gebhart/patrepeval huggingface dataset:
Orthogonal extraction ion mobility spectrometry (2006)

Ion Mobility Spectrometry is a powerful tool for the study of molecular conformations, separation of mass isomers, and analysis of complex mixtures and suppression of chemical background. The factors that limit the capabilities of the technique include its relatively low resolving power and duty cycle. New principle of gas-phase ion separation, based on ion focusing under the influence of electrostatic field and stationary in time gas flow, is proposed. Both analytical calculations and a numerical simulation show that a diffusion-limited resolution of several hundred can be achieved. The new type of ion mobility analyzer is called orthogonal extraction IMS. The proposed ortho-IMS can be interfaced with commercial mass spectrometers and offers the theoretical resolution of several hundred and ion transmission close to 100%.
Plasticizer contamination from vacuum system o-rings in a quadrupole ion trap mass spectrometer (2002)

The outgassing of plasticizers from Buna-N and Viton o-rings under vacuum lead to undesired ion-molecule chemistry in an Electrospray Quadrupole Ion Trap Mass Spectrometer. In experiments with the helium bath gas pressure >1.2 mTorr, or whenever analyte ions were stored for >100 ms, extensive loss of analyte ions by proton transfer or adduction with o-ring plasticizers bis(2-ethylhexyl) phthalate and bis(2-ethylhexyl) adipate occurred. A temporary solution to this contamination problem was found to be overnight refluxing in hexane of all the o-rings in the vacuum system. This procedure alleviated this plasticizer contamination for approximately 100 hours of operation. These results, and those that lead to identification of the contamination as plasticizers outgassing from o-rings are described.
Molecular Mechanism of an Oncogenic Mutation That Alters Membrane Targeting: Glu17Lys Modifies the PIP Lipid Specificity of the AKT1 PH Domain (2008)

The protein kinase AKT1 regulates multiple signaling pathways essential for cell function. Its N-terminal PH domain (AKT1 PH) binds the rare signaling phospholipid phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P(3)], resulting in plasma membrane targeting and phosphoactivation of AKT1 by a membrane-bound kinase. Recently, it was discovered that the Glu17Lys mutation in the AKT1 PH domain is associated with multiple human cancers. This mutation constitutively targets the AKT1 PH domain to the plasma membrane by an unknown mechanism, thereby promoting constitutive AKT1 activation and oncogenesis. To elucidate the molecular mechanism underlying constitutive plasma membrane targeting, this work compares the membrane docking reactions of the isolated wild-type and E17K AKT1 PH domains. In vitro studies reveal that the E17K mutation dramatically increases the affinity for the constitutive plasma membrane lipid PI(4,5)P(2). The resulting PI(4,5)P(2) equilibrium affinity is indistinguishable from that of the standard PI(4,5)P(2) sensor, PLCdelta1 PH domain. Kinetic studies indicate that the effects of E17K on PIP lipid binding arise largely from electrostatic modulation of the dissociation rate. Membrane targeting analysis in live cells confirms that the constitutive targeting of E17K AKT1 PH to plasma membrane, like PLCdelta1 PH, stems from PI(4,5)P(2) binding. Overall, the evidence indicates that the molecular mechanism underlying E17K oncogenesis is a broadened target lipid selectivity that allows high-affinity binding to PI(4,5)P(2). Moreover, the findings strongly implicate the native Glu17 side chain as a key element of PIP lipid specificity in the wild-type AKT1 PH domain. Other PH domains may employ an analogous anionic residue to control PIP specificity.
A single point mutation results in a constitutively activated and feedback-resistant chorismate mutase of Saccharomyces cerevisiae (1989)

The Saccharomyces cerevisiae ARO7 gene product chorismate mutase, a single-branch-point enzyme in the aromatic amino acid biosynthetic pathway, is activated by tryptophan and subject to feedback inhibition by tyrosine. The ARO7 gene was cloned on a 2.05-kilobase EcoRI fragment. Northern (RNA) analysis revealed a 0.95-kilobase poly(A)+ RNA, and DNA sequencing determined a 771-base-pair open reading frame capable of encoding a protein 256 amino acids. In addition, three mutant alleles of ARO7 were cloned and sequenced. These encoded chorismate mutases which were unresponsive to tyrosine and tryptophan and were locked in the on state, exhibiting a 10-fold-increased basal enzyme activity. A single base pair exchange resulting in a threonine-to-isoleucine amino acid substitution in the C-terminal part of the chorismate mutase was found in all mutant strains. In contrast to other enzymes in this pathway, no significant homology between the monofunctional yeast chorismate mutase and the corresponding domains of the two bifunctional Escherichia coli enzymes was found.
Spectral dependence of absorption sensitivity on concentration of oxygenated hemoglobin: pulse oximetry implications (2013)

The sensitivity analysis indicates that the effective absorption coefficient is most sensitive to the concentration of oxygenated hemoglobin in spectral bands centered at 700 and 960 nm. We find that the highest temporal modulation due to heart function for a thick sample, like an arm, is at 940 nm, a significant shift from 710 nm measured for a finger. The most favorable spectral region for a thick transmission sample, such as a forearm, is the domain defined by intervals [900 nm ≤ λ₁ ≤ 1000 nm] and [650 nm ≤ λ₂ ≤ 720 nm]. We evaluated five near-infrared light-emitting diodes (LEDs) for their potential applications in oximetry. The LED with peak emission at 930 nm emits well in this spectral region. Here the temporal noise is low, and the effective absorption coefficient is strongly dependent on the concentration of the oxygenated hemoglobin. High-quality saturation results are obtained through the forearm during a short measurement (30 s).
Lantibiotic Structures as Guidelines for the Design of Peptides That Can Be Modified by Lantibiotic Enzymes (2005)

Lantibiotics are (methyl)lanthionine-containing bacterial peptides. (Methyl)lanthionines are posttranslationally introduced into the prepropeptides by biosynthetic enzymes that dehydrate serines and threonines and couple these dehydrated residues to cysteine residues. Thirty seven lantibiotic primary structures have been proposed to date, but little is known about the substrate specificity of the lantibiotic modifying enzymes. To define rules for the rational design of modified peptides, we compared all known lantibiotic structures by in silico analysis. Although no strict sequence motifs can be defined that govern the modification, statistical analysis demonstrates that dehydratable serines and threonines are more often flanked by hydrophobic than by hydrophilic amino acids. Serine residues escape dehydration more often than threonines. With these rules, novel hexapeptides were designed that either were predicted to become modified or will escape modification. The hexapeptides were fused to the nisin leader and expressed in a Lactococcus lactis strain containing the nisin modifying and export enzymes. The excreted peptides were analyzed by mass spectrometry. All designed fusion peptides were produced, and the presence or absence of modifications was found to be in full agreement with the predictions based on the statistical analysis. These findings demonstrate the feasibility of the rational design of a wide range of novel peptides with dehydrated amino acid residues.
New Directions in the Treatment of Cancer: Inhibition of Signal Transduction (2002)

In recent years, it has become increasingly apparent that proteins regulated by activated oncogenes or mutated tumor suppressor genes are responsible for the transformation of normal cells to malignant cells as well as for malignant characteristics such as uncontrolled cellular proliferation and the development of metastases. These proteins may be soluble factors, receptors on cell surfaces, or intracellular enzymes that produce signals that stimulate cellular development or proliferation. This process is called signal transduction .In many cases, increased amounts of these proteins have been demonstrated in cancer cells (over normal cells) and have been found to carry prognostic significance. New approaches in cancer treatment are being designed to block such proteins; this approach is termed signal transduction inhibition. !Specific protein targets that anticancer therapies have been developed to inhibit include epidermal growth factor receptors, tyrosine kinase, farnesyl transferase, and various promoters of angiogenesis.
[Prevention of antibiotic-associated diarrhea with Lactobacillus sporogens and fructo-oligosaccharides in children. A multicentric double-blind vs placebo study]. (2003)

Prophylaxis with Lactobacillus sporogens, associated to FOS, significantly reduced the number of days and duration of events in children with antibiotic-induced diarrhea.
Expression of bone associated macromolecules by gingival and periodontal ligament fibroblasts (2001)

The expression of hard tissue associated proteins may be used to identify periodontal fibroblasts with the capability to facilitate periodontal regeneration. The aim of this study was to describe, by immunohistochemistry, the distribution of osteocalcin, osteopontin, bone sialoprotein and bone morphogenic proteins-2 and -4 (BMP-2 and BMP-4) within the human periodontium. Furthermore, the expression of mRNA for the above proteins and alkaline phosphatase by gingival and periodontal ligament fibroblasts in vitro was also assessed by reverse transcriptase polymerase chain reaction (RT-PCR). Localization of osteopontin, osteocalcin, BMP-2 and BM P-4 within sections of human periodontal structures was stronger in the periodontal ligament compared to the gingiva. Bone sialoprotein was not detected in either of the soft tissues but, along with osteopontin and osteocalcin, it was localized in the cementum and bone. In vitro, both the gingival and periodontal ligament fibroblasts expressed mRNA for alkaline phosphatase, BMP-2, BMP-4 and osteopontin. Although there were no differences in the expression of alkaline phosphatase and BMP-4 mRNA between the two cell types, we noted significantly higher mRNA levels of osteopontin in the periodontal ligament and BM P-2 in the gingival fibroblasts. Osteocalcin and bone sialoprotein mRNA expression was only noted in the cultured periodontal ligament fibroblasts. From these results, it can be concluded that distinct differences exist between the two fibroblast populations in terms of the localization and mRNA expression of the majority of the hard tissue associated proteins. Furthermore, the elevated in vitro mRNA expression for osteocalcin, osteopontin and bone sialoprotein may be used to identify cells with the potential to facilitate hard tissue formation and hence periodontal regeneration.
Topical Methotrexate Therapy for Psoriasis (1989)

In vitro percutaneous penetration of methotrexate is enhanced with 1-dodecylazacycloheptan-2-one (laurocapram [Azone]). Laurocapram-containing methotrexate formulations provide effective local inhibition of epidermal DNA synthesis in the in vivo hairless mouse and minipig models, providing the biochemical rationale for topical use in the treatment of psoriasis. Topical methotrexate (0.1%, 0.5%, and 1%) in a laurocapram-containing formulation was tested in a two-center double-blind pilot clinical study of 42 patients with plaque psoriasis. Drugs were applied twice a day for six weeks, and lesions were scored weekly for erythema, scale, and elevation. An overall improvement of 50% or more in the combined scores for erythema, scale, and elevation was obtained with 0.1% methotrexate (64% of patients), 0.5% methotrexate (59%), and 1% methotrexate (56%) vs the vehicle alone (25%). These preliminary findings suggest that methotrexate preparations that provide adequate percutaneous absorption may have a beneficial effect in the treatment of psoriasis.
A pharmacokinetic comparison of anrukinzumab, an anti‐ IL‐13 monoclonal antibody, among healthy volunteers, asthma and ulcerative colitis patients (2015)

Anrukinzumab's PK behave like a typical antibody. UC patients were identified to have a faster CL of anrukinzumab than healthy volunteers and asthma patients. This finding suggests a higher dose level may be required for this population.
Discovery of novel hematopoietic cell adhesion molecules from human bone marrow stromal cell membrane protein extracts by a new cell- blotting technique (1994)

In an attempt to define the role of cell adhesion molecules (CAMs) within the bone marrow (BM) microenvironment in normal hematopoiesis and in leukemia development, a novel cell-blotting technique that involved cell adhesion to protein bands after separation by lithium dodecyl sulfate-polyacrylamide gel electrophoresis (LDS-PAGE) and blotting onto polyvinylidene difluoride (PVDF) membrane has been developed. Human BM stromal cell membrane fractions have been prepared from Dexter-type cultures after cell lysis by sonification and differential centrifugations of the sonification contents. The 20,000 g pellets representing membrane fractions have been solubilized by 2% Triton X-100, 0.575% LDS, and 8 mol/L urea in sequential order. The protein extracts are fractionated by LDS-PAGE and screened for CAMs by the new cell-blotting technique. This led to identification of nine protein bands in lanes containing LDS extracts showing adhesion of KG1a (CD34+ progenitor myeloid) cells. Evidence that the BM proteins exhibiting KG1a cell adhesion are novel CAMs is based on the observations that these proteins, in comparison with known CAMs, specifically VCAM-1, CD54, and CD44, show (1) contrasting detergent-solubility properties, (2) different temperature requirement for mediating cell adhesion function, and (3) markedly distinct electrophoretic mobilities. The various cell types tested, notably KG1a, NALM-6, WIL-2, Ramos, HS-Sultan, K562, JY B lymphoblastoid cells, and T lymphoblasts, showed distinctive patterns of binding to different subsets of BM CAMs. These results demonstrate a new approach to studies of molecular mechanisms that may determine specificity of hematopoietic cellular localization within BM microenvironment and may play an important role in controlling hematopoiesis.
Oximes as reversible links in polymer chemistry: dynamic macromolecular stars (2014)

We demonstrate the formation of oxime-functional macromolecular stars that are able to dissociate and reconstruct themselves upon application of a stimulus.
Primary repair with semitendinosus tendon augmentation of acute anterior cruciate ligament injuries (1990)

A retrospective review of 72 acute ACL injuries in 70 athletically active patients (50 recreational and 20 competitive athletes) treated with primary repair and semitendinosus tendon augmentation was conducted (mean follow-up time, 38.5 months). All patients had open primary multiple loop depth-varying suture repair and semitendinosus tendon augmentation at a mean injury to surgery interval of 9.1 days. Fifty-one cases (70.8%) were supplemented with an extraarticular procedure consisting in all cases of an iliotibial band lateral sling reinforcement. All patients underwent 6 weeks of postoperative immobilization followed by a graduated rehabilitation regimen lasting a mean 7.2 months. In 22 of the ACL tears, no other associated injury could be defined at arthrotomy, while in 27, significant medial collateral ligament injuries were noted. Lateral meniscal injuries (24) were more commonly noted than medial meniscal injuries (19). Good to excellent subjective results were reported in 82%, while 77.1% returned to preinjury sport level and participation without limitation. One patient developed "giving way" symptoms and overall, only four patients did not return to sports participation. Objective examination revealed 93.1% to have a 1+ or less Lachman test and 86.1% to have a negative pivot shift. Of 60 knees tested, 93.3% had KT-1000 side-to-side difference values (measured at 25 degrees +/- 5 degrees of flexion with an 89 N load) of less than or equal to 3 mm of anterior displacement. A 100 point Hospital for Special Surgery ligament rating score was used with 25 points assigned to subjective, 45 points to objective, and 30 points to functional assessment. The mean score at followup was 93.1. Analysis of results in patients with or without an extraarticular reinforcement revealed no difference in objective outcome. The incidence of patellofemoral pain was 27.8%. Thirty knees had some degree of loss of range of motion. Loss of terminal flexion was noted in 29, while 5 had loss of terminal extension. No correlation could be found between patellofemoral pain and diminished range of motion. Generalized ligamentous laxity was found in 37.1% of the patients; this was not associated with a poor result. This study suggests that primary repair with semitendinosus tendon augmentation of acute ACL injuries with a graduated rehabilitation regimen provides good subjective, and excellent functional and objective, results in active patients that were followed for more than 3 years.
Constitutive Steroidogenesis in Ovine Large Luteal Cells May Be Mediated by Tonically Active Protein Kinase A1 (2007)

The mechanisms responsible for the increased basal rates of progesterone secretion from large steroidogenic luteal cells (LLC) relative to small steroidogenic luteal cells (SLC) have not been clearly defined. To determine if protein kinase A (PKA) is tonically active in LLC, the adenylate cyclase activator forskolin and a specific PKA inhibitor (PKI) were utilized in a 2 x 2 factorial treatment with each steroidogenic cell type. Progesterone and cAMP production were quantified after the different treatments. In addition, the effects of the treatments on the concentrations and relative phosphorylation status of the steroidogenic acute regulatory (STAR) protein in the two cell types were determined as a measure of PKA activity. Treatment with PKI blocked forskolin-induced increases in progesterone secretion by SLC without affecting the production of cAMP. The treatment of LLC with PKI significantly decreased basal progesterone secretion in the presence or absence of forskolin, indicating that the high level of steroidogenesis in this cell type requires PKA activity. There were no differences in the steady-state concentrations of STAR protein in either cell type after treatment. However, the percentage of relative STAR phosphorylation was higher in the LLC than in SLC, and PKI treatment significantly decreased the phosphorylation of STAR in the LLC. The relative phosphorylation status of STAR and the concentrations of progesterone in the media were significantly correlated with the treatments in both cell types. The amount of progesterone secreted per picogram of cAMP was higher in the LLC than in the SLC, and this was accompanied by a significant increase in the ratio of relative STAR phosphorylation to the steady-state concentration of STAR protein. These data are compatible with the theory that LLC are constitutively steroidogenic, partly because they have tonically active PKA. In addition, the phosphorylation of STAR appears to be a primary activity of PKA in both types of ovine steroidogenic luteal cells.
Animal models for evaluation of compounds against influenza viruses (1975)

Experimental methods for the evaluation of antiviral compounds in mice and ferrets infected with influenza viruses are discussed. BRL 5907, an interferon inducer, is shown to reduce lung lesions in infected mice and the behaviour of standard antiviral compounds is compared using their capacity to reduce the increase in lung weight caused by the virus. In infected ferrets, BRL 5907 reduces the febrile response and virus excretion while allowing full humoral antibody production. Measurement of nasal airway resistance is shown to be a reproducible method of monitoring respiratory distress in infected ferrets.
Platelet-derived growth factor: purification and partial characterization. (1979)

A cationic protein that stimulates DNA synthesis in human cultured cells was isolated from human platelets by ion exchange chromatography, hydrophobic chromatography, gel chromatography, and gel electrophoresis in sodium dodecyl sulfate. The electrophoretic behavior of biologically active or radioiodinated and reduced growth factor indicated that the native protein (approximately 30,000 daltons) was composed of two different polypeptides (approximately 13,000-14,000 and 16,000-17,000 daltons, respectively) linked via reduction-susceptible bonds. The stimulatory activity on human glial cells of the purified product at a concentration of approximately 4 ng/ml (0.13 nM) was equal to that of 1% human serum.
Monitoring of glutamate‐induced excitotoxicity by mitochondrial oxygen consumption (2018)

Dysfunction of mitochondrial activity is often associated with the onset and progress of neurodegenerative diseases. Membrane depolarization induced by Na<sup>+</sup> influx increases intracellular Ca<sup>2+</sup> levels in neurons, which upregulates mitochondrial activity. However, overlimit of Na<sup>+</sup> influx and its prolonged retention ultimately cause excitotoxicity leading to neuronal cell death. To return the membrane potential to the normal level, Na<sup>+</sup> /K<sup>+</sup> -ATPase exchanges intracellular Na<sup>+</sup> with extracellular K<sup>+</sup> by consuming a large amount of ATP. This is a reason why mitochondria are important for maintaining neurons. In addition, astrocytes are thought to be important for supporting neighboring neurons by acting as energy providers and eliminators of excessive neurotransmitters. In this study, we examined the meaning of changes in the mitochondrial oxygen consumption rate (OCR) in primary mouse neuronal populations. By varying the medium constituents and using channel modulators, we found that pyruvate rather than lactate supported OCR levels and conferred on neurons resistance to glutamate-mediated excitotoxicity. Under a pyruvate-restricted condition, our OCR monitoring could detect excitotoxicity induced by glutamate at only 10 μM. The OCR monitoring also revealed the contribution of the N-methyl-D-aspartate receptor and Na<sup>+</sup> /K<sup>+</sup> -ATPase to the toxicity, which allowed evaluating spontaneous excitation. In addition, the OCR monitoring showed that astrocytes preferentially used glutamate, not glutamine, for a substrate of the tricarboxylic acid cycle. This mechanism may be coupled with astrocyte-dependent protection of neurons from glutamate-mediated excitotoxicity. These results suggest that OCR monitoring would provide a new powerful tool to analyze the mechanisms underlying neurotoxicity and protection against it.
Determination of the Radioprotective Effects of Topical Applications of MEA, WR-2721, and N-Acetylcysteine on Murine Skin (1983)

Topical applications of MEA (beta-mercaptoethylamine or cysteamine), WR-2721 [S-2-(3-aminopropylamino)-ethylphosphorothioic acid], and N-acetylcysteine (NAC) were tested for their ability to protect the normal skin of the hind legs of mice against acute and late damage from single doses of 137Cs radiation. No significant protection was observed with either WR-2721 or NAC. MEA was shown to offer significant protection against acute skin damage in both buffered and unbuffered forms, but no significant protection against late contraction. The use of topical MEA on unanesthetized animals breathing carbogen (95% O2, 5% CO2) appears to give an enhanced level of radioprotection over that shown for anesthetized, air-breathing animals.