Miracle-dz/UniFAR-FTUs huggingface dataset:
Incorporating Prior Biologic Information for High-Dimensional Rare Variant Association Studies

Background: Given the increasing scale of rare variant association studies, we introduce a method for high-dimensional studies that integrates multiple sources of data as well as allows for multiple region-specific risk indices. Methods: Our method builds upon the previous Bayesian risk index by integrating external biological variant-specific covariates to help guide the selection of associated variants and regions. Our extension also incorporates a second level of uncertainty as to which regions are associated with the outcome of interest. Results: Using a set of study-based simulations, we show that our approach leads to an increase in power to detect true associations in comparison to several commonly used alternatives. Additionally, the method provides multi-level inference at the pathway, region and variant levels. Conclusion: To demonstrate the flexibility of the method to incorporate various types of information and the applicability to high-dimensional data, we apply our method to a single region within a candidate gene study of second primary breast cancer and to multiple regions within a candidate pathway study of colon cancer.
Efficient generation of counterexamples and witnesses in symbolic model checking

Model checking is an automatic technique for verifying sequential circuit designs and protocols. An efficient search procedure is used to determine whethe or not the specification is satisfied. If it is not satisfied, our technique will produce a counter-example execution trace that shows the cause of the problem. We describe an efficient algorithm to produce counter-examples and witnesses for symbolic model checking algorithms. This algorithm is used in the SMV model checker and works quite well in practice. We also discuss how to extend our technique to more complicated specifications.
Development of an intelligent agent-based mobile phone supply chain simulation system

An intelligent agent-based mobile phone supply chain simulation system is developed, in which a business entity or customer is represented by an intelligent agent. The proposed simulation system has six layers - raw material providers, component manufacturers, product assemblers, product holders, retailers, and final customers. There are two agents in each layer. An agent has a number of engines to implement various functions of the agent. This system can simulate many activities of a business in a supply chain either automatically or manually. The system can be used to study and simulate supply chain management technologies and methodologies.
An oxygen-induced but protein F-independent fibronectin-binding pathway in Streptococcus pyogenes

Protein F is an important fibronectin-binding adhesin of Streptococcus pyogenes (group A streptococcus). However, all previous analyses of protein F have been conducted in a mutant strain which expresses protein F under anaerobic conditions nonpermissive for expression in other strains. In this study, we have examined the fibronectin-binding properties of several protein F-deficient mutants cultured under aerobic conditions and have identified a second pathway for binding fibronectin. Unlike the case with protein F, exposure to an aerobic environment does not induce transcription of a new gene product. Rather, O2 is apparently required for the modification of a protease-resistant cell surface component into a binding-component form. Modification occurred preferentially at a pH of 6.0 or less, and the binding of the modified component to fibronectin required Zn2+. The oxidizing agent Fe(CN)6 could be substituted for O2 and stimulated expression of binding activity under O2-limiting conditions. Streptococcal fibronectin binding mediated by this pathway but not by protein F could be inhibited by laminin and by streptococcal lipoteichoic acid, a molecule previously implicated as the streptococcal adhesin for fibronectin. The non-protein F-binding activity could also substantially enhance the binding of the organism for fibronectin. The non-protein F-binding activity could also substantially enhance the binding of the organism to basement membrane. By using differential inhibition, analyses of binding to non-protein F mutant strains demonstrated that the total level of fibronectin bound under aerobic conditions reflects contributions from both pathways. Because of its dependence on Zn2+, an oxidant, and pH, this binding activity has been designated the ZOP binding pathway.
[Second trimester cerclage of short cervixes: which technique to use? A retrospective study of 25 cases].

OBJECTIVE To evaluate pregnancy outcome after therapeutic or emergency cerclage performed on the basis of clinical or/and ultrasound cervical modifications noted before 26 weeks of gestation and to precise which surgical procedure (Shirodkar or McDonald) is the most appropriate in these indications. PATIENTS AND METHODS Retrospective study between January 1(st) 1996 and December 31(st) 2001 on 25 clinical charts of patients with suspected cervical incompetence who had second trimester cervical cerclage on the basis of clinical or ultrasound cervical length shortening. Patients with first trimester prophylactic cervical cerclage were excluded from analysis. The choice between the two surgical procedures (Shirodkar or McDonald) depended on surgeon preference but the two groups were identical for previous obstetrical history, time of cerclage and cervical modifications. Statistical analysis was performed using Chi 2 test or t-test according to the type of variables. RESULTS In our series, 9 patients had cervical cerclage performed with Shirodkar (S) procedure and 16 had McDonald cerclage (MD). Mean operating time (S: 52 +/- 18 minutes; MD: 39 +/- 3 minutes; p=0.1) and mean hospital stay (S: 5.2 +/- 1.3 days; MD: 5.3 +/- 1.5 days; p=0.9) were not significantly different between the two procedures. The difference in mean gestational age at delivery, (S: 35.7 +/- 3.2 Wks; MD: 33.2 +/- 2.9 Wks; p=0.5) and in the number of premature deliveries before 32 completed weeks (S: 22.2%; MD: 43.7%; p=0.4) better in Shirodkar group didn't reach statistical signification. No statistical difference was noted in the number of admission in neonatal intensive care unit (S: 22.2%; MD: 31.2%; p=0.9) and in neonatal survival (S: 1 neonatal death; MD: 1 neonatal death) between the two groups. CONCLUSION No conclusion regarding the most appropriate cervical cerclage procedure can be drawn from our study. However, Shirodkar procedure seems preferable to us due to tendency in a higher mean gestational age at delivery and because it didn't appeared to be longer or more difficult procedure. Multicentric studies may probably give better knowledge in this topic.
CD151 regulates epithelial cell–cell adhesion through PKC- and Cdc42-dependent actin cytoskeletal reorganization

CD151, a member of the tetraspanin family proteins, tightly associates with integrin α3β1 and localizes at basolateral surfaces of epithelial cells. We found that overexpression of CD151 in A431 cells accelerated intercellular adhesion, whereas treatment of cells with anti-CD151 mAb perturbed the integrity of cortical actin filaments and cell polarity. E-Cadherin puncta formation, indicative of filopodia-based adhesion zipper formation, as well as E-cadherin anchorage to detergent-insoluble cytoskeletal matrix, was enhanced in CD151-overexpressing cells. Levels of GTP-bound Cdc42 and Rac were also elevated in CD151-overexpressing cells, suggesting the role of CD151 in E-cadherin–mediated cell–cell adhesion as a modulator of actin cytoskeletal reorganization. Consistent with this possibility, engagement of CD151 by the substrate-adsorbed anti-CD151 mAb induced prominent Cdc42-dependent filopodial extension, which along with E-cadherin puncta formation, was strongly inhibited by calphostin C, a protein kinase C (PKC) inhibitor. Together, these results indicate that CD151 is involved in epithelial cell–cell adhesion as a modulator of PKC- and Cdc42-dependent actin cytoskeletal reorganization.
Fast and robust 3D T1 mapping using spiral encoding and steady RF excitation at 7 T: application to cardiac manganese enhanced MRI (MEMRI) in mice

Mapping longitudinal relaxation times in 3D is a promising quantitative and non‐invasive imaging tool to assess cardiac remodeling. Few methods are proposed in the literature allowing us to perform 3D T1 mapping. These methods often require long scan times and use a low number of 3D images to calculate T1. In this project, a fast 3D T1 mapping method using a stack‐of‐spirals sampling scheme and regular RF pulse excitation at 7 T is presented. This sequence, combined with a newly developed fitting procedure, allowed us to quantify T1 of the whole mouse heart with a high spatial resolution of 208 × 208 × 315 µm3 in 10–12 min acquisition time. The sensitivity of this method for measuring T1 variations was demonstrated on mouse hearts after several injections of manganese chloride (doses from 25 to 150 µmol kg−1). T1 values were measured in vivo in both pre‐ and post‐contrast experiments. This protocol was also validated on ischemic mice to demonstrate its efficiency to visualize tissue damage induced by a myocardial infarction. This study showed that combining spiral gradient shape and steady RF excitation enabled fast and robust 3D T1 mapping of the entire heart with a high spatial resolution. Copyright © 2015 John Wiley & Sons, Ltd.
Isothermal Crystallization Behavior of Poly(L-lactic acid)/Organo-Montmorillonite Nanocomposites

The isothermal crystallization behavior of poly(L-lactic acid)/organo-montmorillonite nanocomposites (PLLA/OMMT) with different content of OMMT, using a kind of twice-functionalized organoclay (TFC), prepared by melt intercalation process has been investigated by optical depolarizer. In isothermal crystallization from melt, the induction periods (t(i)) and half times for overall PLLA crystallization (100 degrees C <= T-c <= 120 degrees C) were affected by the temperature and the content of TFC in nanocomposites. The kinetic of isothermal crystallization of PLLA/TFC nanocomposites was studied by Avrami theory. Also, polarized optical photomicrographs supplied a direct way to know the role of TFC in PLLA isothermal crystallization process. Wide angle X-ray diffraction (WAXD) patterns showed the nanostructure of PLLA/TFC material, and the PLLA crystalline integrality was changed as the presence of TFC. Adding TFC led to the decrease of equilibrium melting point of nanocomposites, indicating that the layered structure of clay restricted the full formation of crystalline structure of polymer.
Enhanced Navigation Strategies for Teams of Mobile Agents 1

In multi-agent systems engaged in cooperative activities there is an apparent trade-off between the complexity of the individual agents, their sensing capabilities and communication required for accomplishment of particular tasks. One of the main computationally intensive components which affects the complexity of the overall system is the acquisition and maintenance of the environment model where the agents reside. In this paper, in the context of foraging and coordinated traversal task, we will examine control strategies that in the absence of the global model of the environment can substantially improve the performance of the team using additional sensing and communication capabilities. In one case the coordinated strategy is motivated by an ant trail following behavior while in another case the line of sight information is used to constrain the movement of individual agents guaranteeing shorter total traversal times.
A Laplace decomposition algorithm applied to a class of nonlinear differential equations

In this paper, a numerical Laplace transform algorithm which is based on the decomposition method is introduced for the approximate solution of a class of nonlinear differential equations. The technique is described and illustrated with some numerical examples. The results assert that this scheme is rapidly convergent and quite accurate by which it approximates the solution using only few terms of its iterative scheme.
Are Treatment Preferences Relevant in Response to Serotonergic Antidepressants and Cognitive-Behavioral Therapy in Depressed Primary Care Patients? Results from a Randomized Controlled Trial Including a Patients’ Choice Arm

Background: Little is known about the influence of depressed patients’ preferences and expectations about treatments upon treatment outcome. We investigated whether better clinical outcome in depressed primary care patients is associated with receiving their preferred treatment. Methods: Within a randomized placebo-controlled single-centre 10-week trial with 5 arms (sertraline; placebo; cognitive-behavioral group therapy, CBT-G; moderated self-help group control; treatment with sertraline or CBT-G according to patients’ choice), outcomes for 145 primary care patients with mild-to-moderate depressive disorders according to DSM-IV criteria were investigated. Preference for medication versus psychotherapy was assessed at screening using a single item. Post-baseline difference scores for the Hamilton Depression Rating Scale (HAMD-17) were used to assess treatment outcome (mixed-model repeated-measures regression analysis). Results: Depressed patients receiving their preferred treatment (n = 63), whether sertraline or CBT-G, responded significantly better than those who did not receive their preferred therapy (n = 54; p = 0.001). The difference in outcome between both groups was 8.0 points on the HAMD-17 for psychotherapy and 2.9 points on the HAMD-17 for treatment with antidepressants. Results were not explained by differences in depression severity or dropout rates. Conclusions: Patients’ relative preference for medication versus psychotherapy should be considered when offering a treatment because receiving the preferred treatment conveys an additional and clinically relevant benefit (HAMD-17: +2.9 points for drugs; +8.0 points for CBT-G) in outcome.
Face recognition using distributed, mobile computing

This paper describes a distributed computing framework called Blue-Hoc, that uses mobile devices connected using a Bluetooth, wireless ad hoc network. For a network composed of different devices, we have developed a load balancing method to optimize performance of BlueHoc. The eigenfaces technique for face recognition is implemented and used to benchmark performance. With four devices and an 80 subject face database, we can achieve a speedup (including all overheads) of 1.37× without load balancing and with a 40 subject database a speedup of 1.08× with load balancing. Because of fixed communications and initialization costs, the speedup factor can grow as the number of subjects in the recognition system grows. Consequently, by aggregating the computing capabilities of local mobile devices, BlueHoc provides an effective solution for distributed mobile computing.
Improving local search ranking through external logs

The signals used for ranking in local search are very different from web search: in addition to (textual) relevance, measures of (geographic) distance between the user and the search result, as well as measures of popularity of the result are important for effective ranking. Depending on the query and search result, different ways to quantify these factors exist -- for example, it is possible to use customer ratings to quantify the popularity of restaurants, whereas different measures are more appropriate for other types of businesses. Hence, our approach is to capture the different notions of distance/popularity relevant via a number of external data sources (e.g., logs of customer ratings, driving-direction requests, or site accesses). In this paper we will describe the relevant signal contained in a number of such data sources in detail and present methods to integrate these external data sources into the feature generation for local search ranking. In particular, we propose novel backoff methods to alleviate the impact of skew, noise or incomplete data in these logs in a systematic manner. We evaluate our techniques on both human-judged relevance data as well as click-through data from a commercial local search engine.
Red blood cell segmentation using Active Appearance Model

The red blood cell segmentation is an important technology for automatic cell counting, classification and analysis in clinical examination. In this paper, we propose a red blood cell segmentation method based on Active Appearance Models (AAM). The AAM can effectively describe the shape information and texture information of the red blood cell, and separate cells from background precisely. Experimental results show that the AAM can extract cells from background effectively. Besides, compared with many traditional image segmentation methods, the AAM method provides a closed form of the boundary of the cell, so it is no need to perform boundary tracking for cell counting, measurement and analysis.
AutoCyclone: Automatic Mining of Cyclic Online Activities with Robust Tensor Factorization

Given a collection of seasonal time-series, how can we find regular (cyclic) patterns and outliers (i.e. rare events)? These two types of patterns are hidden and mixed in the time-varying activities. How can we robustly separate regular patterns and outliers, without requiring any prior information? We present CycloneM, a unifying model to capture both cyclic patterns and outliers, and CycloneFact, a novel algorithm which solves the above problem. We also present an automatic mining framework AutoCyclone, based on CycloneM and CycloneFact. Our method has the following properties; (a) effective: it captures important cyclic features such as trend and seasonality, and distinguishes regular patterns and rare events clearly; (b) robust and accurate: it detects the above features and patterns accurately against outliers; (c) fast: CycloneFact takes linear time in the data size and typically converges in a few iterations; (d) parameter free: our modeling framework frees the user from having to provide parameter values. Extensive experiments on 4 real datasets demonstrate the benefits of the proposed model and algorithm, in that the model can capture latent cyclic patterns, trends and rare events, and the algorithm outperforms the existing state-of-the-art approaches. CycloneFact was up to 5 times more accurate and 20 times faster than top competitors.
Equality of Opportunity, A Flexible Framework.

Kanbur and Wagstaff (further: KW) criticize something they call the “equality of opportunity” (EOP)approach. Yet, most of the points they make are accepted in that literature and what they propose as an alternative, is just a primitive version of it. Some of the confusion may have arisen because KW do not distinguish the different approaches within the EOP-world (for a discussion, see, e.g., Fleurbaey and Schokkaert, 2012), and mainly focus on the Roemer-inspired applications.
Reinforcement Learning for Motor Primitives

Humans demonstrate a large variety of very complicated motor skills in their day-to-day life. Their agility and adaptability to new control task remains unmatched by the millions of robots laboring on factory floors and roaming research labs. Achieving the abilities of learning and improving new motor skills has become an essential component in order to get a step closer to human-like motor skills. If future robots could acquire their basic task by imitating human demonstrations and subsequently self-improve by trial and error, such robot learning would result into more interesting robot applications as well as large productivity gains in industry. Recent progress in the area of machine learning has yielded several important tools for making progress towards this vision for the future. Two of these recent developments are a novel framework for representing motor primitives using dynamical systems presented in [Ijspeert et al., 2002a,b, 2003, Schaal et al., 2004] and the reduction of reward-related self-improvement to reward-weighted regression by Peters and Schaal [2006c, 2007b]. To date, these two important methods have only been used separately in robot learning; when using them in combination, this could yield a strong basis for learning motor skills. In this diploma thesis, the task of ball-in-a-cup or balero was chosen as a target evaluation platform for the proposed method. We will start by first implementing a simulation platform for the balero task in the physically realistic robot simulator SL [Schaal, 2004]. Subsequently, we obtain human presentations of the task using a VICONTM motion capture system. This data is used for imitations learning and we will show that several very different basic movements exist which can fulfill the task. We implement the framework of motor primitives based on dynamical systems, adapt it for applicability to our task and subsequently discuss how the suggested learning framework works in toy applications. Using the physically realistic simulation, we evaluate our resulting framework in simulation and test it extensively. Final evaluations are planned to take place on a high-speed Barret WAMTM robot arm using a 200Hz vision setup which is currently being created at the Max-Planck Institute for Biological Cybernetics.
Cardiovascular risk management and its impact on hypertension control in primary care in low-resource settings: a cluster-randomized trial.

OBJECTIVE To evaluate a simple cardiovascular risk management package for assessing and managing cardiovascular risk using hypertension as an entry point in primary care facilities in low-resource settings. METHODS Two geographically distant regions in two countries (China and Nigeria) were selected and 10 pairs of primary care facilities in each region were randomly selected and matched. Regions were then randomly assigned to a control group, which received usual care, or to an intervention group, which applied the cardiovascular risk management package. Each facility enrolled 60 consecutive patients with hypertension. Intervention sites educated patients about risk factors at baseline and initiated treatment with hydrochlorothiazide at 4 months in patients at medium risk of a cardiovascular event, according to a standardized treatment algorithm. Systolic blood pressure change from baseline to 12 months was the primary outcome measure. FINDINGS The study included 2397 patients with baseline hypertension: 1191 in 20 intervention facilities and 1206 in 20 control facilities. Systolic and diastolic blood pressure decreased more in intervention patients than in controls. However, at 12 months more than half of patients still had uncontrolled hypertension (systolic blood pressure > 140 mmHg and/or diastolic blood pressure > 90 mmHg). Behavioural risk factors had improved among intervention patients in Nigeria but not in China. Only about 2% of hypertensive patients required referral to the next level of care. CONCLUSION Even in low-resource settings, hypertensive patients can be effectively assessed and managed in primary care facilities.
The other side of the nearly neutral theory, evidence of slightly advantageous back-mutations

We argue that if there is a category of slightly deleterious mutations, then there should be a category of slightly advantageous back-mutations. We show that when there are both slightly deleterious and advantageous back-mutations, there is likely to be an increase in the rate of evolution after a population size expansion. This increase in the rate of evolution is short-lived. However, we show how its signature can be captured by comparing the rate of evolution in species that have undergone population size expansion versus contraction. We test our model by comparing the pattern of evolution in pairs of island and mainland species in which the colonization event was either island-to-mainland (population size expansion) or mainland-to-island (contraction). We show that the predicted pattern of evolution is observed.