gebhart/patrepeval huggingface dataset:
Human DNA Damage Checkpoint Protein hRAD9 Is a 3′ to 5′ Exonuclease (2000)

Human RAD9 protein (hRAD9) is a homolog of the fission yeast Rad9 protein, one of the six so-called checkpoint Rad proteins involved in the early steps of DNA damage checkpoint response in Schizosaccharomyces pombe. It has been shown previously that, in vivo, a highly modified form of hRAD9 makes a ternary complex with two other checkpoint Rad proteins, hRAD1 and hHUS1 (Volkmer, E., and Karnitz, L. M. (1999) J. Biol. Chem. 274, 567-570; St. Onge, R. P., Udell, C. M., Casselman, R., and Davey, S. (1999) Mol. Biol. Cell. 10, 1985-1995). However, the function of this complex is not known at present. To help define the functions of checkpoint Rad proteins in humans, we expressed hRAD9 in Escherichia coli, purified the recombinant protein and characterized it. We found that hRAD9 is a 3' to 5' exonuclease and located the nuclease active site to the region between residues 51 and 91 of the 391-amino acid-long protein. Our results suggest that exonucleolytic processing of primary DNA lesion by hRAD9 may contribute to DNA damage checkpoint response in humans.
The cytoplasmic tail of the T cell receptor ζ chain is required for signaling via CD26 (1995)

The protease dipeptidylpeptidase IV (CD26) provides an alternative activation pathway for T lymphocytes and is involved in several aspects of T cell function. Activation via CD26 requires the expression of the T cell receptor (TcR)/CD3 complex. Here we have investigated the role of the TcR zeta chain for T cell activation via CD26. T cell hybridomas expressing TcR with various deletions in the CD3 zeta chain were transfected with a CD26 cDNA and the response of the transfected cells to anti-CD26 monoclonal antibodies was tested. Our data show that the zeta chain is essential and that at least one YXXL motif in the cytoplasmic tail of the zeta chain is required for CD26-mediated signaling. Other TcR components do not replace the zeta chain.
PLACEMENT OPTIMIZATION OF POSITIONING NODES: MAXIMIZING THE DISTINCTION OF INDOOR ZONES (2019)

Abstract. The performance of an indoor positioning system is highly related to the placement of the transmitting nodes that are used as references for the positioning estimations. In this paper, we propose a methodology that can be used to optimize such a deployment and thus, increase the performance of an indoor positioning system that a) is based on Received Signal Strength (RSS) fingerprinting and b) is orientated towards providing location or zone estimations instead of exact positioning. The optimization process involves 4 fundamental components. Firstly, the modelling of the obstructions in the indoor environment and also the zone modelling. Then, the definition of the performance metric that can be used to evaluate each different deployment scenario, in which case, our proposed metric considers the separation area and distances between the zones in the RSS vector space. The third component is the radio propagation model, required for simulating the RSSs from each node, where a model based on the ray tracing technique is selected. Finally, the last component is the selection of the optimization function that will control and drive the whole optimization process by selecting which deployment schemes to evaluate. For that, the utilization of a Genetic Algorithm is proposed. Although the evaluation of this methodology is outside the paper’s scope, the key factors affecting the optimization performance the most, are expected to be a) the accuracy of the used indoor model and radio propagation model and b) the exact implementation of the optimization function.
A system of parallel and selective microchannels for biosensor sample delivery and containment (2010)

This paper presents an integrated microfluidic system for selectively interrogating parallel biosensors at programmed time intervals. Specifically, the microfluidic system is used for delivering a volume of sample from a single source to a surface-based arrayed biosensor. In this case the biosensors were an array of electrochemical electrodes modified with sample specific capture probes. In addition, the sample was required to be captured, stored and removed for additional laboratory analysis. This was accomplished by a plastic laminate stack in which each thin laminate was patterned by CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> laser ablation to form microchannels and two novel valves. The first valve was a normally closed type opened by heat via an electrically resistive wire. The second valve was a check type integrated into a removable storage chamber. This setup allows for remote and leave-behind sensing applications and also containment of sensed sample for further laboratory analysis.
Secretory dynamics of ghrelin in adolescent girls with anorexia nervosa and healthy adolescents (2005)

Ghrelin is an orexigenic peptide and a growth hormone (GH) secretagogue. Secretory dynamics of ghrelin have not been characterized in adolescents with anorexia nervosa (AN). We hypothesized that, compared with healthy adolescents, girls with AN would have increased ghrelin concentrations measured over 12 h of nocturnal sampling from increased basal and pulsatile secretion, and endogenous ghrelin would independently predict GH and cortisol. We examined ghrelin concentration and secretory dynamics in 22 girls with AN and 18 healthy adolescents 12-18 yr old. Associations between ghrelin, various hormones, and measures of insulin resistance were examined. On Cluster analysis, girls with AN had higher ghrelin concentrations than controls, including total area under the curve (AUC) (P = 0.002), nadir (P = 0.0006), and valley levels (P = 0.002). On deconvolution analysis, secretory burst amplitude (P = 0.03) and burst mass (P = 0.04) were higher in AN, resulting in higher pulsatile (P = 0.05) and total ghrelin secretion (P = 0.03). Fasting ghrelin independently predicted GH burst frequency (r = 0.44, P = 0.005). The nutritional markers body mass index and body fat predicted postglucose and valley ghrelin but not fasting levels. Ghrelin parameters were inversely associated with fasting insulin, homeostasis model assessment of insulin resistance (HOMA-IR), leptin, and IGF-I. HOMA-IR was the most significant predictor of most ghrelin parameters. Valley ghrelin independently predicted cortisol burst frequency (52% of variability), and ghrelin parameters independently predicted total triiodothyronine and LH levels. Higher ghrelin concentrations in adolescents with AN are a consequence of increased secretory burst mass and amplitude. The most important predictor of ghrelin concentration is insulin resistance, and ghrelin in turn predicts GH and cortisol burst frequency.
Hypochlorous Acid Generated by Myeloperoxidase Modifies Adjacent Tryptophan and Glycine Residues in the Catalytic Domain of Matrix Metalloproteinase-7 (Matrilysin) (2003)

Dysregulation of matrix metalloproteinase (MMP) activity is implicated in tissue destruction under inflammatory conditions. An important mechanism controlling enzymatic activity might involve reactive oxygen species generated by phagocytes. Myeloperoxidase, a heme protein secreted by neutrophils, monocytes, and macrophages, uses hydrogen peroxide to generate hypochlorous acid (HOCl). We demonstrate that HOCl inhibits the activity of human matrilysin (MMP-7) in vitro, suggesting that it might limit proteolytic activity during inflammation. When MMP-7 was exposed to HOCl generated by myeloperoxidase, the proteinase lost activity. High performance liquid chromatographic analysis of the tryptic digest of the HOCl-treated proteinase demonstrated the absence of two peptides that were present in the untreated enzyme. Tandem mass spectrometric analysis revealed that both of the lost peptides contained methionine and tryptophan-glycine residues. The methionine residue of one of the peptides had been oxidized to methionine sulfoxide. In contrast, the major product from the other peptide was 4 atomic mass units smaller than its precursor (WG-4). This novel oxidation product was derived though modification of adjacent tryptophan and glycine residues in the catalytic domain of the enzyme. Loss of proteolytic activity was associated with conversion of the precursor peptide to WG-4 but not with methionine oxidation. In contrast, hydrogen peroxide failed to oxidize MMP-7 or to inactivate the enzyme. Thus, HOCl inactivates MMP-7, perhaps by site-specific conversion of tryptophan-glycine to WG-4. This inactivation mechanism is distinct from the well studied mechanisms involving tissue inhibitors of metalloproteinases. Our findings suggest that local pericellular production of HOCl by phagocytes is a physiological mechanism for governing MMP activity during inflammation.
<title>Robotic technologies for outdoor industrial vehicles</title> (2001)

The commercial industries of agriculture, mining, construction, and material handling employ a wide variety of mobile machines, including tractors, combines, Load-Haul-Dump vehicles, trucks, paving machines, fork trucks, and many more. Automation of these vehicles promises to improve productivity, reduce operational costs, and increase safety. Since the vehicles typically operate in difficult environments, under all weather conditions, and in the presence of people and other obstacles, reliable automation faces severe technical challenges. Furthermore, the viable technology solutions are constrained by cost considerations. Fortunately, due to the limited application domain, repetitive nature, and the utility of partial automation for most tasks, robotics technologies can have a profound impact on industrial vehicles. In this paper, we describe a technical approach developed at Carnegie Mellon University for automating mobile machines in several applications, including mass excavation, mining, and agriculture. The approach is introduced via case studies, and the results are presented.
Human‐human hybridomas for the study of anti‐tumor immune response in patients with colorectal cancer (1986)

Human-human hybridoma technology was evaluated for the study of humoral immune reactions of colorectal cancer patients against their own tumors. Six fusions were carried out with lymphocytes from mesenteric lymph nodes from patients with colorectal cancer, using the human B-lymphoma cell line LICR-LON-HMy-2 as fusion partner. A total of 294 wells with cell growth were obtained. Supernatants from 26 of these reacted in enzyme-linked immuno-sorbent assay (ELISA) with one or more colon cancer cell lines. Cells from only one of these wells (D 4213) could be cloned. The clone was shown to produce antibody which by immunocytochemical analysis reacted with a panel of colon cancer cell lines and melanoma cell lines but not with several other cancer cell lines or normal human leukocytes. By immunohistochemical analysis on formalin-fixed paraffin-embedded tissue this antibody reacted strongly with antigen expressed by autologous and allogeneic colorectal cancers. Faint staining could occasionally be observed on normal colon epithelium. D4213 is a hybrid cell line since it is tetraploid and produces kappa and lambda light chains as well as gamma and mu chains, whereas HMy-2 produces only kappa and gamma chains. The study produces only kappa and gamma chains. The study suggests that patients may possess B cells producing antibody reactive with their own malignant cells.
Effect of Protease Digestion and Dephosphorylation on High Emulsifying Properties of Hen Egg Yolk Phosvitin (1998)

The emulsifying properties, particularly the emulsion stability, of phosvitin was found to be higher than those of other food proteins. The emulsifying activity and emulsion stability were greatly decreased by protease and phosphatase treatment. The protease digestion of phosvitin resulted in the peptide cleavage of large fragment (a highly phosphorylated core region, 50 to 210 peptide) and small fragments (N-terminal 1 to 49 and C-terminal 211 to 217 peptides). The large fragment lacking the small fragments did not show the excellent emulsifying properties, suggesting that small fragments of protein moiety play an important role in emulsifying properties. On the other hand, the effect of phosphatase treatment showed that electrostatic repulsive force of phosphate in phosvitin has a significant affect on its emulsifying properties and that the protein moiety with abundant phosphorylated residues is also considered to be essential for the high emulsifying properties. Keywords: Phosvitin, emulsifying property, chymotrypsin, pepsin, trypsin, phosphatase.
Vascular Basis of Alzheimer's Pathogenesis (2002)

Considerable evidence now indicates that Alzheimer's disease (AD) is primarily a vascular disorder. This conclusion is supported by the following evidence: (1) epidemiologic studies linking vascular risk factors to cerebrovascular pathology that can set in motion metabolic, neurodegenerative, and cognitive changes in Alzheimer brains; (2) evidence that AD and vascular dementia (VaD) share many similar risk factors; (3) evidence that pharmacotherapy that improves cerebrovascular insufficiency also improves AD symptoms; (4) evidence that preclinical detection of potential AD is possible from direct or indirect regional cerebral perfusion measurements; (5) evidence of overlapping clinical symptoms in AD and VaD; (6) evidence of parallel cerebrovascular and neurodegenerative pathology in AD and VaD; (7) evidence that cerebral hypoperfusion can trigger hypometabolic, cognitive, and degenerative changes; and (8) evidence that AD clinical symptoms arise from cerebromicrovascular pathology. The collective data presented in this review strongly indicate that the present classification of AD is incorrect and should be changed to that of a vascular disorder. Such a change in classification would accelerate the development of better treatment targets, patient management, diagnosis, and prevention of this disorder by focusing on the root of the problem. In addition, a theoretical capsule summary is presented detailing how AD may develop from chronic cerebral hypoperfusion and the role of critically attained threshold of cerebral hypoperfusion (CATCH) and of vascular nitric oxide derived from endothelial nitric oxide synthase in triggering the cataclysmic cerebromicrovascular pathology.
IndexTV: a MPEG-7 based personalized recommendation system for digital TV (2005)

Digital television is a reality, providing new facilities for multimedia content delivery. Due to the large amount of available content from multiple broadcasters, the use of personalized recommendation techniques can help the user in the process of consuming A/V content. The viewer, who is actually a passive subject, is changed into an active one, who can organize the TV program guide of interest whenever and however he wants, achieving a real "agrave la carte TV". We present an end-to-end system able to offer A/V contents according to the TV viewer's preferences. The system adapts its suggestions to the changes in viewer's behaviour across time
Generalization of a phased array error correction method (2002)

The failure of a single element can seriously degrade the sidelobe pattern of a high performance array and therefore methods to compensate array element failures are required. One recent method considers an N-element array with P plane wave signals incident from known directions /spl thetav/ /sub p/, and processes the received signals from a select set of P contiguous operative array elements. The processing corresponds to that of a P/spl times/P multibeam network which spatially separates the incident signals. Any missing element signal is then reconstructed as a weighted sum of these P separated signals. The method works perfectly for signals from known directions but can lead to spurious responses for other signals. These errors are small when only a few incident signals are reconstructed, but can grow very large with the reconstruction of many, closely spaced known signals, such as required to model a wide clutter region for instance. We generalize the approach to utilize all operative elements in the array and thereby reduce these spurious responses.
ALARMS: alerting and reasoning management system for next generation aircraft hazards (2010)

The Next Generation Air Transportation System will introduce new, advanced sensor technologies into the cockpit. With the introduction of such systems, the responsibilities of the pilot are expected to dramatically increase. In the ALARMS (ALerting And Reasoning Management System) project for NASA, we focus on a key challenge of this environment, the quick and efficient handling of aircraft sensor alerts. It is infeasible to alert the pilot on the state of all subsystems at all times. Furthermore, there is uncertainty as to the true hazard state despite the evidence of the alerts, and there is uncertainty as to the effect and duration of actions taken to address these alerts.
Efficient synchronization primitives for large-scale cache-coherent multiprocessors (1989)

This paper proposes a set of efficient primitives for process synchronization in multiprocessors. The only assumptions made in developing the set of primitives are that hardware combining is not implemented in the inter-connect, and (in one case) that the interconnect supports broadcast.
Gate Tunable Infrared Phonon Anomalies in Bilayer Graphene (2009)

We observe a giant increase of the infrared intensity and a softening of the in-plane antisymmetric phonon mode E(u) ( approximately 0.2 eV) in bilayer graphene as a function of the gate-induced doping. The phonon peak has a pronounced Fano-like asymmetry. We suggest that the intensity growth and the softening originate from the coupling of the phonon mode to the narrow electronic transition between parallel bands of the same character, while the asymmetry is due to the interaction with the continuum of transitions between the lowest hole and electron bands. The growth of the peak can be interpreted as a "charged-phonon" effect observed previously in organic chain conductors and doped fullerenes, which can be tuned in graphene with the gate voltage.
ChemInform Abstract: TOTALSYNTH. VON PROSTAGLANDIN F(2ALPHA) UND E2 ALS NATUERLICH VORKOMMENDE FORMEN (1970)

Abstract Die Prostaglandine F 2α (IIIb) und E 2 (IV), die bislang nur als Racemate dargestellt werden konnten, werden als optisch aktive Formen synthetisiert.
A 280mV-to-1.2V wide-operating-range IA-32 processor in 32nm CMOS (2012)

Near-threshold computing brings the promise of an order of magnitude improvement in energy efficiency over the current generation of microprocessors [1]. However, frequency degradation due to aggressive voltage scaling may not be acceptable across all single-threaded or performance-constrained applications. Enabling the processor to operate over a wide voltage range helps to achieve best possible energy efficiency while satisfying varying performance demands of the applications. This paper describes an IA-32 processor fabricated in 32nm CMOS technology [2], demonstrating a reliable ultra-low voltage operation and energy efficient performance across the wide voltage range from 280mV to 1.2V.
Two-dimensional lenses microfabricated in PDMS for integrated fluidic photonic devices (2006)

Focusing is demonstrated in fluid-filled microfabricated 2D lenses formed by an optical polymer. Such lenses can be integrated into fluidic photonic devices performing flow cytometry for increased detection efficiency and device functionality.
CD8<sup>+</sup>T-cell Responses in Flavivirus-Naive Individuals Following Immunization with a Live-Attenuated Tetravalent Dengue Vaccine Candidate (2015)

We are developing a live-attenuated tetravalent dengue vaccine (TDV) candidate based on an attenuated dengue 2 virus (TDV-2) and 3 chimeric viruses containing the premembrane and envelope genes of dengue viruses (DENVs) -1, -3, and -4 expressed in the context of the attenuated TDV-2 genome (TDV-1, TDV-3, and TDV-4, respectively). In this study, we analyzed and characterized the CD8(+) T-cell response in flavivirus-naive human volunteers vaccinated with 2 doses of TDV 90 days apart via the subcutaneous or intradermal routes. Using peptide arrays and intracellular cytokine staining, we demonstrated that TDV elicits CD8(+) T cells targeting the nonstructural NS1, NS3, and NS5 proteins of TDV-2. The cells were characterized by the production of interferon-γ, tumor necrosis factor-α, and to a lesser extent interleukin-2. Responses were highest on day 90 after the first dose and were still detectable on 180 days after the second dose. In addition, CD8(+) T cells were multifunctional, producing ≥2 cytokines simultaneously, and cross-reactive to NS proteins of the other 3 DENV serotypes. Overall, these findings describe the capacity of our candidate dengue vaccine to elicit cellular immune responses and support the further evaluation of T-cell responses in samples from future TDV clinical trials.
Molecular Mechanisms of Fibrillogenesis and the Protective Role of Amyloid P Component: Two Possible Avenues for Therapy (2007)

Amyloid deposits regress when the supply of fibril precursor proteins is sufficiently reduced, indicating that amyloid fibrils are degradable in vivo. Serum amyloid P component (SAP), a universal constituent of amyloid deposits, efficiently protects amyloid fibrils from proteolysis in vitro, and may contribute to persistence of amyloid in vivo. Drugs that prevent binding of SAP to amyloid fibrils in vivo should therefore promote regression of amyloid and we are actively seeking such agents. A complementary strategy is identification of critical molecular processes in fibrillogenesis as targets for pharmacological intervention. All amyloidogenic variants of apolipoprotein AI contain an additional positive charge in the N-terminal fibrillogenic region of the protein. This is unlikely to be a coincidence and should be informative about amyloidogenesis by this protein. The two amyloidogenic variants of human lysozyme, caused by the first natural mutations found in its gene, provide a particularly powerful model system because both the crystal structure and folding pathways of wild-type lysozyme are so well characterized. The amyloidogenic variant lysozymes have similar 3D crystal structures to the wild type, but are notably less thermostable. They unfold on heating, lose enzymic activity, and aggregate to form amyloid fibrils in vitro.
Comparison of windowing in speech and audio coding (2013)

Speech and audio coding have during the last decade converged to an increasingly unified technology. This contribution discusses one of the remaining fundamental differences between speech and audio paradigms, namely, windowing of the input signal. Audio codecs generally use lapped transforms and apply a perceptual model in the transform domain, whereby temporal continuity is achieved by windowing and overlap-add. Speech codecs on the other hand achieve temporal continuity by using linear predictive filtering, whereby windowing is applied in the residual domain. Despite these fundamental differences, we demonstrate that the two windowing approaches, combined with perceptual modeling, perform very similarly both in terms of perceptual quality and theoretical properties.