LLukas22/scidocs huggingface dataset:
ALOHOMORA: a tool for linkage analysis using 10K SNP array data

SUMMARY
ALOHOMORA is a software tool designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Array. Genotype data are converted into appropriate formats for a number of common linkage programs and subjected to standard quality control routines before linkage runs are started. ALOHOMORA is written in Perl and may be used to perform state-of-the-art linkage scans in small and large families with any genetic model. Options for using different genetic maps or ethnicity-specific allele frequencies are implemented. Graphic outputs of whole-genome multipoint LOD score values are provided for the entire dataset as well as for individual families.


AVAILABILITY
ALOHOMORA is available free of charge for non-commercial research institutions. For more details, see http://gmc.mdc-berlin.de/alohomora/
Wegener granulomatosis: CT and MR findings.

PURPOSE
To demonstrate the spectrum of CT and MR imaging findings in patients with Wegener granulomatosis and to determine how often these findings could be attributed to either direct extension from paranasal or orbital disease sites, remote granulomas, or central nervous system (CNS) vasculitis.


METHODS
We retrospectively reviewed the CT or MR studies of 15 patients with Wegener granulomatosis.


RESULTS
Abnormal findings were seen in 7 patients (5 examined with MR imaging, 2 with CT). Findings included dural thickening and contrast enhancement (3 patients), infarcts (2 patients), regions of hyperintense signal on T2-weighted MR images (2 patients), and abnormal MR signal in the brain stem (2 patients). Three patients with imaging findings of dural enhancement and thickening were thought to have remote granulomatous lesions involving the dura. No patients had extension from sites external to the CNS or clinical findings suggestive of CNS vasculitis.


CONCLUSION
The spectrum of CT and MR findings in Wegener granulomatosis includes dural thickening and enhancements cerebral infarction, and MR signal abnormalities in the brain stem and white matter. Presumed remote granulomatous lesions were the most common causes of CNS findings in this study. Complications related to non-CNS disease (eg, hypertension, endocarditis) also appear to have played a role in some patients.
Cardiorespiratory response to exercise after renal sympathetic denervation in patients with resistant hypertension.

OBJECTIVES
This study sought to investigate the effects of interventional renal sympathetic denervation (RD) on cardiorespiratory response to exercise.


BACKGROUND
RD reduces blood pressure at rest in patients with resistant hypertension.


METHODS
We enrolled 46 patients with therapy-resistant hypertension as extended investigation of the Symplicity HTN-2 (Renal Denervation With Uncontrolled Hypertension) trial. Thirty-seven patients underwent bilateral RD and 9 patients were assigned to the control group. Cardiopulmonary exercise tests were performed at baseline and 3-month follow-up.


RESULTS
In the RD group, compared with baseline examination, blood pressure at rest and at maximum exercise after 3 months was significantly reduced by 31 ± 13/9 ± 13 mm Hg (p < 0.0001) and by 21 ± 20/5 ± 14 mm Hg (p < 0.0001), respectively. Achieved work rate increased by 5 ± 13 W (p = 0.029) whereas peak oxygen uptake remained unchanged. Blood pressure 2 min after exercise was significantly reduced by 29 ± 17/8 ± 15 mm Hg (p < 0.001 for systolic blood pressure; p = 0.002 for diastolic blood pressure). Heart rate at rest decreased after RD (4 ± 11 beats/min; p = 0.028), whereas maximum heart rate and heart rate increase during exercise were not different. Heart rate recovery improved significantly by 4 ± 7 beats/min after renal denervation (p = 0.009). In the control group, there were no significant changes in blood pressure, heart rate, maximum work rate, or ventilatory parameters after 3 months.


CONCLUSIONS
RD reduces blood pressure during exercise without compromising chronotropic competence in patients with resistant hypertension. Heart rate at rest decreased and heart rate recovery improved after the procedure. (Renal Denervation With Uncontrolled Hypertension; [Symplicity HTN-2]; NCT00888433).
The e V ect of level of construal on the temporal distance of activity enactment

A series of four studies demonstrates that, across diVerent operationalizations of level of construal, diVerent types of activities, and for both the self and another person as targets, construing activities in high-level terms fosters perception of the more distal future as appropriate for their enactment. SpeciWcally, the studies show that thinking about superordinate “why” (rather than subordinate “how”) aspects of actions, about the implications of actions for one’s personality (rather than the objects that would be used in performing the action), and about abstract (rather than concrete) aspects of actions leads people to expect the actions to be performed in the more distant future. These results suggest that the association of level of construal and time perspective is bi-directional, in that time perspective aVects level of construal and, in addition, level of construal aVects time perspective. © 2006 Elsevier Inc. All rights reserved.
Using motor imagery in the rehabilitation of hemiparesis.

OBJECTIVE
To examine the effectiveness of using motor imagery training in the rehabilitation of hemiparesis.


DESIGN
A before-after trial with clinical and behavioral analyses of single cases.


SETTING
Academic-affiliated rehabilitation hospital.


PARTICIPANTS
Two survivors of embolic middle cerebral artery stroke that resulted in chronic hemiparesis.


INTERVENTION
A motor imagery training program consisting of imagined wrist movements (extension, pronation-supination) and mental simulations of reaching and object manipulation making use of a mirror box apparatus. Twelve 1-hour experimental sessions were delivered, 3 times a week for 4 consecutive weeks.


MAIN OUTCOME MEASURES
Two clinical assessments, grip strength, 4 wrist functionality measurements, and 3 timed performance tests. All outcome measures were recorded before training began, at 3 times during the intervention month, with 2 additional long-term measurements.


RESULTS
Performance of the paretic limb improved after the imagery intervention, indicated by increases in assessment scores and functionality and decreases in movement times. The improvements over baseline performance remained stable over a 3-month period.


CONCLUSIONS
These results demonstrate the potential for using motor imagery as a cognitive strategy for functional recovery from hemiparesis. The intervention targets the cognitive level of action processing while its effects may be realized in overt behavioral performance.
Pharmacokinetic-pharmacodynamic modeling of levodopa in patients with advanced Parkinson disease.

OBJECTIVES
The aims of the present study were to investigate the pharmacokinetic and pharmacodynamic (pk/pd) relationship of levodopa (l-dopa) in patients with advanced Parkinson disease (PD) and also to evaluate the effect of tolcapone on the pk/pd analysis of l-dopa in 1 patient with severe dyskinesias and fluctuations.


METHODS
The pharmacokinetics (plasma concentrations of l-dopa and 3-O-methyldopa [3-OMD]) and motor effects (global score of the Unified Parkinson's Disease Rating Scale-III) of a single dose of l-dopa (plus the peripheral decarboxylase inhibitor 1:4) were determined in 14 patients with advanced PD. Patients were classified into 2 groups according to Hoehn and Yahr scale (stages 2 and 3). In 1 patient with severe dyskinesias and fluctuations, pk/pd of l-dopa were evaluated before and after coadministration of tolcapone at 100 mg 2 times daily for 1 month. The pk/pd analysis was based on an estimate of the maximal response model with a semiparametric approach to effect site equilibrium.


RESULTS
The highest levels of l-dopa and 3-OMD were observed in patients with stage 3 of Hoehn and Yahr scale. We showed differences in the pk/pd parameters after coadministration of tolcapone in 1 patient as well as the clinical improvement.Univariate analysis showed some significant correlations (P < 0.05) between l-dopa pk/pd parameters and patients' age, duration of l-dopa treatment, and duration of the disease. Multivariate analysis adjusted for patients' age, sex, duration of the disease, and Hoehn and Yahr stage showed that presence of diphasic (dyskinesia-improvement-dyskinesia [DID]) dyskinesias was the only independent predictor of larger threshold level - EC50 (mean concentration at half maximal effect) of l-dopa (P = 0.034).


CONCLUSIONS
The motor complications during long treatment therapy in patients with advanced PD especially with stage 3 Hoehn and Yahr scale were correlated to the higher plasma concentrations of l-dopa. In the presented study, patients with motor complications, especially with DID dyskinesias, exhibited a larger threshold level (EC50). The clinical improvement of a patient who received l-dopa and tolcapone can be explained by tolcapone-induced changes of peripheral and central l-dopa pharmacokinetics, which led to a decrease of l-dopa EC50 and 3-OMD concentrations. Our data indicate that pk/pd analysis may be helpful for monitoring the efficiency of therapeutic strategy applied in PD patients.
A Supervised Learning Approach for Imbalanced Text Classification of Biomedical Literature Triage

A Supervised Learning Approach for Imbalanced Text Classification of Biomedical Literature Triage
Personal FM systems for children with autism spectrum disorders (ASD) and/or attention-deficit hyperactivity disorder (ADHD): an initial investigation.

UNLABELLED
The goal of this initial investigation was to examine the potential benefit of a frequency modulation (FM) system for 11 children diagnosed with autism spectrum disorders (ASD), attention-deficit hyperactivity disorder (ADHD), or both disorders through measures of speech recognition performance in noise, observed classroom behavior, and teacher-rated educational risk and listening behaviors. Use of the FM system resulted in significant average improvements in speech recognition in noise for the children with ASD and ADHD as well as large effect sizes. When compared to typically functioning peers, children with ASD and ADHD had significantly poorer average speech recognition performance in noise without the FM system but comparable average performance when the FM system was used. Similarly, classroom observations yielded a significant increase in on-task behaviors and large effect sizes when the FM system was in use during two separate trial periods. Although teacher ratings on questionnaires showed no significant improvement in the average level of educational risk of participants, they did indicate significant improvement in average listening behaviors during two trial periods with the FM system. Given the significantly better speech recognition in noise, increased on-task behaviors, and improved teacher ratings of listening behaviors with the FM system, these devices may be a viable option for children who have ASD and ADHD in the classroom. However, an individual evaluation including audiological testing and a functional evaluation in the child's primary learning environment will be necessary to determine the benefit of an FM system for a particular student.


LEARNING OUTCOMES
1. The reader will be able to describe the potential benefit of FM systems for children with ASD and/or ADHD. 2. The reader will be able to identify on-task versus off-task listening behaviors in children with ASD and/or ADHD. 3. The reader will be able to explain the components of a successful pre-fit education program that may be necessary prior to fitting an FM system in children with ASD.
Emotional intelligence and its relationship to workplace performance outcomes of leadership effectiveness

Purpose – This study seeks to investigate the relationship between emotional intelligence (EI), personality, cognitive intelligence and leadership effectiveness. Design/methodology/approach – Senior executives ðn 1⁄4 41Þ completed an ability measure of EI (MSCEIT), a measure of personality (16PF5) and a measure of cognitive ability (the Wechsler abbreviated scale of intelligence (WASI)). Leadership effectiveness was assessed using an objective measure of performance and a 3608 assessment involving each leader’s subordinates and direct manager ðn 1⁄4 149Þ: Findings – Correlational and regression analyses revealed that higher EI was associated with higher leadership effectiveness, and that EI explained variance not explained by either personality or IQ. Originality/value – This paper establishes a link between EI and workplace measures of leadership
Design of a randomized controlled trial to assess the comparative effectiveness of a multifaceted intervention to improve adherence to colorectal cancer screening among patients cared for in a community health center

BACKGROUND
Colorectal cancer (CRC) is common and leads to significant morbidity and mortality. Although screening with fecal occult blood testing (FOBT) or endoscopy has been shown to decrease CRC mortality, screening rates remain suboptimal. Screening rates are particularly low for people with low incomes and members of underrepresented minority groups. FOBT should be done annually to detect CRC early and to reduce CRC mortality, but this often does not occur. This paper describes the design of a multifaceted intervention to increase long-term adherence to FOBT among poor, predominantly Latino patients, and the design of a randomized controlled trial (RCT) to test the efficacy of this intervention compared to usual care.


METHODS
In this RCT, patients who are due for repeat FOBT are identified in the electronic health record (EHR) and randomized to receive either usual care or a multifaceted intervention. The usual care group includes multiple point-of-care interventions (e.g., standing orders, EHR reminders), performance measurement, and financial incentives to improve CRC screening rates. The intervention augments usual care through mailed CRC screening test kits, low literacy patient education materials, automated phone and text message reminders, in-person follow up calls from a CRC Screening Coordinator, and communication of results to patients along with a reminder card highlighting when the patient is next due for screening. The primary outcome is completion of FOBT within 6 months of becoming due.


DISCUSSION
The main goal of the study is to determine the comparative effectiveness of the intervention compared to usual care. Additionally, we want to assess whether or not it is possible to achieve high rates of adherence to CRC screening with annual FOBT, which is necessary for reducing CRC mortality. The intervention relies on technology that is increasingly widespread and declining in cost, including EHR systems, automated phone and text messaging, and FOBTs for CRC screening. We took this approach to ensure generalizability and allow us to rapidly disseminate the intervention through networks of community health centers (CHCs) if the RCT shows the intervention to be superior to usual care.


TRIAL REGISTRATION
ClinicalTrials.gov NCT01453894.
Heavy Metal Levels in Vegetables with Growth Stage and Plant Species Variations

Field experiment was conducted to compare and investigate the concentration levels of heavy metals in leafy vegetables with growth stage and plant species variations on an experimental field near the net house of Soil Science Division, Bangladesh Agricultural Research Institute, Joydebpur, Gazipur, Bangladesh during November 2008 to January 2009. Seeds of spinach (Spinacia oleracea), red amaranth (Amaranthus tricolor) and amaranth (Amaranthus oleraseus) were sown on 14 November 2008. Plant and soil samples were collected at different growth stages, such as at 20, 30, 40, and 50 days after sowing (DAS). The concentrations of lead (Pb), cadmium (Cd), nickel (Ni), cobalt (Co), and chromium (Cr) in plant increased with the age of the plant, but the increase was not linear. The rate of increase of concentration of these metals at 20 to 30 DAS was found lower than that at 30 to 40 DAS, except Cr. Heavy metal content gradually increased at the early growing stage and fall during later stages of growth. The significant differences (P < 0.01) were observed between the mean metal concentrations in the three vegetables species. The Pb and Co concentrations in amaranth were found higher compared to those found in spinach and red amaranth. Spinach exhibited higher levels of Cd and Cr than those of other vegetables. However, the three vegetables did not differ significantly in its Ni concentration. The order of heavy metal level in different vegetables was Cd<Co<Pb<Ni<Cr. In vegetable species in respect of heavy metal concentration Cd, Ni, and Cr was highest in spinach and amaranth showed highest concentration in Pb and Co. The highest correlation between soil-plant was found for Cd, while the lowest for Ni. Metal concentrations in the vegetables studied were found lower than the maximum allowable level in India but the concentrations of Cd and Cr were higher than the allowable levels set by the World Health Organization (WHO).
Human rights and the new world order : universality, acceptability and human diversity

This book is divided into two parts, with the first dealing with the examination of the evolution of the concept - human rights, while focusing on the period since the 1948 declaration. In this part, there is an examination of the strands of debates that have characterized the evolutionary nature of the concept, given the socio-political and economic changes since the second world war.
Anti-NMDA-Receptor Encephalitis: Case Report and Literature Review of an Under-Recognized Condition

Anti-N-methyl-D-aspartate receptor (anti-NMDA-R) encephalitis is an immune-mediated syndrome that remains under-recognized despite a growing body of literature. This syndrome has been predominantly described in young females with a constellation of symptoms, including personality changes, autonomic dysfunction and neurologic decompensation. It is commonly associated with mature ovarian teratomas. We describe the classic presentation of anti-NMDA-R encephalitis in three dramatically different patients: Case A, a young woman with ovarian teratoma; Case B, the eldest case reported to date; and Case C, a young male with no identifiable tumor. We review the literature summarizing the differential diagnosis, investigative approach, treatment options and challenges inherent to this disorder. We advocate good supportive care, involvement of multiple health disciplines and use of immune-modulating therapies in patient management. These cases underscore the need for increased awareness and high diagnostic suspicion when approaching the patient with suspected viral encephalitis.
Wavelets for computer graphics: a primer.1

Wavelets are a mathematical tool for hierarchically decomposing functions. They allow a function to be described in terms of a coarse overall shape, plus details that range from broad to narrow. Regardless of whether the function of interest is an image, a curve, or a surface, wavelets offer an elegant technique for representing the levels of detail present. The article is intended to provide people working in computer graphics with some intuition for what wavelets are, as well as to present the mathematical foundations necessary for studying and using them. We discuss the simple case of Haar wavelets in one and two dimensions, and show how they can be used for image compression.<<ETX>>
An empirical Bayes approach to inferring large-scale gene association networks

MOTIVATION
Genetic networks are often described statistically using graphical models (e.g. Bayesian networks). However, inferring the network structure offers a serious challenge in microarray analysis where the sample size is small compared to the number of considered genes. This renders many standard algorithms for graphical models inapplicable, and inferring genetic networks an 'ill-posed' inverse problem.


METHODS
We introduce a novel framework for small-sample inference of graphical models from gene expression data. Specifically, we focus on the so-called graphical Gaussian models (GGMs) that are now frequently used to describe gene association networks and to detect conditionally dependent genes. Our new approach is based on (1) improved (regularized) small-sample point estimates of partial correlation, (2) an exact test of edge inclusion with adaptive estimation of the degree of freedom and (3) a heuristic network search based on false discovery rate multiple testing. Steps (2) and (3) correspond to an empirical Bayes estimate of the network topology.


RESULTS
Using computer simulations, we investigate the sensitivity (power) and specificity (true negative rate) of the proposed framework to estimate GGMs from microarray data. This shows that it is possible to recover the true network topology with high accuracy even for small-sample datasets. Subsequently, we analyze gene expression data from a breast cancer tumor study and illustrate our approach by inferring a corresponding large-scale gene association network for 3883 genes.
The Gifted Child.

Although most commonly associated with intellectual abilities, giftedness in children may present in various ways. Child development specialists find that gifted children can manifest exceptional skills in one or more particular domains. The areas of superior ability may be academic, for example, mathematics, or may take form in other areas, such as in the arts, music, or athletics. No widespread consensus exists for a single definition of giftedness, but in addition to having advanced skills, children with giftedness also make connections easily, display curiosity or love of learning, and acquire new skills rapidly. Discerning how to measure giftedness may be even more challenging. The National Association for Gifted Children defines gifted individuals as “those who demonstrate outstanding levels of aptitude (defined as exceptional ability to reason and learn) or competence (documented performance or achievement in the top 10 percent or rarer in one or more domains).” The US Department of Education is even more vague when defining how to measure giftedness but introduces an important feature regarding sociocultural background that is worth noting. The Department of Education describes gifted children as “those with remarkably high levels of accomplishment when compared with others of their age, experience or environment.outstanding talents are present in children from all cultural groups, across all economic strata, and in all areas of human endeavor.” Identification generally occurs in the early/middle school years. Although requirements vary, schools often use standardized tests measuring academic aptitude and achievement as initial screening, sometimes defining academic giftedness as the top third percentile. However, superior IQ and achievement scores alone do not predict academic success, in part because they do not fully take into account creativity and practical intelligence, aswell as the important personality characteristics contributing to giftedness. Furthermore, such methods fail to identify children who may be exceptional in only one domain. Sociocultural differences contribute significantly as well in performance on standardized testing, and some cultures may value giftedness in certain domains over others. Poverty or discrimination may limit opportunities, and thus identification of some students may be based on potential or aptitude rather than on achievement. The diversity of skills is vast among thosewith high ability, and using a “one size fits all” approach to label giftedness is not appropriate. AUTHOR DISCLOSURE Drs Intagliata and Scharf have disclosed no financial relationships relevant to this article. This commentary does not contain a discussion of an unapproved/investigative use of a commercial product/device.