gebhart/patrepeval huggingface dataset:
Substrate specificity of human kallikrein 2 (hK2) as determined by phage display technology (2002)

Human glandular kallikrein 2 (hK2) is a trypsin-like serine protease expressed predominantly in the prostate epithelium. Recently, hK2 has proven to be a useful marker that can be used in combination with prostate specific antigen for screening and diagnosis of prostate cancer. The cleavage by hK2 of certain substrates in the proteolytic cascade suggest that the kallikrein may be involved in prostate cancer development; however, there has been very little other progress toward its biochemical characterization or elucidation of its true physiological role. In the present work, we adapt phage substrate technology to study the substrate specificity of hK2. A phage-displayed random pentapeptide library with exhaustive diversity was generated and then screened with purified hK2. Phages displaying peptides susceptible to hK2 cleavage were amplified in eight rounds of selection and genes encoding substrates were transferred from the phage to a fluorescent system using cyan fluorescent protein (derived from green fluorescent protein) that enables rapid determination of specificity constants. This study shows that hK2 has a strict preference for Arg in the P1 position, which is further enhanced by a Ser in P'1 position. The scissile bonds identified by phage display substrate selection correspond to those of the natural biological substrates of hK2, which include protein C inhibitor, semenogelins, and fibronectin. Moreover, three new putative hK2 protein substrates, shown elsewhere to be involved in the biology of the cancer, have been identified thus reinforcing the importance of hK2 in prostate cancer development.
Integrative Analysis of Calcium Cycling in Cardiac Muscle (2000)

The control of intracellular calcium is central to regulation of contractile force in cardiac muscle. This review illustrates how analysis of the control of calcium requires an integrated approach in which several systems are considered. Thus, the calcium content of the sarcoplasmic reticulum (SR) is a major determinant of the amount of Ca(2+) released from the SR and the amplitude of the Ca(2+) transient. The amplitude of the transient, in turn, controls Ca(2+) fluxes across the sarcolemma and thence SR content. This control of SR content influences the response to maneuvers that modify, for example, the properties of the SR Ca(2+) release channel or ryanodine receptor. Specifically, modulation of the open probability of the ryanodine receptor produces only transient effects on the Ca(2+) transient as a result of changes of SR content. These interactions between various Ca(2+) fluxes are modified by the Ca(2+) buffering properties of the cell. Finally, we predict that, under some conditions, the above interactions can result in instability (such as alternans) rather than ordered control of contractility.
Studies in Pressure Drop with Lateral Mass Extraction: First Paper: Pressure Gradients for Air Flowing along Porous Tubes with Uniform Extraction at the Walls (1965)

Experiments are described in which the pressure drop and pressure gradient were measured for air flowing through porous tubes with uniform extraction at the walls. A simple correlation is derived and is shown to be approximately consistent with the theoretical work of Silver (1)†. The results may be of particular interest to designers of condenser equipment in which pressure changes are important.
Mucosal Competitive Exclusion to Diminish Colonization of Chickens by Campylobacter jejuni (1994)

Mucosal competitive exclusion flora (MCE) and length of MCE culture storage were studied to determine their influence upon colonization of Campylobacter jejuni in chickens. Day-of-hatch broiler chicks, held in isolation units, were treated with MCE or were left untreated. Thirty to 48 h later, groups of chicks were challenged with serial dilutions of C. jejuni (Strain A74/C). Single challenge doses and treatments were administered to chickens within each isolation unit. After 5 d, chicks were killed and levels of the organism in cecal materials were enumerated. Effective MCE was held at -80 C in 15% glycerol for 3 to 9 mo, and efficacy in inhibiting C. jejuni colonization of fresh and stored MCE cultures was compared. Colonization dose-50% (CD50%; dose needed to colonize one-half of the challenged chicks) and colonization quotients (CQ; log10 colony-forming unit geometric means per gram cecal materials) were determined. Data indicated that in three of five trials a significant reduction (P < .02) in CQ was observed in groups of chicks provided fresh MCE as compared with the control groups. Generally, efficacy of MCE treatment decreased with storage of the cultures. This study defines methods for production of MCE and the advantages and limitations of MCE intervention for C. jejuni colonization in chickens.
Effectiveness of Select Synch (Gonadotropin-Releasing Hormone and Prostaglandin F2α) for Synchronizing Estrus in Replacement Beef Heifers (2004)

Our objective was to determine if a 7-d, gonadotropin-releasing hormone (GnRH) + prostaglandin F2α (PGF2α) protocol (Select Synch) was effective for synchronizing estrus in replacement beef heifers compared with two traditionally used programs. Heifers (n = 637) consisting of Angus, Hereford, Simmental, and Hereford × Angus breeding at three Kansas locations were assigned randomly to each of three treatments: 1) melengestrol acetate (MGA●; 0.5 mg/d per heifer for 14 d) starting on d –31 plus 25 mg of PGF2α administered 17 d later (d 0; MGA + PGF2α; n = 301); 2) two 25-mg injections of PGF2α given 14 d apart (d –14 and 0; 2 × PGF2α; n = 176); or 3) injection of 100 mg of GnRH (d –7) followed by 25 mg of PGF2α (d 0; Select Synch; n = 160). Twice daily observations for estrus began on d –5 and continued until at least d 10. Inseminations were performed 10 to 14 h after first detected estrus. Pregnancy was diagnosed by transrectal ultrasonography between 33 and 37 d after insemination. A greater (P<0.05) percentage of heifers on the MGA + PGF2α (83%) treatment than on the Select Synch (73%) or 2 × PGF2α (71%) treatment were detected in estrus during the target breeding week. Average interval to estrus from the second or only injection of PGF2α was greater (P<0.001) after MGA + PGF2α (72.1 ± 2.5 h) and 2 × PGF2α (71.3 ± 2.5 h) treatments than after the Select Synch (54.3 ± 2.4 h) treatment. Overall conception and pregnancy were not different. There were treatment × location interactions for conception and pregnancy rates. All three programs synchronized estrus, but overall, because more heifers in the MGA + PGF2α treatment were detected in estrus during the target breeding week, this protocol tended to be most effective.
Biocompatibility of Peritoneal Dialysis Fluids: Long-term Exposure of Nonuremic Rats (2004)

Our results show that long-term exposure to different components of PD fluids leads to mesothelial cell damage, submesothelial fibrosis, and neoangiogenesis. Mesothelial cell damage could be connected to the presence of GDP; the other changes were similar for all fluids. Peritoneal transport characteristics did not change in any consistent way and the neoangiogenesis observed was not paralleled by increased solute transport.
Modulation of dihydropyridine-sensitive calcium channels in heart cells by fish oil fatty acids. (1992)

The highly unsaturated n-3 fatty acids from fish oils, eicosapentaenoic acid [EPA; C20:5 (n-3)] and docosahexanoic acid [DHA; C22:6 (n-3)], prevent the toxicity of high concentrations of the cardiac glycoside ouabain to isolated neonatal rat cardiac myocytes. Arachidonic acid [C20:4 (n-6)] lacks such protective action. The protective effect of the n-3 fatty acids is associated with their ability to prevent high levels of cytosolic free calcium from occurring in response to the ouabain. This in turn results, at least in part, from a 30% reduction in calcium influx rate induced by the n-3 fatty acids. This protective effect is simulated by nitrendipine, a dihydropyridine inhibitor of the L-type calcium channels in cardiac myocytes. Nitrendipine (0.1 mM) alone, however, inhibits myocyte contractility, as do verapamil (10 microM) and diltiazem (1.0 microM). EPA or DHA (5 microM) blocks the inhibitory effects of nitrendipine but not those of verapamil or diltiazem. Bay K8644, a known dihydropyridine agonist of L-type calcium channels, produces a ouabain-like effect that is also prevented by EPA or DHA. Specific binding of [3H]nitrendipine to intact myocytes is noncompetitively inhibited by EPA or DHA in a manner that reduces the number of high- and low-affinity binding sites (Bmax) and increases their affinities. The fish oil fatty acids prevent calcium overload from ouabain and Bay K8644. They also prevent a calcium-depleted state in the myocytes caused by the L-type calcium channel blocker nitrendipine. The protective effects of the n-3 fatty acids appear to result from their modulatory effects on nitrendipine-sensitive L-type calcium channels.
Mechanism of Terahertz Electromagnetic Wave Emission from Intrinsic Josephson Junctions (2009)

Using a 3D parallelepiped model of the stack of intrinsic Josephson junctions, we calculate the cavity resonance modes of Josephson plasma waves excited by external electric currents. The cavity modes accompanied by static phase kinks of the order parameter have been intensively investigated. Our calculation shows that the kink phase state is unfavorable, since the static phase kinks reduce the order parameter amplitude and thus the superconducting condensation energy. We point out that the oscillating magnetic field of the cavity mode penetrates the vacuum from the sample surfaces and the energy of the magnetic field plays an important role to determine the orientation of the cavity resonance mode. On the basis of the above discussions, we calculate the I-V characteristic curve, the THz wave emission intensity and the other physical quantities.
Uplink capacity and interference avoidance for two-tier femtocell networks (2009)

Two-tier femtocell networks- comprising a conventional cellular network plus embedded femtocell hotspots- offer an economically viable solution to achieving high cellular user capacity and improved coverage. With universal frequency reuse and DS-CDMA transmission however, the ensuing cross-tier interference causes unacceptable outage probability. This paper develops an uplink capacity analysis and interference avoidance strategy in such a two-tier CDMA network. We evaluate a network-wide area spectral efficiency metric called the operating contour (OC) defined as the feasible combinations of the average number of active macrocell users and femtocell base stations (BS) per cell-site that satisfy a target outage constraint. The capacity analysis provides an accurate characterization of the uplink outage probability, accounting for power control, path loss and shadowing effects. Considering worst case interference at a corner femtocell, results reveal that interference avoidance through a time-hopped CDMA physical layer and sectorized antennas allows about a 7x higher femtocell density, relative to a split spectrum two-tier network with omnidirectional femtocell antennas. A femtocell exclusion region and a tier selection based handoff policy offers modest improvements in the OCs. These results provide guidelines for the design of robust shared spectrum two-tier networks.
Establishing Moore's Law (2006)

Every field has brief formulas or relationships that are useful for back-of-the-envelope calculations. Rarely do these maxims become popular knowledge; even more rarely do they become as ubiquitous and influential as Moore's law, the 40-year-old prediction that the speed of computers will double every year or two. Here, a look at the way in which the legendary law evolved into a self-fulfilling prophecy.
Mrs. Friley Prefers Informal Entertainment (1936)

Eight o'clock on a white morning- I tramped up the hill leading to the lovely brick home of the Frileys'. Just as I went in and was tugging at my galoshes, dripping snow liberally over the mat, Mrs. Friley bade Dr. Friley, now the new president of Iowa State College, and the rest of her family, goodbye. As the bustle subsided she ushered me into the living room.
Two-Dimensional Analysis of Thermal Oxidation of Silicon (1983)

Step-shaped (110) oriented silicon wafers are oxidized in dry O 2 (900–1150°C) and the cross sectional views of oxide are observed by scanning electron microscopy. At lower temperature (900–950°C), the oxide thickness at te edge the reduced compared to the other regions, but the reduction cannot be observed at higher temperatures (1000–1150°C).
Corticotropin-Releasing Hormone-Mediated Neuroprotection against Oxidative Stress Is Associated with the Increased Release of Non-amyloidogenic Amyloid β Precursor Protein and with the Suppression of Nuclear Factor-κB (2000)

The neuropeptide CRH is the central regulator of the hypothalamic-pituitary-adrenal (HPA) stress response system and is implicated in various stress-related conditions. In the neurodegenerative disorder Alzheimer's disease (AD), levels of CRH are decreased. AD pathology is characterized by the deposition of the nonsoluble amyloid beta protein (A beta), oxidative stress, and neuronal cell death. Employing primary neurons and clonal cells, we demonstrate that CRH has a neuroprotective activity in CRH-receptor type 1 (CRH-R1)-expressing neurons against oxidative cell death. The protective effect of CRH was blocked by selective and nonselective CRH-R1 antagonists and by protein kinase A inhibitors. Overexpression of CRH-R1 in clonal hippocampal cells lacking endogenous CRH-receptors established neuroprotection by CRH. The activation of CRH-R1 and neuroprotection are accompanied by an increased release of non-amyloidogenic soluble A beta precursor protein. At the molecular level CRH caused the suppression of the DNA-binding activity and transcriptional activity of the transcription factor NF-kappaB. Suppression of NF-kappaB by overexpression of a super-repressor mutant form of IkappaB-alpha, a specific inhibitor of NF-kappaB, led to protection of the cells against oxidative stress. These data demonstrate a novel cytoprotective effect of CRH that is mediated by CRH-R1 and downstream by suppression of NF-kappaB and indicate CRH as an endogenous protective neuropeptide against oxidative cell death in addition to its function in the HPA-system. Moreover, the protective function of CRH proposes a molecular link between oxidative stress-related degenerative events and the CRH-R1 system.
The RET–Glial Cell-derived Neurotrophic Factor (GDNF) Pathway Stimulates Migration and Chemoattraction of Epithelial Cells (1998)

Embryonic development requires cell migration in response to positional cues. Yet, how groups of cells recognize and translate positional information into morphogenetic movement remains poorly understood. In the developing kidney, the ureteric bud epithelium grows from the nephric duct towards a group of posterior intermediate mesodermal cells, the metanephric mesenchyme, and induces the formation of the adult kidney. The secreted protein GDNF and its receptor RET are required for ureteric bud outgrowth and subsequent branching. However, it is unclear whether the GDNF–RET pathway regulates cell migration, proliferation, survival, or chemotaxis. In this report, we have used the MDCK renal epithelial cell line to show that activation of the RET pathway results in increased cell motility, dissociation of cell adhesion, and the migration towards a localized source of GDNF. Cellular responses to RET activation include the formation of lamellipodia, filopodia, and reorganization of the actin cytoskeleton. These data demonstrate that GDNF is a chemoattractant for RET-expressing epithelial cells and thus account for the developmental defects observed in RET and GDNF mutant mice. Furthermore, the RET-transfected MDCK cells described in this report are a promising model for delineating RET signaling pathways in the renal epithelial cell lineage.
Improved HPLC-radioimmunoassay for quantifying angiotensin II in plasma (1994)

To measure the octapeptide angiotensin II (Ang II) in plasma, we developed a sensitive, specific assay that interfaces solid-phase extraction, HPLC, and RIA. A reversed-phase HPLC system involving isocratic elution at 38 degrees C with a volatile mobile phase of acetonitrile and the ion-pairing reagent heptafluorobutyric acid produced baseline separation of angiotensin peptides. Ang II was collected as a single fraction, concentrated by evaporation to dryness, and measured by RIA after resuspension in RIA buffer. Even including column washing between sample injections to prevent carryover of plasma constituents, two plasma extracts could be processed per hour by HPLC. Assay validation experiments demonstrated < 2% cross-reactivity with Ang II-related peptides; a 75% recovery from plasma at physiological concentrations of Ang II; intra- and interassay precision (CVs) of 6.2% and 10.3%, respectively; and a lower limit of quantification of 1.3 ng/L. Two clinical protocols designed to measure plasma Ang II concentration under basal and stimulated conditions confirmed the utility of the assay.
Decayed MCMC iltering (2002)

Filtering--estimating the state of a partially observable Markov process from a sequence of observations-is one of the most widely studied problems in control theory, AI, and computational statistics. Exact computation of the posterior distribution is generally intractable for large discrete systems and for nonlinear continuous systems, so a good deal of effort has gone into developing robust approximation algorithms. This paper describes a simple stochastic approximation algorithm for filtering called decayed MCMC. The algorithm applies Markov chain Monte Carlo sampling to the space of state trajectories using a proposal distribution that favours flips of more recent state variables. The formal analysis of the algorithm involves a generalization of standard coupling arguments for MCMC convergence. We prove that for any ergodic underlying Markov process, the convergence time of decayed MCMC with inversepolynomial decay remains bounded as the length of the observation sequence grows. We show experimentally that decayed MCMC is at least competitive with other approximation algorithms such as particle filtering.
Impact of curing temperatures and alkaline activators on compressive strength and porosity of ternary blended geopolymer mortars (2018)

Impact of changing temperatures of curing (27, 60 and 90 °C) and types of alkaline activator solution on the properties of geopolymer mortars (GPMs) prepared by combining agricultural and industrial wastes including granulated-blast-furnace-slag (GBFS), fly-ash (FA), and palm-oil-fuel-ash (POFA) was examined. Sodium Hydroxide (NH), Sodium Silicate (NS) and NHNS alkaline solutions were used as alkali activators. Proposed GPMs were synthesized using NH solution of molarity 8 M, ratios of alkaline solution to binder were 0.30, NS to NH was 3.0 and binder to fine aggregate (sand) was 1.5. The mechanical properties of the studied GPMs and the products of reaction were greatly sensitive to the variation of mix compositions, alkaline activators type, and temperatures of curing. Furthermore, the formation of crystalline calcium silicate hydrate (C-S-H), calcium aluminium silicate hydrate (C-A-S-H) together with additional amorphous gel led to the compressive strength enhancement of the GPMs as the content of FA was increased and activated with NS solution. A linear correlation was established between compressive strength, ultrasonic pulse velocity and porosity of the proposed GPMs.
Urethral pressure increase on effort originates from within the urethra, and continence from musculovaginal closure (1995)

The aim of the study was to determine the contribution of intra-abdominal pressure transmission to urinary continence in the female. Five patients with genuine stress incontinence (GSI) were studied. Pressure transmission was measured in equivalent positions inside and outside the urethra and bladder during the Intravaginal Slingplasty procedure, a surgical operation used for treatment of urinary incontinence, and performed under local anaesthesia. A 6 mm diameter channel was created alongside the urethra. Two separate microtransducer catheters appropriately marked for length were inserted, one inside the urethra, and the other inside the described channel. With the vaginal hammock intact, an average of 10 simultaneous pressure measurements were made intraoperatively in response to coughing and straining in equivalent positions inside the urethra, and directly outside. Significantly higher pressure readings were found inside the urethra (P = 0.0025), indicating that an active component within the urethra may have created this pressure rise. After opening out two suburethral vaginal flaps, large quantities of urine were lost on coughing in all patients. Continence was achieved on tightening the suburethral vagina, indicating that an adequately tight vaginal hammock is a critical element in the continence process. The findings of this study question intraabdominal pressure as a mechanism contributing to continence, but support an alternative mechanism, musculovaginal closure of the urethra.
Reliability and Performance of Component Based Software Systems with Restarts, Retries, Reboots and Repairs (2006)

High reliability and performance are vital for software systems handling diverse mission critical applications. Such software systems are usually component based and may possess multiple levels of fault recovery. A number of parameters, including the software architecture, behavior of individual components, underlying hardware, and the fault recovery measures, affect the behavior of such systems, and there is a need for an approach to study them. In this paper we present an integrated approach for modeling and analysis of component based systems with multiple levels of failures and fault recovery both at the software, as well as the hardware level. The approach is useful to analyze attributes such as overall reliability, performance, and machine availabilities for such systems, wherein failures may happen at the software components, the operating system, or at the hardware, and corresponding restarts, retries, reboots or repairs are used for mitigation. Our approach encompasses Markov chain, and queueing network modeling, for estimating system reliability, machine availabilities and performance. The approach is helpful for designing and building better systems and also while improving existing systems
The Effect of Bone Morphogenetic Protein-2 on Rat Intervertebral Disc Cells in Vitro (2003)

The results of this study show that recombinant human bone morphogenetic protein-2 enhances disc matrix production and chondrocytic phenotype of intervertebral disc cells. Recombinant human bone morphogenetic protein-2 increases cell proliferation and sulfated-glycosaminoglycan (proteoglycan) synthesis. It increases mRNA of Type II collagen, aggrecan, and Sox9 genes (chondrocyte specific genes), and osteocalcin, but not Type I collagen or glyceraldehyde phosphate dehydrogenase.
Identification of a Unique Ganglioside Binding Loop within Botulinum Neurotoxins C and D-SA, (2010)

The botulinum neurotoxins (BoNTs) are the most potent protein toxins for humans. There are seven serotypes of BoNTs (A-G) based on a lack of cross antiserum neutralization. BoNTs utilize gangliosides as components of the host receptors for binding and entry into neurons. Members of BoNT/C and BoNT/D serotypes include mosaic toxins that are organized in D/C and C/D toxins. One D/C mosaic toxin, BoNT/D-South Africa (BoNT/D-SA), was not fully neutralized by immunization with BoNT serotype C or D, which stimulated this study. Here the crystal structures of the receptor binding domains of BoNT/C, BoNT/D, and BoNT/D-SA are presented. Biochemical and cell binding studies show that BoNT/C and BoNT/D-SA possess unique mechanisms for ganglioside binding. These studies provide new information about how the BoNTs can enter host cells as well as a basis for understanding the immunological diversity of these neurotoxins.