gebhart/patrepeval huggingface dataset:
Structure and Dynamics of Peptide−Amphiphiles Incorporating Triple-Helical Proteinlike Molecular Architecture (1999)

Organized polymeric assemblies that incorporate bioactive sequences and structures are finding important applications for the study of protein structure-function relationships. We have recently described a heteropolymeric peptide-amphiphile system that forms organized structures in solution and on surfaces. While the overall three-dimensional features of peptide-amphiphiles have been studied previously, the precise environment of specific residues, particularly those within biologically active regions, have not been examined in detail. In the present study, we have used heteronuclear single quantum coherence (HSQC) and inverse-detected 1H-15N NMR spectroscopy to examine the structure and dynamics of a peptide and peptide-amphiphile that incorporate the alpha1(IV)1263-1277 ([IV-H1]) amino acid sequence from type IV collagen. Three variants of the sequence (Gly-Pro-Hyp)4-[IV-H1]-(Gly-Pro-Hyp)4 were constructed with a single 15N-labeled Gly placed in the middle of the N-terminal (Gly-Pro-Hyp)4 region (residue Gly7), in the middle of the [IV-H1] sequence (residue Gly19), or in the middle of the C-terminal (Gly-Pro-Hyp)4 region (residue Gly34). These peptides were also N-terminally acylated with hexanoic acid to create an analogous series of 15N-labeled peptide-amphiphiles. HSQC spectra indicated that both the peptide and the peptide-amphiphile were in triple-helical conformation at low temperature, supporting prior circular dichroism (CD) spectroscopic results. The intensities of the triple-helical cross-peaks were stronger for the peptide-amphiphile, consistent with an enhanced triple-helical thermal stability within the peptide-amphiphile construct compared to that of the peptide alone. Relative relaxation values for the peptide-amphiphile monomeric and trimeric species were consistent with those reported previously for other triple-helical peptides. Relaxation measurements indicated that the triple-helical [IV-H1] region did not appear to be dramatically more flexible than the Gly-Pro-Hyp regions. The angle between Gly N-H bonds and the helix dyad axis, determined from the relaxation data, was within the range expected for triple helices. Overall, the peptide headgroup of the C6-(Gly-Pro-Hyp)4-[IV-H1]-(Gly-Pro-Hyp)4 peptide-amphiphile appears to form a continuous triple helix that behaves similarly, in a dynamic sense, to a triple-helical peptide. The enhanced thermal stability of the peptide-amphiphile compared to the analogous triple-helical peptide, along with the multitude of organized structures formed by lipidlike compounds, suggest that peptide-amphiphiles could be utilized as targeted liposomes, sensors, receptors, or enzymes.
Oral contraceptives and colorectal cancer risk: a meta-analysis (2001)

Several studies have suggested an inverse association between use of combined oral contraceptives (OC) and the risk of colorectal cancer and here we present a meta-analysis of published studies. Articles considered were epidemiological studies published as full papers in English up to June 2000 that included quantitative information on OC use. The pooled relative risks (RR) of colorectal cancer for ever OC use from the 8 case-control studies was 0.81 (95% confidence interval (CI): 0.69-0.94), and the pooled estimate from the 4 cohort studies was 0.84 (95% CI: 0.72-0.97). The pooled estimate from all studies combined was 0.82 (95% CI: 0.74-0.92), without apparent heterogeneity. Duration of use was not associated with a decrease in risk, but there was some indication that the apparent protection was stronger for women who had used OCs more recently (RR = 0.46; 95% CI: 0.30-0.71). A better understanding of this potential relation may help informed choice of contraception.
Characterization of Murine Sarcoma Virus (KIRSTEN) Transformation of Mouse and Human Cells (1971)

SUMMARY Kirsten sarcoma virus induces foci of morphologically altered cells in rat, mouse, and human cells in tissue culture. The kirsten sarcoma virus stock contains two viruses; one forming foci and the other plaques on XC cells. The sarcoma virus particle transforms cells in the absence of murine leukaemia virus but requires murine leukaemia virus for its replication. The high susceptibility of human cells to transformation by kirsten sarcoma virus is related to a function provided to the sarcoma virus by murine leukaemia virus. A large number of kirsten sarcoma virus-transformed mouse and rat cell foci has been isolated, and from these many non-producer clonal lines have been derived and characterized.
Relation of Smoking to the Incidence of Age-related Maculopathy: The Beaver Dam Eye Study (1998)

To date, a number of reports have been published on the relation of cigarette smoking to age-related maculopathy, an important cause of blindness in the United States. However, few studies have examined the relation between smoking and the incidence of age-related maculopathy. In this report, the authors examine this association in persons aged 43-86 years (n = 3,583) at baseline who were participants in the baseline examination and 5-year follow-up of the Beaver Dam Eye Study, Beaver Dam, Wisconsin (1988-1990 and 1993-1995). Exposure data on cigarette smoking were obtained from questions about present and past smoking, duration of smoking, and the number of cigarettes smoked per day. Age-related maculopathy status was determined by grading stereoscopic color fundus photographs using the Wisconsin Age-related Maculopathy Grading System. After controlling for age, sex, vitamin supplement use, and beer consumption, men who smoked greater amounts of cigarettes were more likely to develop early age-related maculopathy (odds ratio (OR) per 10 pack-years smoked = 1.06, 95% confidence interval (CI) 1.00-1.13, p = 0.06) than men who had smoked less. This association was not observed in women. Men (OR = 3.21, 95% CI 1.09-9.45) and women (OR = 2.20, 95% CI 1.04-4.66) who were current smokers at the time of the baseline examination had significantly higher odds of developing large drusen (> or = 250 microns in diameter) after 5 years than those who had never smoked or who quit before the baseline study. Current or past history of cigarette smoking was not related to the incidence of retinal pigment epithelial depigmentation. The authors conclude that smoking appears to be related to the incidence of some lesions associated with early age-related maculopathy.
Effect of polymer architecture on surface properties, plasma protein adsorption, and cellular interactions of pegylated nanoparticles (2008)

The aim of the present study was to evaluate the cellular interaction of nanoparticles (NPs) prepared from different pegylated polymers and elucidate the effect of polymer architecture, for instance, grafted versus block copolymer on their cellular uptake. Fluorescein-labeled NPs of four different polymers, viz., poly(D,L-lactide) (PLA), poly(ethylene glycol)(1%)-graft-poly(D,L-lactide) (PEG(1%)-g-PLA), poly(ethylene glycol)(5%)-graft-poly(D,L-lactide) (PEG(5%)-g-PLA), and (poly(D,L-lactide)-block-poly(ethylene glycol)-block-poly(D,L-lactide))(n) multiblock copolymer (PLA-PEG-PLA)(n) were prepared. These NPs were characterized for their size, zeta-potential, and surface morphology. XPS studies revealed possibility of chemical interaction between PLA-COOH groups and PVA-OH groups, thus making it difficult to be washed off the NP surface completely. Grafted polymer NPs showed more surface PEG coverage than (PLA-PEG-PLA)(n) despite of their comparatively lower PEG content. The results of surface properties were translated into protein binding showing least amount of proteins bound to grafted copolymer NPs as against multiblock copolymer NPs. NPs showed no toxicity to RAW 264.7 cells. Cellular uptake of NPs was temperature and concentration-dependent as well as involved clathrin-mediated processes. Thus, this study confirms the importance of polymer architecture in determining the surface properties and hence, protein binding and cellular interactions of NPs. Also, it was shown that grafted copolymer NPs reduced macrophage uptake as compared to multiblock copolymer although mechanisms different than phagocytosis were involved.
Copy Number Variation in Familial Parkinson Disease (2011)

Copy number variants (CNVs) are known to cause Mendelian forms of Parkinson disease (PD), most notably in SNCA and PARK2. PARK2 has a recessive mode of inheritance; however, recent evidence demonstrates that a single CNV in PARK2 (but not a single missense mutation) may increase risk for PD. We recently performed a genome-wide association study for PD that excluded individuals known to have either a LRRK2 mutation or two PARK2 mutations. Data from the Illumina370Duo arrays were re-clustered using only white individuals with high quality intensity data, and CNV calls were made using two algorithms, PennCNV and QuantiSNP. After quality assessment, the final sample included 816 cases and 856 controls. Results varied between the two CNV calling algorithms for many regions, including the PARK2 locus (genome-wide p = 0.04 for PennCNV and p = 0.13 for QuantiSNP). However, there was consistent evidence with both algorithms for two novel genes, USP32 and DOCK5 (empirical, genome-wide p-values<0.001). PARK2 CNVs tended to be larger, and all instances that were molecularly tested were validated. In contrast, the CNVs in both novel loci were smaller and failed to replicate using real-time PCR, MLPA, and gel electrophoresis. The DOCK5 variation is more akin to a VNTR than a typical CNV and the association is likely caused by artifact due to DNA source. DNA for all the cases was derived from whole blood, while the DNA for all controls was derived from lymphoblast cell lines. The USP32 locus contains many SNPs with low minor allele frequency leading to a loss of heterozygosity that may have been spuriously interpreted by the CNV calling algorithms as support for a deletion. Thus, only the CNVs within the PARK2 locus could be molecularly validated and associated with PD susceptibility.
A Printed Organic Circuit System for Wearable Amperometric Electrochemical Sensors (2018)

Wearable sensor device technologies, which enable continuous monitoring of biological information from the human body, are promising in the fields of sports, healthcare, and medical applications. Further thinness, light weight, flexibility and low-cost are significant requirements for making the devices attachable onto human tissues or clothes like a patch. Here we demonstrate a flexible and printed circuit system consisting of an enzyme-based amperometric sensor, feedback control and amplification circuits based on organic thin-film transistors. The feedback control and amplification circuits based on pseudo-CMOS inverters were successfuly integrated by printing methods on a plastic film. This simple system worked very well like a potentiostat for electrochemical measurements, and enabled the quantitative and real-time measurement of lactate concentration with high sensitivity of 1 V/mM and a short response time of a hundred seconds.
Preferential affinity of high molecular weight high mobility group non-histone chromatin proteins for single-stranded DNA. (1979)

We have subjected proteins dissociated from chicken erythrocyte or calf thymus chromatin by 0.35 M NaCl to sequential chromatography on columns containing immobilized double-stranded DNA and single-stranded DNA. At 0.2 M NaCl, 1 mM Tris . Cl (pH 7.5), the high molecular weight, high mobility group proteins (HMG-1, HMG-2, and HMG-E), were not retained by double-stranded DNA columns, but were retained by single-stranded DNA columns. Thus, in that solvent, those proteins exhibit selective affinity for single-stranded DNA. This suggests that the functions of the high molecular weight, high mobility group proteins might involve destabilizing the DNA double helix by virtue of their preferential affinity for single-stranded DNA.
Ad35 and Ad26 Vaccine Vectors Induce Potent and Cross-Reactive Antibody and T-Cell Responses to Multiple Filovirus Species (2012)

Filoviruses cause sporadic but highly lethal outbreaks of hemorrhagic fever in Africa in the human population. Currently, no drug or vaccine is available for treatment or prevention. A previous study with a vaccine candidate based on the low seroprevalent adenoviruses 26 and 35 (Ad26 and Ad35) was shown to provide protection against homologous Ebola Zaire challenge in non human primates (NHP) if applied in a prime-boost regimen. Here we have aimed to expand this principle to construct and evaluate Ad26 and Ad35 vectors for development of a vaccine to provide universal filovirus protection against all highly lethal strains that have caused major outbreaks in the past. We have therefore performed a phylogenetic analysis of filovirus glycoproteins to select the glycoproteins from two Ebola species (Ebola Zaire and Ebola Sudan/Gulu,), two Marburg strains (Marburg Angola and Marburg Ravn) and added the more distant non-lethal Ebola Ivory Coast species for broadest coverage. Ad26 and Ad35 vectors expressing these five filovirus glycoproteins were evaluated to induce a potent cellular and humoral immune response in mice. All adenoviral vectors induced a humoral immune response after single vaccination in a dose dependent manner that was cross-reactive within the Ebola and Marburg lineages. In addition, both strain-specific as well as cross-reactive T cell responses could be detected. A heterologous Ad26-Ad35 prime-boost regime enhanced mainly the humoral and to a lower extend the cellular immune response against the transgene. Combination of the five selected filovirus glycoproteins in one multivalent vaccine potentially elicits protective immunity in man against all major filovirus strains that have caused lethal outbreaks in the last 20 years.
The Agent of Bacillary Angiomatosis (1990)

The cause of bacillary angiomatosis is a previously uncharacterized rickettsia-like organism, closely related to R. quintana. This method for the identification of an uncultured pathogen may be applicable to other infectious diseases of unknown cause.
Detecting moving shadows: algorithms and evaluation (2003)

Moving shadows need careful consideration in the development of robust dynamic scene analysis systems. Moving shadow detection is critical for accurate object detection in video streams since shadow points are often misclassified as object points, causing errors in segmentation and tracking. Many algorithms have been proposed in the literature that deal with shadows. However, a comparative evaluation of the existing approaches is still lacking. In this paper, we present a comprehensive survey of moving shadow detection approaches. We organize contributions reported in the literature in four classes two of them are statistical and two are deterministic. We also present a comparative empirical evaluation of representative algorithms selected from these four classes. Novel quantitative (detection and discrimination rate) and qualitative metrics (scene and object independence, flexibility to shadow situations, and robustness to noise) are proposed to evaluate these classes of algorithms on a benchmark suite of indoor and outdoor video sequences. These video sequences and associated "ground-truth" data are made available at http://cvrr.ucsd.edu/aton/shadow to allow for others in the community to experiment with new algorithms and metrics.
Increase in long-chain polyunsaturated fatty acid n−6/n−3 ratio in relation to hepatic steatosis in patients with non-alcoholic fatty liver disease (2004)

Hepatic steatosis is a major feature associated with NAFLD (non-alcoholic fatty liver disease). The aims of the present study were to assess the levels of PUFA (polyunsaturated fatty acids) in liver total lipids, triacylglycerols (triglycerides) and phospholipids of NAFLD patients in relation to those in adipose tissue and hepatic indexes related to oxidative stress as factors contributing to hepatic steatosis. Eleven control subjects and 19 patients with NAFLD were studied. Analysis of liver and abdominal adipose tissue fatty acids was carried out by GLC. The liver content of protein carbonyl groups and malondialdehyde were taken as indexes related to oxidative stress. NAFLD patients had a depletion in LCPUFA (long-chain PUFA) of the n -6 and n -3 series in liver triacylglycerols, with decreased 20:4, n -6/18:2, n -6 and (20:5, n -3+22:6, n -3)/18:3, n -3 ratios, whereas liver phospholipids contained higher n -6 and lower n -3 LCPUFA. These findings were accompanied by an enhancement of (i) n -6/ n -3 ratio in liver and adipose tissue, (ii) 18:1, n -9 trans levels in adipose tissue, and (iii) hepatic lipid peroxidation and protein oxidation indexes. It is concluded that a marked enhancement in LCPUFA n -6/ n -3 ratio occurs in the liver of NAFLD patients, a condition that may favour lipid synthesis over oxidation and secretion, thereby leading to steatosis. Depletion of hepatic LCPUFA may result from both defective desaturation of PUFA, due to inadequate intake of precursors, such as 18:3, n -3, and higher intake of the 18:1, n -9 trans isomer leading to desaturase inhibition, and from an increased peroxidation of LCPUFA due to oxidative stress.
Treatment of Endometriosis-Associated Pain with Elagolix, an Oral GnRH Antagonist (2017)

Copyright Â© 2017 Massachusetts Medical Society. BACKGROUND Endometriosis is a chronic, estrogen-dependent condition that causes dysmenorrhea and pelvic pain. Elagolix, an oral, nonpeptide, gonadotropin-releasing hormone (GnRH) antagonist, produced partial to nearly full estrogen suppression in previous studies. METHODS We performed two similar, double-blind, randomized, 6-month phase 3 trials (Elaris Endometriosis I and II [EM-I and EM-II]) to evaluate the effects of two doses of elagolix-150 mg once daily (lower-dose group) and 200 mg twice daily (higher-dose group)-as compared with placebo in women with surgically diagnosed endometriosis and moderate or severe endometriosis-associated pain. The two primary efficacy end points were the proportion of women who had a clinical response with respect to dysmenorrhea and the proportion who had a clinical response with respect to nonmenstrual pelvic pain at 3 months. Each of these end points was measured as a clinically meaningful reduction in the pain score and a decreased or stable use of rescue analgesic agents, as recorded in a daily electronic diary. RESULTS A total of 872 women underwent randomization in Elaris EM-I and 817 in Elaris EM-II; of these women, 653 (74.9%) and 632 (77.4%), respectively, completed the intervention. At 3 months, a significantly greater proportion of women who received each elagolix dose met the clinical response criteria for the two primary end points than did those who received placebo. In Elaris EM-I, the percentage of women who had a clinical response with respect to dysmenorrhea was 46.4% in the lower-dose elagolix group and 75.8% in the higher-dose elagolix group, as compared with 19.6% in the placebo group; in Elaris EM-II, the corresponding percentages were 43.4% and 72.4%, as compared with 22.7% (P&lt;0.001 for all comparisons). In Elaris EM-I, the percentage of women who had a clinical response with respect to nonmenstrual pelvic pain was 50.4% in the lower-dose elagolix group and 54.5% in the higher-dose elagolix group, as compared with 36.5% in the placebo group (P&lt;0.001 for all comparisons); in Elaris EM-II, the corresponding percentages were 49.8% and 57.8%, as compared with 36.5% (P = 0.003 and P&lt;0.001, respectively). The responses with respect to dysmenorrhea and nonmenstrual pelvic pain were sustained at 6 months. Women who received elagolix had higher rates of hot flushes (mostly mild or moderate), higher levels of serum lipids, and greater decreases from baseline in bone mineral density than did those who received placebo; there were no adverse endometrial findings. CONCLUSIONS Both higher and lower doses of elagolix were effective in improving dysmenorrhea and nonmenstrual pelvic pain during a 6-month period in women with endometriosis-associated pain. The two doses of elagolix were associated with hypoestrogenic adverse effects.
Eye Tracking Young Children with Autism (2012)

The rise of accessible commercial eye-tracking systems has fueled a rapid increase in their use in psychological and psychiatric research. By providing a direct, detailed and objective measure of gaze behavior, eye-tracking has become a valuable tool for examining abnormal perceptual strategies in clinical populations and has been used to identify disorder-specific characteristics, promote early identification, and inform treatment. In particular, investigators of autism spectrum disorders (ASD) have benefited from integrating eye-tracking into their research paradigms. Eye-tracking has largely been used in these studies to reveal mechanisms underlying impaired task performance and abnormal brain functioning, particularly during the processing of social information. While older children and adults with ASD comprise the preponderance of research in this area, eye-tracking may be especially useful for studying young children with the disorder as it offers a non-invasive tool for assessing and quantifying early-emerging developmental abnormalities. Implementing eye-tracking with young children with ASD, however, is associated with a number of unique challenges, including issues with compliant behavior resulting from specific task demands and disorder-related psychosocial considerations. In this protocol, we detail methodological considerations for optimizing research design, data acquisition and psychometric analysis while eye-tracking young children with ASD. The provided recommendations are also designed to be more broadly applicable for eye-tracking children with other developmental disabilities. By offering guidelines for best practices in these areas based upon lessons derived from our own work, we hope to help other investigators make sound research design and analysis choices while avoiding common pitfalls that can compromise data acquisition while eye-tracking young children with ASD or other developmental difficulties.
[Synthesis and platelet aggregation inhibitory activity of analogues of 4-([2-(1H-imidazol-1-yl)-1-(4-substituted-phenyl)ethoxy]methyl)benzoic acids]. (1991)

Analogues of 4-([2-(1H-imidazol-1-yl)-1-(4-substituted-phenyl)ethoxy]methyl)benz oic acids were synthesized for searching of more potent and selective thromboxane synthetase inhibitors. All title compounds are first reported. Results of preliminary pharmacological tests showed that all title compounds have activity against thromboxane synthetase, i.e. inhibiting platelet aggregation induced by AA in vitro with rabbit. Compound 15 is the most potent. Its activity is 55.6% of that of Dazoxiben in comparison of IC50. The change of group substituted on benzene would affect inhibitory activity to thromboxane synthetase. Esters are more potent than the parent acids. This is probably due to the greater platelet permeability of the more lipophilic ester prior to intraplatelet deesterification. NBS was applied to the preparation of p-bromoethylbenzoic ester. This method increased the yield and simplified operating process.