increased sickness absence rates. Delegates reported on cases from their own experience where mental health symptoms, particularly stress and depression, were, they believed, related to new intensive forms of ‘people management’. Given the importance of these concerns, the Conference resolved to commission a research report ‘to establish the cost and affect Performance Management processes are having on the workforce and in various sectors, including the amount of management time which is spent implementing them’. The concluding, and perhaps most important, sentence in the resolution requested that this research attempt to establish whether a link could be established between Performance Management processes and the rise in workplace mental health problems.
Does pupil dilation influence subfoveal choroidal laser Doppler flowmetry?

Purpose: The aim of this study was to assess (i) whether pupil dilation with tropicamide influences subfoveal choroidal blood flow, as assessed by continuous laser Doppler flowmetry (LDF) and (ii) if this is the case, whether the effect is due to a haemodynamic response of the drug‐induced dilation.
Parkinson's Disease and Genetics

Background:Idiopathic Parkinson disease (IPD) is a condition of unknown cause. Several factors are believed to contribute to its onset, and many studies have been conducted in search of the possible etiology of Parkinson disease. Review Summary:Genetic factors have become relevant when trying to explain the onset of Parkinson disease. The studies are divided into 2 categories: epidemiological and studies that analyze twins from families with members suffering from Parkinson disease, thus looking for the responsible genetic mutations. In this article we address this controversial topic, reviewing some of the most significant studies trying to provide evidence which relates genetics to Parkinson disease. Conclusion:We present current epidemiological studies and the most important genetic factors related to Parkinson disease, including the latest information currently available on each issue.
The effectiveness of stigma coping orientations: can negative consequences of mental illness labeling be avoided?

Recent research has assigned a prominent role to labeling and stigma as factors that impair the social and psychological functioning of people officially labeled mentally ill. But can the effects of labeling and stigma be overcome by adopting a few simple approaches to coping with these problems? If so, the stigma-induced problems of social awkwardness, demoralization and unemployment emphasized by recent research may not be as severe as claimed. Using a sample of psychiatric patients, we examine this issue by assessing whether patients can ameliorate labeling effects by keeping their history of treatment a secret, educating others about their situation, or avoiding situations in which rejection might occur. None of these coping orientations were effective in diminishing negative labeling effects on unemployment or on psychological distress/demoralization. In fact, the three coping strategies show consistent effects in the direction of producing more harm than good, and with respect to withdrawal-avoidance this effect is significant. Based on these results we argue that stigma is powerfully reinforced by culture and that its effects are not easily overcome by the coping actions of individuals. Using C. Wright Mills's (1967) distinction we conclude that labeling and stigma are "social problems" not "individual troubles. "
Galanin Inhibits Performance on Rodent Memory Tasks

Abstract: Central administration of galanin produces performance deficits on a variety of rodent learning and memory tasks. Galanin impairs acquisition and/or retention of the Morris water task, delayed nonmatching to position, T‐maze delayed alternation, starburst radial maze, and passive avoidance in normal rats. A primary site of action is the ventral hippocampus, with an additional modulatory site in the medial septum‐diagonal band. The behavioral actions of galanin at rat septohippo‐campal sites mediating cognitive processes are consistent with previous reports of inhibitory actions of galanin on acetylcholine release and cholinergically activated transduction at the M1 muscarinic receptor in rat hippocampus. The peptidergic galanin receptor antagonist M40 blocks the inhibitory actions of galanin on memory tasks. Treatment combinations of M40 with an M1 agonist, TZTP, improves performance on delayed nonmatching to position, in rats with 192IgG‐saporin‐induced cholinergic lesions of basal forebrain neurons. Nonpeptide, bioavailable, subtype‐selective galanin receptor antagonists may provide tools to test the hypothesis that antagonism of endogenous galanin, which is overexpressed in the basal forebrain in Alzheimer's patients, can contribute to the alleviation of the cognitive deficits associated with Alzheimer's disease.
The Determination of Sensory Deficits in Children With Hemiplegic Cerebral Palsy

Therapeutic intervention for children with cerebral palsy begins with accurate appraisal of abilities and disabilities. Currently, treatment focuses on the identified motor deficits, with any underlying sensory deficits often being overlooked. Sensory input is an essential component of motor function and motor control. Therefore, the objective of this study was to determine the presence and extent of sensory deficits in school-aged hemiplegic children using a formal clinical sensory battery, as well as somatosensory evoked potentials. A cross-sectional comparative study was performed comparing sensory function in hemiplegic children and healthy controls. Nine hemiplegic children and 41 healthy controls between 4 and 19 years of age were assessed. Hemiplegic children were included if they had a minimum level of receptive language function of 30 to 33 months and expressive language ability of 24 to 27 months, and no severe limitation of joint range of the hand. Significant bilateral sensory deficits (88.8%) were ascertained in hemiplegic children (P < .05), when compared to the performance of the healthy controls. Stereognosis and proprioception were the chief modalities affected bilaterally. The extent of sensory loss did not mirror the severity of motor deficit. Conversely, findings on somatosensory evoked potentials were closely related to motor function. Thus, a clinical sensory evaluation should be an integral part of the assessment of children with cerebral palsy. The likelihood of sensory impairment in one or more modalities on the hemiplegic or nonhemiplegic side is underappreciated and needs to be identified by rehabilitation specialists to maximize the functional potential of these children. (J Child Neurol 1995; 10:300-309).
Parametric Identification of Parallel Hammerstein Systems

This paper proposes a parametric identification method for parallel Hammerstein systems. The linear dynamic parts of the system are modeled by a parametric rational function in the z - or s-domain, while the static nonlinearities are represented by a linear combination of nonlinear basis functions. The identification method uses a three-step procedure to obtain initial estimates. In the first step, the frequency response function of the best linear approximation is estimated for different input excitation levels. In the second step, the power-dependent dynamics are decomposed over a number of parallel orthogonal branches. In the last step, the static nonlinearities are estimated using a linear least squares estimation. Furthermore, an iterative identification scheme is introduced to refine the estimates. This iterative scheme alternately estimates updated parameters for the linear dynamic systems and for the static nonlinearities. The method is illustrated on a simulation and a validation measurement example.
Immunogenicity and protection studies with recombinant mycobacteria and vaccinia vectors coexpressing the 18-kilodalton protein of Mycobacterium leprae

The activation of antigen-specific T lymphocytes is essential for the control of leprosy infection in humans and experimental animals. T cells recognize a variety of protein antigens from Mycobacterium leprae, including the 18-kDa protein, which is limited in distribution among mycobacteria and which is absent from Mycobacterium tuberculosis and the vaccine strain, Mycobacterium bovis BCG. Adjuvant preparations of mycobacterial protein antigens have had limited protective efficacy for experimental infections in animals. Since recombinant vectors may elicit more effective T-cell responses than adjuvant preparations, recombinant vaccinia virus (VV18) and M. bovis BCG (BCG18) vectors expressing the 18-kDa protein of M. leprae were prepared. Both VV18 and BCG18 stimulated anti-18-kDa protein antibody and lymphocyte proliferative responses. Sequential immunization with VV18 followed by BCG18 induced higher levels of specific immunoglobulin G2a antibodies than immunoglobulin G1 antibodies, in contrast to immunization with VV18 or BCG18 alone. The protective efficacy of immunization with VV18 from a challenge with BCG18 was examined in two murine models of mycobacterial infection. After intravenous challenge, mice immunized with recombinant vaccinia virus exhibited lower initial levels of replication and earlier clearance of BCG18 from their spleens than mice immunized with vaccinia virus expressing an unrelated protein. After footpad infection in a dissemination model, there was earlier clearance of BCG18 from specifically immunized mice. However, immunization of mice with VV18 did not prevent a productive mycobacterial infection.
Low cost robots used for practical assignments in programming modules

This paper describes how small, low-cost robots can be used in practical assignments in different programming modules, both for high- and low level programming, and both at undergraduate as well as graduate level. The constructed robots described here are designed to have a diverse use in different type of exercises. The design utilises both an ARM processor used for running a Java virtual machine and an FPGA development board giving the student the ability to develop both high level code and hardware. An additional challenge in engineering education is the distinct change in student population and attitude over the last few years and it is becoming an increasing challenge to keep the students motivated and voluntarily complete the assignments and get them engaged with the lab work. With the presented robot system we facilitate the use of designing increasing difficult tasks to keep individual students challenged trough the whole assignment. The robots has been tested on student groups with good results both in its ability to function as a laboratory tool and in its ability to engage the students.
Design and dynamic study of a 6 kW external rotor permanent magnet Brushless DC motor for electric drivetrains

This paper studies electromagnetic and parametric design and performance analysis of an in-wheel out-runner BLDC (Brushless Direct Current) electric motor designed specifically for automotive applications. Typical design techniques and simulation studies are applied to the BLDC motor. Specifically, design specifications such as the number of turns, winding area, and stator pole height composing the stator structure are obtained and the performance characteristics of the motor are investigated using the finite element method (FEM). Also, the outputs in terms of phase inductances, flux linkages of each stator winding and static torques for different rotor positions are calculated and evaluated. Finally, a dynamical performance analysis is carried out by using a physical electromechanical model the BLDC motor.
Transformation of an α‐helix peptide into a β‐hairpin induced by addition of a fragment results in creation of a coexisting state

Intrinsic rules of determining the tertiary structure of a protein have been unknown partly because physicochemical factors that contribute to stabilization of a protein structure cannot be represented as a linear combination of local interactions. To clarify the rules on the nonlinear term caused by nonlocal interaction in a protein, we tried to transform a peptide that has a fully helical structure (Target Peptide or TP) into a peptide that has a β‐hairpin structure (Designed Peptide or DP) by adding seven residues to the C terminus of TP. According to analyses of nuclear magnetic resonance measurements, while the β‐hairpin structure is stabilized in some DPs, it is evident that the helical structure observed in TP is also persistent and even extended throughout the length of the molecule. As a result, we have produced a peptide molecule that contains both the α‐helix and β‐hairpin conformation at an almost equally populated level. The helical structures contained in these DPs were more stable than the helix in TP, suggesting that stabilizing one conformation does not result in destabilizing the other conformation. These DPs can thus be regarded as an isolated peptide version of the chameleon sequence, which has the capability of changing the secondary structure depending on the context of the surrounding environment in a protein structure. The fact that the transformation of one secondary structure caused stabilization of both the original and the induced structure would shed light on the mechanism of protein folding. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Pre-cesarean Staphylococcus aureus nasal screening and decolonization: a prospective randomized controlled trial

Abstract Objective: Staphylococcus aureus (S. aureus) is a common pathogen in surgical site infections (SSIs). Mupirocin ointment is an effective treatment for nasal carriers. We aimed to investigate whether screening for nasal colonization of S. aureus and treating carriers prior to a cesarean section (CS) decreases the likelihood of SSI. Methods: This is a randomized controlled trial. All participants underwent nasal culture prior to the CS. Nasal carriers of S. aureus were treated with Mupirocin ointment according to a standardized protocol. In the control group, nasal cultures were obtained immediately prior to surgery and carriers were not treated. Results: We recruited 568 patients. Demographic characteristics were comparable between the groups. S. aureus nasal colonization rates were 20.1% and 14.9% in the intervention and control groups, respectively (p = 0.12). S. aureus eradication rate with Mupirocin treatment was 88%. SSI rates were similar in the intervention and control groups (13.1% versus 12.1%, respectively, p = 0.78) and in treated carriers, untreated carriers, and non-carriers (7.4% versus 13.0% versus 13.1%, respectively, p = 0.69). Previous CS was the only factor found to independently predict SSI (OR 2.5, CI 1.09–5.65 p = 0.029). Conclusion: Pre-cesarean screening for nasal S. aureus carriage and decolonization does not appear to be an effective intervention in reducing SSI rates.
Abortive Cycling and the Release of Polymerase for Elongation at the σ54-dependent glnAp2 Promoter (*)

Transcription initiation at the σ54-dependent glnAp2 promoter was studied to follow the state of polymerase as RNA synthesis begins. σ54 polymerase begins transcription in abortive cycling mode, i.e. after the first bond is made, approximately 75% of the time the short RNA is aborted and synthesis must be restarted. Polymerase is capable of abortive initiation until it reaches a position beyond +3 and before +7, at which stage polymerase is released from its promoter contacts and an elongation complex is formed. Initial elongation is accompanied by two transcription bubbles, one moving with the polymerase and the other remaining at the transcription start site. The σ54-associated polymerase shows an earlier and more efficient transition out of abortive initiation mode than prior studies of σ70-associated polymerase.