gebhart/patrepeval huggingface dataset:
Stochastic optimisation with inequality constraints using simultaneous perturbations and penalty functions (2008)

We present a stochastic approximation algorithm based on penalty function method and a simultaneous perturbation gradient estimate for solving stochastic optimisation problems with general inequality constraints. We present a general convergence result that applies to a class of penalty functions including the quadratic penalty function, the augmented Lagrangian, and the absolute penalty function. We also establish an asymptotic normality result for the algorithm with smooth penalty functions under minor assumptions. Numerical results are given to compare the performance of the proposed algorithm with different penalty functions.
Fc-mediated immune precipitation. I. A new role of the Fc-portion of IgG. (1979)

By comparing the amounts of precipitate formed by the reaction between human serum albumin (HSA) and isomolar solutions of rabbit anti-HSA F(ab')2 fragments and of the corresponding intact rabbit anti-HSA IgG, respectively, it was found that the Fc portion of IgG was of great importance for the precipitin reaction. In the present antigen-antibody system, about half of the antigen was precipitated by this mechanism. This effect was called Fc-mediated precipitation and was most clearly expressed in the biologically important zone of low antigen excess and the zone of equivalence. It was found that the pepsin digestion did not change the ability of the F(ab')2 fragments to bind the antigen in comparison to intact IgG. Furthermore, turbidimetric analyses indicated that the Fc portion was involved in the overall mechanism of the precipitin reaction throughout the range of the precipitin curve.
Lebrikizumab Treatment in Adults with Asthma (2011)

Lebrikizumab treatment was associated with improved lung function. Patients with high pretreatment levels of serum periostin had greater improvement in lung function with lebrikizumab than did patients with low periostin levels. (Funded by Genentech; ClinicalTrials.gov number, NCT00930163 .).
Modulation of metabolic brain networks after subthalamic gene therapy for Parkinson's disease (2007)

Parkinson's disease (PD) is characterized by elevated expression of an abnormal metabolic brain network that is reduced by clinically effective treatment. We used fluorodeoxyglucose (FDG) positron emission tomography (PET) to determine the basis for motor improvement in 12 PD patients receiving unilateral subthalamic nucleus (STN) infusion of an adenoassociated virus vector expressing glutamic acid decarboxylase (AAV-GAD). After gene therapy, we observed significant reductions in thalamic metabolism on the operated side as well as concurrent metabolic increases in ipsilateral motor and premotor cortical regions. Abnormal elevations in the activity of metabolic networks associated with motor and cognitive functioning in PD patients were evident at baseline. The activity of the motor-related network declined after surgery and persisted at 1 year. These network changes correlated with improved clinical disability ratings. By contrast, the activity of the cognition-related network did not change after gene transfer. This suggests that modulation of abnormal network activity underlies the clinical outcome observed after unilateral STN AAV-GAD gene therapy. Network biomarkers may be used as physiological assays in early-phase trials of experimental therapies for PD and other neurodegenerative disease.
Experimental and emerging therapies for sepsis and septic shock (2001)

The underlying principles of sepsis therapy have remained unchanged for decades. These include: prompt institution of antimicrobial agents aimed at the inciting pathogen, source control directed at removal of the infection nidus whenever possible, and support of organ dysfunction. Despite advances in antibiotics, surgical techniques and organ support technology, the morbidity and mortality from sepsis-related diseases have remained substantially unchanged (30 - 50%). Immunomodulation of the inflammatory cascade has been suggested as a crucial but inadequately addressed element in the treatment of sepsis. The list of potential therapeutic targets has been growing as more and more mediators are identified in the pathogenesis of sepsis. To date, numerous anti-inflammatory agents, found to have favourable effects in animal models of septic shock, have been tested in a number of clinical trials on thousands of patients. In this first of a three part series, we go through some of the background and current strategies in sepsis therapy. In this review, we include the two novel therapies that have shown clear survival benefit in large, randomised, placebo-controlled, multi-centre trials, low-dose steroids and recombinant activated protein C. Also included in this review are studies on antithrombin III, platelet-activating factor antagonists, complement modulators, nitric oxide synthase inhibitors and caspase inhibitors (apoptosis inhibitors).
Gram‐negative endotoxin: an extraordinary lipid with profound effects on eukaryotic signal transduction 1 (1991)

The lipid A domain of lipopolysaccharide (LPS) is a unique, glucosamine-based phospholipid that makes up the outer monolayer of the outer membrane of most gram-negative bacteria. Because of its profound pharmacological effects on animal cells, especially those of the immune system, lipid A is also known as endotoxin. Despite decades of earlier work, the precise chemistry of endotoxins and the biochemical pathways for their enzymatic synthesis have been elucidated only within the past 5 years. In this review, we summarize the essentials of endotoxin biochemistry and also present recent experiments aimed at identifying surface receptors, signal-transducing elements, transcriptional factors, and key intracellular targets involved in the response of animal cells to endotoxins.
The Effect of Silicone Gel on Basic Fibroblast Growth Factor Levels in Fibroblast Cell Culture (2004)

These results suggest that silicone gel is responsible for increased bFGF levels in normal and fetal dermal fibroblasts. We postulate that silicone gel treats and prevents hypertrophic scar tissue, which contains histologically normal fibroblasts, by modulating expression of growth factors such as bFGF. Our data support the hypothesis that substances that favorably influence wound healing do so by correcting a deficiency or overabundance of the growth factors that orchestrate the tissue repair process.
Numerical computation of individual far-field arrivals excited by an acoustic source in a borehole (1985)

Abstract In this paper, I model the acoustic logging problem and numerically compute individual arrivals at far-field receivers. The ability to compute individual arrivals is useful for examining the sensitivities of each arrival to various factors of interest, as opposed to examining the full waveform as a whole. While the numerical computation of the mode arrivals (Peterson, 1974) and the numerical computation of the first head waves (Tsang and Rader, 1979) have been previously reported, the numerical computation of the entire set of head-wave arrivals is new and is the major contribution of this paper.Following Roever et al. (1974) and others, the full wave field is represented as a sum of contributions from both poles and branchcuts in the complex wavenumber plane. The pole contributions correspond to mode arrivals while the branch cuts are associated with body waves (i.e., head waves). Both the pole and branch cut contributions are computed numerically and results are presented for the cases of a slow and a fast formation. The shear event in the slow formation is found to be relatively small, consistent with observations in measured data. Contrary to existing knowledge, the shear event in the fast formation is also relatively small. The apparent strong shear arrival in the full waveforms is due primarily to the trapped mode pole in the vicinity of cutoff.
Poroelastic Solution for an Inclined Borehole (1997)

The analytical solution for an infinitely long borehole in an isotropic, poroelastic medium, inclined to the far-field principal stresses, is presented. The solution utilizes a loading decomposition scheme which leads to three fundamental problems: a poroelastic plane-strain, an elastic uni-axial, and an elastic antiplane shear problem.
DNA ligation of ultramicro volume using an EWOD microfluidic system with coplanar electrodes (2008)

An automatic ultramicro-volume DNA ligation process using a coplanar electrode type of electrowetting-on-dielectric (EWOD) microfluidic system was designed for economy of reagent. The droplets, containing DNA, a ligation enzyme and a multi-salt reaction buffer, served to complete the ligation using a developed EWOD system. Droplets of ultramicro volume (0.3 µL) were successfully generated from reservoirs between one plate with coplanar electrodes and another plate with a hydrophobic surface free of electrodes. In one successful cloning, the total usage of reagents in an ultramicro-volume EWOD chip was 2.1 µL; no volume was wasted, in comparison with 85% waste with the standard protocol and 80% waste with a free-cover coplanar EWOD chip. The results also show that the entire process was accomplished without damage to the chip surface and without biomaterial annulment. With a design consisting of electrode pathways in a flexible pattern and multiplex reservoirs, an EWOD digital microfluidic system with coplanar electrodes would be improved as an efficient parallel DNA-cloning system in the construction of an artificial library or expression library.
Isolation of a calcium-dependent 35-kilodalton substrate for the epidermal growth factor receptor/kinase from A-431 cells. (1984)

We have isolated a soluble 35-kDa protein from A-431 cells that in the presence of calcium can serve as a substrate for the epidermal growth factor (EGF)-receptor/kinase. The purification procedure exploits the reversible, Ca2+-dependent binding of the 35-kDa protein to the A-431 total particulate fraction. The 35-kDa protein was purified by 1) Ca2+-dependent adsorption to A-431 particulate fractions, 2) release by chelation of Ca2+ with ethyleneglycolbis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid, and 3) chromatography on Sephadex G-100, DEAE-cellulose, and CM-cellulose columns. When a plasma membrane preparation from A-431 cells is used as a source of the EGF-receptor/kinase, the phosphorylation of the 35-kDa protein occurs on tyrosine, is greatly enhanced in the presence of EGF, and occurs only when Ca2+ is added to the standard reaction mixture for phosphorylation. Autophosphorylation of the receptor does not require Ca2+. We have postulated that one of the roles of Ca2+ is to facilitate the interaction of the 35-kDa protein with cellular membranes. Ca2+ enhances, but apparently is not essential for, the direct phosphorylation of the 35-kDa protein by the Triton X-100-solubilized, purified EGF-receptor/kinase. Incubation of intact A-431 cells with EGF at 37 degrees C (but not 0 degrees C) enhances the ability of the particulate fraction prepared from these cells to bind and/or phosphorylate the 35-kDa protein. We suggest that this enhancement in the phosphorylation of the 35-kDa protein, a presumed physiological substrate, is associated with the clustering and internalization of the EGF receptor/kinase complex.
Centrifugal migration of mesenchymal cells in embryonic lung (2008)

Murine lung development begins at embryonic day (E) 9.5. Normal lung structure and function depend on the patterns of localization of differentiated cells. Pulmonary mesenchymal cell lineages have been relatively unexplored. Importantly, there has been no prior evidence of clonality of any lung cells. Herein we use a definitive genetic approach to demonstrate a common origin for proximal and distal pulmonary mesenchymal cells. A retroviral library with 3,400 unique inserts was microinjected into the airway lumen of E11.5 lung buds. After 7-11 days of culture, buds were stained for placental alkaline phosphatase (PLAP). Most PLAP+ cells are peribronchial smooth muscle cells, initially localized laterally near the hilum, then migrating down airways to the subpleural region. Laser-capture microdissection and polymerase chain reaction confirm the clonal identities of PLAP+ cells proximally and distally. Our observation of this fundamental process during lung development opens new avenues for investigation of maladaptive mesenchymal responses in lung diseases.
Performance consideration of an AC coupled gate drive circuit with forward bias for normally-on SiC JFETs (2013)

In this paper, an ac coupled driving circuit for normally-on Silicon Carbide (SiC) Junction Field Effect Transistors (JFETs) is proposed, utilizing forward bias during conduction state. Such driving circuits constitute the basic structure of a grid connected, 5kW photovoltaic (PV) inverter. The prototype is investigated in terms of efficiency, considering both conduction and switching losses and the advantages over a conventional zero biased gate drive are recorded. The adequacy of the particular circuit to efficiently drive a normally-off SiC JFET is also investigated. Simulation studies are carried out by developing new depletion mode (DM) as well as enhancement mode (EM) vertical trench (VT) SiC JFET models in Pspice model editor. The promising theoretical and simulation results are validated via experimental testing in a double pulse tester (DPT). Both DM and EM power devices are tested in a bridge leg configuration and their performance is evaluated, having as a reference point the operational characteristics of a conventional Silicon (Si) based IGBT power switch. Ultimately, a reduction of over 18% in conduction losses is obtained through forward biasing a DM SiC JFET, while switching losses less than 500 μJ are achieved over one switching cycle when operating at 600 V, 20 A.
Integrated conversion of hemicellulose and cellulose from lignocellulosic biomass (2012)

Using gamma-valerolactone (GVL) as solvent, the cellulosic fraction of lignocellulosic biomass can be converted into levulinic acid (LA), while at the same conditions the hemicellulose fraction can be converted into furfural. This process allows for the conversion of hemicellulose and cellulose simultaneously in a single reactor, thus eliminating pre-treatment steps to fractionate biomass and simplifying product separation.
A state space decomposition algorithm for approximate FSM traversal (2002)

Approximate FSM traversal is very useful in many applications of interest, when the size of the problem to be solved is too large to be handled by exact methods. The quality of the approximation strongly depends on how state variables are partitioned to decompose the state space, and exploiting circuit structure appears to be the most promising technique to determine a good state variable partition. In this paper we formulate the state space decomposition problem as a graph problem to be solved on the latch connection graph the FSM under investigation. Structural analysis on that graph is used to determine an initial partition; breaking and aggregation, based on seed generation, clustering, and iterative refinement of the current result, are then performed on the initial solution. Approximate FSM traversal results obtained on the largest ISCAS89 examples show the effectiveness of the proposed algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Analytic comparison of the sensitivities of bulk-wave, surface-wave, and flexural plate-wave ultrasonic gravimetric sensors (1989)

We show that, for small added masses, the sensitivities of bulk-mode, surface-mode, and flexural plate-mode gravimetric ultrasonic sensors are respectively 2/ρλ, ≊1/ρλ, and 1/2ρd, where ρ is the density of the sensor substrate material, λ is the wavelength, and d is the plate thickness of the flexural-mode sensor.
Competition and multiscaling in evolving networks (2001)

The rate at which nodes in a network increase their connectivity depends on their fitness to compete for links. For example, in social networks some individuals acquire more social links than others, or on the www some webpages attract considerably more links than others. We find that this competition for links translates into multiscaling, i.e. a fitness-dependent dynamic exponent, allowing fitter nodes to overcome the more connected but less fit ones. Uncovering this fitter-gets-richer phenomenon can help us understand in quantitative terms the evolution of many competitive systems in nature and society.
The Role of Gut-Glucagon-Like Immunoreactants in the Control of Gastrointestinal Epithelial Cell Renewal (1990)

In vitro and in vivo studies have provided considerable information on the possible physiologic function of circulating gastrointestinal hormones as well as locally acting regulatory peptides in the multifactorial control of adaptive gastrointestinal epithelial cell proliferation and cell renewal. It has been suggested by circumstantial evidences that enteroglucagon (EG; G-GLI I) may act as a trophic factor on the intestinal mucosa which may account for adaptive changes of the small intestine following various stimuli. However, we have shown that there are experimental conditions (germ-free rats after conventionalisation; jejunal self-filling blind loops) in which intestinal hyperplasia does not correspond to an increase in the concentrations of enteroglucagon in plasma or intestinal mucosa. Furthermore, despite a continuous immunoneutralisation of circulating endogenous enteroglucagon by monoclonal antibodies there was an adaptive, hyperplastic response of the ileal remnants after a 70% proximal small bowel resection which was of the same magnitude as in the control group but was even greater considering the increased number of mitoses per crypt. In order to gain additional insight into the putative role of enteroglucagon as an enterotrophic regulatory peptide, an in vitro model was used to investigate the effect of highly purified rat G-GLI I on the proliferative response of primary small intestinal epithelial cells of fetal rats. Whereas there was a well known growth-promoting action of EGF, the proliferation of rat fetal intestinal epithelial cells was inhibited by the addition of purified G-GLI I. These results indicate that enteroglucagon does not act as an enterotrophic factor but provide the first direct evidence consistent with an antitrophic role of enteroglucagon in the small intestine.
Design of a Pneumatically Actuated Transfemoral Prosthesis (2006)

This paper describes the design of an above-knee prosthesis with actively powered knee and ankle joints, both of which are actuated via pneumatic actuators. The prosthesis serves as a laboratory test-bed to validate the design and develop of control interfaces for future self-contained versions (i.e., with onboard hot-gas power and computing), and therefore includes a tether for both pneumatic power and control. The prototype prosthesis provides the full range of motion for both the knee and ankle joints while providing 100% of the knee torque required for fast cadence walking and stair climbing and 76% and 100%, respectively, of the ankle torque required for fast cadence walking and for stair climbing, based on the torques required by a healthy 75 kg subject. The device includes sensors to measure knee and ankle torque and position, in addition to a load cell that measures the interaction force and (sagittal and frontal planes) moments between the user and device.
Enhanced muscle fat oxidation and glucose transport by ACRP30 globular domain: Acetyl–CoA carboxylase inhibition and AMP-activated protein kinase activation (2002)

gACRP30, the globular subunit of adipocyte complement-related protein of 30 kDa (ACRP30), improves insulin sensitivity and increases fatty acid oxidation. The mechanism by which gACRP30 exerts these effects is unknown. Here, we examined if gACRP30 activates AMP-activated protein kinase (AMPK), an enzyme that has been shown to increase muscle fatty acid oxidation and insulin sensitivity. Incubation of rat extensor digitorum longus (EDL), a predominantly fast twitch muscle, with gACRP30 (2.5 micro g/ml) for 30 min led to 2-fold increases in AMPK activity and phosphorylation of both AMPK on Thr-172 and acetyl CoA carboxylase (ACC) on Ser-79. Accordingly, concentration of malonyl CoA was diminished by 30%. In addition, gACRP30 caused a 1.5-fold increase in 2-deoxyglucose uptake. Similar changes in malonyl CoA and ACC were observed in soleus muscle incubated with gACRP30 (2.5 micro g/ml), although no significant changes in AMPK activity or 2-deoxyglucose uptake were detected. When EDL was incubated with full-length hexameric ACRP30 (10 micro g/ml), AMPK activity and ACC phosphorylation were not altered. Administration of gACRP30 (75 micro g) to C57 BL6J mice in vivo led to increased AMPK activity and ACC phosphorylation and decreased malonyl CoA concentration in gastrocnemius muscle within 15-30 min. Both in vivo and in vitro, activation of AMPK was the first effect of gACRP30 and was transient, whereas alterations in malonyl CoA and ACC occurred later and were more sustained. Thus, gACRP30 most likely exerts its actions on muscle fatty acid oxidation by inactivating ACC via activation of AMPK and perhaps other signal transduction proteins.
Lessons Learned and Guidelines for Matrix Acidizing With Viscoelastic Surfactant Diversion in Carbonate Formations (2006)

Abstract To conventionally drill, complete and produce horizontal and multilateral wells with zero skin is not an easy undertaking. Much attention has been given to "best oil field practices" in both drilling and production processes, but the reality is that formation damage will often have to be addressed sometime during the life time of the well. Formation damage due to drilling and scale formation is common problem in carbonate reservoirs that can be re-mediated using chemical means. The success of any treatment however, requires a complete understanding of the problem and a solution that will address the majority of the damage. The solution evolves with time and experience. Extended reach intervals with variable permeability complicate the process. Reservoir and fluid characteristics, cleanup fluid chemistry, and operational considerations must always be considered. The acidizing experience and an improved understanding of how to effectively treat long and heterogeneous intervals in carbonate formations is rapidly evolving in Saudi Arabia. Water injectors, oil producers and wastewater disposal wells have been treated and are reviewed in this study. These wells have different configurations including: vertical, horizontal, extended reach, and multilateral with open hole and cased completions. Several acid placement and diversion techniques have been applied and a specialized treatment package was developed based on the latest coiled tubing and chemical diversion technologies. Laboratory studies, lessons learned and specific design guidelines from both successful and less than expected well treatments are highlighted in this work.
Dendritic Cells Control B Cell Growth and Differentiation (2004)

We propose a model where human dendritic cell (DC) subsets control, in a coordinated fashion, B cell growth and differentiation. Plasmacytoid DCs drive memory B cell differentiation into effector plasma cell via type I interferon and IL-6. Type I interferon activates myeloid DCs that regulate B cell priming and acquisition of memory phenotype via IL-12, IL-6 and Blys/Baff. This model also integrates the role of antigen-specific T cells activated by myeloid DCs. Thus, protective humoral immunity results from a highly coordinated interplay of human DC subsets. This interplay may explain the spreading of immune response to deal with antigenic drift and to maintain an active immunity against mutating microbe. It may also provide an explanation for spreading of the autoimmune repertoire as autoimmunity develops.