Miracle-dz/UniFAR-FTUs huggingface dataset:
Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset

MOTIVATION Identifying groups of co-regulated genes by monitoring their expression over various experimental conditions is complicated by the fact that such co-regulation is condition-specific. Ignoring the context-specific nature of co-regulation significantly reduces the ability of clustering procedures to detect co-expressed genes due to additional 'noise' introduced by non-informative measurements. RESULTS We have developed a novel Bayesian hierarchical model and corresponding computational algorithms for clustering gene expression profiles across diverse experimental conditions and studies that accounts for context-specificity of gene expression patterns. The model is based on the Bayesian infinite mixtures framework and does not require a priori specification of the number of clusters. We demonstrate that explicit modeling of context-specificity results in increased accuracy of the cluster analysis by examining the specificity and sensitivity of clusters in microarray data. We also demonstrate that probabilities of co-expression derived from the posterior distribution of clusterings are valid estimates of statistical significance of created clusters. AVAILABILITY The open-source package gimm is available at http://eh3.uc. edu/gimm.
The prevalence of DSM-IV personality disorders in psychiatric outpatients.

OBJECTIVE The largest clinical epidemiological surveys of personality disorders have been based on unstructured clinical evaluations. However, several recent studies have questioned the accuracy and thoroughness of clinical diagnostic interviews; consequently, clinical epidemiological studies, like community-based studies, should be based on standardized evaluations. The Rhode Island Methods to Improve Diagnostic Assessment and Services project is one of the largest clinical epidemiological studies to use semistructured interviews to assess a wide range of psychiatric disorders conducted in general clinical outpatient practice. In the present report, the authors examined the frequency of DSM-IV personality disorders in a patient group and the comorbidity among them. METHOD Eight hundred fifty-nine psychiatric outpatients were interviewed with the Structured Interview for DSM-IV Personality upon presentation for treatment. RESULTS Slightly less than one-third of the patients were diagnosed with one of the 10 official DSM-IV personality disorders (N=270, 31.4%). When the patients with personality disorder not otherwise specified were included, the rate of any personality disorder increased to almost half of the group (N=391, 45.5%). The majority of patients meeting criteria for one of the specific personality disorders were diagnosed with more than one. Avoidant, borderline, and obsessive-compulsive personality disorder were the most frequent specific diagnoses. CONCLUSIONS Personality disorders, as a group, are among the most frequent disorders treated by psychiatrists. They should be evaluated in all psychiatric patients because their presence can influence the course and treatment of the axis I disorder that patients typically identify as their chief complaint.
DPP-4 inhibitors: focus on safety

Introduction: Dipeptidyl peptidase inhibitors (DPP-4-i) are highly selective inhibitors of the enzyme DPP-4. They act by increasing levels of incretin hormones, which have potent effects on insulin and glucagon release, gastric emptying, and satiety. Our goal is to review the safety issues related to DPP-4-i. Areas covered: This review is based upon a PubMed search of the literature using keywords alogliptin, linagliptin, saxagliptin, sitagliptin and vildagliptin, DPP-4-i, glucagon-like polypeptide-1 agonists, as well as extensive personal clinical trial experience with each of these agents. The current DPP-4-i have very different chemical structures. Saxagliptin has significant cytochrome P450 metabolism and carries a risk of drug interactions. Linagliptin has primarily entero-hepatic excretion, a benefit in renally impaired patients. A concern arose related to congestive heart failure in the SAVOR TIMI trial of saxagliptin. Several major cardiac studies are underway, with two concluded. Despite lingering uncertainty related to pancreatitis and pancreatic cancer, large randomized trials have not shown an increased risk with DPP-4-i treatment. Cutaneous adverse effects occur with a low frequency with some of these agents. Expert opinion: DPP-4-i are an additional choice in the group of anti-hyperglycemics. Their principal advantage is a low incidence of hypoglycemia, making these agents desirable in patients such as the elderly and those with cardiac disease. Several large trials have hinted at less cardiac risk with DPP-4-i than with sulfonylureas. The CAROLINA Trial comparing linagliptin and glimepiride may provide a conclusive answer to this question.
In vitro effects of three new 1,2,4-trioxanes (pentatroxane, thiahexatroxane, and hexatroxanone) on Toxoplasma gondii

The in vitro effects of three synthetic, cis-fused, bicyclic 1,2,4-trioxanes (pentatroxane, thiahexatroxane, and hexatroxanone) against intracellular Toxoplasma gondii were studied. Unactivated peritoneal macrophages were infected with the virulent RH strain of T. gondii and exposed to the 1,2,4-trioxanes at different concentrations. The antitoxoplasmic activity of the drugs was first assessed with [3H]uracil, which is incorporated by the parasite but not the host cell. Pentatroxane and thiahexatroxane were the most active, exhibiting 90% inhibitory concentrations of 6.8 and 5.3 micrograms/ml, respectively. Furthermore, microscopic examination of the infected macrophages after treatment with pentatroxane, thiahexatroxane, and hexatroxanone at their respective 90% inhibitory concentrations confirmed the inhibition of intracellular growth of T. gondii. Their activities were comparable to those of pyrimethamine (1 micrograms/ml) and pyrimethamine (0.1 micrograms/ml) in combination with sulfadiazine (25 micrograms/ml). Pentatroxane and thiahexatroxane were also able to inhibit intracellular growth of T. gondii within nonprofessional phagocytes (HeLa cells), suggesting that the antitoxoplasmic activity was not caused by a macrophage-specific mechanism, such as macrophage activation. However, the 1,2,4-trioxanes were not active against extracellular T. gondii. Pentatroxane and thiahexatroxane are new, promising compounds that deserve further study to assess their usefulness for treating toxoplasmosis.
Molecular markers predicting outcome in hepatocellular carcinoma treated by liver transplantation

Josep M. Llovet Liver Cancer Translational Research Laboratory, Barcelona-Clinic Liver Cancer Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer, Hospital Cl ınic de Barcelona, Universitat de Barcelona, Barcelona, Catalonia, Spain; Mount Sinai Liver Cancer Program, Division of Liver Diseases, Tisch Cancer Institute, Ichan School of Medicine at Mount Sinai, New York, NY; and Instituci o Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
Endogenous fluorophores enable two-photon imaging of the primate eye.

PURPOSE Noninvasive two-photon imaging of a living mammalian eye can reveal details of molecular processes in the retina and RPE. Retinyl esters and all-trans-retinal condensation products are two types of retinoid fluorophores present in these tissues. We measured the content of these two types of retinoids in monkey and human eyes to validate the potential of two-photon imaging for monitoring retinoid changes in human eyes. METHODS Two-photon microscopy (TPM) was used to visualize excised retina from monkey eyes. Retinoid composition and content in human and monkey eyes were quantified by HPLC and mass spectrometry (MS). RESULTS Clear images of inner and outer segments of rods and cones were obtained in primate eyes at different eccentricities. Fluorescence spectra from outer segments revealed a maximum emission at 480 nm indicative of retinols and their esters. In cynomolgus monkey and human retinal extracts, retinyl esters existed predominantly in the 11-cis configuration along with notable levels of 11-cis-retinol, a characteristic of cone-enriched retinas. Average amounts of di-retinoid-pyridinium-ethanolamine (A2E) in primate and human eyes were 160 and 225 pmol/eye, respectively. CONCLUSIONS These data show that human retina contains sufficient amounts of retinoids for two-photon excitation imaging. Greater amounts of 11-cis-retinyl esters relative to rodent retinas contribute to the fluorescence signal from both monkey and human eyes. These observations indicate that TPM imaging found effective in mice could detect early age- and disease-related changes in human retina.
Target tracking using multiple auxiliary particle filtering

Particle filters are a widely used tool to perform Bayesian filtering under nonlinear dynamic and measurement models or non-Gaussian distributions. However, the performance of particle filters plummets when dealing with high-dimensional state spaces. In this paper, we propose a method that makes use of multiple particle filtering to circumvent this difficulty. Multiple particle filters partition the state space and run an individual particle filter for every component. Each particle filter shares information with the rest of the filters to account for the influence of the complete state in the observations collected by sensors. The method considered in this paper uses auxiliary filtering within the MPF framework, outperforming previous algorithms in the literature. The performance of the considered algorithm is tested in a multiple target tracking scenario, with fixed and known number of targets, using a sensor network with a nonlinear measurement model.
The Arabidopsis Gene zinc finger protein 3(ZFP3) Is Involved in Salt Stress and Osmotic Stress Response

Plants are continuously challenged by various abiotic and biotic stresses. To tide over these adversities, plants evolved intricate regulatory networks to adapt these unfavorable environments. So far, many researchers have clarified the molecular and genetic pathways involved in regulation of stress responses. However, the mechanism through which these regulatory networks operate is largely unknown. In this study, we cloned a C2H2-type zinc finger protein gene ZFP3 from Arabidopsis thaliana and investigated its function in salt and osmotic stress response. Our results showed that the expression level of ZFP3 was highly suppressed by NaCl, mannitol and sucrose. Constitutive expression of ZFP3 enhanced tolerance of plants to salt and osmotic stress while the zfp3 mutant plants displays reduced tolerance in Arabidopsis. Gain- and Loss-of-function studies of ZFP3 showed that ZFP3 significantly changes proline accumulation and chlorophyll content. Furthermore, over-expression of ZFP3 induced the expressions of stress-related gene KIN1, RD22, RD29B and AtP5CS1. These results suggest that ZFP3 is involved in salt and osmotic stress response.
Self-Monitoring in Schizophrenia

Many patients suffering from schizophrenia feel dispossessed from some of their actions or thoughts. This dis- possession could result from impaired self-monitoring (SM), defined as the ability to monitor self-willed intentions and actions. SM has been widely studied during the past decades with very different paradigms; central error correction, feed- back distortion, sense of effort, and motor imagery. The present article first reviews the methods used and results obtained in investigation of SM. Second, we address what we consider to be the critical questions that must be answered in order to fully understand the role of SM deficit in schizophrenia: 1) Is SM deficit only impaired in patients with specific symp- toms? 2) Is SM deficit associated with other cognitive processes that are also impaired in patients with schizophrenia? 3) Can SM impairment be characterized as a trait or a state marker? Finally, we discuss the consequences of SM investiga- tion on diagnostic evaluation and therapeutic orientations and we propose future research that we think is essential in or- der to clarify the role of SM in schizophrenia.
A Space Vector Modulation Control Algorithm for VSI Multi – Level Converters

In this paper a novel modular digital control algorithm for multi level inverters is introduced and discussed. This algorithm is essentially based on the duty cycle expression and allows a great simplification, because of its modularity and its simple implementation. The algorithm is particularly suitable for the Multi Point Clamped (MPC) inverters with no constraint on the number of the voltage levels and results faster than the most recent solutions proposed in literature. The modulation techniques considered in the paper are the sub oscillation PWM and, above all, the Space Vector Modulation (SVM), but the proposed algorithm may be employed for the main carrier based PWM control techniques including the “Zero sequence injection”. Simulation of a MPC inverters, controlled with the proposed algorithm, have been made with the help of the MATLAB-SIMULINK® package. For these simulations a mathematical model already known in literature, but adapted to be used within the MATLAB-SIMULINK® environment, has been used. The simulation results show the effectiveness of the MPC model formulation and of the proposed control algorithm.
Generation of a dual RT Env SHIV that is infectious in rhesus macaques

Background The best current animal model for HIV infection and evaluation of antiviral compounds is the Simian–human immunodeficiency virus (SHIV)/macaque system. There are multiple recombinant SHIVs available, but these viruses have limitations in evaluating combination drug strategies for prevention. Drug combinations that target reverse transcriptase (RT, either nRTI or nnRTI) and envelope (entry or fusion inhibitors) have to be tested separately, which does not permit the assessment of additive, synergistic, or antagonistic effects of ARV combinations. We describe construction of a dual SHIV containing both HIV RT and a CCR5‐specific HIV envelope gene in a simian immunodeficiency virus backbone.
Extracranial arteriovenous malformations: natural progression and recurrence after treatment.

BACKGROUND Arteriovenous malformation is a dynamic vascular anomaly; it expands with age and after treatment. This study analyzed the pattern of arteriovenous malformation progression and frequency of recurrence after therapy. METHODS Patients with cutaneous and soft-tissue arteriovenous malformation were reviewed. Progression was defined as advancement to a higher Schobinger stage (I through IV) before treatment. Recurrence was defined as expansion following embolization or resection. The effect of sex, location, size, adolescence, pregnancy, and stage on progression or recurrence was analyzed. RESULTS The study included 272 patients. Children with stage I arteriovenous malformation had a 43.8 percent risk of progression before adolescence and an 82.6 percent risk before adulthood; the remaining children had progression in adulthood. Progression was more common during adolescence (56.0 percent; 95 percent confidence interval, 46.5 to 65.2) compared with childhood (38.8 percent; 95 percent confidence interval, 32.4 to 45.4) (p = 0.002). The average age at progression was 12.7 +/- 11.1 years. Diffuse arteriovenous malformations were more likely to progress compared with localized lesions (p < 0.001). Sex (p = 0.46), location (p = 0.36), and pregnancy (p = 0.20) did not influence expansion. Resection (with or without embolization) had a lower recurrence rate (81 percent) and longer time to recurrence (42.7 percent >1 year), compared with embolization alone (98 percent and 14.4 percent >1 year, respectively) (p < 0.001). Recurrence was less likely when lower staged lesions were treated (p < 0.001) and did not correlate with sex (p = 0.10), location (p = 0.60), size (p = 0.07), or age (p = 0.21). CONCLUSIONS Arteriovenous malformation is likely to progress before adulthood, particularly during adolescence, and usually reexpands following treatment. Resection (with or without embolization) for lower staged or localized arteriovenous malformation offers the best chance for long-term control.
Validity of Two New Brief Instruments to Estimate Vegetable Intake in Adults

Cost effective population-based monitoring tools are needed for nutritional surveillance and interventions. The aim was to evaluate the relative validity of two new brief instruments (three item: VEG3 and five item: VEG5) for estimating usual total vegetable intake in comparison to a 7-day dietary record (7DDR). Sixty-four Australian adult volunteers aged 30 to 69 years (30 males, mean age ± SD 56.3 ± 9.2 years and 34 female mean age ± SD 55.3 ± 10.0 years). Pearson correlations between 7DDR and VEG3 and VEG5 were modest, at 0.50 and 0.56, respectively. VEG3 significantly (p < 0.001) underestimated mean vegetable intake compared to 7DDR measures (2.9 ± 1.3 vs. 3.6 ± 1.6 serves/day, respectively), whereas mean vegetable intake assessed by VEG5 did not differ from 7DDR measures (3.3 ± 1.5 vs. 3.6 ± 1.6 serves/day). VEG5 was also able to correctly identify 95%, 88% and 75% of those subjects not consuming five, four and three serves/day of vegetables according to their 7DDR classification. VEG5, but not VEG3, can estimate usual total vegetable intake of population groups and had superior performance to VEG3 in identifying those not meeting different levels of vegetable intake. VEG5, a brief instrument, shows measurement characteristics useful for population-based monitoring and intervention targeting.
Autogenic entrenchment patterns and terraces due to coupling with lateral erosion in incising alluvial channels

The abandonment of terraces in incising alluvial rivers can be used to infer tectonic and climatic histories. A river incising into alluvium erodes both vertically and laterally as it abandons fill‐cut terraces. We argue that the input of sediment from the valley walls during entrenchment can alter the incision dynamics of a stream by promoting vertical incision over lateral erosion. Using a numerical model, we investigate how valley wall feedbacks may affect incision rates and terrace abandonment as the channel becomes progressively more entrenched in its valley. We postulate that erosion of taller valley walls delivers large pulses of sediment to the incising channel, potentially overwhelming the local sediment transport capacity. Based on field observations, we propose that these pulses of sediment can form talus piles that shield the valley wall from subsequent erosion and potentially force progressive channel narrowing. Our model shows that this positive feedback mechanism can enhance vertical incision relative to 1‐D predictions that ignore lateral erosion. We find that incision is most significantly enhanced when sediment transport rates are low relative to the typical volume of material collapsed from the valley walls. The model also shows a systematic erosion of the youngest terraces when river incision slows down. The autogenic entrenchment due to lateral feedbacks with valley walls should be taken into account in the interpretation of complex‐response terraces.
The Relationship between Dimensions of Personality, Self Concept and Family Influence on Students in the FELDA Scheme in Johore Malaysia

The purpose of this study is to identify the relationship between the dimensions of personality, self-concept and family influence. The sample consists of 214 students from two secondary schools in the FELDA settlement in Johor. Random cluster sampling was carried out. A pilot test was carried out to determine the internal consistency of the questionnaire. The assessment instrument used in this study was the Malay version of the Junior Eysenck Personality Inventory (JEPI) which has a reliability level of 0.5739. The Malay version of the Tennessee Self-concept Scale which has a reliability level of 0.8657 was also used. The family influence questionnaire which has a reliability level of 0.7913 was also used in this study to identify the effects of family influence in the aspects of family cohesiveness, religious and moral aspect and freedom aspect. Descriptive statistic and Pearson's Correlation were used to analyze the relationship between the dimensions of personality, self-concept and family influence. The results show a weak relationship between the dimensions of personality and self-concept, and between the dimensions of personality and family cohesiveness. However, there is no relationship between the dimensions of personality and the religious /moral and freedom aspect. The results also show that there is a strong relationship between self-concept and family cohesiveness and a moderate relationship between self-concept and the religious/moral aspect. However, there is no relationship between self-concept and freedom.
These Aren't the Commands You're Looking For: Addressing False Feedforward in Feature-Rich Software

The names, icons, and tooltips of commands in feature-rich software are an important source of guidance when locating and selecting amongst commands. Unfortunately, these cues can mislead users into believing that a command is appropriate for a given task, when another command would be more appropriate, resulting in wasted time and frustration. In this paper, we present command disambiguation techniques that inform the user of alternative commands before, during, and after an incorrect command has been executed. To inform the design of these techniques, we define categories of false-feedforward errors caused by misleading interface cues, and identify causes for each. Our techniques are the first designed explicitly to solve this problem in feature-rich software. A user study showed enthusiasm for the techniques, and revealed their potential to play a key role in learning of feature-rich software.
Amblyopia treatment outcomes after preschool screening v school entry screening: observational data from a prospective cohort study

Background/aims: Preschool screening for amblyopia has controversially been abandoned in some localities within the United Kingdom, on the basis that there is no clear evidence of benefit to support its continuation. Data collected within a birth cohort study were used to examine visual outcomes at 7½ years in children who did or did not receive preschool vision screening. Methods: Monocular logMAR visual acuity with and without a pinhole was assessed by orthoptists. Contemporary records were used to identify children who had been offered and/or received preschool screening. Results: Of 6081 children, 24.9% had been offered preschool screening and 16.7% had attended. The prevalence of amblyopia was approximately 45% lower in the children who received preschool screening than in those who did not (1.1% v 2.0%, p = 0.05). The mean acuity in the worse seeing eyes after patching treatment was better for amblyopic children who received preschool screening than for those who did not; 0.14 v 0.20 logMAR (p <0.001). These effects did not persist in an intention to screen analysis. Conclusions: Preschool screening at 37 months was associated with an improved treatment outcome for individuals with amblyopia. However, the improvement was clinically small and disappeared when considering all children offered screening rather than only those who received it. Further research is needed into improving the effectiveness of vision screening for preschool children, while in the interim these data do not conflict with current recommendations for school entry screening by orthoptists.