gebhart/patrepeval huggingface dataset:
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database (2017)

The MEROPS database (http://www.ebi.ac.uk/merops/) is an integrated source of information about peptidases, their substrates and inhibitors. The hierarchical classification is: protein-species, family, clan, with an identifier at each level. The MEROPS website moved to the EMBL-EBI in 2017, requiring refactoring of the code-base and services provided. The interface to sequence searching has changed and the MEROPS protein sequence libraries can be searched at the EMBL-EBI with HMMER, FastA and BLASTP. Cross-references have been established between MEROPS and the PANTHER database at both the family and protein-species level, which will help to improve curation and coverage between the resources. Because of the increasing size of the MEROPS sequence collection, in future only sequences of characterized proteins, and from completely sequenced genomes of organisms of evolutionary, medical or commercial significance will be added. As an example, peptidase homologues in four proteomes from the Asgard superphylum of Archaea have been identified and compared to other archaean, bacterial and eukaryote proteomes. This has given insights into the origins and evolution of peptidase families, including an expansion in the number of proteasome components in Asgard archaeotes and as organisms increase in complexity. Novel structures for proteasome complexes in archaea are postulated.
Association between COMT Val158Met polymorphism and competition results of competitive swimmers (2017)

Recent studies have shown the contribution of genetic determinants to athletes' physical ability. However, despite the fact that cognitive abilities like self-control and stress-tolerance influence athletes' competitive performance, few studies to date have investigated the association between genetic polymorphism, which is linked to cognitive ability and athletic performance. The present study investigated the link between single-nucleotide polymorphisms (SNPs), which are known to exert influences on dopaminergic neural function and competitive performance of swimmers. The results have revealed superior competitive performance in competitive swimmers with Met allele of catechol-O-methyltransferase Val158Met polymorphism than those with Val/Val genotype. The investigated SNPs of DRD2 and DRD3 were not associated with swimmer's competitive performance. This finding indicates that genetic polymorphism linked to cognitive ability influences the athletes' performance.
Adeno-Associated Virus Capsids Displaying Immunoglobulin-Binding Domains Permit Antibody-Mediated Vector Retargeting to Specific Cell Surface Receptors (2002)

Recombinant adeno-associated virus type 2 (rAAV2) is a promising vector for human somatic gene therapy. However, its broad host range is a disadvantage for some applications, because it reduces the specificity of the gene transfer. To overcome this limitation, we sought to create a versatile rAAV vector targeting system which would allow us to redirect rAAV binding to specific cell surface receptors by simple coupling of different ligands to its capsid. For this purpose, an immunoglobulin G (IgG) binding domain of protein A, Z34C, was inserted into the AAV2 capsid at amino acid position 587. The resulting AAV2-Z34C mutants could be packaged and purified to high titers and bound to IgG molecules. rAAV2-Z34C vectors coupled to antibodies against CD29 (beta(1)-integrin), CD117 (c-kit receptor), and CXCR4 specifically transduced distinct human hematopoietic cell lines. In marked contrast, no transduction was seen in the absence of antibodies or in the presence of specific blocking reagents. These results demonstrate for the first time that an immunoglobulin binding domain can be inserted into the AAV2 capsid and coupled to various antibodies, which mediate the retargeting of rAAV vectors to specific cell surface receptors.
Efficient mode selection for block-based motion compensated video coding (2002)

A method for efficiently selecting the operating modes within a block-based multi-mode video compression system is described. For a given image region, the optimum combination of modes is selected so as to minimize the overall distortion for a given bit-rate budget. Necessary conditions for optimizing the encoder operation are derived within a rate-constrained product code framework. When rate and distortion dependencies exist between adjacent blocks, the ensuing encoder complexity is surmounted using a dynamic programming strategy based on the Viterbi algorithm so as to achieve the optimum selection of macroblock modes. Results are provided for the emerging H.263 video coding standard.
Atrial G protein-activated K+ channel: expression cloning and molecular properties. (1993)

Activity of several ion channels is controlled by heterotrimeric GTP-binding proteins (G proteins) via a membrane-delimited pathway that does not involve cytoplasmic intermediates. The best studied example is the K+ channel activated by muscarinic agonists in the atrium, which plays a crucial role in regulating the heartbeat. To enable studies of the molecular mechanisms of activation, this channel, denoted KGA, was cloned from a rat atrium cDNA library by functional coupling to coexpressed serotonin type 1A receptors in Xenopus oocytes. KGA displays regions of sequence homology to other inwardly rectifying channels as well as unique regions that may govern G-protein interaction. The expressed KGA channel is activated by serotonin 1A, muscarinic m2, and delta-opioid receptors via G proteins. KGA is activated by guanosine 5'-[gamma-thio]triphosphate in excised patches, confirming activation by a membrane-delimited pathway, and displays a conductance equal to that of the endogenous channel in atrial cells. The hypothesis that similar channels play a role in neuronal inhibition is supported by the cloning of a nearly identical channel (KGB1) from a rat brain cDNA library.
Nanofluidics in Lab-on-a-Chip Devices (2009)

As the field of nanofluidics matures, fundamental discoveries are being applied to lab-on-a-chip analyses. The unique behavior of matter at the nanoscale is adding new functionality to devices that integrate nanopores or nanochannels. (To listen to a podcast about this feature, please go to the Analytical Chemistry website at pubs.acs.org/journal/ancham.).
Continuous field-flow separation of particle populations in a dielectrophoretic chip with three dimensional electrodes (2007)

This letter presents a dielectrophoretic (DEP) separation method of particles under continuous flow. The method consists of flowing two particle populations through a microfluidic channel, in which the vertical walls are the electrodes of the DEP device. The irregular shape of the electrodes generates both electric field and fluid velocity gradients. As a result, the particles that exhibit negative DEP can be trapped in the fluidic dead zones, while the particles that experience positive DEP are concentrated in the regions with high velocity and collected at the outlet. The device was tested with dead and living yeast cells.
Differential expression of human granzymes A, B, and K in natural killer cells and during CD8+ T cell differentiation in peripheral blood (2005)

Abstract NK cells and cytotoxic T lymphocytes can induce apoptosis in virus‐infected and transformed target cells via the granule exocytosis pathway. The key components of the cytolytic granules are perforin and several serine esterases, termed granzymes. While the cellular distribution of human granzymes A (GrA) and B (GrB) has been well characterized much less is known about the expression pattern of human granzyme K (GrK). In this study GrA, GrB, and GrK expression was analyzed in human peripheral blood lymphocytes using flow cytometry. There was a distinct population of GrK expressing CD8 + T cells with a CD27 + /CD28 + /CCR5 high /CCR7 – /perforin –/low /IFN‐γ + memory‐like phenotype, while all CD56 bright NK cells were also positive for GrK. In addition, GrK was also expressed in subpopulations of CD56 + T cells, CD4 + T cells, and TCRγδ + T cells. In contrast, GrB was primarily expressed in CD56 dim NK cells and differentiated memory CD8 + T cells with the CD27 –/low /CD28 –/low /CCR5 –/low /CCR7 – /CD11b + /perforin high phenotype. Only few CD8 + T cells expressed both GrB and GrK. GrA was found to be co‐expressed in all GrB‐ and GrK‐expressing T cells. Our findings suggest that granzyme expression during the differentiation process of memory CD8 + T cells might be as follows: GrA + /GrB – /GrK + → GrA + /GrB + /GrK + → GrA + /GrB + /GrK – .
The Fatty Acid–Binding Protein-2 A54T Polymorphism Is Associated With Renal Disease in Patients With Type 2 Diabetes (2005)

The intestinal fatty-acid binding protein-2 (FABP2) gene codes a protein responsible for the absorption of long-chain fatty acids. To test whether FABP2 is a candidate gene for renal disease in patients with type 2 diabetes, a functional A54T polymorphism was genotyped in 1,042 Brazilians with type 2 diabetes. Patients were classified as having normoalbuminuria (urinary albumin excretion [UAE] <20 microg/min; n = 529), microalbuminuria (UAE 20-199 microg/min; n = 217), or proteinuria (UAE >199 microg/min; n = 160). Patients with end-stage renal disease (ESRD) (n = 136) were also included. The prevalence of the TT genotype was higher in patients with renal involvement compared with those with normoalbuminuria (odds ratio [95% CI] 2.4 [1.1-5.4]) following adjustment for type 2 diabetes duration, BMI, hypertension, A1C, and cholesterol levels. The risk was similar considering different stages of renal involvement. In a second independent patient sample (483 type 2 diabetic Caucasians residing in Massachusetts), a significant association was also observed between the TT genotype and proteinuria or ESRD (2.7 [1.0-7.3]; P = 0.048). This study thus provides evidence that FABP2 confers susceptibility to renal disease in type 2 diabetic patients.
Mitotic Spindle Disruption by Alternating Electric Fields Leads to Improper Chromosome Segregation and Mitotic Catastrophe in Cancer Cells (2015)

Tumor Treating Fields (TTFields) are low intensity, intermediate frequency, alternating electric fields. TTFields are a unique anti-mitotic treatment modality delivered in a continuous, noninvasive manner to the region of a tumor. It was previously postulated that by exerting directional forces on highly polar intracellular elements during mitosis, TTFields could disrupt the normal assembly of spindle microtubules. However there is limited evidence directly linking TTFields to an effect on microtubules. Here we report that TTFields decrease the ratio between polymerized and total tubulin, and prevent proper mitotic spindle assembly. The aberrant mitotic events induced by TTFields lead to abnormal chromosome segregation, cellular multinucleation, and caspase dependent apoptosis of daughter cells. The effect of TTFields on cell viability and clonogenic survival substantially depends upon the cell division rate. We show that by extending the duration of exposure to TTFields, slowly dividing cells can be affected to a similar extent as rapidly dividing cells.
No increase of calcitonin gene–related peptide in jugular blood during migraine (2005)

Increased calcitonin gene-related peptide (CGRP) in external jugular venous blood during migraine attack is one of the most cited findings in the headache literature. The finding has not been convincingly reproduced and is based on comparison with historic control subjects. The validity of this finding is important for the understanding of migraine. We therefore investigated the issue using an intrapatient comparison design and two different CGRP assays. We sampled blood from the external jugular and cubital vein during, as well as outside of, an attack of migraine without aura. We succeeded in 17 patients, whereas only cubital fossa blood could be sampled in an additional 4 patients. CGRP was measured with the same assay as most previous studies (assay I) and furthermore with a more sensitive and validated assay (assay II). For assay I, mean CGRP concentration in external jugular venous blood during attack was 17.18 pmol/L compared with 15.88 pmol/L outside of attack. Mean difference was 1.81 pmol/L (95% confidence interval [CI]: -2.88, 6.41; p = 0.44). In peripheral blood during attack, CGRP was 16.86 pmol/L compared with 17.57 pmol/L outside of attack. Mean difference was -0.79 pmol/L (95% CI: -4.64, 3.06; p = 0.69). For assay II, external jugular venous blood concentration of CGRP during attack was 32.59 pmol/L compared with 30.59 pmol/L outside of attack; mean difference was 2.00 pmol/L (standard error, 2.39; 95% CI: -3.07, 7.07; p = 0.416). In peripheral blood during attack, CGRP was 33.37 pmol/L compared with 31.84 pmol/L outside of attack; mean difference was 1.53 pmol/L (standard error, 1.90; 95% CI: -2.46, 5.51; p = 0.431). Thus, no difference between CGRP level in external jugular or cubital fossa blood during and outside of attack was found. No difference was found between external jugular and peripheral venous blood. Thus, previous findings of increased CGRP level in external jugular or cubital fossa venous blood could not be confirmed. Our finding strongly suggests that CGRP is not increased in jugular venous blood during migraine without aura. CGRP cannot be used as a biomarker to validate human or animal models of migraine.
An individualized plastic intraoral device for the collection of human parotid saliva. (1984)

A new individualized, non-invasive device for the collection of parotid saliva is described which offers the following advantages: automatic placement in the proper position for saliva collection by patients without the help of a technician, lack of deadspace, lack of salivary leakage around the device, elimination of cross contamination between patients, and unlimited re-use. Because of its simplicity, it is an ideal device for routine collection of parotid saliva samples in therapeutic drug monitoring, biochemical monitoring of exposure to toxic materials, and detection of secretory component deficiencies of immune system disorders.
Platelet lysate modulates MMP-2 and MMP-9 expression, matrix deposition and cell-to-matrix adhesion in keratinocytes and fibroblasts (2010)

Cell-matrix interactions are an essential element of wound healing, while platelet derivatives are used in clinical settings for the treatment of chronic wounds. We used a platelet lysate (PL), which had been previously shown to accelerate in vitro the wounding of HaCaT keratinocytes and fibroblasts (J Cell Mol Med, 13, 2009, 2030; Br J Dermatol, 159, 2008, 537), to study the modulation of MMP-2 and MMP-9 collagenase expression, collagen type I and III production and syndecan-4 expression and rearrangement in these cells. Zymography and Western blot analyses showed that exposure to 20% (v/v) PL for 24 h induced an apparently ERK1/2- and p38-dependent, NF-kappaB-independent, translational upregulation of MMP-9 in HaCaT, while HaCaT MMP-2 and fibroblast collagenases were almost unaffected. The use of in-cell ELISA showed that PL induced an increase in the collagen III production of fibroblasts. In-cell ELISA and immunofluorescence microscopy revealed an increase in the expression of syndecan-4 and its rearrangement to form focal adhesions in both cell types after PL exposure. Taken together, data indicate that PL promotes keratinocyte epithelialization and regulates fibroblast matrix deposition, thus providing a molecular basis for the ability of this platelet derivative to heal severe and problematic wounds without leading to heavy scarring and keloid formation.
The Use of Hypothermia as a Treatment for Traumatic Brain Injury (2009)

Hypothermia has been shown to have neuroprotective effects and may have benefit in the treatment of head injuries. However, it is a controversial treatment in traumatic brain injury, and to date, there are no specific recommendations for its use. This article examines six research studies investigating the use of hypothermia as a treatment in patients with traumatic brain injury. All studies were prospective trials and compared a controlled normothermia group with a hypothermia group. Studies were compared by sample population, methods of hypothermia, outcomes, and conclusions. The leading variable in each study was hypothermia. However, each study used a different method of cooling, goal temperature, and duration of cooling. Through the comparison of these studies, a recommendation for change in practice cannot be made. Nevertheless, there may be benefits to hypothermia in traumatic brain injury, and suggestions for future research are identified.
A Tough Nut to Crack (2015)

The purpose of our project is to explore the measurement of cognitive skills in the domain of science through collaborative problem solving tasks, measure the collaborative skills, and gauge the potential feasibility of using game-like environments with avatar representation for the purposes of assessing the relevant skills. We are comparing students' performance in two conditions. In one condition, students work individually with two virtual agents in a game-like task. In the second condition, dyads of students work collaboratively with two virtual agents in the similar game-like task through a chat box. Our research is motivated by the distributed nature of cognition, extant research on computer-supported collaborative learning (CSCL) which has shown great value of collaborative activities for learning, and the framework for the Programme for International Student Assessment (PISA) framework. This chapter focuses on the development and implementation of a conceptual model to measure individuals' cognitive and social skills through collaborative activities.
Transesterification kinetics of soybean oil 1 (1986)

Abstract Transesterification of soybean oil (SBO) and other triglycerides with alcohols, in the presence of a catalyst, yields fatty esters and glycerol. Di‐ and monoglycerides are intermediates. Reactions are consecutive and reversible. Rate constants have been determined for each reaction with a computerized kinetic program. The effects of the type of alcohol, 1‐butanol or methanol (MeOH); molar ratio of alcohol to SBO; type and amount of catalyst; and reaction temperature on rate constants and kinetic order were examined. Forward reactions appear to be pseudo‐first order or second order depending upon conditions used. Reverse reactions appear to be second order. At a molar ratio of MeOH/SBO of 6:1, a shunt reaction was observed. Energy of activation was determined for all forward and reverse reactions under a variety of experimental conditions from plots of log k vs 1/T. Values ranged from 8–20 kcal/mol.
Intrasystem Entanglement Generator and Unambiguos Bell States Discriminator on Chip (2019)

Bell measurements, jointly projecting two qubits onto the so-called Bell basis, constitute a crucial step in many quantum computation and communication protocols, including dense coding, quantum repeaters, and teleportation-based quantum computation. A problem is the impossibility of deterministic unambiguous Bell measurements using passive linear optics, even when arbitrarily many auxiliary photons, photon-number-resolving detectors, and dynamical (conditionally changing) networks are available. Current proposals for going over the 50% upper bound without using experimentally challenging nonlinearities rely on using entangled photon ancilla states and a sufficiently large interferometer to combine the signal and ancilla modes. We demonstrate that the novel Multiple Rail architecture, based on the propagation of a single photon in a complex multipath optical circuit (or multiwaveguide optical circuit), provides the possibility to perform deterministic Bell measurements so to unambiguously discrimate all four Bell States.
Pharmacokinetics of 125I-labeled insulin glargine (HOE 901) in healthy men: comparison with NPH insulin and the influence of different subcutaneous injection sites. (2000)

OBJECTIVE: To determine the subcutaneous absorption rates and the appearance in plasma of 3 formulations of the long-acting human insulin analog insulin glargine (HOE 901) differing only in zinc content (15, 30, and 80 microg/ml). RESEARCH DESIGN AND METHODS: We conducted 2 studies. Study 1 compared the subcutaneous abdominal injection of 0.15 U/kg of 125I-labeled insulin glargine[15], insulin glargine[80], NPH insulin, and placebo. In study 2, 0.2 U/kg of insulin glargine[30] was injected into the arm, leg, and abdominal regions. Both studies had a randomized crossover design; each enrolled 12 healthy men, aged 18-50 years. RESULTS: In study 1, the time in hours for 25% of the administered radioactivity to disappear after bolus subcutaneous injection (T75%) for NPH insulin indicated a significantly faster absorption rate compared with the 2 insulin glargine formulations (3.2 vs. 8.8 and 11.0 h, respectively P &amp;lt; 0.0001). Mean residual radioactivity with NPH insulin was also significantly lower at 24 h (21.9 vs. 43.8 and 52.2%, P &amp;lt; 0.0001). The calculated plasma exogenous insulin concentrations after NPH insulin were substantially higher than those with insulin glargine, reaching a peak within the first 6 h after administration before declining. Insulin glargine, however, did not exhibit a distinct peak. Weighted average plasma glucose concentration between 0 and 6 h was significantly lower after NPH compared with insulin glargine (P &amp;lt; 0.001). In study 2, there were no significant differences in the absorption characteristics of insulin glargine between the 3 injection sites (T75% = 11.9, 15.3, and 13.2 h for arm, leg, and abdomen, respectively) or in residual radioactivity at 24 h. CONCLUSIONS: Subcutaneous absorption of insulin glargine is delayed compared with NPH insulin. There is little or no difference in the absorption rate of insulin glargine between the main subcutaneous injection sites.
An overview of query optimization in relational systems (1998)

Article Free Access Share on An overview of query optimization in relational systems Author: Surajit Chaudhuri Microsoft Research, One Microsoft Way, Redmond, WA Microsoft Research, One Microsoft Way, Redmond, WAView Profile Authors Info & Claims PODS '98: Proceedings of the seventeenth ACM SIGACT-SIGMOD-SIGART symposium on Principles of database systemsMay 1998 Pages 34–43https://doi.org/10.1145/275487.275492Online:01 May 1998Publication History 339citation7,618DownloadsMetricsTotal Citations339Total Downloads7,618Last 12 Months350Last 6 weeks69 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF