Miracle-dz/UniFAR-FTUs huggingface dataset:
Principal-components analysis of shape fluctuations of single DNA molecules

Thermal fluctuations agitate molecules in solution over a broad range of times and distances. By passively watching the shape fluctuations of a thermally driven biomolecule, one can infer properties of the underlying interactions that determine the motion. We applied this concept to single molecules of fluorescently labeled λ-DNA, a key model system for polymer physics. In contrast to most other single-molecule DNA experiments, we examined the unstretched, equilibrium state of DNA by using an anti-Brownian electrokinetic trap to confine the center of mass of the DNA without perturbing its internal dynamics. We analyze the long-wavelength conformational normal modes, calculate their spring constants, and measure linear and nonlinear couplings between modes. The modes show strong signs of nonlinear hydrodynamics, a feature of the underlying equations of polymer dynamics that has not previously been reported and is neglected in the widely used Rouse and Zimm approximations.
Zone Based Feature Extraction and Statistical Classification Technique for Kannada Handwritten Numeral Recognition

This paper presents the zone based feature extraction and statistical classification technique for Kannada handwritten numeral recognition. The Kannada handwritten numeral database required for the experimentation is collected from the different individuals and are preprocessed for feature extraction. The binary images fitted in a particular window size are partitioned into a number of regions and a real value is computed by the density of one’s to represent the image. The statistical classifier build for the experimentation and on Kannada handwritten numeral database found better classification and recognition rate. Keywords-Handwritten Kannada numeral data; Feature extraction; statistical classifier; Feature matching technique
The Kinetics of L-selectin Tethers and the Mechanics of Selectin-mediated Rolling

Two mechanisms have been proposed for regulating rolling velocities on selectins. These are (a) the intrinsic kinetics of bond dissociation, and (b) the reactive compliance, i.e., the susceptibility of the bond dissociation reaction to applied force. To determine which of these mechanisms explains the 7.5–11.5-fold faster rolling of leukocytes on L-selectin than on E- and P-selectins, we have compared the three selectins by examining the dissociation of transient tethers. We find that the intrinsic kinetics for tether bond dissociation are 7–10-fold more rapid for L-selectin than for E- and P-selectins, and are proportional to the rolling velocities through these selectins. The durations of pauses during rolling correspond to the duration of transient tethers on low density substrates. Moreover, applied force increases dissociation kinetics less for L-selectin than for E- and P-selectins, demonstrating that reactive compliance is not responsible for the faster rolling through L-selectin. Further measurements provide a biochemical and biophysical framework for understanding the molecular basis of rolling. Displacements of tethered cells during flow reversal, and measurements of the distance between successive pauses during rolling provide estimates of the length of a tether and the length of the adhesive contact zone, and suggest that rolling occurs with as few as two tethers per contact zone. Tether bond lifetime is an exponential function of the force on the bond, and the upper limit for the tether bond spring constant is of the same order of magnitude as the estimated elastic spring constant of the lectin–EGF unit. Shear uniquely enhances the rate of L-selectin transient tether formation, and conversion of tethers to rolling adhesions, providing further understanding of the shear threshold requirement for rolling through L-selectin.
Ageing and Development: Theories and Research

With increasing numbers of the population living into old age, we need a better understanding of the nature and experience of ageing in all its aspects. Up to now, very few texts have considered this in any depth, but 'Ageing and Development', a new volume in the Texts in Developmental Psychology series, provides a detailed and comprehensive overview of the theories and research in adult development into old age. The classic early accounts of theorists such as Jung and Erikson are considered, as well as their present day successors. Particular attention is given to theories of adjustment to loss, and to the threat of loss, which dominate current gerontological research. A notable feature of the book is the separate section devoted to the psychology of advanced old age, to life in states of physical and/or mental frailty, and to the survival of the self in these circumstances. There is a strong emphasis throughout on up-to-date empirical research and illustrative case examples. The reader is constantly encouraged to take a critical perspective, to understand the strengths and limitations of different studies, and to think about the issues raised in terms of their own lives.
Prevalence and Predictors of Pulmonary Embolism in Korean Patients with Exacerbation of Chronic Obstructive Pulmonary Disease

Background: Data concerning the rate of pulmonary embolism (PE) in Asian patients with chronic obstructive pulmonary disease (COPD) exacerbation are sparse, and no study has shown predictors of PE in these patients. Objectives: The purpose of the present study was to investigate the prevalence and predictors of PE in Korean patients with COPD exacerbation. Methods: Hospitalized patients with COPD exacerbations were prospectively enrolled into this study and underwent computed tomography (CT) pulmonary angiography and indirect CT venography. Results: The most common cause of COPD exacerbation was lower respiratory tract infection (82%; n = 84), followed by PE (5%; n = 5). Eight patients (8%) had venous thromboembolism, and deep vein thrombosis (DVT) was seen in 6%, with proximal DVT in 4%. On multivariate analysis, the absence of symptoms of respiratory infection and plasma D-dimer elevation (≥500 µg/l) were significant factors predicting PE in patients with COPD exacerbations (odds ratio 31, 95% confidence interval 2-563, p = 0.02, and odds ratio 25, 95% confidence interval 1-464, p = 0.03, respectively). Conclusions: PE comprises approximately 5% of the etiologies of COPD exacerbations in Koreans. The absence of symptoms suggestive of respiratory infection and elevated plasma D-dimer levels were significant predictors of PE in this population.
Ionic Liquids as Advanced Lubricant Fluids

Ionic liquids (ILs) are finding technological applications as chemical reaction media and engineering fluids. Some emerging fields are those of lubrication, surface engineering and nanotechnology. ILs are thermally stable, non-flammable highly polar fluids with negligible volatility, these characteristics make them ideal candidates for new lubricants under severe conditions, were conventional oils and greases or solid lubricants fail. Such conditions include ultra-high vacuum and extreme temperatures. Other very promising areas which depend on the interaction between IL molecules and material surfaces are the use of ILs in the lubrication of microelectromechanic and nanoelectromechanic systems (MEMS and NEMS), the friction and wear reduction of reactive light alloys and the modification of nanophases.
LooM: An Anonymity Quantification Method in Pervasive Computing Environments

We propose a novel anonymity quantification method for privacy protection in pervasive computing environments. Its main feature is that it can quantitatively control anonymity by a single value (disclosure threshold value) using a classification algorithm of the decision tree. The value is not affected by the user set size or the contents of private information. This property was confirmed by evaluation using sample databases. In order to decide the disclosure threshold value for controlling anonymity, we established a model of privacy information disclosure that achieves a balance (equilibrium point) between users' privacy protection requirements and service providers' disclosure requirements. Applying Web questionnaire data to this model we found the equilibrium point for each service
Acculturation and Psychological Distress Among Non-Western Muslim Migrants - a Population-Based Survey

Background: Political and social developments point at increasing marginalization of Muslim migrants, but little is known about its consequences for the mental health of this particular group. Aim: To explore the relationship between acculturation and psychological distress among first-generation Muslim migrants from Turkey and Morocco in the Netherlands. Methods: A cross-sectional study. Respondents were interviewed in their preferred language. Acculturation was measured with the Lowlands Acculturation Scale (LAS) and psychological distress with the Kessler Psychological Distress Scale (K10). Data were complete for 321 subjects and analyzed with multivariate linear regression. Results: Less skills for living in Dutch society was associated with distress (p = 0.032). Feelings of loss were related to distress among Moroccans (p = 0.037). There was an interaction between traditionalism and ethnic background ( p = 0.037); traditionalism was related to less distress among Moroccans (p = 0.020), but not among Turkish. Finally, there was an interaction by gender among Turks (p = 0.029); conservative norms and values seemed to be related to distress among men (p = 0.062), not women. Conclusion: Successful contact and participation in Dutch society, and maintenance of heritage culture and identity were moderately associated with less psychological distress. Improving mastery of the dominant language in host societies, and allowing migrants to preserve their traditions, might be effective measures in improving the mental well-being of migrants.
Is Cognitive Case Formulation Science or Science Fiction

As with all systematic models of therapy, cognitive therapy distills a theory to the understanding of particular cases through the case formulation method. This article sets out criteria to evaluate whether cognitive case formulation follows the process of scientific inquiry, and it questions whether the formulation method meets these criteria. In terms of the evidence base for the cognitive theory that underpins cognitive case formulation, the research suggests that although the descriptive elements of cognitive theory are substantiated, the explanatory elements have received less support. In terms of the scientific status of the cognitive case formulation process, current evidence for the reliability of the cognitive case formulation method is modest, at best. There is a striking paucity of research examining the validity of cognitive case formulations or the impact of cognitive case formulation on therapy outcome. Implications for the clinical use of cognitive case formulation within a scientist-practitioner model are discussed, and potential programs of research to evaluate the case formulation method are described.
Heuristic-based Genetic Operation in Classifier Systems

This thesis focuses on improving the Accuracy-based Learning Classifier System (XCS), a Machine Learning technique that attempts to build general and accurate rules. Adapted from the induction concept, a new approach named Rule Combining (RC) draws conclusions from the experience. It learns more efficient in terms of speed and space requirement compared to the original XCS that employs Darwinian genetic operation. Furthermore, RC allows an additional capability of performing feature selection.
Increased Infiltration of Macrophages in Omental Adipose Tissue Is Associated With Marked Hepatic Lesions in Morbid Human Obesity

In human obesity, white adipose tissue (WAT) is enriched in macrophages. How macrophage infiltration in WAT contributes to the complications of obesity is unknown. This study tested the hypothesis that recruitment of macrophages in omental WAT is associated with hepatic damage in obese patients. Paired biopsies of subcutaneous and omental WAT and a liver biopsy were collected during gastric surgery in 46 obese women and 9 obese men (BMI 47.9 ± 0.93 kg/m2). The number of HAM56+ macrophages in WAT was quantified microscopically, and correlations with clinical and biological parameters and histological liver pathology were investigated. There were twice as many macrophages in omental as in subcutaneous WAT (P < 0.0001). After adjustment for age, omental WAT macrophage infiltration was correlated to fasting glucose and insulin, quantitative insulin sensitivity check index, triglycerides, aspartate aminotransferase (AST), and γ-glutamyltranspeptidase. We propose an easy equation to estimate the amount of macrophages in omental WAT. Increased macrophage accumulation specifically in omental WAT was associated with hepatic fibroinflammatory lesions (P = 0.01). The best predictive model for the severity of hepatic damage includes adiponectinemia, AST, and omental WAT macrophages. These data suggest that the presence of macrophages in omental WAT participates in the cellular mechanisms favoring hepatic fibroinflammatory lesions in obese patients.
Acylation of Escherichia coli Hemolysin: A Unique Protein Lipidation Mechanism Underlying Toxin Function

SUMMARY The pore-forming hemolysin (HlyA) of Escherichia coli represents a unique class of bacterial toxins that require a posttranslational modification for activity. The inactive protoxin pro-HlyA is activated intracellularly by amide linkage of fatty acids to two internal lysine residues 126 amino acids apart, directed by the cosynthesized HlyC protein with acyl carrier protein as the fatty acid donor. This action distinguishes HlyC from all bacterial acyltransferases such as the lipid A, lux-specific, and nodulation acyltransferases, and from eukaryotic transferases such as N-myristoyl transferases, prenyltransferases, and thioester palmitoyltransferases. Most lipids directly attached to proteins may be classed as N-terminal amide-linked and internal ester-linked acyl groups and C-terminal ether-linked isoprenoid groups. The acylation of HlyA and related toxins does not equate to these but does appear related to a small number of eukaryotic proteins that include inflammatory cytokines and mitogenic and cholinergic receptors. While the location and structure of lipid moieties on proteins vary, there are common effects on membrane affinity and/or protein-protein interactions. Despite being acylated at two residues, HlyA does not possess a “double-anchor” motif and does not have an electrostatic switch, although its dependence on calcium binding for activity suggests that the calcium-myristoyl switch may have relevance. The acyl chains on HlyA may provide anchorage points onto the surface of the host cell lipid bilayer. These could then enhance protein-protein interactions either between HlyA and components of a host signal transduction pathway to influence cytokine production or between HlyA monomers to bring about oligomerization during pore formation.
FESAS IDE: An Integrated Development Environment for Autonomic Computing

While Autonomic Computing can ease the maintenance of systems through adaptations [1], the development of Autonomic Computing systems itself introduces a high complexity. Literature suggests that reusable processes for the development and reusable components in the adaptation logic can reduce the complexity. Existing approaches aim to reduce this complexity with tools and frameworks for specific tasks in the development of the adaptation logic of Autonomic Computing systems. However, to the best of our knowledge, none of these approaches offer an Integrated Development Environment (IDE) for it. In this paper, we extend FESAS - our framework for building reusable adaptation logic components - with Eclipse plug-ins integrated into the FESAS IDE for a simplified development of MAPE components as well as a process for deployment of the components. In this paper, we present these tools. Further, we evaluate their potential to ease the development of self-adaptive systems within five example cases. Last, we discuss the benefits and limitations of the FESAS IDE.
Analysis of monopole antenna over a ground plane by a Meshless Local Petrov-Galerkin method

In this work, two different configurations of a monopole mounted over a ground plane have their input admittance determined by a meshless numerical simulation. The Meshless Local Petrov-Galerkin is used with shape functions generated by Moving Least Squares. Boundary conditions are imposed by a collocation scheme that avoids numerical integrations. The proposed axisymmetric analysis has a simple implementation. The results are in agreement with theoretical data and simulations found in the literature.
Grid vs. arbitrary placement of files for generating animated photomosaics

A traditional photomosaic is a still image where a larger picture is created by selectively arranging small picture tiles on a blank, gridded canvas. We show interesting and engaging animations can be generated from an evolutionary search for the final photomosaic image. We then investigate two different tile placement strategies for generating the animations. In the first strategy tiles can only be placed in fixed cells in a 2 dimensional grid and it is not possible for tiles to overlap. This strategy is implemented with a genetic algorithm. In the second strategy, which is implemented using genetic programming, the tiles can be placed in any position and at an arbitrary rotation. It is possible for one tile to be placed on top of another so a method for dealing with overlap is needed. We have investigated three methods for dealing with overlap. The second strategy generates more engaging animations but at considerably increased computational cost. We conclude that evolutionary search can be used to produce very engaging animations in which a target image gradually emerges from an initial random collection of tiles.
A Review of Psychological Literature on the Health and Wellbeing Benefits of Biophilic Design

Abstract: Biophilic design has received increasing attention as a design philosophy in recent years. This review paper focused on the three Biophilic design categories as proposed by Stephen Kellert and Elizabeth Calabrese in “The Practice of Biophilic Design”. Psychological, peer reviewed literature supporting the benefits of Biophilic design was searched for through the lens of restorative environments. Results indicate that there exists much evidence supporting certain attributes of Biophilic design (such as the presence of natural elements), while empirical evidence for other attributes (such as the use of natural materials or processes) is lacking. The review concludes with a call for more research on restorative environments and Biophilic design.
Dexamethasone Increases Cdc42 Expression in Human TM-1 Cells

Abstract Purpose: Changes in the cytoskeletal organization of the human trabecular meshwork (HTM) is thought to be responsible for primary open-angle glaucoma (POAG) pathologies. Cdc42 is a Rho GTPase; Rho GTPases are important modulatory agents of the cytoskeleton. This study aimed to investigate the effects of dexamethasone (DEX) on Cdc42 in a transformed HTM cell line, TM-1 to understand the molecular pathologies underlying POAG. Methods: TM-1 cells were cultured in vitro. The cultures were treated with DEX at 10−6 and 10−7 M for 1–4 days. Cdc42 was silenced using small interfering RNA (siRNA). The expression levels of Cdc42 in the TM-1 cells were measured using reverse transcription (RT)–PCR, western blotting analysis and immunofluorescence. Its downstream effectors, p21-activated kinase phosphorylation (phospho-PAK) and myosin light chain kinase (MLCK), were measured using western blotting analysis. In addition, the F-actin of TM-1 cells was stained using phalloidin. Results: The mRNA and protein levels of Cdc42 showed an increase in TM-1 cells with DEX treatment and a decrease in TM-1 cells transfected with Cdc42 siRNA. Moreover, phospho-PAK levels increased, whereas MLCK levels appeared to decrease, with DEX treatment. The F-actin of DEX-treated TM-1 cells displayed a rearrangement. Cdc42 siRNA decreased the expression of Cdc42 and its related proteins, resulting in an attenuation of the effects of DEX on Cdc42 and F-actin organization in TM-1 cells. Conclusions: DEX increases Cdc42 expression in TM-1. This may represent a potential mechanism of DEX-induced HTM cytoskeletal rearrangement.
Senataxin Plays an Essential Role with DNA Damage Response Proteins in Meiotic Recombination and Gene Silencing

Senataxin, mutated in the human genetic disorder ataxia with oculomotor apraxia type 2 (AOA2), plays an important role in maintaining genome integrity by coordination of transcription, DNA replication, and the DNA damage response. We demonstrate that senataxin is essential for spermatogenesis and that it functions at two stages in meiosis during crossing-over in homologous recombination and in meiotic sex chromosome inactivation (MSCI). Disruption of the Setx gene caused persistence of DNA double-strand breaks, a defect in disassembly of Rad51 filaments, accumulation of DNA:RNA hybrids (R-loops), and ultimately a failure of crossing-over. Senataxin localised to the XY body in a Brca1-dependent manner, and in its absence there was incomplete localisation of DNA damage response proteins to the XY chromosomes and ATR was retained on the axial elements of these chromosomes, failing to diffuse out into chromatin. Furthermore persistence of RNA polymerase II activity, altered ubH2A distribution, and abnormal XY-linked gene expression in Setx−/− revealed an essential role for senataxin in MSCI. These data support key roles for senataxin in coordinating meiotic crossing-over with transcription and in gene silencing to protect the integrity of the genome.
A new point of NP-hardness for unique games

We show that distinguishing 1/2-satisfiable Unique-Games instances from (3/8 + ε)-satisfiable instances is NP-hard (for all ε > 0). A consequence is that we match or improve the best known c vs. s NP-hardness result for Unique-Games for all values of c (except for c very close to 0). For these c, ours is the first hardness result showing that it helps to take the alphabet size larger than 2. Our NP-hardness reductions are quasilinear-size and thus show nearly full exponential time is required, assuming the ETH.
Concurrent aflatoxicosis and caecal coccidiosis in broilers

A farm of two broiler flocks fed from one day old to 56 days of age a diet naturally contaminated with high level of Aflatoxin (AF), were suffered from caecal coccidiosis at 35 days of age Aflatoxin levels in feed commodities and mixed feed were determined using ELISA test. Results of ELISA showed that the average level of corn, soybean and mixed feeds contamination with aflatoxin were 1915, ppb, 229 ppb and 860 ppb respectively. Diagnosis of caecal coccidiosis was confirmed by clinical signs, post-mortem findings, fecal oocyst excretion per gram, oocyt size, morphological characteristic of eggs, lesion score and schizonts size. The significance of AF as predisposing factor to coccidiosis infection was discussed.