gebhart/patrepeval huggingface dataset:
β-Secretase (BACE1) Inhibitors with High in Vivo Efficacy Suitable for Clinical Evaluation in Alzheimer’s Disease (2013)

An extensive fluorine scan of 1,3-oxazines revealed the power of fluorine(s) to lower the pKa and thereby dramatically change the pharmacological profile of this class of BACE1 inhibitors. The CF3 substituted oxazine 89, a potent and highly brain penetrant BACE1 inhibitor, was able to reduce significantly CSF Aβ40 and 42 in rats at oral doses as low as 1 mg/kg. The effect was long lasting, showing a significant reduction of Aβ40 and 42 even after 24 h. In contrast to 89, compound 1b lacking the CF3 group was virtually inactive in vivo.
The assaulted nurse: short-term and long-term responses. (1989)

The purpose of this prospective study was to identify attitudinal changes and to describe the emotional, cognitive, social, and biophysiological short- and long-term reactions of nursing staff being physically assaulted by a patient. Sixty-one assaulted nursing staff at the University of California Los Angeles Neuropsychiatric Institute comprised the sample. Responses to the assault were elicited through weekly self-report questionnaires and interviews at week 1 and week 6. Follow-up questionnaires were completed at 6 months to 1 year following the assault. Sixty-seven percent (41/61) of the staff met the "responder" criteria during week 1. Eighteen percent (11/61) of the assaulted staff continued to experience moderate to severe responses 6 weeks following the assault. Long-term follow-up showed that 21% (8/39) of the staff were responders at 6 months, and 16% (4/25) were responders at 1 year. Two overall trends were evident: an overall decrease in the frequency of moderate to severe responses in each of the four categories from weeks 1 to 6, with increases during weeks 3 and 4, and a higher frequency of moderate, rather than intense and severe, responses throughout the 6 week period. No significant changes in attitudes were found. The data support the need for formalized clinical, educational, and administrative programs to assist staff in coping with this stressful work experience.
Identification of two essential histidine residues of ribonuclease T2 from Aspergillus oryzae (1990)

Ribonuclease (RNase) T2 from Aspergillus oryzae was modified by diethyl pyrocarbonate and iodoacetic acid. RNase T2 was rapidly inactivated by diethyl pyrocarbonate above pH 6.0 and by incorporation of a carboxymethyl group. No inactivation occurred in the presence of 3'AMP. 1H-NMR titration and photo-chemically induced dynamic nuclear polarization experiments demonstrated that two histidine residues were involved in the active site of RNase T2. Furthermore, analysis of inactive carboxymethylated RNase T2 showed that both His53 and His115 were partially modified to yield a total of one mole of N tau-carboxymethylhistidine/mole enzyme. The results indicate that the two histidine residues in the active site of RNase T2 are essential for catalysis and that modification of either His53 or His115 inactivates the enzyme.
Investigating the use of the coanda effect to create novel unmanned aerial vehicles. (2009)

In recent years the demand for Unmanned Aerial Vehicles (UAV&amp;apos;s) has increased rapidly across many different industries and they are used for various applications. Such systems have the ability to enter dangerous or inaccessible environments and allow vital information to be collected without human risk. In order to carry out a task, a UAV has to face many different challenges. This has led to the development of novel platforms that move away from traditional aircraft design in order to make them more capable. A good example of this type of craft is one which uses the Coanda Effect to assist propulsion. This effect was discovered in 1930 by Henri-Marie Coanda who found that if a thin film of air is directed over a curved body, then the air follows the curve. When used to propel a UAV, the Coanda Effect also entrains air from above and lowers the air pressure in this region, which in turn generates more lift. Many organizations have attempted to use this phenomenon to aid the lift of various unusual air vehicles.
Five-year efficacy and safety of asfotase alfa therapy for adults and adolescents with hypophosphatasia (2018)

Hypophosphatasia (HPP) features low tissue-nonspecific alkaline phosphatase (TNSALP) isoenzyme activity resulting in extracellular accumulation of its substrates including pyridoxal 5'-phosphate (PLP), the principal circulating form of vitamin B6, and inorganic pyrophosphate (PPi), a potent inhibitor of mineralization. Asfotase alfa is an enzyme replacement therapy developed to treat HPP. This multinational, randomized, open-label study (NCT01163149; EudraCT 2010-019850-42) evaluated the efficacy and safety of asfotase alfa in adults and adolescents 13-66 years of age with HPP. The study comprised a 6-month primary treatment period and a 4.5-year extension phase. In the primary treatment period, 19 patients were randomized to receive asfotase alfa 0.3 mg/kg/d subcutaneously (SC; n = 7), asfotase alfa 0.5 mg/kg/d SC (n = 6), or no treatment (control; n = 6) for 6 months. In the extension phase, patients received asfotase alfa (0.5 mg/kg/d for 6 mo-1 y, then 1 mg/kg/d 6 d/wk). During the primary treatment period, changes from Baseline to Month 6 in plasma PLP and PPi concentrations (coprimary efficacy measure) were greater in the combined asfotase alfa group compared with the control group, reaching statistical significance for PLP (P = 0.0285) but not for PPi (P = 0.0715). However, for the total cohort, the within subject changes in both PLP and PPi after 6 months and over 5 years of treatment with asfotase alfa were significant (P < 0.05). Secondary efficacy measures included transiliac crest histomorphometry, dual-energy X-ray absorptiometry (DXA), and the 6-Minute Walk Test (6MWT). A significant decrease from Baseline in mineralization lag time was observed in the combined asfotase alfa group at Year 1. There were no significant differences between treated and control patients in DXA mean bone mineral density results at 6 months; Z-scores and T-scores were within the expected range for age at Baseline and remained so over 5 years of treatment. On the 6MWT, median (min, max) distance walked increased from 355 (10, 620; n = 19) meters before treatment to 450 (280, 707; n = 13) meters at 5 years (P < 0.05). Results for the exploratory outcome measures suggested improvements in gross motor function, muscle strength, and patient-reported functional disability over 5 years of treatment. There were no deaths during this study. Asfotase alfa was generally well tolerated; the most common adverse events were mild to moderate injection site reactions. This study suggests that in adults and adolescents with pediatric-onset HPP, treatment with asfotase alfa is associated with normalization of circulating TNSALP substrate levels and improved functional abilities.
Dextran Sodium Sulfate-Induced Inflammation Alters the Expression of Proteins by Intestinal Escherichia coli Strains in a Gnotobiotic Mouse Model (2011)

To identify Escherichia coli proteins involved in adaptation to intestinal inflammation, mice were monoassociated with the colitogenic E. coli strain UNC or with the probiotic E. coli strain Nissle. Intestinal inflammation was induced by treating the mice with 3.5% dextran sodium sulfate (DSS). Differentially expressed proteins in E. coli strains collected from cecal contents were identified by 2-dimensional difference gel electrophoresis. In both strains, acute inflammation led to the downregulation of pathways involved in carbohydrate breakdown and energy generation. Accordingly, DSS-treated mice had lower concentrations of bacterial fermentation products in their cecal contents than control mice. Differentially expressed proteins also included the Fe-S cluster repair protein NfuA, the tryptophanase TnaA, and the uncharacterized protein YggE. NfuA expression was 3-fold higher in E. coli strains from DSS-treated than from control mice. Reporter experiments confirmed the induction of nfuA in response to iron deprivation, mimicking Fe-S cluster destruction by inflammation. YggE expression, which has been reported to reduce the intracellular level of reactive oxygen species, was 4- to 8-fold higher in E. coli Nissle than in E. coli UNC. This was confirmed by in vitro reporter gene assays indicating that Nissle is better equipped to cope with oxidative stress than UNC. Nissle isolated from DSS-treated and control mice had TnaA levels 4- to 7-fold-higher than those of UNC. Levels of indole resulting from the TnaA reaction were higher in control animals associated with E. coli Nissle. Because of its anti-inflammatory effect, indole is hypothesized to be involved in the extension of the remission phase in ulcerative colitis described for E. coli Nissle.
Backbone Cyclic Peptide Antagonists, Derived from the Insect Pheromone Biosynthesis Activating Neuropeptide, Inhibit Sex Pheromone Biosynthesis in Moths (1999)

We describe an application of the backbone cyclization and cycloscan concept for the design and synthesis of pheromone biosynthesis activating neuropeptide (PBAN) antagonists capable of inhibiting sex pheromone biosynthesis in Heliothis peltigera female moths. Two backbone cyclic (BBC) sub-libraries were designed and synthesized. The structure of the first sub-library ([Arg27]PBAN27-33NH2, termed the Ser sub-library) was based on the active C-terminal hexapeptide sequence (Tyr-Phe-Ser-Pro-Arg-Leu-NH2) of PBAN1-33NH2, which was found to comprise its active core. The second sub-library ([Arg27, D-Phe30]PBAN27-33NH2, termed the D-Phe sub-library) was based on the sequence of the lead antagonist Arg-Tyr-Phe-(D)Phe-Pro-Arg-Leu-NH2. In both sub-libraries the Pro residue was replaced by an Nalpha(omega-amino-alkyl)Gly building unit having various lengths of the alkyl chain. All the cyclic peptides in each sub-library had the same primary sequence and the same location of the ring. The members of each library differed from each other by the bridge size and bridge chemistry. Screening of the two libraries for pheromonotropic antagonists resulted in the disclosure of four compounds that fully inhibited sex pheromone biosynthesis at 1 nmol and were devoid of agonistic activity. All antagonistic peptides originated from the D-Phe sub-library. Substitution of the D-Phe30 amino acid with a Ser resulted in a loss of antagonistic activity. Agonistic activities were exhibited by peptides from both sub-libraries.
The use of parasitic elements to remove potential E-plane scan blindnesses in high dielectric substrate microstrip patch probe-fed phased arrays (2002)

The effect of parasitic elements on the scan performance of probe-fed microstrip patch arrays is thoroughly investigated using a rigorous full-wave analysis. In the analysis the probe feed is accurately modelled using a special attachment mode [Aberle and Pozar, 1991], thus providing accurate scan impedance variation and other related scanning characteristics. A technique is introduced that significantly reduces the reflection coefficient magnitude at potential scan blindnesses, without losing power to a grating lobe. This method is suitable for patches mounted on high dielectric material, due to the small size of these elements (relative to the free space wavelength, /spl lambda//sub 0/).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
ATP is a potent stimulator of the activation and formation of rodent osteoclasts (1998)

1. There is increasing evidence that extracellular ATP acts directly on bone cells via P2 receptors. In normal rat osteoclasts, ATP activates both non-selective cation channels and Ca2+-dependent K+ channels. In this study we investigated the action of ATP on the formation of osteoclasts and on the ultimate function of these cells, namely resorption pit formation. 2. We found that ATP stimulated resorption pit formation up to 5.6-fold when osteoclast-containing bone cell populations from neonatal rats were cultured for 26 h on ivory discs, with a maximum effect occurring at relatively low concentrations (0.2-2 microM). The stimulatory effect of ATP was amplified greatly when osteoclasts were activated by culture in acidified media (pH 6.9-7.0). Pit formation by acid-activated osteoclasts in the absence of ATP was inhibited by apyrase, an ecto-ATPase and by suramin, an antagonist of P2 receptors. 3. Over the same concentration range at which rat osteoclast activation occurred (0.2-2 microM), ATP also enhanced osteoclast formation in 10 day mouse marrow cultures, by up to 3.3-fold, with corresponding increases in resorption pit formation. Higher concentrations of ATP (20-200 microM) reduced or blocked osteoclast formation. Adenosine, a P1 receptor agonist, was without effect on either osteoclast activation or formation. 4. These results suggest that low levels of extracellular ATP may play a fundamental role in modulating both the resorptive function and formation of mammalian osteoclasts.
Novel Algorithmic Methods in Mapping of Atrial and Ventricular Tachycardia (2014)

In LQ atrial and ventricular electrograms, the novel LAT methods (B-LATOnset, B-LATCoM, and U-LATSlope-hybrid) show less variation than the conventional methods. The U-LATSlope-hybrid, a hybrid method that accurately detects the maximal negative unipolar slope, is associated with the highest accuracy in algorithmic mapping of atrial tachycardia/ventricular tachycardia.
Eukaryotic cells grown on microcarrier beads offer a cost-efficient way to propagate Chlamydia trachomatis. (1992)

The use of microcarrier cell culture as a method for the in vitro propagation of the obligate intracellular bacterial parasite, Chlamydia trachomatis, is described. The microcarrier beads proved to be a more cost-effective means to propagate C. trachomatis than traditional tissue culture flasks or roller bottles without sacrificing yields or infectivity. In addition, microcarrier cell culture was found to be a much simpler technique to study the intracellular development of these bacteria.
DNA Repair and Resistance to Topoisomerase I Inhibitors: Mechanisms, Biomarkers and Therapeutic Targets (2012)

Irinotecan and topotecan are derivatives of the naturally occurring cytotoxic compound camptothecin that are used in the treatment of patients with colorectal cancer, either as single agents or in combination with radiotherapy and/or other chemotherapy drugs. They are inhibitors of DNA topoisomerase I (Top I) and exert their cytotoxic effects in replicating cells by inducing DNA strand breaks. A wide range of DNA repair proteins is involved in the recognition and repair of these breaks, and depletion or inhibition of some of these proteins increases the cytotoxic effects of Top I inhibitors. Building on these laboratory observations, ongoing translational research is aiming to establish whether this mechanistic information can be used to improve the treatment of patients with certain types of cancer. Two potential strategies are under investigation: (1) individualising treatment by evaluating levels and/or patterns of expression of DNA repair proteins that predict clinical response to Top I inhibitors, and (2) developing small molecule inhibitors of these repair enzymes to overcome tumour resistance and improve outcomes. This review summarises the current status of these research endeavours, focusing on the key roles of tyrosyl DNA phosphodiesterase 1 (Tdp1) and poly(ADP-ribose) polymerase (PARP), and examines the pre-clinical and clinical data that support the potential value of these and other DNA repair proteins as predictive markers and therapeutic targets. Since irinotecan is increasingly being combined with radiotherapy, the potential for these proteins to act as predictive biomarkers for both Top I inhibitors and radiation is proposed, and the possibility of synergistic potentiation of chemoradiation regimes by Tdp1 and/or PARP inhibitors is considered.
Analysis of CYP7A1 gene regulation in HepG2 cells by reverse-transcriptase polymerase chain reaction (1997)

grantor: University of Toronto
Clustered p53 immunostaining: a novel pattern associated with prostate cancer progression. (1996)

Abnormal p53 protein accumulation is typically defined as present when greater than 5 or 10% of cancer cells stain positively. We present a novel approach whereby immunopositivity is defined when 15 or more cells within a 300 x 400-micrometer(2) field exhibit p53 protein accumulation; a feature that we have called "clustered" staining. We assessed p53 immunostaining of moderately differentiated, clinically localized prostate cancers derived from two patient groups: those without cancer recurrence 5 years after radical prostatectomy, and those in whom cancer had recurred following radical prostatectomy. Clustered p53 immunopositivity was present in 10 (63%) of 16 patients in the recurrent group and in only 7 (21%) of 33 in the nonrecurrent group. Clustered p53 staining was clearly associated with cancer recurrence (P < 0.01). This refinement of a commonly used assay may help define the biological aggressiveness of a cancer.
Critical Role of Hypoxia Sensor - HIF-1&#945; in VEGF Gene Activation. Implications for Angiogenesis and Tissue Injury Healing (2012)

Vascular injury of esophageal and gastrointestinal mucosa caused by injurious and ulcerogenic factors leads to the cessation of blood flow, ischemia, and hypoxia and tissue necrosis in form of erosions or ulcers. The re-establishment of blood vessels through the process of angiogenesis--formation of new blood vessels--is critical for healing of tissue injury because is essential for delivery of oxygen and nutrients to the healing site. Hypoxia increases expression of hypoxia inducible factor (HIF-1), which serves as hypoxia sensor and activates compensatory and adaptive mechanisms. However, the molecular mechanisms and the role of HIF-1α in hypoxia-driven cellular and molecular events of angiogenesis in gastrointestinal injury healing have not been fully explored. The review discusses the novel molecular mechanisms of angiogenesis in gastric and esophageal mucosa with focus on HIF1α and VEGF interactions during healing of gastric mucosal injury and esophageal ulcers. HIF-1α is upregulated by gastric mucosal injury and esophageal ulcers; this upregulation correlates with VEGF gene activation and initiation of angiogenesis. The non-steroidal anti-inflammatory drugs (NSAIDs) interfere with hypoxia-induced HIF-1α accumulation, VEGF gene activation and angiogenesis through upregulation of von Hippel- Lindau (VHL) tumor suppressor, which activates degradation of HIF-1α protein. HIF-1α is a transcription factor that under hypoxic conditions, accumulates in endothelial cells and can bind to VEGF gene promoter and induce VEGF gene expression. In order to activate the VEGF gene, HIF-1α must be transported to the nucleus. Recent evidence implicates importins as key mechanism in this process.
The Role of Internal Water Molecules in the Structure and Function of the Rhodopsin Family of G Protein‐Coupled Receptors (2006)

Not so watered down. In this review, we summarize the role of water molecules embedded in the transmembrane bundle of G protein-coupled receptors in stabilizing intra- and interhelical interactions, and their use for building computer-generated homology models.
Increased efficiency of folding and peptide loading of mutant MHC class I molecules (2000)

Class I molecules, encoded by diverse alleles at several loci of the major histocompatibility complex (MHC) are assembled in the endoplasmic reticulum (ER) from heavy chain, beta2 microglobulin and peptide in association with accessory proteins of the peptide loading complex. We show here, that mutations in the alpha2 domain (Q115A; D122A) of the human class I allele HLA-A2 cause a lack of apparent association with the loading complex and a faster assembly. Despite the drastically reduced association with the TAP loading complex, i. e. less than 20 % of HLA-A2 expressed in the cells can be co-precipitated with either TAP, calreticulin or tapasin, the mutant proteins are expressed on the cell surface in a stable conformation, and bind a complex set of peptides almost identical to that of wild-type HLA-A2. Furthermore, the mutant class I molecules are more rapidly exported from the ER than wild-type HLA-A2 and undergo faster maturation. The mutation Q115A does not destroy a binding site for the loading complex as this HLA-A2 mutant associates with the loading complex when peptide supply is limited. The association of class I molecules with the TAP-associated loading complex appears to be a reflection of how quickly the stable conformation is gained.
Desferrioxamine induces erythropoietin gene expression and hypoxia- inducible factor 1 DNA-binding activity: implications for models of hypoxia signal transduction (1993)

Erythropoietin (EPO) gene transcription is activated in kidney cells in vivo and in Hep3B cells exposed to hypoxia or cobalt chloride. Hypoxia-inducible factor 1 (HIF-1) is a nuclear factor that binds to the hypoxia-inducible enhancer of the EPO gene at a site that is required for transcriptional activation. HIF-1 DNA-binding activity is induced by hypoxia or cobalt chloride treatment of Hep3B cells. We report that treatment of Hep3B cells with desferrioxamine (DFX) induced HIF-1 activity and EPO RNA expression with kinetics similar to the induction of HIF-1 by hypoxia or cobalt chloride. Induction by each of these stimuli was inhibited by cycloheximide, indicating a requirement for de novo protein synthesis. DFX appears to induce HIF-1 by chelating iron as induction was inhibited by coadministration of ferrous ammonium sulfate. DFX administration to mice transiently increased EPO RNA levels in the kidney. As previously shown for hypoxia and cobalt treatment, DFX also induced HIF-1 activity in non-EPO-producing cells, suggesting the existence of a common hypoxia signal-transduction pathway leading to HIF-1 induction in different cell types.
Scheduling algorithms for message transmission over a satellite broadcast system (2002)

This paper addresses scheduling algorithms for message transmissions over a satellite broadcast system. The system is expected to deliver messages of widely varied length. Our objective is to find a scheduling algorithm that exhibits good delay performance for messages of all sizes. We show that classical scheduling algorithms such as first-come-first-serve and round-robin perform poorly in this environment. We study two alternative schemes. The first, gives preemptive priority to the message with the shortest remaining processing time (SRPT). This scheme is known to minimize overall average message delays, but results in disproportionately large delays for long messages. The second scheme, serves messages based on a dynamic priority function, where a message's priority varies based on how long the message has been in the system as well as its length. This scheme results in somewhat larger overall average delays, but it is more fair to long messages.