Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational detection of cis-regulatory modules

MOTIVATION The transcriptional regulation of a metazoan gene depends on the cooperative action of multiple transcription factors that bind to cis-regulatory modules (CRMs) located in the neighborhood of the gene. By integrating multiple signals, CRMs confer an organism specific spatial and temporal rate of transcription. RESULTS Based on the hypothesis that genes that are needed in exactly the same conditions might share similar regulatory switches, we have developed a novel methodology to find CRMs in a set of coexpressed or coregulated genes. The ModuleSearcher algorithm finds for a given gene set the best scoring combination of transcription factor binding sites within a sequence window using an A(*)procedure for tree searching. To keep the level of noise low, we use DNA sequences that are most likely to contain functional cis-regulatory information, namely conserved regions between human and mouse orthologous genes. The ModuleScanner performs genomic searches with a predicted CRM or with a user-defined CRM known from the literature to find possible target genes. The validity of a set of putative targets is checked using Gene Ontology annotations. We demonstrate the use and effectiveness of the ModuleSearcher and ModuleScanner algorithms and test their specificity and sensitivity on semi-artificial data. Next, we search for a module in a cluster of gene expression profiles of human cell cycle genes. AVAILABILITY The ModuleSearcher is available as a web service within the TOUCAN workbench for regulatory sequence analysis, which can be downloaded from http://www.esat. kuleuven.ac. be/~dna/BioI.
3D Face Recognition Based on Multiple Keypoint Descriptors and Sparse Representation

Recent years have witnessed a growing interest in developing methods for 3D face recognition. However, 3D scans often suffer from the problems of missing parts, large facial expressions, and occlusions. To be useful in real-world applications, a 3D face recognition approach should be able to handle these challenges. In this paper, we propose a novel general approach to deal with the 3D face recognition problem by making use of multiple keypoint descriptors (MKD) and the sparse representation-based classification (SRC). We call the proposed method 3DMKDSRC for short. Specifically, with 3DMKDSRC, each 3D face scan is represented as a set of descriptor vectors extracted from keypoints by meshSIFT. Descriptor vectors of gallery samples form the gallery dictionary. Given a probe 3D face scan, its descriptors are extracted at first and then its identity can be determined by using a multitask SRC. The proposed 3DMKDSRC approach does not require the pre-alignment between two face scans and is quite robust to the problems of missing data, occlusions and expressions. Its superiority over the other leading 3D face recognition schemes has been corroborated by extensive experiments conducted on three benchmark databases, Bosphorus, GavabDB, and FRGC2.0. The Matlab source code for 3DMKDSRC and the related evaluation results are publicly available at http://sse.tongji. edu.cn/linzhang/3dmkdsrcface/3dmkdsrc.htm.
The iron K-shell features of MXB 1728-34 from a simultaneous Chandra-RXTE observation

We report on a simultaneous Chandra and RossiXTE observation of the low-mass X-ray binary atoll bursting source MXB 1728-34 performed on 2002 March 3-5. We fit the 1.2-35 keV continuum spectrum with a blackbody plus a Comptonized component. Large residuals at 6-10 keV can be fitted by a broad ( keV) Gaussian emission line or, alternatively, by two absorption edges associated with lowly ionized iron and Fe XXV/XXVI at ~7.1 keV and ~9 keV, respectively. In this interpretation, we find no evidence of broad emission lines between 6 and 7 keV. We test our alternative model of the iron K shell region by reanalysing a previous BeppoSAX observation of MXB 1728-34, finding a general agreement with our new spectral model.
Dimensionality and the Dynamics of Human Unstable Equilibrium

Abstract Maintaining an unstable equilibrium requires that multiple joints be coordinated so that the center of mass is kept above the base of support. The authors' aim in the present study was to discover the underlying dynamics of local (foot, hip, or head) and global (center of mass) components involved in balance control and how those dynamics are affected by changes in the available information. Participants (N = 6) had to maintain their balance on an unstable platform. Using dimensional analyses (largest Lyapunov exponent and correlation dimension), the authors examined the active degrees of freedom involved in balance control. Results indicated a similarity in dimension between local (joints) and global (center of mass) components, between a fixed point and a limit cycle. The behavior of the center of mass was found to be more predictable than the behavior of its local constituents. In addition, the available visual information affected the predictability of the postural behavior, which suggests that vision is used in the stabilization of the low-dimensional dynamics underlying balance control.
THE SARCOPLASMIC RETICULUM AND TRANSVERSE TUBULES OF THE FROG'S SARTORIUS

The sarcoplasmic reticulum of the frog's sartorius muscle was examined by electron microscopy following sequential fixation in glutaraldehyde and osmium tetroxide and embedding in Epon. The earlier results of Porter and Palade on Ambystoma muscle were confirmed in the sartorius. In addition, the transverse tubules were observed to be continuous across the width of the fiber, a set of flat intermediate cisternae was seen to connect the terminal cisternae to the longitudinal tubules in the A band, and the continuous reticulum collar at the center of the A band was found to be perforated by circular and elongated pores (the fenestrated collar). The transverse tubules have a volume about 0.3 per cent of the fiber volume, and a surface area about 7 times the outer cylindrical surface area for a fiber 100 µ in diameter. The terminal cisternae, the intermediate cisternae, and the longitudinal tubules together with the fenestrated collar each have a volume of 4 to 5 per cent of the fiber volume and a surface area 40 to 50 times the outer surface area of a fiber 100 µ in diameter. Some evidence for continuity of the transverse tubules with the fiber surface is presented, but this is thought to be not so convincing as evidence presented by others. The results are discussed in terms of a possible mechanism for a role of the transverse tubules and sarcoplasmic reticulum in excitation-contraction coupling, as suggested by their morphology and a variety of physiological studies. In this scheme, the transverse tubules are thought to be electrically coupled to the terminal cisternae, so that depolarization of the fiber surface spreads inward along the transverse tubules and to the terminal cisternae, initiating the release of a contraction-activating substance.
Morphological Evidence for a Change in the Pattern of Aortic Wall Shear Stress With Age

Objective—The distribution of atherosclerosis around branch sites changes with age in human and rabbit aortas. We tested whether that reflects a change in the pattern of wall shear stress by examining shear-dependent morphological features of endothelial cells. Methods and Results—Endothelial cells and their nuclei align and elongate with applied shear. These parameters were examined in the descending thoracic aorta of immature and mature rabbits. The use of Häutchen preparations, fluorescent stains, and automated image analysis allowed nuclear morphology to be mapped reliably at high resolution over large areas. Cells and their nuclei were most elongated downstream of branch ostia in immature aortas but upstream of them in mature aortas. Elongation was generally greater in mature animals, and nuclei aligned toward the ostia more in these animals, consistent with a greater flow into the branch. Morphology away from branches was indicative of helical flow in the aorta, with greatest shear on the dorsal wall, at both ages. Conclusion—The data are consistent with age-related changes in the pattern of shear around aortic branches. Maps of nuclear elongation closely resembled maps of lesion frequency. The association was positive, implying that lesions occur at sites of high shear stress at both ages.
Physical activity intensity, sedentary time, and body composition in preschoolers.

BACKGROUND Detailed associations between physical activity (PA) subcomponents, sedentary time, and body composition in preschoolers remain unclear. OBJECTIVE We examined the magnitude of associations between objectively measured PA subcomponents and sedentary time with body composition in 4-y-old children. DESIGN We conducted a cross-sectional study in 398 preschool children recruited from the Southampton Women's Survey. PA was measured by using accelerometry, and body composition was measured by using dual-energy X-ray absorptiometry. Associations between light physical activity, moderate physical activity (MPA), vigorous physical activity (VPA), and moderate-to-vigorous physical activity (MVPA) intensity; sedentary time; and body composition were analyzed by using repeated-measures linear regression with adjustment for age, sex, birth weight, maternal education, maternal BMI, smoking during pregnancy, and sleep duration. Sedentary time and PA were also mutually adjusted for one another to determine whether they were independently related to adiposity. RESULTS VPA was the only intensity of PA to exhibit strong inverse associations with both total adiposity [P < 0.001 for percentage of body fat and fat mass index (FMI)] and abdominal adiposity (P = 0.002 for trunk FMI). MVPA was inversely associated with total adiposity (P = 0.018 for percentage of body fat; P = 0.022 for FMI) but only because of the contribution of VPA, because MPA was unrelated to fatness (P ≥ 0.077). No associations were shown between the time spent sedentary and body composition (P ≥ 0.11). CONCLUSIONS In preschoolers, the time spent in VPA is strongly and independently associated with lower adiposity. In contrast, the time spent sedentary and in low-to-moderate-intensity PA was unrelated to adiposity. These results indicate that efforts to challenge pediatric obesity may benefit from prioritizing VPA.
SCRY: Extending SPARQL with Custom Data Processing Methods for the Life Sciences

An ever-growing amount of life science databases are (partially) exposed as RDF graphs (e.g. UniProt, TCGA, DisGeNET, Human Protein Atlas), complementing traditional methods to disseminate biodata. The SPARQL query language provides a powerful tool to rapidly retrieve and integrate this data. However, the inability to incorporate custom data processing methods in SPARQL queries inhibits its application in many life science use cases. It should take far less effort to integrate data processing methods, such as BLAST, with SPARQL. We propose an effective framework for extending SPARQL with custom methods should fulfill four key requirements: generality, reusability, interoperability and scalability. We present SCRY, the SPARQL compatible service layer, which provides custom data processing within SPARQL queries. SCRY is a lightweight SPARQL endpoint that interprets parts of basic graph patterns as input for user defined procedures, generating an RDF graph against which the query is resolved on-demand. SCRY’s federationoriented design allows for easy integration with existing endpoints, extending SPARQL’s functionality to include custom data processing methods in a decoupled, standards-compliant, tool independent manner. We demonstrate the power of this approach by performing statistical analysis of a benchmark, and by incorporating BLAST in a query which simultaneously finds the tissues expressing Hemoglobin β and its homologs.
The Swarm Simulation System: A Toolkit for Building Multi-Agent Simulations

Swarm is a multi-agent software platform for the simulation of complex adaptive systems. In the Swarm system the basic unit of si8mulation is the swarm, a collection of agents executing a schedule of actions. Swarm supports hierarchical modeling approaches whereby agents can be composed of swarms of other agents in nested structures. Swarm provides object oriented libraries of reusable components for building models and analyzing, displaying, and controlling experiments on those models. Swarm is currently available as a beta version in full, free source code form. It requires the GNU C Compiler, Unix, and X Windows. More information about Swarm can be obtained from our web pages, [ Swarm ].
The Role and Issues of Clustering Technique in Designing Maintainable Object Oriented System

: Object Oriented Software development technique has become very popular and is being used by most of the software development companies. Although maintenance may be turn out to be easier for Object Oriented System. But it is unlikely that the maintenance burden will be completely disappearing. It has always been a crucial issue for software project developers. Still, maintenance consumes a large portion of software development cost. Therefore it is worthwhile to develop Object Oriented System keeping maintainability as a key issue in design phase. This paper investigates the use of clustering technique of data mining in maintenance of software system using object oriented metrics. The presented work evaluates the K-means clustering method by applying it to the commercial software system. The experimental work of software maintenance for the sample data is being simulated on Matlab.
WHAT DOES THERAPIST PRESENCE LOOK LIKE IN THE THERAPEUTIC ENCOUNTER? A RATIONAL-EMPIRICAL STUDY OF THE VERBAL AND NON-VERBAL BEHAVIOURAL MARKERS OF PRESENCE

Humanistic approaches to psychotherapy recognize therapeutic presence as necessary to sharpening one’s attunement to ongoing dynamics of intra and interpersonal processes, to promoting empathy and in developing a strong working alliance. Despite its purported value, however, little empirical research has explored the nature of presence in the psychotherapeutic encounter. Following a task analytic methodology, the current study used both rational (model building) and empirical (observational) strategies to investigate how highly present therapists manifest presence through verbal and non-verbal behaviours. As part of a larger research program this study ‘s aim was to observe behavioral markers of therapeutic presence that will inform an observational measure for examining this phenomenon at an in-session, process level of analysis. Results from the present study show that therapist presence is linked to a constellation of verbal and non-verbal markers that reflect four modes of expression, which were named ‘here’, ‘now’, ‘open’, and ‘communion’. The final model that emerged included prominent behaviours such as stable/poised body posture, unwavering eye gaze, responsive nodding and facial expressions, and vitality in face, body, and vocal tone. Implications for the development of an observational measure are discussed, along with limitations and suggestions for future research.
Effects of hyperbaric nitrogen-induced narcosis on response-selection processes

Certain underwater circumstances carry risk of inert gas narcosis. Impairment of sensorimotor information processing due to narcosis, induced by normobaric nitrous oxide or high partial nitrogen pressure, has been broadly evidenced, by a lengthening of the reaction time (RT). However, the locus of this effect remains a matter of debate. We examined whether inert gas narcosis affects the response-selection stage of sensorimotor information processing. We compared an air normobaric condition with a hyperbaric condition in which 10 subjects were subjected to 6 absolute atmospheres of 8.33% O2 Nitrox. In both conditions, subjects performed a between-hand choice-RT task in which we explicitly manipulated the stimulus–response association rule. The effect of this manipulation (which is supposed to affect response-selection processes) was modified by inert gas narcosis. It is concluded, therefore, that response selection processes are among the loci involved in the effect of inert gas narcosis on information processing. Practitioner Summary: Does inert gas narcosis affect the response-selection stage of sensorimotor-information processing? Subjects performed a RT task in which response-selection processes were explicitly manipulated. The well-known ‘compatibility’ effect was modified by inert gas narcosis compared with control condition: response-selection processes are among the loci involved in the effect of inert gas narcosis on information processing.
Stress Theory, Health, and Health Care: Self-care Technology and Self-Identity Reinvigoration

How does self-care technology influence self-concept in patients with chronic health care needs? Progressive patient reliance on self-care is tantamount to the extension of independence and self-reliance in all countries with populations experiencing chronic health challenges. With remarkable advancements in medical technology of late, understanding the effects of self-care technology on patient well-being is critical. This work explores existing literature on the intersection of medical care and technological interventions in populations dealing with chronic illnesses, through the lens of a researcher involved with the HOPE Project in Hawai'i exploring technology use by patients undergoing dialysis treatments. The perspective of this researcher is of note: a patient with type 1 diabetes implementing self-care technology every day. The interplay of self-identity and self-concept is discussed. Stress theory identifies critical areas of risk for patients with chronic medical needs: perceptions of self-efficacy, social support availability and maintenance, and patient experiences as medical patients and social organisms. Research involving self-care technology shows marked improvement in perceptions of self-efficacy, perceptions of social support availability, and positive gains in the lives of people dealing with chronic illnesses. The overarching discussion of human rights must include the narratives of people struggling to find success with chronic illnesses.
Functional Dissection of the PE Domain Responsible for Translocation of PE_PGRS33 across the Mycobacterial Cell Wall

PE are peculiar exported mycobacterial proteins over-represented in pathogenic mycobacterial species. They are characterized by an N-terminal domain of about 110 amino acids (PE domain) which has been demonstrated to be responsible for their export and localization. In this paper, we characterize the PE domain of PE_PGRS33 (PERv1818c), one of the best characterized PE proteins. We constructed several mutated proteins in which portions of the PE domain were deleted or subjected to defined mutations. These proteins were expressed in different mycobacterial species and their localization was characterized. We confirmed that the PE domain is essential for PE_PGRS33 surface localization, and demonstrated that a PE domain lacking its first 30 amino acids loses its function. However, single amino acid substitutions in two regions extremely well conserved within the N-terminal domain of all PE proteins had some effect on the stability of PE_PGRS33, but not on its localization. Using Mycobacterium marinum we could show that the type VII secretion system ESX-5 is essential for PE_PGRS33 export. Moreover, in M. marinum, but not in Mycobacterium bovis BCG and in Mycobacterium tuberculosis, the PE domain of PE_PGRS33 is processed and secreted into the culture medium when expressed in the absence of the PGRS domain. Finally, using chimeric proteins in which different portions of the PERv1818c domain were fused to the N-terminus of the green fluorescent protein, we could hypothesize that the first 30 amino acids of the PE domain contain a sequence that allows protein translocation.
Wideband Propagation Measurements and Analysis of Indoor Radio Channel at 5GHz and 18GHz Using Directive Antennas

Wideband radio propagation measurements at the 4.8 to 5.2GHz and 18 to 19GHz frequency bands using directive antennas were made in the foyer of Main Lecture Theatre(MLT) Nanyang Technological University, Singapore. The area is characterized by high glass panel and zigzag shape with few indoor trees and scattering objects within. Frequency responses of the channel were collected and then transformed to the time domain for analysis by using the Inverse Fast Fourier Transform (IFFT). The collected data was classified into Line Of Sight (LOS) and Obstructed Sight (OBS) at 5GHz and 18GHz band for analysis. The characteristics of the channel were analyzed and compared in terms of path loss and RMS delay spread for these two frequency bands. The exponent values (n) were found less than the free space propagation power law exponent of 2.0 for the LOS areas, and larger than 2.5 for the OBS areas at both these two frequency bands. The RMS delay values obtained here were relative small compared with the results reported by other researchers[1][2] using omni-directional antennas. The use of directive antennas significantly decreases the RMS delay spread and hence reduces the ISI for the Wireless LAN. Key-Words:Indoor Radio Propagation,Multipath,Path Loss,RMS Delay Spread,Wireless LAN, ISI Proc.pp.6171-6175
Practice Evaluation in Social Work

Summary: Practice evaluation strategies range in style from the formal-analytic tools of single-subject designs, software applications such as Singwin, rapid assessment instruments, and evidence-based practice algorithms, to the everyday informal-interactive tools of supervision, consultation with colleagues, use of client statements, and clinical experience. Though survey studies have consistently demonstrated that social workers prefer and most often use informal-interactive tools, scholarship in social work continues to demote the informal-interactive tool preference to a necessary but insufficient expertise for evaluating practice. Findings: Drawing on advances in the cognitive and phenomenological sciences, the purpose of this study is to introduce theory and research for reinterpreting the informal-interactive tool preference as a phenomenologically necessary, cognitively sufficient, and stand-alone expertise for evaluating practice effectiveness. To reinterpret the informal-interactive tool preference, this study will use a dual-process theory situated in a phenomenological context. Application: As the informal-interactive tool preference is theoretically and phenomenologically delineated, scholarship in social work can re-evaluate its tendency to promulgate the formal-analytic tools social workers do not prefer, while demoting the informal-interactive tools social workers do prefer. [Article copies available for a fee from The Haworth Document Delivery Service: 1-800-HAWORTH. E-mail address: <docdelivery@ haworthpress.com> Website: <http://www.HaworthPress. com> © 2006 by The Haworth Press, Inc. All rights reserved. ]
Applications of High Content Screening in Life Science Research

Over the last decade, imaging as a detection mode for cell based assays has opened a new world of opportunities to measure “phenotypic endpoints” in both current and developing biological models. These “high content” methods combine multiple measurements of cell physiology, whether it comes from sub-cellular compartments, multicellular structures, or model organisms. The resulting multifaceted data can be used to derive new insights into complex phenomena from cell differentiation to compound pharmacology and toxicity. Exploring the major application areas through review of the growing compendium of literature provides evidence that this technology is having a tangible impact on drug discovery and the life sciences.