gebhart/patrepeval huggingface dataset:
Inhibition of Type I and Type II Phospholipase A2 by Phosphatidyl-Ethanolamine Linked to Polymeric Carriers (1998)

We have previously shown that cell surface proteoglycans protect the cell membrane from the action of extracellular phospholipase A2 (PLA2) enzymes [Dan, P., Nitzan, D. W., Dagan, A., Ginsburg, I., and Yedgar, S. (1996) FEBS Lett. 383, 75-78]. Cell-impermeable PLA2 inhibitors (ExPLIs) were prepared by linking phosphatidylethanolamine (PE) to polymeric carriers, specifically, carboxymethylcellulose, heparin, or hyaluronic acid. The structure of these inhibitors enables the incorporation of their PE moiety into the membrane while the polymer remains at the membrane surface. In the present study, we show that the ExPLIs are effective inhibitors of the hydrolysis of different phospholipids in biological (Escherichia coli) and model (phospholipid vesicle) membranes, by diverse types of PLA2 enzymes, specifically human recombinant synovial fluid and C. atrox (type II), as well as Naja mocambique and porcine pancreatic (type I) PLA2. It is proposed that the external polymers of the ExPLIs, which are anchored to the membrane by the PE, mimic the naturally occurring cell surface proteoglycans and similarly protect membranes from the action of exogenous PLA2.
Automatic synthesis using genetic programming of an improved general-purpose controller for industrially representative plants (2003)

Most real-world controllers are composed of proportional, integrative, and derivative Signal processing blocks. The so-called PID controller was invented and patented by A. Callender and A.B. Stevenson (1939). Later J.G. Ziegler and N.B. Nichols (1942) developed mathematical rules for automatically selecting the parameter values for PID controllers. In their influential book, K.J. Astrom and T. Hagglund (1995) developed a world-beating PID controller that outperforms the 1942 Ziegler-Nichols rules on an industrially representative set of plants. In this paper, we approached the problem of automatic synthesis of a controller using genetic programming without requiring in advance that the topology of the plant be the conventional PID topology. We present a genetically evolved controller that outperforms the automatic tuning rules developed by Astrom and Hagglund in 1995 for the industrially representative set of plants specified by Astrom and Hagglund.
Therapeutic response to intravenous infusions of glucocerebrosidase in a patient with Gaucher disease. (1990)

Enzyme replacement has been under consideration as a therapeutic strategy for patients with Gaucher disease for more than two decades. Previous studies indicated that single injections of purified glucocerebrosidase reduced the amount of storage material in the liver. It was important to determine whether administration of exogenous enzyme on a regular basis would be of clinical benefit. We report here that weekly i.v. infusions of a macrophage-targeted preparation of human placental glucocerebrosidase in a child with type 1 Gaucher disease increased hemoglobin from 6.9 +/- 0.8 g/dl (+/- 1 SD) to 10.2 +/- 0.4 g/dl (+/- 1 SD) over a 20-week period. The platelet count also increased from a pretreatment value of 30,000 +/- 7000/mm3 (+/- 1 SD) to 54,000 +/- 11,000/mm3 (+/- 1 SD). Phagocytic activity in the spleen decreased during the period of enzyme administration, and there was radiographic evidence of skeletal improvement. These observations document objective clinical responses to enzyme supplementation in a patient with a sphingolipid storage disorder.
Transcriptional control of high molecular weight keratin gene expression in multistage mouse skin carcinogenesis. (1988)

Monospecific antikeratin antisera and specific complementary DNA probes were used to analyze expression of keratin genes in newborn mouse skin and skin papillomas and carcinomas by indirect immunofluorescence, immunoblotting, and in situ hybridization. Tumors were induced by initiation with 7,12-dimethylbenz[a]anthracene and promotion with 12-O-tetradecanoylphorbol-13-acetate. Type I epidermal keratin K14 protein (Mr 55,000) is found in all living layers of the newborn skin but is most abundant in the lower strata. K1 (Mr 67,000) and K10 (Mr 59,000) proteins are predominantly suprabasal and K1 is processed in the stratum corneum. Transcripts for K14 were confined largely to the basal cell layer by in situ hybridization. Transcripts for K1 and K10 were highly expressed in suprabasal cells including the granular cell layer. In benign tumors, distribution of K14 protein is similar to that in newborn skin, while the abundance of K1 and K10 appears to be somewhat reduced although the tissue distribution remains suprabasal. Transcription of K14 is aberrant in benign tumors and transcripts persist throughout much of the suprabasal cell layers. Transcripts of K1 and K10 are normally distributed in papillomas but grain density is less intense than in newborn epidermis. Keratin expression in carcinomas is highly disturbed. K14 protein and transcripts are highly expressed in all strata in carcinomas while protein and transcripts for K1 and K10 are essentially absent. These results suggest that papilloma cells fail to respond to or generate signals to regulate K14 expression in the differentiating suprabasal cell layers and may not fully express their suprabasal cell keratins. Carcinomas fail to express suprabasal cell keratins and this is regulated at the transcriptional level. The loss of suprabasal keratin expression may provide a marker for malignant conversion in the mouse skin carcinogenesis model.
Double-Blind Controlled Study on the Effects of Dietary Diacylglycerol on Postprandial Serum and Chylomicron Triacylglycerol Responses in Healthy Humans (2000)

In the usual range of fat intake (10-44 g), postprandial response after ingestion of DG emulsion was significantly less than that after ingestion of TG emulsion in healthy human subjects.
Effects of thromboxane A2 receptor blockade on oliguric ischemic acute renal failure in conscious rats. (1993)

To investigate the potential pathogenetic and therapeutic roles of thromboxane A2 (TXA2) and its receptor blockade, respectively, in the early phase of ischemic acute renal failure (ARF), renal function, TXB2 excretion, and the effects of the specific TXA2 receptor antagonist sulotroban (SU) in a model of unilateral renal artery occlusion in conscious female Sprague-Dawley rats were studied. Occlusion of the left renal artery for 1 h in untreated (i.e., vehicle-treated) rats (N = 8) resulted in oliguric ARF. In SU-treated rats (N = 8), the drug was given as an i.v. bolus of 5 mg/kg body wt, followed by a continuous infusion of 0.5 mg/min.kg body wt from 1 h before and during ischemia and for 6 h after reflow. After 1 h of ischemia, urine volume of left ischemic kidneys from untreated rats had decreased from 13.2 +/- 2.8 to 1.0 +/- 0.3 and 0.5 +/- 0.2 microL/min.100 g at 2 and 6 h of reflow, respectively, and GFR had decreased from 0.32 +/- 0.04 mL/min.100 g body wt to undetectable values. At 6 h of reflow, medullary Na-K-ATPase was slightly (P < 0.05) reduced in left ischemic kidneys, whereas medullary and papillary enzyme activities were compensatorily increased (P < 0.01) in right intact kidneys. The ADP/O ratio of cortical mitochondria was 41% (P < 0.05) and ATP synthesis was 77% (P < 0.01) lower than in right intact kidneys.(ABSTRACT TRUNCATED AT 250 WORDS)
Nanostructured Hydrogels for Three‐Dimensional Cell Culture Through Self‐Assembly of Fluorenylmethoxycarbonyl–Dipeptides (2006)

A number of short peptide amphiphiles consisting of dipeptides linked to fluorenylmethoxycarbonyl spontaneously form fibrous hydrogels under physiological conditions (see figure). The structural and physical properties of these gels are dictated by the amino acid sequence of the peptide building blocks, and the gels support the three-dimensional cell culture of chondrocytes.
Simultaneous photoacoustic microscopy of microvascular anatomy, oxygen saturation, and blood flow (2015)

Capitalizing on the optical absorption of hemoglobin, photoacoustic microscopy (PAM) is uniquely capable of anatomical and functional characterization of the intact microcirculation in vivo. However, PAM of the metabolic rate of oxygen (MRO<sub>2</sub>) at the microscopic level remains an unmet challenge, mainly due to the inability to simultaneously quantify microvascular diameter, oxygen saturation of hemoglobin (sO<sub>2</sub>), and blood flow at the same spatial scale. To fill this technical gap, we have developed a multi-parametric PAM platform. By analyzing both the sO<sub>2</sub>-encoded spectral dependence and the flow-induced temporal decorrelation of photoacoustic signals generated by the raster-scanned mouse ear vasculature, we demonstrated-for the first time-simultaneous wide-field PAM of all three parameters down to the capillary level in vivo.
Reflections of the Environment in Memory (1991)

Availability of human memories for specific items shows reliable relationships to frequency, recency, and pattern of prior exposures to the item. These relationships have defied a systematic theoretical treatment. A number of environmental sources ( New York Times, parental speech, electronic mail) are examined to show that the probability that a memory will be needed also shows reliable relationships to frequency, recency, and pattern of prior exposures. Moreover, the environmental relationships are the same as the memory relationships. It is argued that human memory has the form it does because it is adapted to these environmental relationships. Models for both the environment and human memory are described. Among the memory phenomena addressed are the practice function, the retention function, the effect of spacing of practice, and the relationship between degree of practice and retention.
Plasma Levels of cAMP, cGMP and CGRP in Sildenafil-Induced Headache (2004)

Sildenafil, a selective inhibitor of the cyclic guanosine monophosphate (cGMP) degrading phosphodiestrase 5 (PDE5), induced migraine without aura in 10 of 12 migraine patients and in healthy subjects it induced significantly more headache than placebo. The aim of the present study was to determine whether the pain-inducing effects of sildenafil would be reflected in plasma levels of important signalling molecules in migraine: cGMP, cyclic adenosine monophosphate (cAMP) and calcitonin gene-related peptide (CGRP). Ten healthy subjects (four women, six men) and 12 patients (12 women) suffering from migraine without aura were included in two separate double-blind, placebo-controlled, cross-over studies in which placebo or sildenafil 100 mg was administered orally. Plasma levels of CGRP, cAMP and cGMP were determined in blood from the antecubital vein. Despite the ability of sildenafil to induce headache and migraine, no significant differences in plasma levels of CGRP, cGMP and cAMP were detected after sildenafil compared with placebo. In conclusion, plasma levels of CGRP, cGMP and cAMP remain normal during sildenafil-induced headache or migraine. However, since previous studies indicate an important role of these signalling molecules, the present study questions whether cAMP and cGMP in peripheral blood can be used for monitoring pathophysiological events in headache and migraine mechanisms.
Soluble Elastin Fragments in Serum Are Elevated in Acute Aortic Dissection (2003)

The sELAF level in serum may be a useful marker for helping in the diagnosis and screening of AAD and may also help to distinguish AAD from AMI.
Activity-Based Protein Profiling Reveals Broad Reactivity of the Nerve Agent Sarin (2009)

Elucidation of noncholinesterase protein targets of organophosphates, and nerve agents in particular, may reveal additional mechanisms for their high toxicity as well as clues for novel therapeutic approaches toward intoxications with these agents. Within this framework, we here describe the synthesis of the activity-based probe 3, which contains a phosphonofluoridate moiety, a P-Me moiety, and a biotinylated O-alkyl group, and its use in activity-based protein profiling with two relevant biological samples, that is, rhesus monkey liver and cultured human A549 lung cells. In this way, we have unearthed eight serine hydrolases (fatty acid synthase, acylpeptide hydrolase, dipeptidyl peptidase 9, prolyl oligopeptidase, carboxylesterase, long-chain acyl coenzyme A thioesterase, PAF acetylhydrolase 1b, and esterase D/S-formyl glutathione hydrolase) as targets that are modified by the nerve agent sarin. It is also shown that the newly developed probe 3 might find its way into the development of alternative, less laborious purification protocols for human butyrylcholinesterase, a potent bioscavenger currently under clinical investigation as a prophylactic/therapeutic for nerve agent intoxications.
EFFECT OF HEN EGG PRODUCTION AND PROTEIN COMPOSITION ON TEXTURAL PROPERTIES OF EGG ALBUMEN GELS (2001)

The effect of hen age, strain and dietary amino acid intake on the egg albumen gel textural properties was studied in two experiments by textural profile analysis (TPA) and uniaxial compression (UC) tests. In experiment 1, eggs from 4 different hen flocks were heat processed industrially. Egg rejection due to poor albumen gelling was correlated to hen age (r = 0.502), albumen dry matter (r =−0.632), gel hardness of 1 st compression (r =−0.765), and gel work of 1 st compression (r =−0.740) in TPA. In experiment 2 two hen strains, representing two levels of egg production, were fed diets with supplementation of L‐lysine, methionine or both amino acids compared to a control diet. The lysine intake ranged from 818–1272 mg/hen/day and methionine intake from 377–575 mg/hen/day among hen groups, but without significant effect on the albumen gel texture parameters. The hen strains differed significantly in egg production (P&lt;0.001), physical (P&lt;0.001), chemical (P&lt;0.05) and gel textural parameters of egg albumen (P&lt;0.01). Hen age was essential, and correlated to the industrial egg rejection (r = 0.729), albumen dry matter (r =−0.902) and gel stress at fracture (r =−0.884). Albumen gels with high fracture stress values were found to contain a modified form of ovofransferrin.
A case study of secure ATM switch booting (2002)

This paper examines a few techniques for booting Asynchronous Transfer Mode (ATM) switches securely over an insecure network. Each of these techniques assume a different trust model. This work is being carried out in the context of the Fairisle ATM switch environment. In this environment we are envisaging an open multi-service network where ATM switches are booted with third party software, possibly using a third party booting service. Hence we are faced with an increased security threat, compared with a closed network environment, in ensuring that the switch has been booted with authorised and authenticated boot code. In this paper, we examines these threats and presents three schemes of countering the threats.
An APAF-1·Cytochrome c Multimeric Complex Is a Functional Apoptosome That Activates Procaspase-9 (1999)

We report here the reconstitution of the de novo procaspase-9 activation pathway using highly purified cytochrome c, recombinant APAF-1, and recombinant procaspase-9. APAF-1 binds and hydrolyzes ATP or dATP to ADP or dADP, respectively. The hydrolysis of ATP/dATP and the binding of cytochrome c promote APAF-1 oligomerization, forming a large multimeric APAF-1.cytochrome c complex. Such a complex can be isolated using gel filtration chromatography and is by itself sufficient to recruit and activate procaspase-9. The stoichiometric ratio of procaspase-9 to APAF-1 is approximately 1 to 1 in the complex. Once activated, caspase-9 disassociates from the complex and becomes available to cleave and activate downstream caspases such as caspase-3.
Well Performance Diagnosis with Temperature Profile Measurements (2011)

Abstract The measurement of the temperature profile of a well has been a primary part of production logs since the inception of these logs and continues to be a routine production logging measurement. In recent years, the increasing application of fiber-optic based distributed temperature sensors, either permanently installed in the well completion, or temporarily deployed, has provided a source for additional temperature profile data. In this paper, we present methodologies for interpreting numerous conditions in wells from temperature profiles. For each method, the underlying theory of the interpretation, and one or more field examples are presented. The most fundamental well property that can often be obtained from a temperature profile is the well's inflow profile - the locations and relative rates of inflow along the well. Simple analytical methods for interpreting the flow profiles of vertical oil producing wells are presented along with examples of this interpretation. Another key application of temperature profile measurements, particularly for horizontal wells, is the location of water or gas entries in oil-producing wells. We will show how water or gas entries create temperature anomalies along horizontal wells caused by the differences in the Joule-Thomson coefficients of the different phases or by the water or gas source being from below or above the well depth, as in a coning situation. We illustrate how such water or gas inflows can be quantitatively identified by applying standard inversion methods to the measured temperature profiles, yielding the locations and rates of water or gas entries. Another growing application of temperature profile measurements is the analysis of stimulation treatment (fracturing or acidizing) fluid placement. Temperature profiles measured during treatment pumping, during a flowback period, or after shut-in can be analyzed to determine the amount of stimulation fluid placed in different completed intervals along the well. A related analysis method using transient temperature profile measurements provides a means of determining layer properties of permeability, skin factor, and damage depth. This method can be applied before a stimulation treatment to aid the stimulation design, or post-job to evaluate treatment results.
Burkholderia ambifaria sp. nov., a novel member of the Burkholderia cepacia complex including biocontrol and cystic fibrosis-related isolates. (2001)

A polyphasic taxonomic study, including amplified fragment length polymorphism (AFLP) fingerprinting, DNA-DNA hybridizations, DNA base-ratio determinations, phylogenetic analysis, whole-cell fatty acid analyses and an extensive biochemical characterization, was performed on 19 Burkholderia cepacia-like isolates from the environment and cystic fibrosis (CF) patients. Several of the environmental isolates have attracted considerable interest due to their biocontrol properties. The polyphasic taxonomic data showed that the strains represent a new member of the B. cepacia complex, for which the name Burkholderia ambifaria sp. nov. is proposed. The type strain is strain LMG 19182T. B. ambifaria can be differentiated from the other members of the B. cepacia complex by means of AFLP fingerprinting, whole-cell fatty acid analysis, biochemical tests (including ornithine and lysine decarboxylase activity, acidification of sucrose and beta-haemolysis) and a newly developed recA gene-based PCR assay. 16S rDNA-based RFLP analysis and PCR tests allowed differentiation of B. ambifaria from Burkholderia multivorans, Burkholderia vietnamiensis and B. cepacia genomovar VI, but not from B. cepacia genomovars I and III and Burkholderia stabilis. The finding that this new taxon includes both strains isolated from CF patients and potentially useful biocontrol strains supports the general consensus that the large-scale use of biocontrol strains belonging to the B. cepacia complex would be ill-advised until more is known about their potential pathogenic mechanisms.
Uterotonic Plants and their Bioactive Constituents (2010)

Abnormalities in the process of uterine muscle contractility during pregnancy and birth can have major clinical implications, including preterm labour, which is the single largest cause of maternal and prenatal mortality in the Western world and a major contributor to childhood developmental problems. In contrast, induction of labour may be necessary in certain conditions. Currently used interventional therapies to suppress (tocolytic agents) or to induce (uterotonic agents) uterine contractions lack potency and/or selectivity and can have harmful side effects for mother and baby. Nature's diversity has always been, and still is, one of the biggest resources of therapeutic lead compounds. Many natural products exhibit biological activity against unrelated targets, thus providing researchers with starting points for drug development. In this review we will provide an overview of uterine muscle physiology, describe currently available biological screening procedures for testing of uterotonic plant compounds and will summarise traditionally-used uterotonic plants, their active components and their mechanisms, primarily focusing on uterotonic active circular plant peptides called cyclotides. Finally we will comment on the discovery of novel cyclotide-producing plant species and the possibility for the development of novel plant-derived uterotonic and tocolytic drugs.
Development of Next Generation Stevia Sweetener: Rebaudioside M (2014)

This work aims to review and showcase the unique properties of rebaudioside M as a natural non-caloric potential sweetener in food and beverage products. To determine the potential of rebaudioside M, isolated from <i>Stevia rebaudiana</i> Bertoni, as a high potency sweetener, we examined it with the Beidler Model. This model estimated that rebaudioside M is 200-350 times more potent than sucrose. Numerous sensory evaluations of rebaudioside M's taste attributes illustrated that this steviol glycoside possesses a clean, sweet taste with a slightly bitter or licorice aftertaste. The major reaction pathways in aqueous solutions (pH 2-8) for rebaudioside M are similar to rebaudioside A. Herein we demonstrate that rebaudioside M could be of great interest to the global food industry because it is well-suited for blending and is functional in a wide variety of food and beverage products.
New β-Strand Templates Constrained by Huisgen Cycloaddition (2012)

New peptidic templates constrained into a β-strand geometry by linking acetylene and azide containing P(1) and P(3) residues of a tripeptide by Huisgen cycloaddition are presented. The conformations of the macrocycles are defined by NMR studies and those that best define a β-strand are shown to be potent inhibitors of the protease calpain. The β-strand templates presented and defined here are prepared under optimized conditions that should be suitable for targeting a range of proteases and other applications requiring such a geometry.