Miracle-dz/UniFAR-FTUs huggingface dataset:
Interaction of Calreticulin with CD40 Ligand, TRAIL and Fas Ligand

The molecular chaperone calreticulin has been shown to bind C1q and mannan‐binding lectin (MBL), which are constituents of the innate immune defence system. C1q and MBL do not share a large sequence identity but have a similar overall molecular architecture: an N‐terminal triple‐helical collagen‐like domain and a C‐terminal globular domain with ligand‐binding properties. C1q is a hetero‐trimer, while MBL is a homo‐trimer, but due to the presence of N‐terminal cysteines they both form higher order oligomers of trimers, which are the mature functional molecules. The same molecular architecture is utilized by many other functionally diverse molecules and in this work the interaction of calreticulin with C1q and structurally similar molecules was investigated. In addition to C1q and MBL, CD40 ligand (CD40L), tumour necrosis factor‐related apoptosis‐inducing ligand (TRAIL) and Fas ligand (FasL) were found to bind calreticulin strongly. A low level or no binding was observed for adiponectin, tumour necrosis factor‐α (TNF‐α), CD30L, surfactant protein‐A and ‐D and collagen VIII. The interaction with calreticulin required a conformational change in CD40L, TRAIL and FasL and showed the same characteristics as calreticulin’s interaction with C1q and MBL: a time‐dependent saturable binding to immobilized protein, which was initially sensitive to salt but gradually developed into a salt‐insensitive interaction. Thus, the interaction requires a structural change in the interaction partner and leads to a conformational change in calreticulin itself. The implications of these results are that calreticulin may function as a general response modifier for a whole group of immunologically important proteins.
CPAF: A Chlamydial Protease in Search of an Authentic Substrate

Bacteria in the genus Chlamydia are major human pathogens that cause an intracellular infection. A chlamydial protease, CPAF, has been proposed as an important virulence factor that cleaves or degrades at least 16 host proteins, thereby altering multiple cellular processes. We examined 11 published CPAF substrates and found that there was no detectable proteolysis when CPAF activity was inhibited during cell processing. We show that the reported proteolysis of these putative CPAF substrates was due to enzymatic activity in cell lysates rather than in intact cells. Nevertheless, Chlamydia-infected cells displayed Chlamydia-host interactions, such as Golgi reorganization, apoptosis resistance, and host cytoskeletal remodeling, that have been attributed to CPAF-dependent proteolysis of host proteins. Our findings suggest that other mechanisms may be responsible for these Chlamydia-host interactions, and raise concerns about all published CPAF substrates and the proposed roles of CPAF in chlamydial pathogenesis.
Psoriasis Patients Are Enriched for Genetic Variants That Protect against HIV-1 Disease

An important paradigm in evolutionary genetics is that of a delicate balance between genetic variants that favorably boost host control of infection but which may unfavorably increase susceptibility to autoimmune disease. Here, we investigated whether patients with psoriasis, a common immune-mediated disease of the skin, are enriched for genetic variants that limit the ability of HIV-1 virus to replicate after infection. We analyzed the HLA class I and class II alleles of 1,727 Caucasian psoriasis cases and 3,581 controls and found that psoriasis patients are significantly more likely than controls to have gene variants that are protective against HIV-1 disease. This includes several HLA class I alleles associated with HIV-1 control; amino acid residues at HLA-B positions 67, 70, and 97 that mediate HIV-1 peptide binding; and the deletion polymorphism rs67384697 associated with high surface expression of HLA-C. We also found that the compound genotype KIR3DS1 plus HLA-B Bw4-80I, which respectively encode a natural killer cell activating receptor and its putative ligand, significantly increased psoriasis susceptibility. This compound genotype has also been associated with delay of progression to AIDS. Together, our results suggest that genetic variants that contribute to anti-viral immunity may predispose to the development of psoriasis.
Another Look at Job and Life Satisfaction among Employees: Evidence from a Developing Country

Organizational literature has demonstrated remarkable attention to the relationship between job and life satisfaction. Approaching the relationship between job and life satisfaction from an attitu-dinal perspective, the present study was conducted to examine the relationship between job and life satisfaction in Southern Saudi Arabia. It also aimed to investigate the contribution of demo-graphic and socioeconomic variables in predicting job and life satisfaction. The results of Pearson correlation analysis and hierarchical regression analysis revealed a statistically significant rela-tionship between job and life satisfaction, even after controlling for demographic and socioeconomic variables. The results also suggested that job satisfaction and life satisfaction were positively and reciprocally related. Having controlled for demographic and socioeconomic variables, the age variable was uniquely predicted job satisfaction. Additionally, Tukey’s post-hoc test showed that participants whose age ranged from 40 to 50 were more satisfied with their jobs (M = 3.73; SD = 0.35) than those from 18 to 28 and from 29 to 39. That is, older employees were more satisfied with their jobs than younger employees.
Statistical Optimization in High Dimensions

We consider optimization problems whose parameters are known only approximately, based on noisy samples. Of particular interest is the high-dimensional regime, where the number of samples is roughly equal to the dimensionality of the problem, and the noise magnitude may greatly exceed the magnitude of the signal itself. This setup falls far outside the traditional scope of Robust and Stochastic optimization. We propose three algorithms to address this setting, combining ideas from statistics, machine learning, and robust optimization. In the important case where noise artificially increases the dimensionality of the parameters, we show that combining robust optimization and dimensionality reduction can result in high-quality solutions at greatly reduced computational cost.
An Emergency Warning Message Dissemination Policy of Vehicular Ad Hoc Network

In vehicular ad hoc network, emergency warning messages exchange could improve vehicle safety. Emergency warning messages should be exchanged with high reliability and low delay. Currently, reliability of emergency warning messages is guaranteed by repeating broadcast. In current research, how many times repeated broadcast per second was not discussed. In this paper, a speed-based broadcast rate model is proposed. The main idea of the method was to model the message creation and broadcast system as a queuing system. With the relationship model of vehicle speed and message creation number was established, and the transfer delay of emergency message was limited, the basic model to calculate the optimized repeating broadcast rate was proposed. Experiment results showed that the method had balanced reliability and transfer delay of emergency message broadcast with simple operation.
Ethical Dimensions of Shared Ethnicity, Language, and Immigration Experience.

In this article I illustrate how some commonalities that I share with my participants―ethnic background, native language, and immigration experience―create unexpected ethical concerns. I explore how these commonalities facilitate the establishment of rapid intimacy, at the same time creating the temptations of overidentification and blurring the boundaries between researcher and participants. Drawing on three episodes from my ethnographic field work, I demonstrate how the mundane and taken-for-granted encounters with informants (used synonymously with participants) reveal the seeds of ethical dilemmas when put under the powerful and critical lens of reflexivity. Instead of viewing ethics as adherence to a set of codes, I explore reflexivity as ethical practice. Researchers continually make on-the-fly decisions in the field and take corresponding actions without the luxury of careful forethought. I argue that such decisions need to be unpacked after the event to examine if they carry ethical implications with them.
The Johnson Typologies of Intimate Partner Violence: An Investigation of Their Representation in a General Population of New Zealand Women

Typologies of intimate partner violence (IPV) can inform practice and aid with the development of interventions. To maintain utility, typologies should be constantly reviewed in light of emerging results generated from internal and external validation. The presented study is an empirical exploration of the M. P. Johnson (2008) typology of IPV using data gathered from the New Zealand replication of the World Health Organization Violence Against Women survey. We could not identify all types of IPV described by Johnson, and we suggest that mutually exclusive types of violent relationships do not exist. Further exploration of the validity of the Johnson typologies, including an exploration of the utility of categorization for suggesting appropriate responses to IPV, is required.
Effects of Phosphorothioate Oligodeoxynucleotide on Hemoglobin-induced Damage to Intestinal Mucosa

Some “blood substitutes,” such as human diaspirin cross-linked hemoglobin DBBF-Hb, can damage the intestinal mucosa. This response may be due to release of free iron from Hb leading to production of reactive oxygen species (ROS). Phosphorothioate oligodeoxynucleotides can bind and sequester iron. Therefore experiments were performed to test whether PS-ODN, composed of ten consecutive cytidines “C-10,” reduces Hb-induced ROS generation and damage in the mucosa. Anesthetized Sprague-Dawley rats (4–6 per group) were injected arterially with 1 mg C-10, followed two minutes later by 50 mg DBBF-Hb. The positive controls received only DBBF-Hb and the negative controls either saline or PS-ODN followed by saline. Either ROS formation was monitored using a fluorescence technique, or the intestine was fixed for microscopy after 8 or 30 min. Sixty villi per rat were assigned an epithelial integrity index (EI), ranging from 1 (intact) to 3 (some cell–cell and cell–basement membrane separation). Pretreatment with PS-ODN significantly exacerbated DBBF-Hb-induced ROS formation, and PS-ODN groups showed significantly more epithelial damage near Peyer's patches, (EI of 1.93 ± 0.06 (SEM) at 8 minutes and 1.31 ± 0.04 at thirty minutes), than the negative controls, (1.11 ± 0.02 at both 8 and 30 minutes), or the positive controls (1.43 ± 0.05 at 8 minutes and 1.20 ± 0.03 at 30 minutes) ( p < 0.05). However, mast cell degranulation, eosinophil accumulation and goblet cell secretion were significantly reduced in the DBBF-Hb groups pre-treated with PS-ODN. Thus, PS-ODN, although an iron chelator, can significantly enhance epithelial damage caused by DBBF-Hb in the rat intestinal mucosa near Peyer's patches, possibly by formation of the ferryl component of the hemoglobin.
Diospyrin, a bisnaphthoquinone: a novel inhibitor of type I DNA topoisomerase of Leishmania donovani.

Diospyrin is a plant product that has significant inhibitory effect on the growth of Leishmania donovani promastigotes. This compound inhibits the catalytic activity of DNA topoisomerase I of the parasite. Like camptothecin, it induces topoisomerase I mediated DNA cleavage in vitro. Treatment of DNA with diospyrin before addition of topoisomerase I has no effect. Preincubation of topoisomerase I with diospyrin before the addition of DNA in the relaxation reaction increases this inhibition. Our results suggest that this bis-naphthoquinone compound exerts its inhibitory effect by binding with the enzyme and stabilizing the topoisomerase I-DNA "cleavable complex. " Diospyrin is a specific inhibitor of the parasitic topoisomerase I. It does not inhibit type II topoisomerase of L. donovani and requires much higher concentrations to inhibit type I topoisomerase of calf thymus. The potent inhibitory effect of diospyrin on type I DNA topoisomerase from L. donovani can be exploited for rational drug design in human leishmaniasis.
Time-resolved X-ray spectroscopies of chemical systems: New perspectives

The past 3–5 years have witnessed a dramatic increase in the number of time-resolved X-ray spectroscopic studies, mainly driven by novel technical and methodological developments. The latter include (i) the high repetition rate optical pump/X-ray probe studies, which have greatly boosted the signal-to-noise ratio for picosecond (ps) X-ray absorption spectroscopy studies, while enabling ps X-ray emission spectroscopy (XES) at synchrotrons; (ii) the X-ray free electron lasers (XFELs) are a game changer and have allowed the first femtosecond (fs) XES and resonant inelastic X-ray scattering experiments to be carried out; (iii) XFELs are also opening the road to the development of non-linear X-ray methods. In this perspective, I will mainly focus on the most recent technical developments and briefly address some examples of scientific questions that have been addressed thanks to them. I will look at the novel opportunities in the horizon.
Disintegrated Rural Development? Neo‐endogenous Rural Development, Planning and Place‐Shaping in Diffused Power Contexts

What is the role of the state in promoting sustainable rural communities? Only a few years ago any discussion of this question would have alluded to the concept of integrated rural development. Today the concept of governance is internationally used to address such questions, reflecting a recognition of the changing role of the state (at all levels) and the greater propensity for public, private and voluntary sectors to interact at multiple scales in diffused power contexts together with attempts to mobilise local actors. This article asks whether the concept, integrated rural development, still has any meaning in the context of the new rural governance and begins to link this to re-theorisations of concepts of spatial planning, place-shaping, capacity-building and neo-endogenous development, and offers illustrations from the north of Scotland. The article concludes by suggesting that initiatives such as the EU’s LEADER programme might be recast explicitly as a transnational experiment in doing ‘disintegrated rural development’, addressing the challenges of neo-endogenous rural development, multi-scalar governance, an enabling, generative state and the transformation of mainstream policies.
Geodesic‐Controlled Developable Surfaces for Modeling Paper Bending

We present a novel and effective method for modeling a developable surface to simulate paper bending in interactive and animation applications. The method exploits the representation of a developable surface as the envelope of rectifying planes of a curve in 3D, which is therefore necessarily a geodesic on the surface. We manipulate the geodesic to provide intuitive shape control for modeling paper bending. Our method ensures a natural continuous isometric deformation from a piece of bent paper to its flat state without any stretching. Test examples show that the new scheme is fast, accurate, and easy to use, thus providing an effective approach to interactive paper bending. We also show how to handle non‐convex piecewise smooth developable surfaces.
An octopus-bioinspired solution to movement and manipulation for soft robots

Soft robotics is a challenging and promising branch of robotics. It can drive significant improvements across various fields of traditional robotics, and contribute solutions to basic problems such as locomotion and manipulation in unstructured environments. A challenging task for soft robotics is to build and control soft robots able to exert effective forces. In recent years, biology has inspired several solutions to such complex problems. This study aims at investigating the smart solution that the Octopus vulgaris adopts to perform a crawling movement, with the same limbs used for grasping and manipulation. An ad hoc robot was designed and built taking as a reference a biological hypothesis on crawling. A silicone arm with cables embedded to replicate the functionality of the arm muscles of the octopus was built. This novel arm is capable of pushing-based locomotion and object grasping, mimicking the movements that octopuses adopt when crawling. The results support the biological observations and clearly show a suitable way to build a more complex soft robot that, with minimum control, can perform diverse tasks.
ITEP-TH-05 / 09 Holographic Gauge Mediation

We discuss gravitational backgrounds where supersymmetry is broken at the end of a warped throat, and the SUSY-breaking is transmitted to the Standard Model via gauginos which live in (part of) the bulk of the throat geometry. We find that the leading effect arises from splittings of certain “messenger mesons,” which are adjoint KK-modes of the D-branes supporting the Standard Model gauge group. This picture is a gravity dual of a strongly coupled field theory where SUSY is broken in a hidden sector and transmitted to the Standard Model via a relative of semi-direct gauge mediation.
Prediction of Intrauterine Pressure From Electrohysterography Using Optimal Linear Filtering

We propose a method of predicting intrauterine pressure (IUP) from external electrohysterograms (EHG) using a causal FIR Wiener filter. IUP and 8-channel EHG data were collected simultaneously from 14 laboring patients at term, and prediction models were trained and tested using 10-min windows for each patient and channel. RMS prediction error varied between 5-14 mmHg across all patients. We performed a 4-way analysis of variance on the RMS error, which varied across patients, channels, time (test window) and model (train window). The patient-channel interaction was the most significant factor while channel alone was not significant, indicating that different channels produced significantly different RMS errors depending on the patient. The channel-time factor was significant due to single-channel bursty noise, while time was a significant factor due to multichannel bursty noise. The time-model interaction was not significant, supporting the assumption that the random process generating the IUP and EHG signals was stationary. The results demonstrate the capabilities of optimal linear filter in predicting IUP from external EHG and offer insight into the factors that affect prediction error of IUP from multichannel EHG recordings
The Genotoxic and Cytotoxic Effects of Bisphenol-A (BPA) in MCF-7 Cell Line and Amniocytes

Bisphenol-A (BPA) is an industrial xenoestrogen used widely in our living environment. Recently, several studies suggested that BPA has destructive effects on DNA and chromosomes in normal body cells via estrogen receptors (ER). Therefore, BPA could be considered as an important mediator in many diseases such as cancer. However, there are still many controversial issues which need clarification. In this study, we investigated the BPA-induced chromosomal damages in MCF-7 cell line, ER-positive and negative amniocyte cells. Cytotoxicity and genotoxicity effects of BPA were also compared between these three cell groups. Expression of estrogen receptors was determined using immunocytochemistry technique. The cell cytotoxicity of BPA was measured by MTT assay. Classic cytogenetic technique was carried out for the investigation of chromosome damage. BPA, in addition to cytotoxicity, had remarkable genotoxicity at concentrations close to the traceable levels in tissues or biological fluids. Although some differences were observed in the amount of damages between ER-positive and negative fetal cells, interestingly, these differences were not significant. The present study showed that BPA could lead to chromosomal aberrations in both ER-dependent and independent pathways at some concentrations or in cell types yet not reported. Also, BPA could probably be considered as a facilitator for some predisposed cells to be cancerous by raising the chromosome instability levels. Finally, estrogen receptor seems to have a different role in cytotoxicity and genotoxicity effects.
Combining article content and Web usage for literature recommendation in digital libraries

In a large‐scale digital library, it is essential to recommend a small number of useful and related articles to users. In this paper, a literature recommendation framework for digital libraries is proposed that dynamically provides recommendations to an active user when browsing a new article. This framework extends our previous work that considers only Web usage data by utilizing content information of articles when making recommendations. Methods that make use of pure content data, pure Web usage data, and both content and usage data are developed and compared using the data collected from our university's electronic thesis and dissertation (ETD) system. The experimental results demonstrate that content data and usage data are complements of each other and hybrid methods that take into account of both types of information tend to achieve more accurate recommendations.
Fault estimation—a standard problem approach

This paper presents a range of optimization based approaches to fault diagnosis. A variety of fault diagnosis problems are reformulated in the so‐called standard problem set‐up introduced in the literature on robust control. Once the standard problem formulations are given, the fault diagnosis problems can be solved by standard optimization techniques. The proposed methods include (1) fault diagnosis (fault estimation, (FE)) for systems with model uncertainties; FE for systems with parametric faults, and FE for a class of nonlinear systems. Copyright © 2002 John Wiley & Sons, Ltd.
Planning plausible human motions for navigation and collision avoidance

This thesis investigates the plausibility of computer-generated human motions for navigation and collision avoidance. To navigate a human character through obstacles in an virtual environment, the problem is often tackled by finding the shortest possible path to the destination with smoothest motions available. This is because such solution is regarded as cost-effective and free-flowing in that it implicitly minimises the biomechanical efforts and potentially precludes anomalies such as frequent and sudden change of behaviours, and hence more plausible to human eyes. Previous research addresses this problem in two stages: finding the shortest collision-free path (motion planning) and then fitting motions onto this path accordingly (motion synthesis). This conventional approach is not optimal because the decoupling of these two stages introduces two problems. First, it forces the motion-planning stage to deliberately simplify the collision model to avoid obstacles. Secondly, it over-constrains the motion-synthesis stage to approximate motions to a sub-optimal trajectory. This often results in implausible animations that travel along erratic long paths while making frequent and sudden behaviour changes. In this research, I argue that to provide more plausible navigation and collision avoidance animation, close-proximity interaction with obstacles is crucial. To address this, I propose to combine motion planning and motion synthesis to search for shorter and smoother solutions. The intuition is that by incorporating precise collision detection and avoidance with motion capture database queries, we will be able to plan fine-scale interactions between obstacles and moving crowds. The results demonstrate that my approach can discover shorter paths with steadier behaviour transitions in scene navigation and crowd avoidance. In addition, this thesis attempts to propose a set of metrics that can be used to evaluate the plausibility of computer-generated navigation animations.