Miracle-dz/UniFAR-FTUs huggingface dataset:
Solution structures of DNA.RNA hybrids with purine-rich and pyrimidine-rich strands: comparison with the homologous DNA and RNA duplexes.

The structures of d(GAAGAGAAGC). d(GCTTCTCTTC), d(GAAGAGAAGC). r(GCUUCUCUUC), r(GAAGAGAAGC). d(GCTTCTCTTC), and r(GAAGAGAAGC). r(GCUUCUCUUC) have been determined in solution from NMR data. Globally, the pure DNA and RNA duplexes were in the B and A forms, respectively. The two DNA.RNA hybrids were neither A nor B, but closer globally to the A than the B form. However, the thermodynamically less stable d(GAAGAGAAGC). r(GCUUCUCUUC) duplex has a significantly different conformation from r(GAAGAGAAGC). d(GCTTCTCTTC). Structures were calculated based on the NMR data, using restrained molecular dynamics. A new approach to the treatment of conformational averaging based on a prioriprobabilities has been used. The nucleotides were treated by fitting the scalar coupling data and NOE time courses to a two-state model comprising N and S sugar puckers each with a different glycosidic torsion angle, and the mole fraction of the S state. Restraint sets for different distributions of N and S states within molecules were constructed, such that each nucleotide was weighted in the ensemble according to the mole fractions (or a prioriprobabilities). The individual nucleotide conformations were strongly restrained, whereas the internucleotide restraints were set relatively loosely. Ensembles of conformations were generated and assessed by comparison of the NOEs calculated from ensemble-averaged relaxation matrices with the experimental NOEs. The ensemble averages accounted for the experimental data much better than any individual member, or for structures calculated assuming a single unique conformation. The two hybrids populated different degrees of conformational space. There was a general trend in minor and major groove widths in the order d(GAAGAGAAGC). d(GCTTCTCTTC), d(GAAGAGAAGC). r(GCUUCUCUUC), r(GAAGAGAAGC). d(GCTTCTCTTC), r(GAAGAGAAGC). r(GCUUCUCUUC) and a similar progression in global character from B-like to A-like structures. Furthermore, r(GAAGAGAAGC). d(GCTTCTCTTC) showed a greater dispersion of conformations in the ensemble than d(GAAGAGAAGC). r(GCUUCUCUUC), reflecting the greater flexibility of the sugars. If conformational averaging of the nucleotides is ignored, incorrect virtual structures are produced that nevertheless are able to satisfy a substantial fraction of the experimental data.
Active Specific Immunotherapy with Autologous Tumor cell vaccines for Stage II Colon Cancer: Logistics, Efficacy, Safety and Immunological Pharmacodynamics

In the area of cancer treatment, immunotherapy with vaccines has suffered in the last 5 years, due to many clinical trial failures. One must keep in mind however, that many of the clinical trials conducted in the past decade were performed without the benefit of sound regulatory guidance or validated and compliant manufacturing processes. This has clearly been the case for patient specific, tumor cell vaccine therapy. The safety concerns that emanated within the regulatory agencies from the Somatic Cell Therapy concepts, translated to active specific immunotherapy with vaccines. Fortunately, in the past 5 years advances in understanding the immune system, improved design of clinical trials, improvement and compliance of manufacturing processes provided opportunities to significantly improve efficacy and safety. Clearly, the vaccine research establishment has learned the importance of not just selecting antigens but the requirement of tumor associated immunogens that can stimulate a functional immune response. Also, it has become clear that immunotherapy works best in situations of minimal residual disease. Finally, more realistic endpoints in clinical trials have been recognized and accepted by oversight review committees. This commentary describes the “trials and tribulations” of developing a patient specific, autologous tumor cell vaccine for therapy of Stage II colon cancer.
Swedish universities Scales of Personality (SSP): construction, internal consistency and normative data

Objective: A thorough revision of the Karolinska Scales of Personality (KSP) was made by reducing the number of items and improving the psychometric quality as concerns face validity, internal consistency and response differentiation. The revised version was labelled The Swedish universities Scales of Personality (SSP) and now include 91 items divided into 13 scales.
They Choose to Attend Academic Summer Camps? A Mixed Methods Study Exploring the Impact of a NASA Academic Summer Pre-Engineering Camp On Middle School Students in a Latino Community

Early exposure to engineering and mathematics career opportunities has been indicated to influence students’ decisions regarding their academic majors and career goals. This study utilized mixed methods to analyze how changes in middle school students’ affective characteristics might be linked to their future career decision-making, following participation in an integrated science, technology, engineering, and mathematics summer camp. As part of the summer camp, rising sixththrough eighth-grade students attended a weeklong learning experience based on a specific engineering context. Each grade level cohort participated with their same grade peers in a 36-hour, 6-day event focused on sparking their interest in engineering careers and developing their content knowledge in select science and mathematics content areas. Pre-post testing was conducted with 65 students of diverse backgrounds in grades six through eight to measure their self-reported engineering-related self-efficacy, knowledge of engineering careers, and motivation to pursue future engineering classes and careers. In addition, interviews were conducted to examine any changes in middle school camp participants’ affective characteristics of motivation, self-efficacy, and self-determination.
A physiologically based pharmacokinetic model for trichloroethylene and its metabolites, chloral hydrate, trichloroacetate, dichloroacetate, trichloroethanol, and trichloroethanol glucuronide in B6C3F1 mice.

A six-compartment physiologically based pharmacokinetic (PBPK) model for the B6C3F1 mouse was developed for trichloroethylene (TCE) and was linked with five metabolite submodels consisting of four compartments each. The PBPK model for TCE and the metabolite submodels described oral uptake and metabolism of TCE to chloral hydrate (CH). CH was further metabolized to trichloroethanol (TCOH) and trichloroacetic acid (TCA). TCA was excreted in urine and, to a lesser degree, metabolized to dichloroacetic acid (DCA). DCA was further metabolized. The majority of TCOH was glucuronidated (TCOG) and excreted in the urine and feces. TCOH was also excreted in urine or converted back to CH. Partition coefficient (PC) values for TCE were determined by vial equilibrium, and PC values for nonvolatile metabolites were determined by centrifugation. The largest PC values for TCE were the fat/blood (36.4) and the blood/air (15.9) values. Tissue/blood PC values for the water-soluble metabolites were low, with all PC values under 2.0. Mice were given bolus oral doses of 300, 600, 1200, and 2000 mg/kg TCE dissolved in corn oil. At various time points, mice were sacrificed, and blood, liver, lung, fat, and urine were collected and assayed for TCE and metabolites. The 1200 mg/kg dose group was used to calibrate the PBPK model for TCE and its metabolites. Urinary excretion rate constant values were 0. 06/hr/kg for CH, 1.14/hr/kg for TCOH, 32.8/hr/kg for TCOG, and 1. 55/hr/kg for TCA. A fecal excretion rate constant value for TCOG was 4.61/hr/kg. For oral bolus dosing of TCE with 300, 600, and 2000 mg/kg, model predictions of TCE and several metabolites were in general agreement with observations. This PBPK model for TCE and metabolites is the most comprehensive PBPK model constructed for P450-mediated metabolism of TCE in the B6C3F1 mouse.
Mathematical Analysis of Hepatic High Density Lipoprotein Transport Based on Quantitative Imaging Data*

Hepatocytes internalize high density lipoprotein (HDL) at the basolateral membrane. Most HDL is recycled while some is shuttled to the canalicular membrane by transcytosis. Here, transport of HDL was analyzed by mathematical modeling based on measurements in polarized hepatic HepG2 cells. Recycling of HDL from basolateral sorting endosomes was modeled by applying the rapid equilibrium approach. Analytical expressions were derived, which describe in one model the transport of HDL to the subapical compartment/apical recycling compartment, the biliary canaliculus (BC), and to late endosomes and lysosomes (LE/LYS). Apical endocytosis of HDL predicted by the model was confirmed for rhodamine-dextran and fluorescent asialoorosomucoid, markers for LE/LYS in living HepG2 cells. Budding of endocytic vesicles from the BC was directly observed by time lapse imaging of a fluorescent lipid probe. Based on fitted kinetic parameters and their covariance matrix a Monte Carlo simulation of HDL transport in hepatocytes was performed. The model was used to quantitatively assess release of HDL-associated free cholesterol by scavenger receptor BI. It is shown that only 6% of HDL-associated sterol reaches the BC as a constituent of the HDL particles, whereas the remaining sterol is rapidly released from HDL and shuttled to the BC by non-vesicular transport.
Bony labyrinth morphometry indicates locomotor adaptations in the squirrel-related clade (Rodentia, Mammalia)

The semicircular canals (SCs) of the inner ear detect angular acceleration and are located in the bony labyrinth of the petrosal bone. Based on high-resolution computed tomography, we created a size-independent database of the bony labyrinth of 50 mammalian species especially rodents of the squirrel-related clade comprising taxa with fossorial, arboreal and gliding adaptations. Our sampling also includes gliding marsupials, actively flying bats, the arboreal tree shrew and subterranean species. The morphometric anatomy of the SCs was correlated to the locomotion mode. Even if the phylogenetic signal cannot entirely be excluded, the main significance for functional morphological studies has been found in the diameter of the SCs, whereas the radius of curvature is of minor interest. Additionally, we found clear differences in the bias angle of the canals between subterranean and gliding taxa, but also between sciurids and glirids. The sensitivity of the inner ear correlates with the locomotion mode, with a higher sensitivity of the SCs in fossorial species than in flying taxa. We conclude that the inner ear of flying and gliding mammals is less sensitive due to the large information flow into this sense organ during locomotion.
A double heads static cluster algorithm for wireless sensor networks

Since sensor nodes are generally deployed in surveillance areas by airplane and cannonball, node's position is affected by many factors, which leads to unevenly distribution. Maybe nodes in some areas are very thick, while nodes in other areas are very thin. Unevenly distribution phenomenon brings many disadvantages in network management, such as unbalanced energy dissipation between nodes, nodes premature death and network lifetime short. To solve those disadvantages, a double heads static cluster (DHSC) algorithm is presented, in which nodes density area is central at each cluster. Cluster is static after formulation. In additional, two cluster heads, a main cluster head which is selected in thick and an assistant cluster head which is selected in thin area, are used to reduce single cluster head's energy dissipation load. The main cluster head collects and fuses data inner-cluster, and the assistant cluster head routes data inter-cluster. Simulation result in MATLAB shows that DHSC achieves improvement on network lifetime.
G Protein βγ Subunits Regulate Cell Adhesion through Rap1a and Its Effector Radil

The activation of several G protein-coupled receptors is known to regulate the adhesive properties of cells in different contexts. Here, we reveal that Gβγ subunits of heterotrimeric G proteins regulate cell-matrix adhesiveness by activating Rap1a-dependent inside-out signals and integrin activation. We show that Gβγ subunits enter in a protein complex with activated Rap1a and its effector Radil and establish that this complex is required downstream of receptor stimulation for the activation of integrins and the positive modulation of cell-matrix adhesiveness. Moreover, we demonstrate that Gβγ and activated Rap1a promote the translocation of Radil to the plasma membrane at sites of cell-matrix contacts. These results add to the molecular understanding of how G protein-coupled receptors impinge on cell adhesion and suggest that the Gβγ·Rap1·Radil complex plays important roles in this process.
Association Between Meibomian Gland Changes and Aging, Sex, or Tear Function

Purpose: To study changes in the lid margin and meibomian glands and their association with aging, sex, and tear function. Methods: We examined 354 eyes in 177 subjects (76 men and 101 women; 21-93 years; mean age, 63.0 ± 14.3 years) with no ocular symptoms or ocular surface disorders. Anatomic changes in the lid margin were studied using slit-lamp biomicroscopy. Meibomian gland function and morphology were evaluated on the basis of meibum expression and meibography, respectively. Tear function and ocular surface epithelium were assessed with the Schirmer test, by tear film break-up time, and with a fluorescein staining test. Results: Eyes with abnormal lid margin anatomy, hyposecretion of meibum, and meibomian gland dropout were seen in 26 (7.3%), 46 (12.4%), and 68 eyes (18.6%), respectively, with a significant association between each finding and aging (P = <0.0001, 0.0498, and <0.0001, respectively). In patients ≤69 years of age, no significant association was found between meibomian gland-related findings and sex. However, a high incidence of abnormal lid margin and gland dropout was noted in men ⩾70 years of age compared with women. No significant association was found between changes in the lid margin and meibomian glands and tear function in patients ⩾40 years of age. Conclusion: Among symptom-free subjects, we found that changes in the lid margin and meibomian glands were closely related to aging. Among elderly subjects, changes in the anatomic lid margin and meibomian gland morphology were observed more frequently in men than in women. Tear function showed no association with either changes in the lid margin or function of the meibomian glands.
Antimicrobial resistance in Salmonella isolated from animals and their environment in England and Wales from 1988 to 1999

Resistance to 16 antimicrobial agents was monitored in 109,125 Salmonella cultures isolated from animals, their environment and feedstuffs between 1988 and 1999. The sensitivity of the 6512 isolates of Salmonella enterica enterica serotype Dublin to all the antimicrobial agents tested varied from 98.2 per cent in 1997 to 99.7 per cent in 1990 and 1996. In contrast, among 28,053 isolates of Salmonella enterica enterica serotype Typhimurium, there was a marked decrease in their sensitivity to all the antimicrobial agents tested, from 57.4 per cent in 1992 to 7.6 per cent in 1995, owing to the widespread occurrence in farm animals of S Typhimurium isolates of the definitive type DT104, resistant to ampicillin, sulphonamides, streptomycin, chloramphenicol and tetracyclines, although the percentage of sensitive isolates increased to 18.4 per cent in 1999, when the incidence of DT104 had decreased. Some isolates of DT104 also showed an increase in resistance to potentiated sulphonamides (2.4 per cent in 1989 to 19.2 per cent in 1999) and nalidixic acid (0 per cent in 1992, 3.8 per cent in 1995 to a peak of 16.9 per cent in 1998). In 1996, 5.1 per cent of 1086 isolates of S Typhimurium from cattle and 35.9 per cent of 192 isolates of S Typhimurium from poultry showed resistance to nalidixic acid. Of the other 74,528 Salmonella isolates, the percentage of strains sensitive to all the antimicrobials tested decreased slightly from 88.2 per cent in 1988 to 70.6 per cent in 1996 and then increased slightly to 73.7 per cent in 1999. The commonest of these other Salmonella serotypes was Salmonella Enteritidis (20,982), which remained predominantly susceptible (ranging from 81.4 to 97.4 per cent) during the study period. Few isolates were resistant to commonly used veterinary antimicrobials, for example, furazolidone, the use of which was banned in 1990, and the aminoglycoside, apramycin.
Location and sizes of forsterite grains in protoplanetary disks Interpretation from the Herschel DIGIT programme

Context. The spectra of protoplanetary disks contain mid- and far- infrared emission features produced by forsterite dust grains. The spectral features contain information about the forsterite temperature, chemical composition and grain size. Aims. We aim to characterize how the 23 and 69 μm features can be used to constrain the physical locations of forsterite in disks. We check for consistency between two independent forsterite Temperature measurements: the I23/I69 feature strength ratio and the shape of the 69 μm band. Methods. We performed radiative transfer modeling to study the effect of disk properties to the forsterite spectral features. Temperature-dependent forsterite opacities were considered in self-consistent models to compute forsterite emission from protoplanetary disks. Results. Modelling grids are presented to study the effects of grain size, disk gaps, radial mixing and optical depth to the forsterite features. Independent temperature estimates derived from the I23/I69 feature strength ratio and the 69 μm band shape are most inconsistent for HD 141569 and Oph IRS 48. A case study of the disk of HD 141569 shows two solutions to fit the forsterite spectrum. A model with T ~ 40 K, iron-rich (~ 0−1% Fe) and 1 μm forsterite grains, and a model with warmer (T ~ 100 K), iron-free, and larger (10 μm) grains. Conclusions. We find that for disks with low upper limits of the 69 μm feature (most notably in flat, self-shadowed disks), the forsterite must be hot, and thus close to the star. We find no correlation between disk gaps and the presence or absence of forsterite features. We argue that the 69 μm feature of the evolved transitional disks HD 141569 and Oph IRS 48 is most likely a tracer of larger (i.e. ≳10 μm) forsterite grains.
Lack of macrophage migration inhibitory factor suppresses innate immune response in murine dextran sulfate sodium-induced colitis

Objective. Macrophage migration inhibitory factor (MIF) plays an important role in the development of inflammatory diseases. Recent studies have indicated an association of MIF with gastrointestinal inflammation including colitis, but the mechanism by which MIF exacerbates gut inflammation has not been fully clarified. In this study, in order further to clarify the role of MIF in intestinal inflammation, we investigated the association of MIF with innate immunity in experimental colitis using MIF-deficient mice. Material and methods. Colitis was induced by treating mice with 3% dextran sulfate sodium (DSS) solution for 7 days. The expressions of chemokines in the colon were determined by reverse transcriptase-polymerase chain reaction (RT-PCR). Myeloperoxidase activity in the colon was measured and immunohistochemistry for F4/80 was analyzed. Results. DSS treatment increased the level of myeloperoxidase activity and infiltration of F4/80-stained cells in the colon, and up-regulated the mRNA expressions in macrophage inflammatory protein (MIP)-1α, MIP-2, macrophage chemotaxic protein (MCP)-1, and interferon inducible protein (IP)-10 in wild-type mice. In contrast, this increase and up-regulation were not observed in the colon of MIF-deficient mice treated with DSS. Conclusion. Our findings indicate that a lack of MIF suppresses the innate immune response in DSS-induced colitis.
Identification by the Phage-display Technique of Peptides That Bind to H7 Flagellin of Escherichia coli

The four peptides interacting with H7 flagellin of Escherichia coli were selected from a phage display library. The library was selected four times, and the interacting phage peptides were competitively eluted with H7 flagellin. An enzyme-linked immunosorbent assay (ELISA) showed that these peptides were reactive with the H7 flagellin in a dose-dependent manner. Among them, a D1 phage clone showed the highest binding affinity to the H7 flagellin. We synthesized the D1 peptide (LHIHRPTLSIQG) corresponding to the peptide-encoding region of the D1 phage clone. The synthetic peptide showed micro-molar affinity (EC50 value=1.9 μM) for the H7 flagellin. Furthermore, this D1 peptide interacted more specifically with the H7 flagellin than with the other flagellins (H1, H5, H12, or H23) of E. coli. In situ hybridization clearly showed that the peptide only detected those cells harboring the H7 flagellin gene (fliC). The peptide may specifically bind to the H7 flagellin on the cell surface. These results suggest that the phage-display technique could be used as a tool for identifying peptides as an alternative to using a ligand as a diagnostic reagent in food products or in clinical testing.
Information geometry and estimation of Toeplitz covariance matrices

The estimation of covariance matrix is of fundamental importance in radar signal processing. Recent work has shown that information geometry provides a novel approach to estimating the covariance matrix. Prior work has shown that an information geometry inspired covariance matrix estimator provides significant gains (in SINR loss terms) over several standard estimators, such as the loaded sample matrix inversion (LSMI). In this paper, some techniques for computing the covariance matrix, inspired by information geometry, are presented. It is found that some algorithms provide superior performance when the number of samples is small.
Capital Asset Pricing Model Without Borrowing or Short Sales

Using a new utility framework, the author constructs a capital asset pricing model (CAPM) without borrowing or short sales. According to the new utility framework, borrowing at the risk-free rate and short sales of the zero-beta portfolio cause a decline in risk tolerance. This rules-out a linear investment frontier. Instead, the frontier is described as an upward-sloping, convex curve that consists of many efficient portfolios. In the absence of short sales, the linear regression between asset returns and asset betas holds only in special cases. Also, the intercept of the regression is unique to each efficient portfolio. Using the proposed model, the author explains empirical violations of traditional CAPMs including the Equity Premium Puzzle and the predictive power of non-beta factors such as market size, P/E and book-to-market ratios.
Striatal dopamine loss and discriminative sensory dysfunction in Parkinson's disease

Patients with Parkinson's disease (PD) have higher‐order discriminative sensory dysfunction including prolonged somesthetic temporal discrimination threshold (sTDT). We studied the effect of striatal dopamine loss on the prolongation of sTDT and also studied the impact of prolonged sTDT values on the various parkinsonian motor deficits.
The Malay dilemma revisited : race dynamics in modern Malaysia / by M. Bakri Musa

The Malay Dilemma Revisited is a critical and balanced analysis of Malaysia's preferential race policy and its impact on the nation's delicate race dynamics and economy. Unlike America's affirmative action, Malaysia's version is far more aggressive and pervasive and has been remarkably successful in creating a sizable and stable Bumiputra middle class.