Miracle-dz/UniFAR-FTUs huggingface dataset:
Differing Requirements for CCR4, E-Selectin, and α4β1 for the Migration of Memory CD4 and Activated T Cells to Dermal Inflammation

CCR4 on T cells is suggested to mediate skin homing in mice. Our objective was to determine the interaction of CCR4, E-selectin ligand (ESL), and α4β1 on memory and activated T cells in recruitment to dermal inflammation. mAbs to rat CCR4 were developed. CCR4 was on 5–21% of memory CD4 cells, and 20% were also ESL+. Anti–TCR-activated CD4 and CD8 cells were 40–55% CCR4+, and ∼75% of both CCR4+ and CCR4− cells were ESL+. CCR4+ memory CD4 cells migrated 4- to 7-fold more to dermal inflammation induced by IFN-γ, TNF, TLR agonists, and delayed-type hypersensitivity than CCR4− cells. CCR4+ activated CD4 cells migrated only 5–50% more than CCR4− cells to these sites. E-selectin blockade inhibited ∼60% of CCR4+ activated CD4 cell migration but was less effective on memory cells where α4β1 was more important. Anti-α4β1 also inhibited CCR4− activated CD4 cells more than CCR4+ cells. Anti–E-selectin reduced activated CD8 more than CD4 cell migration. These findings modify our understanding of CCR4, ESL, α4β1, and dermal tropism. There is no strict relationship between CCR4 and ESL for skin homing of CD4 cells, because the activation state and inflammatory stimulus are critical determinants. Dermal homing memory CD4 cells express CCR4 and depend more on α4β1 than ESL. Activated CD4 cells do not require CCR4, but CCR4+ cells are more dependent on ESL than on α4β1, and CCR4− cells preferentially use α4β1. The differentiation from activated to memory CD4 cells increases the dependence on CCR4 for skin homing and decreases the requirement for ESL.
Cryo-Electron Tomography of Frozen-Hydrated Sections of Eukaryotic Cells

Electron tomography (ET) of chemically fixed, plastic embedded and sectioned specimens has become a useful method for studies of 3-D cell structure [1]. Fixation, embedding, and staining make biological samples comparatively resilient to the electron beam, which enables a routine application of ET to plastic sections. However, plastic embedded specimens can suffer artifacts from fixation, dehydration, sectioning, and section collapse during electron irradiation [2,3]. Consequently, there is great current interest in cryo-ET of unfixed and unstained frozen-hydrated samples, which allows visualization of cellular structures in a near-to-native state. To date, cryo-ET has been used primarily for specimens that can be embedded in vitreous ice by plunge freezing, such as macromolecular complexes, isolated organelles and small bacterial cells, because the sample thickness that can be imaged by cryo-EM is limited to ~0.5 mm [4]. Thus cryo-ET of eukaryotic cells has been restricted to very thin regions of the cell like lamellipodia or flagella [5,6]. Here we show that cryo-microtomy permits cryo-ET of samples like yeasts and mitotic mammalian cells that are thick enough to require high-pressure freezing for vitrification.
Algorithms for Multiple Basis Pursuit Denoising

We address the problem of learning a joint sparse approximation of several signals over a dictionary. We pose the problem as a matrix approximation problem with a row-sparsity inducing penalization on the coefficient matrix. We propose a simple algorithm based on iterative shrinking for solving the problem. At the present time, such a problem is solved either by using a Second-Order Cone programming or by means of a MFocuss algorithm. While the former algorithm is computationally expensive, the latter is efficient but present some pitfalls like presences of fixed points which are undesiderable when solving a convex problem. By analyzing the optimality conditions of the problem, we derive a simple algorithm. The algorithm we propose is efficient and is guaranteed to converge to the optimal solution, up to a given tolerance. Furthermore, by means of a reweighte
DTKI: A New Formalized PKI with Verifiable Trusted Parties

The security of public key validation protocols for web-based applications has recently attracted attention because of weaknesses in the certificate authority model, and consequent attacks. Recent proposals using public logs have succeeded in making certificate management more transparent and verifiable. However, those proposals involve a fixed set of authorities. This means an oligopoly is created. Another problem with current log-based system is their heavy reliance on trusted parties that monitor the logs. We propose a distributed transparent key infrastructure (DTKI), which greatly reduces the oligopoly of service providers and allows verification of the behaviour of trusted parties. In addition, this paper formalises the public log data structure and provides a formal analysis of the security that DTKI guarantees.
Low‐ to high‐fidelity simulation – a continuum of medical education?

Context Changes in medical training and culture have reduced the acceptability of the traditional apprenticeship style training in medicine and influenced the growth of clinical skills training. Simulation is an educational technique that allows interactive, and at times immersive, activity by recreating all or part of a clinical experience without exposing patients to the associated risks. The number and range of commercially available technologies used in simulation for education of health care professionals is growing exponentially. These range from simple part‐task training models to highly sophisticated computer driven models.
Changes in small intestinal chromogranin A-immunoreactive cell densities in patients with irritable bowel syndrome after receiving dietary guidance

Chromogranin A (CgA) is a common marker for enteroendocrine cells in the gut, and CgA-immunoreactive cell densities are abnormal in patients with irritable bowel syndrome (IBS). The majority of patients with IBS report that their symptoms develop after consuming certain foodstuffs. In the present study, we investigated the effects of dietary guidance on the total enteroendocrine cell densities in the small intestine, as detected by CgA. A total of 14 patients with IBS underwent a gastroscopy with duodenal biopsies and 11 of them also underwent a colonoscopy, with biopsy samples obtained from the ileum. Fourteen control subjects were also included. Each patient received 3 sessions of dietary guidance. Gastroscopies and colonoscopies were performed on both the controls and patients with IBS (at baseline and at 3–9 months after receiving guidance). Biopsy samples obtained from the duodenum and ileum were immunostained for CgA using the avidin-biotin complex (ABC) method and were quantified using computerized image analysis. The density of CgA-immunoreactive cells in the duodenum (mean ± SEM values) in the control subjects was 235.9±31.9 cells/mm2; in the patients with IBS, the density was 36.9±9.8 and 103.7±16.9 cells/mm2 before and after they received dietary guidance, respectively (P=0.007). The density of CgA-immunoreactive cells in the ileum in the control subjects was 47.4±8.3 cells/mm2; in the patients with IBS, the density was 48.4±8.1 and 17.9±4.4 cells/mm2, before and after they received dietary guidance, respectively (P=0.0006). These data indicate that changes in CgA-immunoreactive cell densities in patients with IBS after receiving dietary guidance may reflect a change in the densities of the small intestinal enteroendocrine cells, which may contribute to an improvement in the IBS symptoms.
Effects of ageing on touch

A decline in the main sensory modalities is well reported to occur with ageing. This article outlines the normal pathways involved in touch sensation and includes a review of available evidence relating to the study of ageing and touch. The authors try to use what is known about the neuroanatomy and neurophysiology of ageing to explain the impact on some broad functional deficits seen in the elderly population. The importance of understanding how the normal ageing process affects touch sensation is emphasised.
Hunter-Gatherer Energetics and Human Obesity

Western lifestyles differ markedly from those of our hunter-gatherer ancestors, and these differences in diet and activity level are often implicated in the global obesity pandemic. However, few physiological data for hunter-gatherer populations are available to test these models of obesity. In this study, we used the doubly-labeled water method to measure total daily energy expenditure (kCal/day) in Hadza hunter-gatherers to test whether foragers expend more energy each day than their Western counterparts. As expected, physical activity level, PAL, was greater among Hadza foragers than among Westerners. Nonetheless, average daily energy expenditure of traditional Hadza foragers was no different than that of Westerners after controlling for body size. The metabolic cost of walking (kcal kg−1 m−1) and resting (kcal kg−1 s−1) were also similar among Hadza and Western groups. The similarity in metabolic rates across a broad range of cultures challenges current models of obesity suggesting that Western lifestyles lead to decreased energy expenditure. We hypothesize that human daily energy expenditure may be an evolved physiological trait largely independent of cultural differences.
Territoriality and behaviour on and around large vertical publicly-shared displays

We investigate behaviours on, and around, large vertical displays during concurrent usage. Using an observational field study, we identify fundamental patterns of how people use existing public displays: their orientation, positioning, group identification, and behaviour within and between social groups just-before, during, and just-after usage. These results are then used to motivate a controlled experiment where two individuals or two pairs of individuals complete tasks concurrently on a simulated large vertical display. Results from our controlled study demonstrates that vertical surface territories are similar to those found in horizontal tabletops in function, but their definitions and social conventions are different. In addition, the nature of use-while-standing systems results in more complex and dynamic physical territories around the display. We show that the anthropological notion of personal space must be slightly refined for application to vertical displays.
Modeling in-network processing and aggregation in sensor networks: algorithms and evaluation

The rapid advances in processor, memory and radio technology have enabled the development of distributed networks of sensor nodes capable of sensing and communicating using wireless media. The basic operation in sensor networks is the systematic gathering and transmission of sensed data to the end-user. The severe energy constraints and limited computing capabilities of the sensors present major challenges to sensor network design. We propose two new protocols for in-network processing and data aggregation, DEEPADS (distributed energy-efficient protocol for aggregation of data in sensor networks) and C-DEEPADS (clustered-DEEPADS) that maximize the lifetime of the sensor network. Simulation results show that our protocols perform better than these existing approaches: directed diffusion (Intanagonwiwat, C. et al., 2003), LEACH (Heinzelman, W. et al., 2002), PEDAP and PEDAP-PA (Tan, H.O. and Korpeoglu, I., 2003.). The two-tier hierarchical approach of C-DEEPADS is optimal in terms of maximizing the system lifetime as well as reducing-the end-to-end latency
Maize Seeds Submitted to Thermotherapy and Analyzed by Dynamic Speckle

: The quality of the seeds used for sowing is fundamental for a high productivity and quality of the crop. Therefore, eradicating pathogens is essential for the plant to develop in the best possible way. The eradication of those pathogens can be accomplished by means of treatments that consist of the application of substances to the seeds or by performing physical procedures. Thermotherapy is a physical treatment, in which the seed is exposed to a given thermal energy, such as heated air or steam, and can be highly efficient for controlling those pathogens, in addition to reducing environmental damage and costs. The present work aimed to evaluate the efficiency of thermotherapy in two ways: wet heat (water) and dry heat (water vapor), both at 60 °C, alternating the exposure time to the thermal sources. The treatment with humid heat with a time of exposure of 5 min was the most efficient, since it presented higher germination percentages (83%) and less occurrence of Fusarium sp. (33%). It was observed that the most efficient thermotherapy is in the control of Fusarium , the most aggressive is for the quality of the seed. The quality of the treatments was evaluated through standard methodologies, according to the rules for seed analysis, such as germination and sanitation tests. Biospeckle laser was used to identify the microbial activity in these seeds, through activity maps generated by laser speckle contrast analysis (LASCA) processing. In this way, the research involving thermotherapy can be done by varying the temperature and the time of exposure to obtain values that considerably reduce the pathogenic agents and preserve the quality, in order to maintain the values of germination and vigor acceptable for commercialization.
The Leucine-Responsive Regulatory Protein, Lrp, Activates Transcription of the fim Operon in Salmonella enterica Serovar Typhimurium via the fimZ Regulatory Gene

ABSTRACT The fim operon of Salmonella enterica serovar Typhimurium encodes type 1 fimbriae. The expression of fim is controlled in response to environmental signals through a complex regulatory cascade involving the proteins FimW, FimY, and FimZ and a genetic locus, fimU, that encodes a rare arginine tRNA. We discovered that a knockout mutation in lrp, the gene that codes for the leucine-responsive regulatory protein (Lrp), inhibited fim transcription. The loss of fim gene expression was accompanied by a corresponding loss of the mannose-sensitive hemagglutination that is a characteristic of type 1 fimbriae. Normal type 1 fimbrial expression was restored following the introduction into the knockout mutant of a plasmid carrying a functional copy of the lrp gene. Electrophoretic mobility shift analysis revealed no interactions between purified Lrp protein and the regulatory region of the fimA, fimU, or fimW gene. Instead, Lrp produced protein-DNA complexes with the regulatory region of the fimZ gene, and the nature of these complexes was leucine sensitive. DNase I footprinting showed that Lrp binds within a region between −65 and −170 with respect to the fimZ transcription start site, consistent with the binding and wrapping of the DNA in this upstream region. Ectopic expression of the fimZ gene from an inducible promoter caused Lrp-independent type 1 fimbriation in serovar Typhimurium. These data show that Lrp makes a positive contribution to fim gene expression through direct interaction with the fimZ promoter region, possibly by antagonizing the binding of the H-NS global repressor protein.
Effect of Green Tea (Camellia sinensis) Solution on Color Change of Silorane- and Methacrylate-Based Composite Resins

Color change is an undesirable but avoidable effect in composite resin. Limited research has been conducted on the effect of green tea solution on silorane- and methacrylate-based composite resins. In this study, we used 30 silorane- and methacrylate-based composite resin disks (shade A3) (6 mm in diameter and 2 mm in thickness) prepared from Filtek P90 and Filtek Z250. Specimens were divided into six groups (n = 5), and each group was immersed in three green tea solutions at different concentrations (1%, 2%, and 3%) for 6 hours. Color assessment was performed with a spectrophotometer based on CIE*Lab theory, and results were subjected to statistical analysis using one-way ANOVA and independent t-test. Significant differences were observed in Δi* between the two composite disks after immersion in tea solutions (p < 0.05). Color change in silorane-based composite resin was higher than that in methacrylate-based resin; this color change was the highest when silorane-based composite resin was immersed in 3% green tea solution (ΔE = 3.85).
Retinal image motion alone does not control disconjugate postsaccadic eye drift.

1. In these experiments, postsaccadic ocular drift was induced by postsaccadic motion of the visual scene. In the most important case, the scene was moved in one eye but not the other. Six human subjects viewed the interior of a full-field hemisphere filled with a random-dot pattern. During training, eye movements were recorded by the electrooculogram. A computer detected the end of every saccade and immediately moved the pattern horizontally in the same or, in different experiments, in the opposite direction as the saccade. The pattern motion was exponential with an amplitude of 25% of the size of the antecedent saccade and a time constant of 50 ms. Before and after 3-4 h of such training, movements of both eyes were measured simultaneously by the eye coil-magnetic field method while subjects looked between stationary targets for calibration, explored the visual pattern with saccades, or made saccades in the dark to measure the effects of adaptation on postsaccadic ocular drift. The amplitude of this drift was expressed as a percentage of the size of the antecedent saccade. 2. In monocular experiments, subjects viewed the random-dot pattern with one eye. The other eye was patched. With two subjects, the pattern drifted backward in the direction opposite to the saccade; with the third, it drifted onward. The induced ocular drift was exponential, always in the direction to reduce retinal image motion, had zero latency, and persisted in the dark. After training, drift in the dark changed by 6.7% in agreement with our prior study with binocular vision, which produced a change of 6.0%. 3. In a dichoptic arrangement, one eye regarded the moveable random-dot pattern; the other, through mirrors, saw a different random-dot pattern (with similar spacing, contrast, and distance) that was stationary. These visual patterns were not fuseable and did not evoke subjective diplopia. In this case, the induced change in postsaccadic drift in the same three subjects was only 4.8%. In all cases the changes in postsaccadic drift were conjugate--they obeyed Hering's law. 4. Normal human saccades are characterized by essentially no postsaccadic drift in the abducting eye and a pronounced onward drift (approximately 4%) in the adducting eye. After training, this abduction-adduction asymmetry was preserved in the light and dark with monocular or dichoptic viewing, indicating again that all adaptive changes were conjugate. 5. When the subjects viewed the adapting stimulus after training, the zero-latency, postsaccadic drift always increased from levels in the dark. (ABSTRACT TRUNCATED AT 400 WORDS)
Preferential Logics: the Predicate Calculus Case

Suppose a knowledge base contains information on how the world generally behaves and in particular contains the information that birds, normally fly. Suppose that we obtain the information that Tweety is a bird, why should we conclude that it is plausible that Tweety flies? The answer to this question is unexpectedly sophisticated since the obvious substitution rule has to be rejected. Our answer to this question is based on an extension to predicate calculus of the ideas presented in [7]. Preferential consequence relations over predicate calculi are defined. In addition to the rules satisfied by those relations in the propositional case, they satisfy two rules dealing with quantifiers. These rules are not enough to enable us to conclude that Tweety flies. The rational closure construction defined in [7] should be generalized to the predicate calculus case and, in the rational closure, Tweety should fly.
Time and Temperature Effects of Ultrasound Treatments on the Resistant Starch Content of Canna edulis Ker

SORAYA RESTI PANGESTIKA. Time and Temperature Effects of Ultrasound Treatments on the Resistant Starch Content of Canna edulis Ker. Under guidance of ADIL BASUKI AHZA. Ultrasonication was applied to Ganyong (Canna edulis Ker) starch for three treatment of times (15, 30, and 45 minutes) at controlled temperature (30, 45, and 60C). Ganyong as a local indigenous plant was chosen as the material in this study because it has big potential to produce resistant starch from its high content of amylose compared to other tuber’s starch, such as cassava, sweet potato, yam and arrowroot. Ultrasonication at 60C and 45 minute was chosen as best treatment combination in this study due to the highest yield of resistant starch produced. Native canna starch was observed to have 1.45±0.24 % of resistant starch, however the number significantly increased to 48.19 ± 0.84% of resistant starch after modification (p<0.05). Further physicochemical changes of native and modified starch were observed. The results showed that there were no significant changes in the proximate analysis profiles before and after treatment. However, the ultrasonication significantly influence the pasting profiles (p<0.05) which was also expected due to the increase of starch granule size range from 30-160 μm to 45-179 μm after modification. The morphological changes were clearly observed by SEM and PLM, which showed swollen granule with rougher surface and fissures after modification. Thermal analysis using DSC did not significantly influenced the gelatinization temperature of the granule starch, however the increase of enthalpy (∆H) occured from 2.99 to 10.86 J/kg. This result indicated the increase of resistant starch within canna starch granule.
Investigation of Injection- and Radiation-Thermal Processes in Thin Gate Dielectric Films of MIS Structures

In order to modify the gate dielectric of MIS structures we suggest to implement the injection-thermal treatment which consists in the high-field injection of electrons of set density into the thin dielectric film and the subsequent annealing of the structure. We investigate an influence of modes of the injection-thermal treatment onto the modification of MIS structures. We demonstrate that the processes of MIS structure modification taking place at the injection-thermal treatment in many respects are identical to the processes taking place at the radiation-thermal treatment. We study an influence of modes of the high-field electron injection into the gate dielectric of MIS structure onto densities of charge defects and the injection hardness of samples. Besides, we research an influence of doping of the silicone dioxide film by phosphorus onto the same characteristics.
PEG-based hydrogel-coated test strip for on-site urea determination

Abstract The urea test strip was prepared using polyethyleneglycol based hydrogel, urease and commercial pH-indicator paper. The swelling behavior of hydrogel indicated the ability of the urea to penetrate into the matrix and allowing the test strip to respond in a short time. The color formed on the strip was distinguished by naked eyes in one minute at room temperature. The linear range for urea was 20–200 mg/dL. The assays have good reproducibility. Relative standard deviation values were found within the range of 3.37–12.95% and 1.68–9.54% for intra- and inter-day assays, respectively. Graphical Abstract