gebhart/patrepeval huggingface dataset:
Structure-based discovery of fiber-binding compounds that reduce the cytotoxicity of amyloid beta (2013)

Amyloid protein aggregates are associated with dozens of devastating diseases including Alzheimer's, Parkinson's, ALS, and diabetes type 2. While structure-based discovery of compounds has been effective in combating numerous infectious and metabolic diseases, ignorance of amyloid structure has hindered similar approaches to amyloid disease. Here we show that knowledge of the atomic structure of one of the adhesive, steric-zipper segments of the amyloid-beta (Aβ) protein of Alzheimer's disease, when coupled with computational methods, identifies eight diverse but mainly flat compounds and three compound derivatives that reduce Aβ cytotoxicity against mammalian cells by up to 90%. Although these compounds bind to Aβ fibers, they do not reduce fiber formation of Aβ. Structure-activity relationship studies of the fiber-binding compounds and their derivatives suggest that compound binding increases fiber stability and decreases fiber toxicity, perhaps by shifting the equilibrium of Aβ from oligomers to fibers. DOI:http://dx.doi.org/10.7554/eLife.00857.001.
Reduction of the Rate of Poliovirus Protein Synthesis through Large-Scale Codon Deoptimization Causes Attenuation of Viral Virulence by Lowering Specific Infectivity (2006)

Exploring the utility of de novo gene synthesis with the aim of designing stably attenuated polioviruses (PV), we followed two strategies to construct PV variants containing synthetic replacements of the capsid coding sequences either by deoptimizing synonymous codon usage (PV-AB) or by maximizing synonymous codon position changes of the existing wild-type (wt) poliovirus codons (PV-SD). Despite 934 nucleotide changes in the capsid coding region, PV-SD RNA produced virus with wild-type characteristics. In contrast, no viable virus was recovered from PV-AB RNA carrying 680 silent mutations, due to a reduction of genome translation and replication below a critical level. After subcloning of smaller portions of the AB capsid coding sequence into the wt background, several viable viruses were obtained with a wide range of phenotypes corresponding to their efficiency of directing genome translation. Surprisingly, when inoculated with equal infectious doses (PFU), even the most replication-deficient viruses appeared to be as pathogenic in PV-sensitive CD155tg (transgenic) mice as the PV(M) wild type. However, infection with equal amounts of virus particles revealed a neuroattenuated phenotype over 100-fold. Direct analysis indicated a striking reduction of the specific infectivity of PV-AB-type virus particles. Due to the distribution effect of many silent mutations over large genome segments, codon-deoptimized viruses should have genetically stable phenotypes, and they may prove suitable as attenuated substrates for the production of poliovirus vaccines.
Gingerols: a novel class of vanilloid receptor (VR1) agonists (2002)

1. Gingerols, the pungent constituents of ginger, were synthesized and assessed as agonists of the capsaicin-activated VR1 (vanilloid) receptor. 2. [6]-Gingerol and [8]-gingerol evoked capsaicin-like intracellular Ca(2+) transients and ion currents in cultured DRG neurones. These effects of gingerols were blocked by capsazepine, the VR1 receptor antagonist. 3. The potency of gingerols increased with increasing size of the side chain and with the overall hydrophobicity in the series. 4. We conclude that gingerols represent a novel class of naturally occurring VR1 receptor agonists that may contribute to the medicinal properties of ginger, which have been known for centuries. The gingerol structure may be used as a template for the development of drugs acting as moderately potent activators of the VR1 receptor.
Targeted gene delivery of BMPR2 attenuates pulmonary hypertension (2011)

Pulmonary arterial hypertension (PAH) remains a fatal disease despite modern pharmacotherapy. Mutations in the gene for bone morphogenetic protein receptor type II (BMPR2) lead to reduced BMPR2 expression, which is causally linked to PAH. BMPR2 is predominantly expressed on pulmonary endothelium and has complex interactions with transforming growth factor (TGF)-β signalling mechanisms. Our objectives were to assess the effect on PAH of upregulating BMPR2 by targeted adenoviral BMPR2 gene delivery to the pulmonary vascular endothelium. We used two established rat models of PAH: chronic hypoxia and monocrotaline (MCT). In both hypertensive models, those receiving BMPR2 had less right ventricular hypertrophy, less pulmonary vascular resistance, improved cardiac function and reduced vascular remodelling. In the MCT model, there was an increase in TGF-β, which was prevented by BMPR2 treatment. In vitro, TGF-β1-induced endothelial-mesenchymal transition (EndMT) in human pulmonary microvascular endothelial cells, which was associated with reduced BMPR2 expression. EndMT was partially ameliorated by stimulating BMPR2 signalling with appropriate ligands even in the ongoing presence of TGF-β1. Collectively, these results indicate therapeutic potential for upregulation of the BMPR2 axis in PAH, which may be, in part, mediated by countering the remodelling effects of TGF-β.
Improved Fluorescence and Dual Color Detection with Enhanced Blue and Green Variants of the Green Fluorescent Protein (1998)

The green fluorescent protein (GFP) from the jellyfish Aequorea victoria is a versatile reporter protein for monitoring gene expression and protein localization in a variety of systems. Applications using GFP reporters have expanded greatly due to the availability of mutants with altered spectral properties, including several blue emission variants, all of which contain the single point mutation Tyr-66 to His in the chromophore region of the protein. However, previously described "BFP" reporters have limited utility, primarily due to relatively dim fluorescence and low expression levels attained in higher eukaryotes with such variants. To improve upon these qualities, we have combined a blue emission mutant of GFP containing four point mutations (Phe-64 to Leu, Ser-65 to Thr, Tyr-66 to His, and Tyr-145 to Phe) with a synthetic gene sequence containing codons preferentially found in highly expressed human proteins. These mutations were chosen to optimize expression of properly folded fluorescent protein in mammalian cells cultured at 37 degreesC and to maximize signal intensity. The combination of improved fluorescence and higher expression levels yield an enhanced blue fluorescent protein that provides greater sensitivity and is suitable for dual color detection with green-emitting fluorophores.
Adult-derived stem cells and their potential for use in tissue repair and molecular medicine (2005)

This report reviews three categories of precursor cells present within adults. The first category of precursor cell, the epiblast-like stem cell, has the potential of forming cells from all three embryonic germ layer lineages, e.g., ectoderm, mesoderm, and endoderm. The second category of precursor cell, the germ layer lineage stem cell, consists of three separate cells. Each of the three cells is committed to form cells limited to a specific embryonic germ layer lineage. Thus the second category consists of germ layer lineage ectodermal stem cells, germ layer lineage mesodermal stem cells, and germ layer lineage endodermal stem cells. The third category of precursor cells, progenitor cells, contains a multitude of cells. These cells are committed to form specific cell and tissue types and are the immediate precursors to the differentiated cells and tissues of the adult. The three categories of precursor cells can be readily isolated from adult tissues. They can be distinguished from each other based on their size, growth in cell culture, expressed genes, cell surface markers, and potential for differentiation. This report also discusses new findings. These findings include the karyotypic analysis of germ layer lineage stem cells; the appearance of dopaminergic neurons after implantation of naive adult pluripotent stem cells into a 6-hydroxydopamine-lesioned Parkinson's model; and the use of adult stem cells as transport mechanisms for exogenous genetic material. We conclude by discussing the potential roles of adult-derived precursor cells as building blocks for tissue repair and as delivery vehicles for molecular medicine.
The pH dependence of quantitative ristocetin-induced platelet aggregation: theoretical and practical implications-a new device for maintenance of platelet-rich plasma pH (1976)

Quantitative ristocetin-induced platelet aggregation of normal platelet- rich plasma (PRP) decreased with time after PRP preparation. An increase in p H of the PRP with time proved to be responsible for this finding. Diffusion of CO2from the plasma is the prime determinant of the change in pH. Since a complex combination of factors influences CO2 diffusion (surface area-to-volume relationship, capping, mixing, etc.) The change in pH is variable with time. Thus, quantitative ristocetin aggregation should be pH controlled. A simple device for maintaining PRP pH constant by control of the ambient pCO2 was designed and found effective in keeping both pH and quantitative ristocetin aggregation constant over a prolonged period of time. It can be adapted for use in platelet aggregation studies employing other reagents. The pH dependence of ristocetin-induced platelet aggregation is consistent with other data supporting an elctrostatic interaction between the platelet, von Willebrand factor, and ristocetin. We favor a model wherein ristocetin neutralizes some of the platelet's negative change and permits the von Willebrand factor to bridge sites on separate platelets to induce agglutination.
Substrate Activity Screening:  A Fragment-Based Method for the Rapid Identification of Nonpeptidic Protease Inhibitors (2005)

A new fragment-based method for the rapid development of novel and distinct classes of nonpeptidic protease inhibitors, Substrate Activity Screening (SAS), is described. This method consists of three steps: (1) a library of N-acyl aminocoumarins with diverse, low molecular weight N-acyl groups is screened to identify protease substrates using a simple fluorescence-based assay, (2) the identified N-acyl aminocoumarin substrates are optimized by rapid analogue synthesis and evaluation, and (3) the optimized substrates are converted to inhibitors by direct replacement of the aminocoumarin with known mechanism-based pharmacophores. The SAS method was successfully applied to the cysteine protease cathepsin S, which is implicated in autoimmune diseases. Multiple distinct classes of nonpeptidic substrates were identified upon screening an N-acyl aminocoumarin library. Two of the nonpeptidic substrate classes were optimized to substrates with >8000-fold improvements in cleavage efficiency for each class. Select nonpeptidic substrates were then directly converted to low molecular weight, novel aldehyde inhibitors with nanomolar affinity to cathepsin S. This study demonstrates the unique characteristics and merits of this first substrate-based method for the rapid identification and optimization of weak fragments and provides the framework for the development of completely nonpeptidic inhibitors to many different proteases.
Detailed Characterization of Neuroprotection by a Rescue Factor Humanin against Various Alzheimer's Disease-Relevant Insults (2001)

A novel factor, termed Humanin (HN), antagonizes against neurotoxicity by various types of familial Alzheimer's disease (AD) genes [V642I and K595N/M596L (NL) mutants of amyloid precursor protein (APP), M146L-presenilin (PS) 1, and N141I-PS2] and by Abeta1-43 with clear action specificity ineffective on neurotoxicity by polyglutamine repeat Q79 or superoxide dismutase 1 mutants. Here we report that HN can also inhibit neurotoxicity by other AD-relevant insults: other familial AD genes (A617G-APP, L648P-APP, A246E-PS1, L286V-PS1, C410Y-PS1, and H163R-PS1), APP stimulation by anti-APP antibody, and other Abeta peptides (Abeta1-42 and Abeta25-35). The action specificity was further indicated by the finding that HN could not suppress neurotoxicity by glutamate or prion fragment. Against the AD-relevant insults, essential roles of Cys(8) and Ser(14) were commonly indicated, and the domain from Pro(3) to Pro(19) was responsible for the rescue action of HN, in which seven residues turned out to be essential. We also compared the neuroprotective action of S14G HN (HNG) with that of activity-dependent neurotrophic factor, IGF-I, or basic FGF for the antagonism against various AD-relevant insults (V642I-APP, NL-APP, M146L-PS1, N141I-PS2, and Abeta1-43). Although all of these factors could abolish neurotoxicity by Abeta1-43, only HNG could abolish cytotoxicities by all of them. HN and HN derivative peptides may provide a new insight into the study of AD pathophysiology and allow new avenues for the development of therapeutic interventions for various forms of AD.
Temporal and real-time databases: a survey (1995)

A temporal database contains time-varying data. In a real-time database transactions have deadlines or timing constraints. In this paper we review the substantial research in these two previously separate areas. First we characterize the time domain; then we investigate temporal and real-time data models. We evaluate temporal and real-time query languages along several dimensions. We examine temporal and real-time DBMS implementation. Finally, we summarize major research accomplishments to date and list several unanswered research questions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
17??-ESTRADIOL (E2) ADMINISTRATION AFTER MAJOR BLOOD LOSS IMPROVES LIVER ATP, 3-HOUR SURVIVAL AND ALSO LONG-TERM SURVIVAL FOLLOWING PROLONGED HYPOTENSION (3 HOUR) AND FLUID RESUSCITATION (2006)

Although E2 administration after trauma-hemorrhage (T-H) and fluid resuscitation produces salutary effects on organ functions, it is not known if E2 has any beneficial effects after major blood loss in the absence of fluid resuscitation. Male SD rats ∼250 g) underwent T-H (tissue trauma, BP 40 mmHg in 10 min and maintained at that BP by further blood withdrawal until maximum bleed out [MBO, 60% of total blood volume] occurred [45±5 min]). E2 i.v. (1 mg/Kg, 0.4 ml/Kg volume i.e., 120 μL/300 g BW) or vehicle (cyclodextrin, CD) was then infused. No additional fluid was given for 3 h. If rats survived, they received Ringer's lactate, 4 × the MBO volume. A customfabricated 31P coil was placed on the surface of the rat's liver after laparotomy in another group, and spectra acquired using 4.7T NMR spectroscopy via a 31P coil in real time before and during hemorrhagic shock. Shock increased phosphomonoester and Pi with a concomitant decrease in β-ATP in both groups. The β-ATP:Pi ratio was at a life-sustaining level in the E2 group as compared to the CD group. The 3-h survival is shown in Fig. Since E2 infusion after major blood loss maintains higher liver ATP levels during severe hypotension, markedly improves 3-h survival rates without fluid resuscitation and increases long-term survival after resuscitation, E2 is a novel hormone for preserving essential cellular energy status under conditions in which fluid resuscitation is not possible for a period of 3 hrs following severe blood loss. (DARPA W81XWH-05-2-0046). Approved for Public Release, Distribution Unlimited.Figure
RETRACTED: Pyrrolidine dithiocarbamate attenuates the development of acute and chronic inflammation (2002)

The nuclear factor-kappaB (NF-kappaB) is a transcription factor which plays a pivotal role in the induction of genes involved in physiological processes as well as in the response to injury and inflammation. Dithiocarbamates are antioxidants which are potent inhibitors of NF-kappaB. We postulated that pyrrolidine dithiocarbamate (PDTC) would attenuate inflammation. In the present study we investigate the effects of PDTC in animal models of acute and chronic inflammation (carrageenan-induced pleurisy and collagen-induced arthritis). We report here for the first time that PDTC (given at 100, 30 or 10 mg kg(-1) i.p. in the pleurisy model or at 10 mg kg(-1) i.p. every 48 h in the arthritis model) exerts potent anti-inflammatory effects (e.g. significant reduction of (A) pleural exudate formation, (B) polymorphonuclear cell infiltration, (C) lipid peroxidation, (D) inducible nitric oxide synthase (iNOS) activity and nitric oxide production (E) plasma and pleural exudates levels of interleukin-1beta and tumour necrosis factor-alpha, (F) histological injury and (G) delayed development of clinical indicators). Furthermore, PDTC reduced immunohistochemical evidence of (A) formation of nitrotyrosine, (B) activation of poly (ADP-ribose) polymerase (PARP), (C) expression of iNOS and (D) expression of cyclo-oxygenase-2 (COX-2) in the lungs of carrageenan-treated mice and in the joints from collagen-treated mice. Additionally, Western blotting and immunohistochemical analysis of lung tissue revealed that PDTC prevented degradation of IKB-alpha and translocation of NF-kappaB from the cytoplasm into the nucleus. Taken together, our results clearly demonstrate that prevention of the activation of NF-kappaB by PDTC reduces the development of acute and chronic inflammation. Therefore, inhibition of NF-kappaB may represent a novel approach for the therapy of inflammation.
Detection of Cardiac Allograft Rejection and Response to Immunosuppressive Therapy With Peripheral Blood Gene Expression (2004)

These data demonstrate that peripheral blood expression profiles correlate with biopsy-proven allograft rejection. Intermediate expression profiles of treated rejection suggest persistent immune activation despite normalization of the EMB. If validated in larger studies, expression profiling may prove to be a more sensitive screening test for allograft rejection than EMB.
Chlamydia pneumoniae in a Free-Ranging Giant Barred Frog ( Mixophyes iteratus ) from Australia (1999)

The koala biovar of Chlamydia pneumoniae was identified in lung tissue from a sick, free-ranging giant barred frog (Mixophyes iteratus) by using electron microscopy, C. pneumoniae-specific fluorescent-antibody staining, cell culture, and sequencing of the ompA, ompB and 16S rRNA genes. This is the first report of a chlamydial strain infecting both a homeotherm and a poikilotherm and only the fourth host (in addition to humans, koalas, and horses) to be naturally infected with this species of Chlamydia. The frog had severe, chronic, mononuclear pneumonia and nonregenerative anemia and pancytopenia.
On the Effect of FWM in Coherent Optical OFDM Systems (2008)

We derive the channel capacity of CO-OFDM systems limited by FWM. Simulations confirm that Peak-to-Average-Power-Ratio reduction techniques are suitable for FWM mitigation. These techniques can utilize the decreased capacity to significantly increase the system reach.
A double-blind comparison of diflunisal and aspirin in the treatment of post-operative pain after episiotomy (1978)

A double-blind randomized trial was carried out in 161 primiparous women suffering from moderate to severe post-episiotomy pain to compare the analgesic efficacy of single doses of diflunisal (125 mg, 250 mg, of 500 mg), aspirin (600 mg), and placebo. The results of pain rating assessments made before and at hourly intervals after drug administration showed that both the active drugs were more effective than placebo and produced similar pain relief over the first 4 hours. The analgesic efficacy of aspirin tailed off after 4 hours but pain relief with 500 mg diflunisal was still evident after 8 hours. Over 65% of patients in the diflunisal group had effective relief of pain at 8 hours whereas there was no significant difference between the aspirin and placebo-treated groups by the seventh and eighth hour.
Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli (2002)

We present the complete genome sequence of uropathogenic Escherichia coli, strain CFT073. A three-way genome comparison of the CFT073, enterohemorrhagic E. coli EDL933, and laboratory strain MG1655 reveals that, amazingly, only 39.2% of their combined (nonredundant) set of proteins actually are common to all three strains. The pathogen genomes are as different from each other as each pathogen is from the benign strain. The difference in disease potential between O157:H7 and CFT073 is reflected in the absence of genes for type III secretion system or phage- and plasmid-encoded toxins found in some classes of diarrheagenic E. coli. The CFT073 genome is particularly rich in genes that encode potential fimbrial adhesins, autotransporters, iron-sequestration systems, and phase-switch recombinases. Striking differences exist between the large pathogenicity islands of CFT073 and two other well-studied uropathogenic E. coli strains, J96 and 536. Comparisons indicate that extraintestinal pathogenic E. coli arose independently from multiple clonal lineages. The different E. coli pathotypes have maintained a remarkable synteny of common, vertically evolved genes, whereas many islands interrupting this common backbone have been acquired by different horizontal transfer events in each strain.
Multifunctional Nanowire Bioscaffolds on Titanium (2007)

This paper reports a new fabrication of multifunctional nanowire bioscaffolds directly on titanium (Ti) through a simple and scale-up easy hydrothermal reaction of alkali with the Ti metal without using any seeds, templates, TiO2 powder, or stabilizers. The nanowires root firmly inside the Ti substrate and grow on top to eventually self-assemble into macroporous scaffolds. The effects of the alkali concentration, reaction time, and temperature on the bioscaffold morphologies were investigated. The novel solid-state chemistry for the nanowires' downward/upward co-growth and the accompanied self-assembly were tackled. Thus-formed coating of scaffolds on the metal implant surface, mimicking the natural extracellular matrix in structure, can promote cell adhesion and proliferation on Ti implant and perform controlled on-site drug release and photocatalytic sterilization.
Multispectral digital microscopy for in vivo monitoring of oral neoplasia in the hamster cheek pouch model of carcinogenesis (2005)

In this study we use a multi-spectral digital microscope (MDM) to measure multi-spectral auto-fluorescence and reflectance images of the hamster cheek pouch model of DMBA (dimethylbenz[alpha]anthracene)- induced oral carcinogenesis. The multi-spectral images are analyzed both in the RGB (red, green, blue) color space as well as in the YCbCr (luminance, chromatic minus blue, chromatic minus red) color space. Mean image intensity, standard deviation, skewness, and kurtosis are selected as features to design a classification algorithm to discriminate normal mucosa from neoplastic tissue. The best diagnostic performance is achieved using features extracted from the YCbCr space, indicating the importance of chromatic information for classification. A sensitivity of 96% and a specificity of 84% were achieved in separating normal from abnormal cheek pouch lesions. The results of this study suggest that a simple and inexpensive MDM has the potential to provide a cost-effective and accurate alternative to standard white light endoscopy.
Cloning and expression of the human erythropoietin gene. (1985)

The human erythropoietin gene has been isolated from a genomic phage library by using mixed 20-mer and 17-mer oligonucleotide probes. The entire coding region of the gene is contained in a 5.4-kilobase HindIII-BamHI fragment. The gene contains four intervening sequences (1562 base pairs) and five exons (582 base pairs). It encodes a 27-amino acid signal peptide and a 166-amino acid mature protein with a calculated Mr of 18,399. The erythropoietin gene, when introduced into Chinese hamster ovary cells, produces erythropoietin that is biologically active in vitro and in vivo.