Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for association between novel polymorphisms in the PRODH gene and schizophrenia in a Chinese population

Haploinsufficiency for or mutation in at least one gene from the velocardiofacial syndrome (VCFS) region at chromosome 22q11 is implicated in psychosis. Linkage disequilibrium mapping of the region in patients identified a segment containing two genes, proline dehydrogenase (PRODH) and DGCR6, as candidates [Liu et al., 2002a ] and by analysis of additional polymorphisms the PRODH gene was associated with schizophrenia in adult and early onset patients. In the present study we provide additional evidence in support of genetic association between PRODH and schizophrenia in a Chinese population. We analyzed the PRODH gene in a samples of schizophrenic patients and their families from Sichuan, SW China consisting of 528 family trios and sibling pairs. We genotyped six SNPs, PRODH*1195C → T, PRODH*1482C → T, PRODH*1483A → G, PRODH*1766A → G, PRODH*1852G → A PRODH*1945T → C, two of which (PRODH*1483A → G and PRODH*1852G → A) have not been previously reported. We found association with schizophrenia for two haplotypes consisting of PRODH*1945T → C and PRODH*1852G → A (Global P = 0.006), and PRODH*1852G → A and PRODH*1766A → G (Global P = 0.01) which include one of the newly identified markers. After six‐fold Bonferroni correction for multiple testing the PRODH*1945T‐C/PRODH*1852G‐A haplotypes remained significant. This is a sub‐haplotype of the PRODH haplotype previously associated with schizophrenia and it also maps to the 3′ region of the gene, indicating that this is the region most likely to contain the underlying risk alleles. Overall this finding supports a role for the PRODH locus in schizophrenia. © 2004 Wiley‐Liss, Inc.
Horse-shoe lung-rediscovered via volume rendered images

Abstract Horseshoe lung, usually associated with pulmonary venolobar syndrome, is a rare congenital anomaly involving the fusion of the postero-basal segments of the right and left lungs across the midline. The fused segment or the isthmus lies posterior to the pericardium and anterior to the aorta.The associated pulmonary venolobar syndrome involves anomalous systemic arterial supply and anomlaous systemic venous drainage of the right lung. With the advent of MDCT imaging, we can diagnose this rare condition as well all its associated anomalies non-invasively. Volume-rendered techniques greatly simplify the complex anatomy and provide easy understanding of the same.
Latent Dynamic Space-Time Volumes for Predicting Human Facial Behavior in Videos

Author(s): Sikka, Karan | Advisor(s): Ngyuen, Truong | Abstract: Enabling machines to understand non-verbal facial behavior from visual data is crucial for building smart interactive systems. This thesis focusses on human behavior analysis in videos. Previous state-of-the-art methods generally employed global temporal pooling approaches that, (i) assume presence of a single uniform event spanning the sequence, and (ii) discard temporal ordering by squashing all information along the temporal dimension. In this dissertation we focus on two specific modeling challenges unaddressed by previous approaches. First issue is training with weak labels that only provide video-level annotations and are much cheaper to obtain than fine (frame-level) annotations. The second concerns modeling temporal dynamics during prediction, as facial expressions are dynamic actions with sub-events. We propose to tackle these issues by proposing methods based on Weakly Supervised Latent Variable Models (WSLVM) and evaluate them on real-world spontaneous expressions. We begin with addressing these challenges by combining Multiple Instance Learning (MIL) framework and Multiple Segment representation (MS-MIL). MS-MIL can simultaneously classify and localize target behavior in videos despite training with weak annotations. However, this method lacks the capability to explicitly model multiple latent concepts or global temporal order. We address this issue in the next chapter by explicitly modeling temporal orderings by learning an exemplar Hidden Markov Model for each sequence. This algorithm models dependencies between segments but is limited in its modeling capacity due to the use of generative modeling. Chapter~4 extends MIL to learn multiple discriminative concepts in a novel formulation for joint clustering and classification. This algorithm shows consistent performance improvement but does not capture temporal structure. We finally present a unified learning framework that combines the strengths of the previously proposed algorithms in that it (i) addresses weakly labeled data (ii) learns multiple discriminative concepts, and (iii) models the temporal ordering structure of the concepts. This method is a novel WSLVM that models a video as a sequence of automatically mined, multiple discriminative sub-events with a loose temporal structure. We show both qualitative and quantitative results highlighting improvements over state-of-the-art algorithms by jointly addressing weak labels and temporal dynamics.
Privacy Preserving Collaborative Filtering

As machine learning and data mining techniques continue to grow in popularity, it has become ever more important to develop methods that preserve user security. One important problem in the field of machine learning is recommendation, which seeks to predict user ratings for unrated items using previous rating information. We focus specifically on the approach of similarity based collaborative filtering (CF) for recommendation, which involves computing similarity coefficients between items in order to extrapolate ratings for unrated items. We analyze an existing protocol for accomplishing privacy preserving collaborative filtering and identify potential vulnerabilities caused by a malicious server. We propose a modified protocol for privacy preserving collaborative filtering which eliminates the identified vulnerabilities. We implement the proposed system and evaluate the tradeoffs between the two systems in terms of performance and security.
Hiding behind Hydrophobicity

Proteomics of membrane proteins is essential for the understanding of cellular function. However, mass spectrometric analysis of membrane proteomes has been less successful than the proteomic determination of soluble proteins. To elucidate the mystery of transmembrane proteins in mass spectrometry, we present a detailed statistical analysis of experimental data derived from chloroplast membranes. This approach was further accomplished by the analysis of the Arabidopsis thaliana proteome after in silico digestion. We demonstrate that both the length and the hydrophobicity of the proteolytic fragments containing transmembrane segments are major determinants for detection by mass spectrometry. Based on a comparative analysis, we discuss possibilities to overcome the problem and provide possible protocols to shift the hydrophobicity of transmembrane segment-containing peptides to facilitate their detection.
Genotyping African haplotypes in ATM using a co‐spotted single‐base extension assay

Human genetic analysis, including population genetic studies, increasingly calls for cost‐effective, high‐throughput methods for the rapid screening of single nucleotide polymorphisms (SNPs) across many individuals. The modified single‐base extension assay described here (arrayed SBE) is a highly accurate and robust method for SNP genotyping that can deliver genotypes at 3.5 cents each, following PCR. Specifically, amino‐modified probe/target pairs were prehybridized, then co‐spotted in a microarray format prior to enzymatic addition of allele‐specific nucleotides. Probe/target identity was determined solely by its physical location on the array rather than by hybridization to a complementary target, resulting in a call rate of 99–100%. These innovations result in an inexpensive, accurate assay with exceptional signal‐to‐noise ratios, depending on the glass surface employed. Comparison of glass slides from three different manufacturers indicated that aldehyde‐based Zyomyx slides provided superior performance for this assay. Arrayed SBE was applied to study the geographic distribution of three African‐specific haplotypes in the human ATM gene. Four selectively neutral markers, which define the haplotypes H5, H6, and H7, were screened in a total of 415 individuals. Region‐specific haplotype frequencies were consistent with patterns of human migration across and outside of Africa, suggesting a possible haplotype origin in East Africa. Arrayed SBE was a robust tool for this analysis that could be applied to any situation requiring the genotyping of a few SNPs in many individuals. Hum Mutat 22:214–221, 2003. © 2003 Wiley‐Liss, Inc.
Design of Three-Dimensional Optical Circuit Devices by Using Topology Optimization Method With Function-Expansion-Based Refractive Index Distribution

We extend topology optimization method with function-expansion-based refractive index distribution to optimization for three-dimensional optical circuits, in which a refractive index distribution in a design region is expressed by an expansion with some analytical functions. Three-branch optical waveguides have been optimized as numerical examples. Equally branching three-branch waveguides are achieved using our method. A limitation of topology optimization in two dimensions and dependency of initial structure are also shown.
Robust guaranteed cost control for BTT vehicle based on LMI

BTT(Bank-to-Turn) vehicle is a kind of typical nonlinear system which has parametric uncertainty and heavy exogenous disturbance. This paper presents a partial linearization method use of robust guaranteed cost control techniques for the design and analysis of BTT vehicle control laws to make the model closer to the actual system. Considering the practical model of BTT vehicle, we employed partial linearization rather than complete linearization in system modeling, in order to prevent the system errors caused by low accuracy in complete linearization. Under the circumstance of satisfying Lipschitz conditions, Lyapunov function was employed to get the sufficient condition for the robust control law of the BTT vehicle system to exist, and transformed into a feasible solution with linear matrix inequalities method. The numerical simulation results show the algorithm can makes up the characteristic distortion of nonlinear system for excessive simplification model, so that the designed control law becomes more reasonable and effective.
Trait Mindfulness and Player Experience

Mindfulness in a general sense is defined as being in the present without having thoughts about past or future. In this study, we have investigated the effect of trait mindfulness on gameplay experience. Specifically, we examined the associations between trait mindfulness and engagement, enjoyment and competence after a game session. Participants (N = 102) first completed a questionnaire packet, and then played a fast-paced video game developed for the purpose of this study (while being eye tracked). Finally, they completed another questionnaire to assess their player experience. Results showed that trait mindfulness was negatively associated with engagement, but positively associated with competence. There was no significant relationship between mindfulness and player enjoyment. The theoretical implications for the unexpected negative association between mindfulness and engagement and the planned future efforts of this work in progress are discussed.
Modeling Nonstationary Emotion Dynamics in Dyads Using a Semiparametric Time-Varying Vector Autoregressive Model

Emotion dynamics often arise in an interpersonal context, such as a romantic relationship. As time passes, emotion dynamics are prone to change, leading to nonstationarity (e.g., time-lagged relations that differ across periods). Several models have been developed to account for nonstationarity in dynamics; for example, a time-varying dynamic factor model (Chow, Zu, Shifren, & Zhang, 2011). The use of such models, however, is limited because they are not implemented in standard software. We present a statistical data-driven model, the semiparametric time-varying vector autoregressive (TV-VAR) model. The TV-VAR model is based on wellstudied generalized additive models (GAM; Wood, 2006), implemented in the software R, and has well-functioning default settings, making it very user friendly. The TV-VAR can explicitly model changes in temporal dependency—for
Evidence that metyrapone can act as a stressor: effect on pituitary‐adrenal hormones, plasma glucose and brain c‐fos induction

Metyrapone, a 11‐β steroid hydroxylase inhibitor that blocks stress‐induced glucocorticoid release, is extensively used to study the physiological and behavioural roles of glucocorticoids. However, there is circumstancial evidence suggesting that metyrapone could act as a pharmacological stressor. Thus, the effects of various doses of metyrapone on two well‐characterized stress markers (ACTH and glucose) were studied in male rats. Metyrapone administration, while exerting a modest effect on plasma corticosterone levels, dose‐dependently increased plasma ACTH and glucose levels. Using the highest doses previously tested (200 mg/kg) we further observed, as evaluated by fos‐like immunoreactivity (FLI), a strong activation of a wide range of brain areas, including the parvocellular region of the hypothalamic paraventricular nucleus (PVNp), the origin of the main ACTH secretagogues. Metyrapone‐induced FLI was observed in neocortical and allocortical areas, in several limbic, thalamic and hypothalamic nuclei and, to a lesser extent, in the brainstem. In a final experiment, a dose–response study of metyrapone‐induced FLI was carried out focusing on selected brain areas. The study revealed that the paraventricular thalamic nucleus and central amygdala were the areas most sensitive to metyrapone as they responded even to the lowest dose of the drug. Most areas, among them the PVNp, only showed enhanced FLI with the two highest doses, i.e. when it was associated with ACTH and glucose responses. These data suggest that some of the effects of metyrapone could be due to its stressful properties rather than its ability to inhibit glucocorticoid synthesis. The exact mechanisms involved remain to be established.
Laser in situ keratomileusis for undercorrection after radial keratotomy.

PURPOSE To assess the safety and efficacy of excimer laser in situ keratomileusis (LASIK) in treating residual myopia and/or astigmatism following refractive keratotomy. METHODS Fourteen eyes that had previously undergone radial and/or arcuate keratotomy were included. The surgeries were performed using the Chiron Automated Microkeratome and the VISX 20/20B excimer laser. RESULTS Average follow-up was 12.64+/-5.02 months. Mean spherical equivalent refraction was reduced from -3.48+/-3.52 D preoperatively to -0.04+/-0.87 D postoperatively. At the last follow-up examination there were 8 eyes (57.1%) with a refraction within+/-0.50 D, and 10 eyes (71.4%) within +/-1.00 D of emmetropia. Uncorrected visual acuity was 20/20 or better in 4 eyes (28.6%) and 20/40 or better in 10 eyes (71.4%). Vector analysis of the astigmatic correction showed an index of success of 80%. There was no significant loss (> or = or =2 lines) of spectacle-corrected visual acuity. We observed interface epithelial ingrowth in one eye. CONCLUSIONS The correction of residual myopia and/or astigmatism with LASIK in eyes with prior refractive keratotomy proved to be safe and effective. Careful preoperative evaluation may help to avoid complications such as reopening of incisions during surgery or postoperative ingrowth of epithelium beneath the corneal flap.
Simulation Evaluation Using a Modified Lasater Clinical Judgment Rubric

Aim. The purpose of this study was to describe the process of evaluating senior nursing students in the simulation laboratory using a modified Lasater Clinical Judgment Rubric (LCJR). Background. The LCJR is a clinical evaluation tool used to measure outcomes in simulated learning settings. The LCJR was revised to provide numeric grading and clarity regarding expectations of clinical competency. Method. The study was conducted over two years with students enrolled in their final bachelor of science in nursing semester (Phase 1, n = 86; Phase 2, n = 102) using high‐fidelity simulation. Results. The modified rubric measured student performance more holistically than a procedural checklist and provided objective criteria for evaluation. Conclusion. A well‐constructed rubric provides a mechanism to evaluate student performance in simulation by focusing on clinical reasoning essential for patient safety and allowing numeric evaluation of performance.
A New Efficient Construction on Probabilistic Tree Embeddings

In this paper we describe a simple and efficient algorithm to construct FRT embeddings (optimal probabilistic tree embeddings) on graphs. For a graph with $n$ vertices and $m$ edges the algorithm runs in $O(m\log n+n\log^2 n)$ time. With the efficient FRT construction, we show that FRT trees are Ramsey partitions with asymptotically tight bound, and we give tighter bounds on coefficient than previous Ramsey partitions, hence improving other results on a series of distance oracles.
XRCC2 and XRCC3 Gene Polymorphismand Risk of Pancreatic Cancer

OBJECTIVESXRCC2 and XRCC3 are key components of the homologous recombination (HR) machinery that repairs DNA double-strand breaks. We hypothesized that the altered HR repair capacity conferred by single nucleotide polymorphisms (SNPs) would modify individual susceptibility to sporadic pancreatic cancer.METHODSIn a hospital-based case-control study, genomic DNA and exposure information was obtained from 468 patients with pathologically confirmed pancreatic adenocarcinoma and 498 frequency-matched healthy controls at M.D. Anderson Cancer Center during January 2000 to September 2006. Genotypes of XRCC2 31479 G>A (Arg188His) and XRCC3 17893 A>G and 18067 C>T (Thr241Met) were determined using the Masscode technology. Unconditional logistic regression models were used to estimate the odds ratio (OR) and its 95% confidence interval (CI) in non-Hispanic whites (408 cases and 449 controls). RESULTSThe distribution of genotype frequencies was not different between cases and controls. We observed a significant effect modification between XRCC2 polymorphism and smoking status and pack-year of smoking in modifying pancreatic cancer risk (P value for interaction 0.02 and 0.05, respectively). Compared with never-smokers carrying the XRCC2 Arg188Arg genotype, the OR (95% CI) for individuals carrying the 188His allele was 2.32 (1.25–4.31) among ever-smokers, 1.43 (0.59–3.48) among light smokers (<22 pack-years), and 3.42 (1.47–7.96) among heavy smokers (≥22 pack-years). The two XRCC3 SNPs are in strong linkage disequilibrium, but there was no suggestive association between XRCC3 genotype and the risk of pancreatic cancer.CONCLUSIONXRCC2 Arg188His polymorphism may be one of the genetic modifiers for smoking-related pancreatic cancer.
The efficacy of oral treatment with pramiconazole in pityriasis versicolor: a phase II a trial

Although the patient was treated with topical prednicarbate ointment twice a day for several months, the skin lesion on the proximal nail fold and the nail dystrophy did not show improvement. Lesions of porokeratosis of Mibelli start as small, brownish papules that slowly enlarge to form irregular, annular, hyperkeratotic or verrucous plaques. Although porokeratosis of Mibelli can appear at any age, the onset is usually during childhood. Porokeratosis of Mibelli can occur practically anywhere on the body, but normally it is localized to the extremities where lesions may involve palms and soles. Nail involvement of porokeratosis is extremely rare and, to date, there has been only one case report of nail involvement in porokeratosis of Mibelli and two case reports of onychodystrophy in linear porokeratosis. Since onychodystrophy in porokeratosis has rarely been described before, the exact pathogenesis of porokeratotic nail has not yet been elucidated. It is possible that nail changes occur once the atypical hyperproliferative keratinocytes involve the nail matrix and nail bed, ultimately resulting in whole nail destruction. Pterygium is known to develop during the healing of disease involving the proximal nail fold and various conditions such as lichen planus, trauma, atherosclerosis, onychotillomania, Raynaud’s phenomenon, systemic lupus erythematosus, toxic epidermal necrolysis and graft-versus-host disease. Treatment modalities for porokeratosis of Mibelli include excision with skin grafting, electrodessication, cryotherapy, dermabrasion, carbon dioxide laser, topical 5-fluorouracil and oral retinoids. However, although these treatments are effective, relapses usually occur several weeks or months after discontinuation of therapy. Moreover, there is no clear recommendation, especially when pterygium is formed. Dorsal pterygium formation by porokeratosis of Mibelli is rare, but it is important for the clinician to recognize this phenomenon and we suggest that porokeratosis of Mibelli should also be considered as one cause of pterygium formation. Therefore, the clinician should explain the possibility of nail change to the patient when the lesion of porokeratosis is near the proximal nail fold.
Serum ischemia-modified albumin and malondialdehyde levels and superoxide dismutase activity in patients with fibromyalgia.

BACKGROUND The aim of the study was to determine serum ischemia modified albumin and malondialdehyde levels as markers of oxidative stress and serum superoxide dismutase activity as a marker of antioxidant defense and their associations with clinical outcomes in patients with fibromyalgia. METHODS 59 patients with fibromyalgia and 38 age and gender matched healthy controls were included in the study. The diagnosis of fibromyalgia was based on the classification criteria declared by American College of Rheumatology in 1990. All patients underwent the clinical assessment, consisting of evaluation for tender point count, visual analogue scale for pain, fibromyalgia impact questionnaire, multidimensional assessment of fatigue, Beck anxiety inventory, Beck depression inventory, and the health assessment questionnaire. Serum levels of ischemia modified albumin, malondialdehyde, and superoxide dismutase activities were measured using colorimetric methods. RESULTS Malondialdehyde levels of fibromyalgia patients were significantly higher than they were in the control group. Ischemia modified albumin levels in the fibromyalgia group were not significantly different from the control values. There was no significant correlation between ischemia modified albumin and malondialdehyde and clinical measures with the exception that malondialdehyde levels positively correlated with health assessment questionnaire scores. CONCLUSIONS We concluded that increased malondialdehyde levels in patients with fibromyalgia could be considered as a sign of increased oxidative stress. Ischemia modified albumin values were not in concordance with malondialdehyde levels and could not be considered as an oxidative stress marker in the follow-up of fibromyalgia. Further studies are needed to investigate IMA levels in newly diagnosed fibromyalgia patients.