gebhart/patrepeval huggingface dataset:
Hyperinsulinemia. A link between hypertension obesity and glucose intolerance. (1985)

Hypertension and glucose intolerance, determined in a random population sample (n = 2,475), showed a highly significant (P less than 0.001) association from the mildest levels of both conditions, independent of the confounding effects of age, sex, obesity, and antihypertensive medications. Summary rate ratios for hypertension were 1.48 (1.18-1.87) in abnormal tolerance and 2.26 (1.69-2.84) in diabetes compared with normal tolerance. Altogether, 83.4% of the hypertensives were either glucose-intolerant or obese--both established insulin-resistant conditions. Fasting and post-load insulin levels in a representative subgroup (n = 1,241) were significantly elevated in hypertension independent of obesity, glucose intolerance, age, and antihypertensive medications. The mean increment in summed 1- and 2-h insulin levels (milliunits per liter) compared with nonobese normotensives with normal tolerance was 12 for hypertension alone, 47 for obesity alone, 52 for abnormal tolerance alone, and 124 when all three conditions were present. The prevalence of concentrations (milliequivalents per liter) of erythrocyte Na+ greater than or equal to 7.0, K+ less than 92.5, and plasma K+ greater than or equal to 4.5 in a subsample of 59 individuals with all combinations of abnormal tolerance obesity and hypertension was compared with those in 30 individuals free of these conditions. Altogether, 88.1% of the former vs. 40.0% of the latter group presented at least one of these three markers of internal cation imbalance (P less than 0.001). We conclude that insulin resistance and/or hyperinsulinemia (a) are present in the majority of hypertensives, (b) constitute a common pathophysiologic feature of obesity, glucose intolerance, and hypertension, possibly explaining their ubiquitous association, and (c) may be linked to the increased peripheral vascular resistance of hypertension, which is putatively related to elevated intracellular sodium concentration.
The Fidelity of DNA Polymerase β during Distributive and Processive DNA Synthesis (1999)

During base excision repair, DNA polymerase beta fills 1-6-nucleotide gaps processively, reflecting a contribution of both its 8- and 31-kDa domains to DNA binding. Here we report the fidelity of pol beta during synthesis to fill gaps of 1, 5, 6, or >300 nucleotides. Error rates during distributive synthesis by recombinant rat and human polymerase (pol) beta with a 390-base gap are similar to each other and to previous values with pol beta purified from tissues. The base substitution fidelity of human pol beta when processively filling a 5-nucleotide gap is similar to that with a 361-nucleotide gap, but "closely-spaced" substitutions are produced at a rate at least 60-fold higher than for distributive synthesis. Base substitution fidelity when filling a 1-nucleotide gap is higher than when filling a 5-nucleotide gap, suggesting a contribution of the 8-kDa domain to the dNTP binding pocket and/or a difference in base stacking or DNA structure imposed by pol beta. Nonetheless, 1-nucleotide gap filling is inaccurate, even generating complex substitution-addition errors. Finally, the single-base deletion error rate during processive synthesis to fill a 6-nucleotide gap is indistinguishable from that of distributive synthesis to fill a 390-nucleotide gap. Thus the mechanism of processivity by pol beta does not allow the enzyme to suppress template misalignments.
Prediction of protein binding sites and hot spots (2011)

Abstract Protein–protein interactions are involved in the majority of cell processes, and their detailed structural and functional characterization has become one of the most important challenges in current structural biology. The first ideal goal is to determine the structure of the specific complex formed upon interaction of two or more given proteins. However, since this is not always technically possible, the practical approach is often to locate and characterize the protein residues that are involved in the interaction. This can be achieved by experimental means at expense of time and cost, so a growing number of computer tools are becoming available to complement experimental efforts. Reported methods for interface prediction are based on sequence information or on structural data, and make use of a variety of evolutionary, geometrical, and physicochemical parameters. As we show here, computer predictions can achieve a high degree of success, and they are of practical use to guide mutational experiments as well as to explain functional and mechanistic aspects of the interaction. Interestingly, it has been found that typically only a few of the interacting residues contribute significantly to the binding energy. The identification of such hot‐spot residues is important for understanding basic aspects of protein association. In addition, these residues have received recent attention as possible targets for drug design, so several computer methods have been developed to predict them. We will review here existing computer approaches for the prediction of protein binding sites and hot‐spot residues, with a discussion on their applicability and limitations. © 2011 John Wiley &amp; Sons, Ltd. WIREs Comput Mol Sci 2011 1 680–698 DOI: 10.1002/wcms.45 This article is categorized under: Structure and Mechanism &gt; Computational Biochemistry and Biophysics
Prediction of survival without morbidity for infants born at under 33 weeks gestational age: a user-friendly graphical tool (2011)

This graphical tool provides an improved and easily interpretable method to predict survival without major morbidity for very preterm infants at the time of birth. These curves are especially useful for small and large for GA infants.
Tubulin detyrosination is a frequent occurrence in breast cancers of poor prognosis. (2001)

Tubulin, the dimeric subunit of microtubules, is a major cell protein that is centrally involved in cell division. Tubulin is subject to specific enzymatic posttranslational modifications including cyclic tyrosine removal and addition at the COOH terminus of the alpha-subunit. Tubulin is normally extensively tyrosinated in cycling cells. However, we have previously shown that detyrosinated tubulin accumulates in cancer cells during tumor progression in nude mice. Tubulin detyrosination, resulting from suppression of tubulin tyrosine ligase and the resulting unbalanced activity of tubulin-carboxypeptidase, apparently represents a strong selective advantage for cancer cells. We have now analyzed the occurrence and significance of tubulin detyrosination in human breast tumors. We studied a total of 134 breast cancer tumors from patients with or without known complications over a follow-up period of 31 +/- 10 months. The mean age of the patients at the time of diagnosis was 57 years. For each patient, detailed data concerning the histology and extension of the tumor were available. Tumor cells containing detyrosinated tubulin were visualized by immunohistochemical staining of paraffin-embedded tissue sections. Cancer cells with detyrosinated tubulin were observed in 53% of the tumors and were predominant in 19.4% of the tumors. Tubulin detyrosination correlated to a high degree of significance (P < 0.001) with a high Scarf-Bloom-Richardson (SBR) grade, a known marker of tumor aggressiveness. Among SBR grade 1 tumors, 3.8% were strongly positive for tubulin detyrosination compared with 65.4% of the SBR grade 3 tumors. The SBR component showing the strongest correlation with tubulin detyrosination was the mitotic score. In the entire patient population, neither the SBR grade nor the detyrosination index had significant prognostic value (P = 0.11, P = 0.27, respectively), whereas a combined index was significantly correlated with the clinical outcome (P = 0.02). A preliminary subgroup analysis indicated that tubulin detyrosination may define high- and low- risk groups in breast cancer tumors with an SBR grade of 2. Our study shows that tubulin detyrosination is a frequent occurrence in breast cancer, easy to detect, and linked to tumor aggressiveness.
Commercialization of high 600V GaN-on-silicon power HEMTs and diodes (2013)

With power conversion losses endemic in all areas of electricity consumption, broadly categorized into motion control (accounting for around 50% of total electrical energy use), lighting, air conditioning, and information technology, consumers, governments and utilities are finding ways to achieve higher efficiency. Manufacturers of data servers, telecom systems, solar power inverters and drives for motor control are focused on reducing power conversion losses while simultaneously shrinking the size of power systems. Although silicon has historically been the base device material used by the power conversion industry, it is rapidly reaching its physical performance limits. GaN semiconductors solutions reduce power conversion loss by over 50% in a significantly smaller form factor and at a lower cost, when device design, fabrication technology and application design are holistically combined to deliver superior end products.
End-to-End Representation Learning for Correlation Filter Based Tracking (2017)

The Correlation Filter is an algorithm that trains a linear template to discriminate between images and their translations. It is well suited to object tracking because its formulation in the Fourier domain provides a fast solution, enabling the detector to be re-trained once per frame. Previous works that use the Correlation Filter, however, have adopted features that were either manually designed or trained for a different task. This work is the first to overcome this limitation by interpreting the Correlation Filter learner, which has a closed-form solution, as a differentiable layer in a deep neural network. This enables learning deep features that are tightly coupled to the Correlation Filter. Experiments illustrate that our method has the important practical benefit of allowing lightweight architectures to achieve state-of-the-art performance at high framerates.
Highly Selective Cyclic Peptide Ligands for NeutrAvidin and Avidin Identified by Phage Display (2006)

Screening combinatorial libraries of conformationally constrained peptides against macromolecular targets is utilized in identifying novel drug leads and in developing new reagents for chemical biology. In methods such as phage-display selections, biotinylated macromolecular targets are often immobilized on avidin- and streptavidin-functionalized supports. Thus, the characterization of peptides that bind avidin and streptavidin is necessary for accurate interpretation of screening and selection results. Toward this goal, we panned a phage-displayed cyclic peptide library against NeutrAvidin, a chemically deglycosylated version of avidin. The selection produced a highly homologous consensus motif (Asp-Arg/Leu-Ala-Ser/Thr-Pro-Tyr/Trp). Two of these cyclic peptides, CDRATPYC and CDRASPYC, bound both NeutrAvidin and avidin with low-micromolar dissociation constants, whereas their acyclic counterparts had negligible affinity (< 80-fold). Moreover, these cyclic peptides were very specific for their targets and did not bind the structurally and functionally similar protein, streptavidin. Thus, we have identified a new class of cyclic peptides, distinct from the much-studied streptavidin-binding His-Pro-Gln peptide motif. These results will not only allow for discriminating between desired and background cyclic peptide motifs in selections and screens but also provide a new protein/peptide model system and a useful reagent in chemical biology that can have utility in protein immobilization, purification, and chemical tagging.
THE AMNIOTIC MEMBRANE: A SUITABLE BIOLOGICAL DRESSING TO PREVENT INFECTION IN THERMAL BURNS (2000)

SUMMARY: The development of wound sepsis is the most common cause of mortality and morbidity among burn patients. A variety of dressings have been used to cover, reduce burn wound sepsis and promote wound healing. The aim of this study was to compare the effectiveness of amniotic membrane with the classical method of treatment in thermal burn patients in reducing wound sepsis. Two-hundred patients, with less than 20% of total body surface, who suffered from second degree superficial and deep-thickness burns, were selected randomly and divided into two groups of 100 patients each. The first group was treated with classical method of antibiotic ointment and gauze bandage. The second group was covered with amniotic membranes procured from hepatitis-, syphilis- and HIV-seronegative mothers having undergone cesarean deliveries. The wounds were inspected for any signs of infection daily for 10 days, then on weekly basis for 4 weeks and finally monthly for 6 months. All cases were treated on an outpatient basis. In the amnion and classical methods, 2 and 17 cases of infection were respectively observed. These were hospitalized and treated successfully by debridement and administration of appropriate systemic and local antibiotics. Despite possible dangers of disease transmission, which can be overcome with appropriate precautions, we recommend the widespread use of this procedure.
Bismuth-Coated Carbon Electrodes for Anodic Stripping Voltammetry (2000)

Bismuth-coated carbon electrodes display an attractive stripping voltammetric performance which compares favorably with that of common mercury-film electrodes. These bismuth-film electrodes are prepared by adding 400 microg/L (ppb) bismuth(III) directly to the sample solution and simultanously depositing the bismuth and target metals on the glassy-carbon or carbon-fiber substrate. Stripping voltammetric measurements of microgram per liter levels of cadmium, lead, thallium, and zinc in nondeaerated solutions yielded well-defined peaks, along with a low background, following short deposition periods. Detection limit of 1.1 and 0.3 ppb lead are obtained following 2- and 10-min deposition, respectively. Changes in the peak potentials (compared to those observed at mercury electrodes) offer new selectivity dimensions. Scanning electron microscopy sheds useful insights into the different morphologies of the bismuth deposits on the carbon substrates. The in situ bismuth-plated electrodes exhibit a wide accessible potential window (-1.2 to -0.2 V) that permits quantitation of most metals measured at mercury electrodes (except of copper, antimony, and bismuth itself). Numerous key experimental variables have been characterized and optimized. High reproducibility was indicated from the relative standard deviations (2.4 and 4.4%) for 22 repetitive measurements of 80 microg/L cadmium and lead, respectively. Such an attractive use of "mercury-free", environmetally friendly electrodes (with a performance equivalent to that of mercury ones) offers great promise to centralized and decentralized testing of trace metals.
Polyamide-6 Polymerization in the VK Tube Reactor with Baffle Structure (2002)

The melt flow mechanism of polyamide-6 (PA6) was simulated with the mathematical flow model and tested by Particle Image Velotrimitry (PIV). The complete mathematical model for PA6 polymerization while flowing through the VK tube reactor was established according to PA6 hydrolytic polymerization kinetics. The characteristic data such as residence time, caprolactam conversion and the degree of polymerization (D. P.), at every stage of polymerization reaction and at every point of the VK tube were presented for the melt flowing through ten alternate conical baffles in VK tube.
Zinc-finger Nucleases as a Novel Therapeutic Strategy for Targeting Hepatitis B Virus DNAs (2010)

Hepatitis B virus (HBV) chronically infects 350-400 million people worldwide and causes >1 million deaths yearly. Current therapies prevent new viral genome formation, but do not target pre-existing viral genomic DNA, thus curing only approximately 1/2 of patients. We targeted HBV DNA for cleavage using zinc-finger nucleases (ZFNs), which cleave as dimers. Co-transfection of our ZFN pair with a target plasmid containing the HBV genome resulted in specific cleavage. After 3 days in culture, 26% of the target remained linear, whereas approximately10% was cleaved and misjoined tail-to-tail. Notably, ZFN treatment decreased levels of the hepatitis C virus pregenomic RNA by 29%. A portion of cleaved plasmids are repaired in cells, often with deletions and insertions. To track misrepair, we introduced an XbaI restriction site in the spacer between the ZFN sites. Targeted cleavage and misrepair destroys the XbaI site. After 3 days in culture, approximately 6% of plasmids were XbaI-resistant. Thirteen of 16 clones sequenced contained frameshift mutations that would lead to truncations of the viral core protein. These results demonstrate, for the first time, the possibility of targeting episomal viral DNA genomes using ZFNs.
A systematic review and economic evaluation of statins for the prevention of coronary events (2007)

There is evidence to suggest that statin therapy is associated with a statistically significant reduction in the risk of primary and secondary cardiovascular events. As the confidence intervals for each outcome in each prevention category overlap, it is not possible to differentiate, in terms of relative risk, between the effectiveness of statins in primary and secondary prevention. However, the absolute risk of CHD death/non-fatal MI is higher, and the number needed to treat to avoid such an event is consequently lower, in secondary than in primary prevention. The generalisability of these results is limited by the exclusion, in some studies, of patients who were hypersensitive to, intolerant of, or known to be unresponsive to, statins, or who were not adequately compliant with study medication during a placebo run-in phase. Consequently, the treatment effect may be reduced when statins are used in an unselected population. The results of the economic modelling show that statin therapy in secondary prevention is likely to be considered cost-effective. In primary prevention, the cost-effectiveness ratios are dependent on the level of CHD risk and age, but the results for the CVD analyses offer support for the more aggressive treatment recommendation issued by recent guidelines in UK. Evidence on clinical endpoints for rosuvastatin is awaited from on-going trials. The potential targeting of statins at low-risk populations is however associated with major uncertainties, particularly the likely uptake and long-term compliance to lifelong medication by asymptomatic younger patients. The targeting, assessment and monitoring of low-risk patients in primary care would be a major resource implication for the NHS. These areas require further research.
Antibody mediated lung targeting of long-circulating emulsions. (1997)

Monoclonal antibody 34A, which specifically binds to a surface glycoprotein (thrombomodulin) of the pulmonary endothelial cell surface in mice, has been conjugated to the surface of long-circulating emulsions composed of Castor oil, phosphatidylcholine and polyethylene glycol coupled to distearoylphosphatidyl-ethanolamine. These antibody-containing emulsions were found capable of binding to the lung when injected into mice through the tail vein. The level of lung accumulation of these emulsions depends on the amount of antibodies conjugated to the surface of the emulsions. With an input antibody to lipid ratio of 2:1 (w/w), 30% injected emulsions were found in the lung 30 minutes after administration. Such high level accumulation can be blocked by co-administration of free 34A antibody, indicating that the binding is specific and 34A antibody mediated. Kinetic studies showed that emulsion targeting to the lung was very rapid. Five minutes after tail vein injection, the total amount of emulsion found in the lung was the highest among the time points examined, indicating the completion of lung binding. However, about 50% of the initially bound emulsions remained bound for more than 4 hours. These results indicate that the targeted drug delivery using oil-in-water emulsions could be very useful to enhance the therapeutic efficacy of lipophilic drugs.
Nano-liposomal irinotecan and 5-FU/LV (N+F) for the treatment of advanced PDAC: Memorial Sloan Kettering (MSK) Single Cancer Center Evaluation. (2018)

471 Background: Therapy options for advanced pancreatic adenocarcinoma (PDAC) are finite. NAPOLI-1, a phase III randomized trial, demonstrated the efficacy of N+F following progression on gemcitabine (G) based therapy (mPFS 3.1 mo, mOS 6.1 mo). There are limited additional data on the safety and efficacy of N+F following FDA approval in October 2015. We examined the post approval safety, tolerability and effectiveness of N+F in advanced PDAC patients at MSK. Methods: A retrospective chart review was conducted of all patients treated with N+F from Feb 2016 and ending in Aug 2017. Using the EMR and institutional database, information was extracted pertaining to demographics, performance status (ECOG), prior therapies, dose, duration of N+F, adverse events, PFS, OS and treatment response per RECIST. Results:N = 56 identified. Demographics: M/F 29/27, age 68 (range 42-88), prior lines of palliative chemotherapy (0/1/2/3/ &gt; 3, 4/20/21/11). Median PFS was 2.9 months and median OS was 5.3 months. There was a significant difference in PFS, OS and prior lines of therapy between patients who previously progressed on irinotecan (N = 27) versus not (N = 29); PFS = 2.4 v 4.8 mo, p = 0.0154; OS = 3.9 v 8.4 mo, p = 0.0021; 2 v 1 line. ECOG score was not predictive of PFS or OS. There were 19 dose reductions (DR), most frequent reasons: fatigue (42%) and diarrhea (37%). Regarding RECIST: PR = 2 (4%), SD = 19 (34%). 10/43 (23%) experienced &gt; 50% CA 19-9 reduction. Dose reductions were not associated with worse outcomes, in fact, patients with 1 or more DR experienced significantly longer PFS v none (DR 2, not reached; DR 1, 5.2 mo; DR 0, 2.5 mo, p = 0.0185). For the subset who received sequential therapy with G+nab-paclitaxel (P) followed by N+F (N = 25) mOS of 25.4 mo. Conclusions: These data support the safety and efficacy of N+F, re-inforcing results of NAPOLI-1. Patients whose disease previously progressed on irinotecan fared significantly worse than patients who did not, when treated with N+F. N+F appears active even in patients requiring DR. Sequential therapy with G+P followed by N+F demonstrates encouraging mOS. Collectively these findings underscore the utility of N+F in the therapy of advanced PDAC.
HLA-DR-Promiscuous T Cell Epitopes from Plasmodium falciparum Pre-Erythrocytic-Stage Antigens Restricted by Multiple HLA Class II Alleles (2000)

Previously, we identified and established the antigenicity of 17 CD8+ T cell epitopes from five P. falciparum Ags that are restricted by multiple common HLA class I alleles. Here, we report the identification of 11 peptides from the same Ags, cicumsporozoite protein, sporozoite surface protein 2, exported protein-1, and liver-stage Ag-1, that bind between at least five and up to 11 different HLA-DR molecules representative of the most common HLA-DR Ags worldwide. These peptides recall lymphoproliferative and cytokine responses in immune individuals experimentally immunized with radiation-attenuated Plasmodium falciparum sporozoites (irradiated sporozoites) or semi-immune individuals naturally exposed to malaria in Irian Jaya or Kenya. We establish that all peptides are recognized by individuals of each of the three populations, and that the frequency and magnitude of helper T lymphocyte responses to each peptide is influenced by the intensity of exposure to P. falciparum sporozoites. Mean frequencies of lymphoproliferative responses are 53.2% (irradiated sporozoites) vs 22.4% (Kenyan) vs 5.8% (Javanese), and mean frequencies of IFN-gamma responses are 66.3% (irradiated sporozoites) vs 27.3% (Kenyan) vs 8. 7% (Javanese). The identification of HLA class II degenerate T cell epitopes from P. falciparum validates our predictive strategy in a biologically relevant system and supports the potential for developing a broadly efficacious epitope-based vaccine against malaria focused on a limited number of peptide specificities.