gebhart/patrepeval huggingface dataset:
Hyaluronan Enhances Contraction of Collagen by Smooth Muscle Cells and Adventitial Fibroblasts (2001)

Remodeling contributes to restenosis when cells shrink the artery wall at sites of injury. This may be analogous to wound healing, where tissue remodeling achieves wound contraction. Hyaluronan (HA) is prominent in wound matrix and inhibits fetal scarring. HA is also produced in the artery wall after angioplasty, where it may inhibit constrictive remodeling. This hypothesis was tested in vitro using a model of matrix contraction. Primate aortic smooth muscle cells and adventitial fibroblasts were seeded into collagen I gels containing increasing amounts of HA (0% to 50%, wt/wt). Both cell types reduced the diameter of collagen alone approximately 65% at 18 hours. HA significantly increased gel contraction (diameter in mm: 0% HA, 7. 7+/-0.9; 2%, 7.1+/-0.7; 10%, 6.7+/-0.5; 50%, 5.6+/-0.9; P<0.05 for >/=10%), cell spreading and telopodia, and pericellular accumulation of collagen fibrils. These effects were mediated in part by cellular HA binding, because an antibody against CD44 receptors blocked pericellular collagen accumulation and enhanced gel contraction without altering cell shape. The role of CD44 was specific, because inhibiting receptor for hyaluronic acid-mediated motility (RHAMM) had no effect. Blocking ss(1)-integrins completely inhibited contraction of collagen, but gels containing HA required CD44 and ss(1)-integrin blockade for complete inhibition. Enhanced collagen reorganization and contraction were not attributable to increased collagenase activity, because the metalloproteinase inhibitor batimastat had no effect. In summary, HA enhanced collagen reorganization by the cell types most likely to mediate constrictive remodeling after angioplasty. These effects were CD44-dependent, thus providing a potential target for therapies to prevent constrictive remodeling and restenosis.
Inferring relative proportions of DNA variants from sequencing electropherograms (2009)

Supplementary data are available at Bioinformatics online.
Mapping applications onto a cache coherent multiprocessor (1992)

The authors present a technique to compute the communication times of programs on cache coherent distributed shared memory systems. Simulated annealing is used to obtain near-optimal mappings of program tasks onto processors. Various cost parameters are explored for determining efficient mappings of the program tasks onto the processors in the presence of cache coherence protocols. The techniques were demonstrated using the Sequent Balance multiprocessor and the Jacobi iteration problem. Measurement results confirm that the estimate of communication time is fairly accurate. The importance of accurate estimation of communication time for efficient mapping of program tasks in the presence of the cache coherence protocol was verified using measurements on the Balance multiprocessor. >
Imaging Local Electrochemical Current via Surface Plasmon Resonance (2010)

We demonstrated an electrochemical microscopy technique based on the detection of variations in local electrochemical current from optical signals arising from surface plasmon resonance. It enables local electrochemical measurements (such as voltammetry and amperometry) with high spatial resolution and sensitivity, because the signal varies with current density rather than current. The imaging technique is noninvasive, scanning-free, and fast, and it constitutes a powerful tool for studying heterogeneous surface reactions and for analyzing trace chemicals.
Constitutive Signaling from an Engineered IL7 Receptor Promotes Durable Tumor Elimination by Tumor-Redirected T Cells (2017)

Successful adoptive T-cell immunotherapy of solid tumors will require improved expansion and cytotoxicity of tumor-directed T cells within tumors. Providing recombinant or transgenic cytokines may produce the desired benefits but is associated with significant toxicities, constraining clinical use. To circumvent this limitation, we constructed a constitutively signaling cytokine receptor, C7R, which potently triggers the IL7 signaling axis but is unresponsive to extracellular cytokine. This strategy augments modified T-cell function following antigen exposure, but avoids stimulating bystander lymphocytes. Coexpressing the C7R with a tumor-directed chimeric antigen receptor (CAR) increased T-cell proliferation, survival, and antitumor activity during repeated exposure to tumor cells, without T-cell dysfunction or autonomous T-cell growth. Furthermore, C7R-coexpressing CAR T cells were active against metastatic neuroblastoma and orthotopic glioblastoma xenograft models even at cell doses that had been ineffective without C7R support. C7R may thus be able to enhance antigen-specific T-cell therapies against cancer.<b>Significance:</b> The constitutively signaling C7R system developed here delivers potent IL7 stimulation to CAR T cells, increasing their persistence and antitumor activity against multiple preclinical tumor models, supporting its clinical development. <i>Cancer Discov; 7(11); 1238-47. ©2017 AACR.</i><i>This article is highlighted in the In This Issue feature, p. 1201</i>.
Acute sensory neuropathy‐neuronopathy from pyridoxine overdose (1987)

We report two patients who developed an acute, profound, and permanent sensory deficit after treatment with massive doses of parenteral pyridoxine. Aside from rapid onset, their clinical picture resembles that described in chronic pyridoxine neurotoxicity. It also is consonant with experimental models of acute pyridoxine intoxication and is probably secondary to a sensory ganglion neuronopathy. These patients also had transient autonomic dysfunction, mild weakness, nystagmus, lethargy, and respiratory depression. These previously undocumented features may be attributable to either the preservative used in the parenteral pyridoxine preparation or to the exceptionally high doses of pyridoxine these patients received.
Personalization and Evaluation of a Real-Time Depth-Based Full Body Tracker (2013)

Reconstructing a three-dimensional representation of human motion in real-time constitutes an important research topic with applications in sports sciences, human-computer-interaction, and the movie industry. In this paper, we contribute with a robust algorithm for estimating a personalized human body model from just two sequentially captured depth images that is more accurate and runs an order of magnitude faster than the current state-of-the-art procedure. Then, we employ the estimated body model to track the pose in real-time from a stream of depth images using a tracking algorithm that combines local pose optimization and a stabilizing dataBase look-up. Together, this enables accurate pose tracking that is more accurate than previous approaches. As a further contribution, we evaluate and compare our algorithm to previous work on a comprehensive benchmark dataset containing more than 15 minutes of challenging motions. This dataset comprises calibrated marker-Based motion capture data, depth data, as well as ground truth tracking results and is publicly available for research purposes.
Variability of a bacterial surface protein and disease expression in a possible mouse model of systemic Lyme borreliosis. (1994)

During persistent infection of scid mice with Borrelia turicatae, an agent of relapsing fever and neuroborreliosis, there was variation in the surface proteins the bacteria expressed and in disease manifestations over time. Two serotypes, A and B, were isolated from the mice, cloned by limiting dilution, and further characterized. The only discernible difference between the two variants was in the size of the major surface protein they expressed: serotype A had a variable major protein (Vmp) of 23,000, and serotype B had a Vmp of 20,000. When other scid mice were inoculated with clonal populations of A and B, the infections were similar with respect to onset and degree of spirochetemia, involvement of the eye and heart, and occurrence of a peripheral vestibular disorder. However, there were differences between the serotypes in other respects: (a) serotype B but not A caused reddened and significantly enlarged joints, markedly impaired performance on a walking bar, and severe arthritis by histologic examination; (b) serotype A but not B invaded the central nervous system during early infection; and (c) serotype A penetrated monolayers of human umbilical vein endothelial cells more readily than did serotype B. The combination of arthritis, myocarditis, and neurologic disease resembled human Lyme borreliosis. The findings indicate that differences in disease expression are determined by variable surface proteins of the bacterium and that scid mouse infections with B. turicatae provide a model for the study of the pathogenesis of Lyme borreliosis and other persistent spirochetal diseases.
Urinary NGAL Marks Cystic Disease in HIV-Associated Nephropathy (2009)

Nephrosis and a rapid decline in kidney function characterize HIV-associated nephropathy (HIVAN). Histologically, HIVAN is a collapsing focal segmental glomerulosclerosis with prominent tubular damage. We explored the expression of neutrophil gelatinase-associated lipocalin (NGAL), a marker of tubular injury, to determine whether this protein has the potential to aid in the noninvasive diagnosis of HIVAN. We found that expression of urinary NGAL was much higher in patients with biopsy-proven HIVAN than in HIV-positive and HIV-negative patients with other forms of chronic kidney disease. In the HIV-transgenic mouse model of HIVAN, NGAL mRNA was abundant in dilated, microcystic segments of the nephron. In contrast, urinary NGAL did not correlate with proteinuria in human or in mouse models. These data show that marked upregulation of NGAL accompanies HIVAN and support further study of uNGAL levels in large cohorts to aid in the noninvasive diagnosis of HIVAN and screen for HIVAN-related tubular damage.
Double-Strand Hydrolysis of Plasmid DNA by Dicerium Complexes at 37 °C (2001)

Significant effort has been made to develop synthetic metal complexes that hydrolyze DNA. Here we report a new dicerium complex, Ce(2)(HXTA) (HXTA = 5-methyl-2-hydroxy-1,3-xylene-alpha,alpha-diamine-N,N,N',N'-tetraacetic acid), which can hydrolyze DNA at pH 8 and 37 degrees C. This complex hydrolyzes DNA restriction fragments to give products with high regioselectivity, affording >90% 5'-OPO(3) and 3'-OH ends, like the products of DNA hydrolyzing enzymes. Ce(2)(HXTA) also hydrolyzes Litmus 29 plasmid DNA to afford both nicked and linear DNA. Analysis of the relative amounts of supercoiled, nicked, and linear DNA present show that there is one double-strand cleavage per ten single-strand cleavages, indicating that the linear DNA formed cannot be the result of two random single-strand cleavage events. The kinetics of nicked and linear DNA formation are comparable, both being associated with apparent first-order rate constants of approximately 1 x 10(-)(4) s(-)(1) for complex concentrations of 10(-)(5)-10(-)(4) M. These observations suggest that similar factors affect the hydrolysis of the first and second DNA strands and that cleaving the phosphodiester bond is likely the rate determining step in both cases. This is the first detailed study of a metal complex shown to mimic DNA hydrolases in their capability to effect double-strand DNA hydrolysis regioselectively at the 3'-O-P bond.
Risk Factors for Hepatocellular Carcinoma among Patients with Chronic Liver Disease (1993)

Patients with hepatitis C virus infection have a greatly increased risk of liver cancer. Further studies are required to clarify the roles of other risk factors, including drinking and smoking habits.
Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies (2008)

The EPISNPmpi parallel computing program provides an effective computing tool for epistasis testing in large scale GWAS, and the epiSNP serial computing programs are convenient tools for epistasis analysis in small scale GWAS using commonly available computer hardware.
Dispersion and Characterization of Pharmaceutical Dry Powder Aerosols (1998)

Dry powder inhalers may be employed for the delivery of drugs to the lungs for the treatment of pulmonary and systemic diseases. Dry powder inhalers consist of a formulation, metering system and delivery device. The formulation consists of small drug particles (median aerodynamic diameter < 5 μm) usually combined with large excipient particles (30-125 μm). The physico-chemical properties of particles influence flow, fluidization and dispersion. An aerosol is passively inhaled by means of the inspiratory effort of the patient. Active devices use independent energy sources to deliver the aerosol. The aerodynamic particle size of an aerosol significantly effects lung deposition. Inertial deposition of particles, as a function of their aerodynamic diameter, allows measurement of the drug mass in a specific size range. The fine particle dose, or fine particle fraction (FPF) of the metered dose, is the simplest expression of the aerosol particle size. Passive inhalers have been reported to administer up to 50% FPF and active inhalers up to 70% FPF. The criteria for optimal inhaler performance must be defined to facilitate the rapid growth in research and development in this field.
Spatial learning and memory in aging C57BL/6 mice (1998)

We evaluated spatial behaviors as a function of age in C57BL/6 mice (4, 16, and 24 months). Simple exploration was measured in an open field, spatial memory was assessed with spontaneous alternation in a Y maze, and spatial learning and memory were measured using a well hole-board with water rewards. The results indicate significant age-related decreases in exploration, significantly less alternation in the Y maze for the two older age groups, and significant age-related impairments in reference and working memory with the hole-board task. Deficits in the hole-board were not due to a lack of exploration, or time to complete the task. A factor analysis indicated that the behavioral measures factor differently with each other as a function of age, and a step-wise regression of the behavioral measures with age indicated that each task uniquely and independently revealed age-related impairments. In conclusion, the three tasks reported here can form a battery of tests to examine changes in spatially mediated behaviors and in the molecular/physiological mechanisms within the limbic system of the aging brain.
Probability, Random Processes, and Estimation Theory for Engineers (1986)

1. (Note: Each chapter concludes with Problems and References)2. Introduction to Probability3. Random Variables4. Functions of Random Variables5. Averages6. Vector Random Variables7. Estimation and Decision Theory I8. Random Sequences9. Random Processes10. Mean-Square Calculus11. Stationary Processes and Sequences12. Estimation Theory II13. Appendix: Review of Relevant Mathematics14. Index15. Information for Using the Program Disk
Neuronal Cyclooxygenase 2 Expression in the Hippocampal Formation as a Function of the Clinical Progression of Alzheimer Disease (2001)

Neuronal COX-2 content in subsets of hippocampal pyramidal neurons may be an indicator of progression of dementia in early AD.
Molecular and functional characterization of the Salmonella typhimurium invasion genes invB and invC: homology of InvC to the F0F1 ATPase family of proteins (1994)

Entry into intestinal epithelial cells is an essential step in the pathogenesis of Salmonella infections. Our laboratory has previously identified a genetic locus, inv, that is necessary for efficient entry of Salmonella typhimurium into cultured epithelial cells. We have carried out a molecular and functional analysis of invB and invC, two members of this locus. The nucleotide sequence of these genes indicated that invB and invC encode polypeptides with molecular masses of 15 and 47 kDa, respectively. Polypeptides with the predicted sizes were observed when these genes were expressed under the control of a T7 promoter. Strains carrying nonpolar mutations in these genes were constructed, and their phenotypes were examined in a variety of assays. A mutation in invC rendered S. typhimurium defective in their ability to enter cultured epithelial cells, while mutations in invB did not. Comparison of the predicted sequences of InvB and InvC with translated sequences in GenBank revealed that these polypeptides are similar to the Shigella spp. proteins Spa15 and Spa47, which are involved in the surface presentation of the invasion protein antigens (Ipa) of these organisms. In addition, InvC showed significant similarity to a protein family which shares sequence homology with the catalytic beta subunit of the F0F1 ATPase from a number of microorganisms. Consistent with this finding, purified preparations of InvC showed significant ATPase activity. Site-directed mutagenesis of a residue essential for the catalytical function of this family of proteins resulted in a protein devoid of ATPase activity and unable to complement an invC mutant of S. typhimurium. These results suggest that InvC may energize the protein export apparatus encoded in the inv locus which is required for the surface presentation of determinants needed for the entry of Salmonella species into mammalian cells. The role of InvB in this process remains uncertain.
MDM2 Antagonist Nutlin-3 Suppresses the Proliferation and Differentiation of Human Pre-Osteoclasts Through a p53-Dependent Pathway (2007)

These findings indicate that Nutlin-3 abrogates both pre-osteoclastic proliferation and differentiation through a p53-dependent pathway and may have therapeutic implications for those neoplastic diseases characterized by an abnormal osteoclastic activity.
Class III Homeodomain-Leucine Zipper Gene Family Members Have Overlapping, Antagonistic, and Distinct Roles in Arabidopsis Development (2004)

The Arabidopsis thaliana genome contains five class III homeodomain-leucine zipper genes. We have isolated loss-of-function alleles for each family member for use in genetic analysis. This gene family regulates apical embryo patterning, embryonic shoot meristem formation, organ polarity, vascular development, and meristem function. Genetic analyses revealed a complex pattern of overlapping functions, some of which are not readily inferred by phylogenetic relationships or by gene expression patterns. The PHABULOSA and PHAVOLUTA genes perform overlapping functions with REVOLUTA, whereas the PHABULOSA, PHAVOLUTA, and CORONA/ATHB15 genes perform overlapping functions distinct from REVOLUTA. Furthermore, ATHB8 and CORONA encode functions that are both antagonistic to those of REVOLUTA within certain tissues and overlapping with REVOLUTA in other tissues. Differences in expression patterns explain some of these genetic interactions, whereas other interactions are likely attributable to differences in protein function as indicated by cross-complementation studies.
Complexation behavior of trivalent actinides and lanthanides with 1,10-phenanthroline-2,9-dicarboxylic acid based ligands: insight from density functional theory (2012)

We have investigated the complexation behavior of preorganized 1,10-phenanthroline-2,9-dicarboxylic acid (PDA) based ligands with trivalent lanthanides and actinides using density functional theory with various GGA type exchange-correlation functionals and different basis sets. New ligands have been designed from PDA through functionalization with soft donor atoms such as sulfur, resulting in mono-thio-dicarboxylic acids (TCA/TCA1) and di-thio-dicarboxylic acid (THIO). It has been found that selectivity in terms of complexation energy of actinides over lanthanides is the maximum with TCA1 where the metal-ligand binding is through the O atoms. This unusual feature where a softer actinide metal ion is bonded strongly with hard donor oxygen atoms has been explained using the popular chemical concepts, viz., Pearson's Hard-Soft-Acid-Base (HSAB) principle and the frontier orbital theory of chemical reactivity as proposed by Fukui. Detailed analysis within the framework of the HSAB principle indicates that the presence of softer nitrogen atoms in the phenanthroline moiety (which also act as donors to the metal ion) has a profound influence in changing the soft nature of the actinide ion, which in turn binds with the hard oxygen atoms in a stronger way as compared to the valence isoelectronic lanthanide ion. Also, the trends in the variation of calculated values of the metal-ligand bond distances and the corresponding complex formation energies have been rationalized using the Fukui reactivity indices corresponding to the metal ions and the donor sites. All the calculations have also been done in the presence of solvent. The "intra-ligand synergistic effect" demonstrated here for PDA or TCA1 with soft and hard donor centers might be very important in designing new ligands for selective extraction of various metal ions in a competitive environment. However, for TCA and THIO ligands with only soft donor centers, "intra-ligand synergism" may not be very efficient although reports are available demonstrating soft-soft inter-ligand synergism. Nevertheless, in the case of TCA and THIO complexes, a shorter Am-S bond distance in conjunction with lower metal ion charge and a higher percentage of orbital interaction energy corroborate the presence of a higher degree of covalency in Am-S bonds, which in turn may be responsible for selectivity towards Am(3+).
Loss of Caveolin-1 in Bronchiolization in Lung Fibrosis (2007)

Bronchiolization is a key process in fibrosing lung in which the proliferative status of bronchiolar epithelium changes, leading to abnormal epithelial morphology. Within the context that caveolin-1 acts to suppress epithelial proliferation, we postulated that stimulating epithelial injury would lead to caveolin-1 downregulation and encourage proliferation. The present study evaluates the expression of caveolin-1, especially in bronchiolization, in C57BL/6J mice with bleomycin-induced lung fibrosis and in various types of re-epithelialization in human interstitial pneumonias (IPs). Immunohistochemically, levels of caveolin-1 decreased in the bronchiolar epithelium of mice treated with bleomycin. Levels of caveolin-1 mRNA in the whole lung were decreased at 7 and 14 days. Caveolin-1 mRNA was also decreased in laser-capture microdissection- retrieved bronchiolar epithelial cells at 7 days. Among patients with 12 IPs, including four usual IPs (UIPs) and eight nonspecific IPs (NSIPs), whole lung caveolin-1 was significantly decreased compared with 12 controls at both mRNA and protein levels. By scoring immunointensity, caveolin-1 was significantly reduced in bronchiolization and squamous metaplasia as well as in bronchiolar epithelium in 23 IPs (12 UIPs and 11 NSIPs) compared with bronchiolar epithelium from seven controls. These data suggested that loss of caveolin-1 is associated with abnormal re-epithelialization in lung fibrosis.
A knowledge-based environment for assessment of color similarity (2002)

A discussion is given on a knowledge-based approach to the representation and implementation of the similarity evaluation of colors; all the aspects involved in color description and the relationships between color descriptions and similarity judgments may be explicitly represented in a quantitative, rigorous and reliable way. The authors choose CIELUV, which provides a flexible and powerful numerical description of color appearance, as the color description space and fuzzy logic as the knowledge representation language for modelling human judgments in the universe of discourse of CIELUV measures. An explanatory example of color image retrieval based on similarity measure is provided to aid the presentation of tools and strategies of the knowledge-based environment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>