Miracle-dz/UniFAR-FTUs huggingface dataset:
A probabilistic method for testing and estimating selection differences between populations

Human populations around the world encounter various environmental challenges and, consequently, develop genetic adaptations to different selection forces. Identifying the differences in natural selection between populations is critical for understanding the roles of specific genetic variants in evolutionary adaptation. Although numerous methods have been developed to detect genetic loci under recent directional selection, a probabilistic solution for testing and quantifying selection differences between populations is lacking. Here we report the development of a probabilistic method for testing and estimating selection differences between populations. By use of a probabilistic model of genetic drift and selection, we showed that logarithm odds ratios of allele frequencies provide estimates of the differences in selection coefficients between populations. The estimates approximate a normal distribution, and variance can be estimated using genome-wide variants. This allows us to quantify differences in selection coefficients and to determine the confidence intervals of the estimate. Our work also revealed the link between genetic association testing and hypothesis testing of selection differences. It therefore supplies a solution for hypothesis testing of selection differences. This method was applied to a genome-wide data analysis of Han and Tibetan populations. The results confirmed that both the EPAS1 and EGLN1 genes are under statistically different selection in Han and Tibetan populations. We further estimated differences in the selection coefficients for genetic variants involved in melanin formation and determined their confidence intervals between continental population groups. Application of the method to empirical data demonstrated the outstanding capability of this novel approach for testing and quantifying differences in natural selection.
Regulatory implications of a novel mode of interaction of calmodulin with a double IQ‐motif target sequence from murine dilute myosin V

Apo‐Calmodulin acts as the light chain for unconventional myosin V, and treatment with Ca2+ can cause dissociation of calmodulin from the 6IQ region of the myosin heavy chain. The effects of Ca2+ on the stoichiometry and affinity of interactions of calmodulin and its two domains with two myosin‐V peptides (IQ3 and IQ4) have therefore been quantified in vitro, using fluorescence and near‐ and far‐UV CD. The results with separate domains show their differential affinity in interactions with the IQ motif, with the apo‐N domain interacting surprisingly weakly. Contrary to expectations, the effect of Ca2+ on the interactions of either peptide with either isolated domain is to increase affinity, reducing the Kd at physiological ionic strengths by >200‐fold to ∼75 nM for the N domain, and ∼10‐fold to ∼15 nM for the C domain. Under suitable conditions, intact (holo‐ or apo‐) calmodulin can bind up to two IQ‐target sequences. Interactions of apo‐ and holo‐calmodulin with the double‐length, concatenated sequence (IQ34) can result in complex stoichiometries. Strikingly, holo‐calmodulin forms a high‐affinity 1:1 complex with IQ34 in a novel mode of interaction, as a “bridged” structure wherein two calmodulin domains interact with adjacent IQ motifs. This apparently imposes a steric requirement for the α‐helical target sequence to be discontinuous, possibly in the central region, and a model structure is illustrated. Such a mode of interaction could account for the Ca2+‐dependent regulation of myosin V in vitro motility, by changing the structure of the regulatory complex, and paradoxically causing calmodulin dissociation through a change in stoichiometry, rather than a Ca2+‐dependent reduction in affinity.
DSL-driven generation of Graphical User Interfaces

Domain-specific languages (DSLs) are becoming more and more popular. However, the number of DSLs is still small when comparing to the number of existing applications. The results of our previous research showed that it is possible to speed up the DSL development process by aiding the first development phases (design and implementation). More specifically it is possible to generate DSLs from existing GUIs (Graphical User Interfaces) of component-based applications. Now we want to use the generated DSLs and their models to generate new user interfaces or even whole new applications. To verify this claim, in this paper we use existing technologies which simplify the creation of web applications: iTasks. We also describe stereotypes of creating GUIs which we used to extract data from existing applications and to generate new applications. In the last part of this paper we limit the types of applications, which can be used for extraction based on our experiments with the prototype.
A Distributed Real-Time Operating System with Distributed Shared Memory for Embedded Control Systems

The paper presents a distributed real-time operating system (DRTOS) that provides a distributed shared memory (DSM) service for distributed control systems. Model-based design has become popular in embedded control software design and the source code of software modules can be generated from a controller model. The generated software modules exchange their input and output values through shared variables. We develop a DRTOS with a real-time DSM service to provide a location-transparent environment, in which distributed software modules can exchange input and output values through the DSM. The DRTOS is an extension to OSEK OS. We use a real-time network called FlexRay, which is based on a TDMA (Time Division Multiple Access) protocol. The consistency of the DSM is maintained according to the order of data transfer through FlexRay, not using inter-node synchronization. The worst case response time of the DSM is predictable if the FlexRay communication is well configured.
API Changes-How Much Would You Allow ?

Once a software library is deployed, it is extremely difficult to modify published types. Every new version has to preserve backward compatibility with existing applications. This limits the number of changes that may be applied to the public classes defined in the library. We present a tool that assists developers in maintaining the consistency of a shared library with the existing software. It allows for greater flexibility in evolving the library’s functionality by supporting a wide range of changes.
Pinpointed muscle force control in consideration Of human motion and external force

The main focus of our research is to control the load of selected muscles by using a power-assisting device, thus enabling pinpointed motion support, rehabilitation and training by explicitly specifying the target muscles. In our past research, a control method was proposed for static human motion. And the result of simulation and experiments showed that it is possible to control the force of selected muscle individually. However, the past method we proposed was only considered for constant posture, which led to a large effect of non-target muscle. In this paper, a new pinpointed muscle force control method was proposed to reduce the effect of non-target muscle by human motion and external force. Human motion and external force was optimized individually in a double-loop searching algorithm, which reduced the computational cost. By calculating the posture step by step, this method can also be used for a quasi-static motion. The validity of this method was confirmed by measuring surface EMG signals for each muscle.
Polish tagger TaKIPI: rule based construction and optimization

A large number of different tags, limited corpora and the free word order are the main causes of low accuracy of tagging in Polish (automatic disambiguation of morphological descriptions) by applying commonly used techniques based on stochastic modelling. In the paper the rule-based architecture of the TaKIPI Polish tagger combining handwritten and automatically extracted rules is presented. The possibilities of optimisation of its parameters and component are discussed, including the possibility of using different methods of rules extraction, than C4.5 Decision Trees applied initially. The main goal of this paper is to explore a range of promising rule-based classifiers and investigate their impact on the accuracy of tagging. Simple techniques of combing classifiers are also tested. The performed experiments have shown that even a simple combination of different classifiers can increase the tagger’s accuracy by almost one percent.
Development of the joint attention with a new face tracking method for multiple people

This thesis aims to develop a system for multiple objects tracking and joint attention between a human and a robot. We propose a new method (modified Multi-CAMSHIFT, MMC), which is based on the characteristics of color and shape probability distribution, to solve the tracking problems for multiple objects. The color information is calculated by MMC improved from CAMSHIFT theory. The shape information is calculated by the procedure of Scharr kernel mask. We calculate color histogram and orientation histogram respectively, and use the adaptive feature selection for optimal tracking. Eyes-pair fast extracting is included for judging face or non-face regions. Our proposed MMC is based on adaptive multi-resolution (AMR) framework for reducing computation. After finding human faces, we find the direction of each human face, and research the human-robot interaction between human and robot that is called joint attention. We construct the joint attention with static and dynamic information of a human, which are edge detector and optical flow, respectively. The static and dynamic information have complementary characteristics. We use support vector machine (SVM) for learning model. Utilizing both static and dynamic information acquired from observing a humanpsilas gaze shift enables the robot to efficiently acquire joint attention ability and to naturally interact with the human. From experiment results, the proposed modified Multi-CAMSHIFT was successfully applied to multiple faces tracking and the development of the joint attention.
Analyzing User Behavior : A Trace Analysis of the NCAR Archival Storage System Technical Report UCSC-SSRC-1202 March 2012

In this work we examine the user behavior of the National Center for Atmospheric Research’s (NCAR) archive. In particular we characterized user sessions and examined namespace locality of accesses within those sessions. Preliminary results suggest within a single session, repeat file accesses are uncommon, and that accessed files are localized within a small set of directories. This work provides a baseline and preliminary results for a more detailed future study.
Bacterial Plasminogen Receptors Utilize Host Plasminogen System for Effective Invasion and Dissemination

In order for invasive pathogens to migrate beyond the site of infection, host physiological barriers such as the extracellular matrix, the basement membrane, and encapsulating fibrin network must be degraded. To circumvent these impediments, proteolytic enzymes facilitate the dissemination of the microorganism. Recruitment of host proteases to the bacterial surface represents a particularly effective mechanism for enhancing invasiveness. Plasmin is a broad spectrum serine protease that degrades fibrin, extracellular matrices, and connective tissue. A large number of pathogens express plasminogen receptors which immobilize plasmin(ogen) on the bacterial surface. Surface-bound plasminogen is then activated by plasminogen activators to plasmin through limited proteolysis thus triggering the development of a proteolytic surface on the bacteria and eventually assisting the spread of bacteria. The host hemostatic system plays an important role in systemic infection. The interplay between hemostatic processes such as coagulation and fibrinolysis and the inflammatory response constitutes essential components of host defense and bacterial invasion. The goal of this paper is to highlight mechanisms whereby pathogenic bacteria, by engaging surface receptors, utilize and exploit the host plasminogen and fibrinolytic system for the successful dissemination within the host.
School Water, Sanitation, and Hygiene, Soil-Transmitted Helminths, and Schistosomes: National Mapping in Ethiopia

Background It is thought that improving water, sanitation, and hygiene (WASH) might reduce the transmission of schistosomes and soil-transmitted helminths, owing to their life cycles. However, few large-scale studies have yet assessed the real extent of associations between WASH and these parasites. Methodology/Principal Findings In the 2013–2014 Ethiopian national mapping of infections with these parasites, school WASH was assessed alongside infection intensity in children, mostly between 10 and 15 years of age. Scores were constructed reflecting exposure to schistosomes arising from water collection for schools, from freshwater sources, and the adequacy of school sanitation and hygiene facilities. Kendall’s τb was used to test the WASH scores against the school-level arithmetic mean intensity of infection with each parasite, in schools with at least one child positive for the parasite in question. WASH and parasitology data were available for 1,645 schools. More frequent collection of water for schools, from open freshwater sources was associated with statistically significantly higher Schistosoma mansoni infection intensity (Kendall’s τb = 0.097, 95% confidence interval, CI: 0.011 to 0.18), better sanitation was associated with significantly lower Ascaris lumbricoides intensity (Kendall’s τb = -0.067, 95% CI: -0.11 to -0.023) and borderline significant lower hookworm intensity (Kendall’s τb = -0.039, 95% CI: -0.090 to 0.012, P = 0.067), and better hygiene was associated with significantly lower hookworm intensity (Kendall’s τb = -0.076, 95% CI: -0.13 to -0.020). However, no significant differences were observed when comparing sanitation and infection with S. mansoni or Trichuris trichiura, or hygiene and infection with A. lumbricoides or T. trichiura. Conclusions/Significance Improving school WASH may reduce transmission of these parasites. However, different forms of WASH appear to have different effects on infection with the various parasites, with our analysis finding the strongest associations between water and S. mansoni, sanitation and A. lumbricoides, and hygiene and hookworm.
A new method of detecting human eyelids based on deformable templates

In this work a new method of automatically detecting human eyelids using deformable templates is proposed. Deformable templates are often used in eye's feature detection although there are several drawbacks such as high computational complexity, unexpected shrinking of the templates, adjusting the weights of energy terms and failure of orientation adjustment. Based on the analysis on these problems, an improved template for eyelid edge detection with several new ideas is presented. The problems of unexpected shrinking of templates, adjusting the weights of energy terms and failure of orientation adjustment are overcome by using a new kind of potential field and accurate estimations of the template parameters. Experiments show that the eyelid template and the optimization method are effective even for complex changes in facial images, such as eye opening and closing, obvious irises movements and rotations of heads in small angles.
Evolutionary spectral clustering by incorporating temporal smoothness

Evolutionary clustering is an emerging research area essential to important applications such as clustering dynamic Web and blog contents and clustering data streams. In evolutionary clustering, a good clustering result should fit the current data well, while simultaneously not deviate too dramatically from the recent history. To fulfill this dual purpose, a measure of temporal smoothness is integrated in the overall measure of clustering quality. In this paper, we propose two frameworks that incorporate temporal smoothness in evolutionary spectral clustering. For both frameworks, we start with intuitions gained from the well-known k-means clustering problem, and then propose and solve corresponding cost functions for the evolutionary spectral clustering problems. Our solutions to the evolutionary spectral clustering problems provide more stable and consistent clustering results that are less sensitive to short-term noises while at the same time are adaptive to long-term cluster drifts. Furthermore, we demonstrate that our methods provide the optimal solutions to the relaxed versions of the corresponding evolutionary k-means clustering problems. Performance experiments over a number of real and synthetic data sets illustrate our evolutionary spectral clustering methods provide more robust clustering results that are not sensitive to noise and can adapt to data drifts.
Molecular Characterization and Expression Analysis of Triticum aestivum Squamosa-Promoter Binding Protein-Box Genes Involved in Ear Development

Wheat (Triticum aestivum L.) is one of the most important crops in the world. Squamosa-promoter binding protein (SBP)-box genes play a critical role in regulating flower and fruit development. In this study, 10 novel SBP-box genes (TaSPL genes) were isolated from wheat ((Triticum aestivum L.) cultivar Yanzhan 4110). Phylogenetic analysis classified the TaSPL genes into five groups (G1–G5). The motif combinations and expression patterns of the TaSPL genes varied among the five groups with each having own distinctive characteristics: TaSPL20/21 in G1 and TaSPL17 in G2 mainly expressed in the shoot apical meristem and the young ear, and their expression levels responded to development of the ear; TaSPL6/15 belonging to G3 were upregulated and TaSPL1/23 in G4 were downregulated during grain development; the gene in G5 (TaSPL3) expressed constitutively. Thus, the consistency of the phylogenetic analysis, motif compositions, and expression patterns of the TaSPL genes revealed specific gene structures and functions. On the other hand, the diverse gene structures and different expression patterns suggested that wheat SBP-box genes have a wide range of functions. The results also suggest a potential role for wheat SBP-box genes in ear development. This study provides a significant beginning of functional analysis of SBP-box genes in wheat.
A Molecular Biology Database Digest

Computational Biology or Bioinformatics has been defined as the application of mathematical and Computer Science methods to solving problems in Molecular Biology that require large scale data, computation, and analysis [18]. As expected, Molecular Biology databases play an essential role in Computational Biology research and development. This paper introduces into current Molecular Biology databases, stressing data modeling, data acquisition, data retrieval, and the integration of Molecular Biology data from different sources. This paper is primarily intended for an audience of computer scientists with a limited background in Biology.
Functional Regulation of ClC-3 in the Migration of Vascular Smooth Muscle Cells

Migration of vascular smooth muscle cells (VSMCs) into neointima contributes to atherosclerosis and restenosis. This migration requires coordinated plasmalemmal fluxes of water and ions. Here, we show that aortic VSMC migration depends on the regulation of transmembrane Cl− flux by ClC-3, a Cl− channel/transporter. The contribution of ClC-3 to plasmalemmal Cl− current was studied in VSMCs by electrophysiological recordings. Cl− current was negligible in cells perfused with 0 [Ca2+]. Raising intracellular [Ca2+] to 0.5 &mgr;M activated a Cl− current (ICl.Ca), approximately half of which was eliminated on inhibition by KN-93 of calmodulin-dependent protein kinase II. ICl.Ca was also halved by inositol-3,4,5,6-tetrakisphosphate, a cellular signal with the biological function of specifically preventing calmodulin-dependent protein kinase II from activating ICl.Ca. Gene disruption of ClC-3 reduced ICl.Ca by 50%. Moreover, ICl.Ca in the ClC-3 null VSMCs was not affected by either KN-93 or inositol-3,4,5,6-tetrakisphosphate. We conclude that ICl.Ca is composed of 2 components, one is ClC-3 independent whereas the other is ClC-3 dependent, activated by calmodulin-dependent protein kinase II and inhibited by inositol-3,4,5,6-tetrakisphosphate. We also assayed VSMC migration in transwell assays. Migration was halved in ClC-3 null cells versus wild-type cells. In addition, inhibition of ClC-3 by niflumic acid, KN-93, or inositol-3,4,5,6-tetrakisphosphate each reduced cell migration in wild-type cells but not in ClC-3 null cells. These cell-signaling roles of ClC-3 in VSMC migration suggest new therapeutic approaches to vascular remodeling diseases.
Why Mozart compositions during pregnancy should be exposed in the night. Study on apoptotic index of Rattus norvegicus offsprings’ brain neurons

Objectives: To analyze the optimal time to expose Mozart compositions(in the night/ dark) by measuring brain neural apoptotic index of Rattus norvegicus offsprings Materials and Methods: This study used experimental random-ized post test only control group design in pregnant Rattus norvegicus . Subjects were divided into three groups at random, ie control group, 1 (1 hour Mozart exposure in dark) and 2 (1 hour Mozart in light), each comprised 8 females. After delivery, 2 heaviest Rattus norvegicus offsprings were chosen, totally 15 neonates in each group, then they were sacrificed with decapita-tion and the brain was prepared and stained using TUNEL assay method and the index of neurons cell apoptosis was calculated using microscope in 1000x magnification. This study was conducted at the Faculty of Veterinary Medicine, University of Airlangga, after conducting ethical feasibility test. Results: There were no miscarriages, congenital malformation, preterm birth and deaths in all groups. The control group's neural apoptosis index was 55.98 ± 4.12, group one 24.87±3.45 and group two 23.82±3.89. Based on statistical test result, there was no significant difference of apoptosis index between treatment group 1 and treatment group 2, with p value 0,836 but significant difference was found between control group and treatment group 1 (p=0.002) and between control group and treatment group 2 (p=0.009). In dark group we found the lower average of apoptotic index, the lowest apoptotic index, 9 of 15 had the lowest, the heaviest head weight and 4 of 15 subjects had the heaviest head weight Conclusion: There was no significant difference between the pro-vision of Mozart music in dark and light on brain neuron of Rattus norvegicus offsprings although lower average in the dark group especially if the extreme value exluded. In the dark group: we found the lower average of apoptotic index, the lowest apoptotic index, biggest proportion of the lowest index, the heaviest head and biggest proportion of heaviest head.
Report From the CoalFace: Lessons Learnt Building A General-Purpose Always-On Provenance System

Over the past year we have implemented OPUS, an always-on system for observed provenance capture in user-space. In this paper we present some important lessons for anyone hoping to implement a general purpose provenance system operating at user-level. In particular, we highlight the problems and solutions associated with the explosion of interposition requirements attributable to function variants, challenges in maintaining semantic equivalence with POSIX and the importance of deactivating function interception in response to runtime errors. We also provide some insights on choosing the right database to manage provenance data.