gebhart/patrepeval huggingface dataset:
Anticonvulsant activity of some 4-aminobenzamides (1984)

A series of 4- aminobenzamides of some simple primary and secondary amines were prepared and evaluated for anticonvulsant effects. The compounds were tested in mice against seizures induced by electroshock and pentylenetetrazole ( metrazole ) and in the rotorod assay for neurologic deficit. For those N-alkyl amides tested, 4-amino-N- amylbenzamide (6) was the most potent against maximal electroshock seizures (MES): ED50 = 42.98 mg/kg; however, the N- cyclohexylbenzamide (8) showed the greatest protective index (PI = TD50/ED50), 2.8. The introduction of a second aromatic ring produced more potent compounds, with d,l-4-amino-N-(alpha-methylbenzyl)-benzamide (12) showing the highest level of activity. This compound has an anti-MES ED50 of 18.02 mg/kg in mice when administered intraperitoneally (ip) and a TD50 of 170.78 mg/kg (PI = 9.5) in the same species. These data compare quite favorably with those for phenobarbital and phenytoin in the same assays.
Advances on the Understanding of the Origins of Synaptic Pathology in AD (2007)

Although Alzheimer's disease (AD) was first discovered a century ago, we are still facing a lack of definitive diagnosis during the patient's lifetime and are unable to prescribe a curative treatment. However, the past 10 years have seen a "revamping" of the main hypothesis about AD pathogenesis and the hope to foresee possible treatment. AD is no longer considered an irreversible disease. A major refinement of the classic beta-amyloid cascade describing amyloid fibrils as neurotoxins has been made to integrate the key scientific evidences demonstrating that the first pathological event occurring in AD early stages affects synaptic function and maintenance. A concept fully compatible with synapse loss being the best pathological correlate of AD rather than other described neuropathological hallmarks (amyloid plaques, neurofibrillary tangles or neuronal death). The notion that synaptic alterations might be reverted, thus offering a potential curability, was confirmed by immunotherapy experiments targeting beta-amyloid protein in transgenic AD mice in which cognitive functions were improved despite no reduction in the amyloid plaques burden. The updated amyloid cascade now integrates the synapse failure triggered by soluble Abeta-oligomers. Still no consensus has been reached on the most toxic Abeta conformations, neither on their site of production nor on their extra- versus intra-cellular actions. Evidence shows that soluble Abeta oligomers or ADDLs bind selectively to neurons at their synaptic loci, and trigger major changes in synapse composition and morphology, which ultimately leads to dendritic spine loss. However, the exact mechanism is not yet fully understood but is suspected to involve some membrane receptor(s).
A Real-Time Wide Area Differential GPS System (1997)

This paper describes the system architecture, algorithms, and results from an operating Wide Area Differential GPS (WADGPS) system spanning the continental United States (CONUS). With single-frequency GPS user equipment and improved positioning algorithms, real-time root mean square (RMS) user position accuracy is typically better than 25 cm in the horizontal components and 50 cm in the vertical with current levels of ionospheric activity. Dual-frequency users have a slightly degraded accuracy of 35 cm horizontal and 75 cm vertical. There may be some degradation in single-frequency positioning during solar maximum or ionospheric storms. We expect that improvements in smoothing and editing techniques for the dual-frequency user will yield better positions than those yielded for single-frequency users during peak solar activity. In addition to commercial applications, the software for estimation of the WADGPS corrections is being adapted for use in the Federal Aviation Administration's (FAA) Wide Area Augmentation System (WAAS) and will be installed in the FAA's National Satellite Test Bed (NSTB).
Studies on poly-β-hydroxybutyrate synthase activity of Nostoc muscorum (2006)

This study compares the PHB synthase activity of Nostoc muscorum, a N(2)-fixing cyanobacterium under control (grown in usual BG-11 medium), nitrogen (N) and phosphorus (P) deprivation and chemoheterotrophic conditions. Specific activity of PHB synthase did not depict significant variations in the latter three types of cultures, except for the control one, where a significantly lower activity was recorded. PHB synthase activity was detected only in the soluble fractions of both the control as well as cells incubated under chemoheterotrophic conditions. A K(m) of 80.2 microM DL-beta-hydroxybutyryl-CoA and V(max) of 197.5 nmol thiobenzoate (TNB) mg protein(-1)min(-1) were observed for the enzyme. PHB synthase remained insensitive to acetyl-CoA, ATP, NADP, NADPH supplementation under in vitro condition. Addition of acetyl phosphate was found to activate the enzyme and the level of activation was dependent on the concentration of acetyl phosphate supplementation. Inhibition of PHB synthase in 2,3-butanedione supplemented cultures and reactivation following acetyl phosphate addition proved the post-translational control of acetyl phosphate over PHB synthase.
A Practical Guide to Approaching Biased Agonism at G Protein Coupled Receptors (2017)

Biased agonism, the ability of a receptor to differentially activate downstream signaling pathways depending on binding of a "biased" agonist compared to a "balanced" agonist, is a well-established paradigm for G protein-coupled receptor (GPCR) signaling. Biased agonists have the promise to act as smarter drugs by specifically targeting pathogenic or therapeutic signaling pathways while avoiding others that could lead to side effects. A number of biased agonists targeting a wide array of GPCRs have been described, primarily based on their signaling in pharmacological assays. However, with the promise of biased agonists as novel therapeutics, comes the peril of not fully characterizing and understanding the activities of these compounds. Indeed, it is likely that some of the compounds that have been described as biased, may not be if quantitative approaches for bias assessment are used. Moreover, cell specific effects can result in "system bias" that cannot be accounted by current approaches for quantifying ligand bias. Other confounding includes kinetic effects which can alter apparent bias and differential propagation of biological signal that results in different levels of amplification of reporters downstream of the same effector. Moreover, the effects of biased agonists frequently cannot be predicted from their pharmacological profiles, and must be tested in the <i>vivo</i> physiological context. Thus, the development of biased agonists as drugs requires a detailed pharmacological characterization, involving both qualitative and quantitative approaches, and a detailed physiological characterization. With this understanding, we stand on the edge of a new era of smarter drugs that target GPCRs.
Heme-regulated eIF2α kinase activated Atf4 signaling pathway in oxidative stress and erythropoiesis (2012)

Heme-regulated eIF2α kinase (Hri) is necessary for balanced synthesis of heme and globin. In addition, Hri deficiency exacerbates the phenotypic severity of β-thalassemia intermedia in mice. Activation of Hri during heme deficiency and in β-thalassemia increases eIF2α phosphorylation and inhibits globin translation. Under endoplasmic reticulum stress and nutrient starvation, eIF2α phosphorylation also induces the Atf4 signaling pathway to mitigate stress. Although the function of Hri in regulating globin translation is well established, its role in Atf4 signaling in erythroid precursors is not known. Here, we report the role of the Hri-activated Atf4 signaling pathway in reducing oxidative stress and in promoting erythroid differentiation during erythropoiesis. On acute oxidative stress, Hri(-/-) erythroblasts suffered from increased levels of reactive oxygen species (ROS) and apoptosis. During chronic iron deficiency in vivo, Hri is necessary both to reduce oxidative stress and to promote erythroid differentiation. Hri(-/-) mice developed ineffective erythropoiesis during iron deficiency with inhibition of differentiation at the basophilic erythroblast stage. This inhibition is recapitulated during ex vivo differentiation of Hri(-/-) fetal liver erythroid progenitors. Importantly, the Hri-eIF2αP-Atf4 pathway was activated and required for erythroid differentiation. We further demonstrate the potential of modulating Hri-eIF2αP-Atf4 signaling with chemical compounds as pharmaceutical therapies for β-thalassemia.
Interaction of Syndecan and α6β4 Integrin Cytoplasmic Domains (2010)

The alpha6beta4 integrin is a laminin 332 (LN332) receptor central to the formation of hemidesmosomes in epithelial layers. However, the integrin becomes phosphorylated by keratinocytes responding to epidermal growth factor in skin wounds or by squamous cell carcinomas that overexpress/hyperactivate the tyrosine kinase ErbB2, epidermal growth factor receptor, or c-Met. We show here that the beta4-dependent signaling in A431 human squamous carcinoma cells is dependent on the syndecan family of matrix receptors. Yeast two-hybrid analysis identifies an interaction within the distal third (amino acids 1473-1752) of the beta4 cytoplasmic domain and the conserved C2 region of the syndecan cytoplasmic domain. Via its C2 region, Sdc1 forms a complex with the alpha6beta4 integrin along with the receptor tyrosine kinase ErbB2 and the cytoplasmic kinase Fyn in A431 cells. Engagement of LN332 or clustering of the alpha6beta4 integrin with integrin-specific antibodies causes phosphorylation of ErbB2, Fyn, and the beta4 subunit as well as activation of phosphatidylinositol 3-kinase and Akt and their assimilation into this complex. This leads to phosphatidylinositol 3-kinase-dependent cell spreading and Akt-dependent protection from apoptosis. This is disrupted by RNA interference silencing of Sdc1 but can be rescued by mouse Sdc1 or Sdc4 but not by syndecan mutants lacking their C-terminal C2 region. This disruption does not prevent the phosphorylation of ErbB2 or Fyn but blocks the Fyn-mediated phosphorylation of the beta4 tail. We propose that syndecans engage the distal region of the beta4 cytoplasmic domain and bring it to the plasma membrane, where it can be acted upon by Src family kinases.
Benzo[d]imidazole Transient Receptor Potential Vanilloid 1 Antagonists for the Treatment of Pain: Discovery of trans-2-(2-{2-[2-(4-Trifluoromethyl-phenyl)-vinyl]-1H-benzimidazol-5-yl}-phenyl)-propan-2-ol (Mavatrep) (2015)

Reported herein is the design, synthesis, and pharmacologic characterization of a class of TRPV1 antagonists constructed on a benzo[d]imidazole platform that evolved from a biaryl amide lead. This design composes three sections: a 2-substituted 5-phenyl headgroup attached to the benzo[d]imidazole platform, which is tethered at the two position to a phenyl tail group. Optimization of this design led to the identification of 4 (mavatrep), comprising a trifluoromethyl-phenyl-vinyl tail. In a TRPV1 functional assay, using cells expressing recombinant human TRPV1 channels, 4 antagonized capsaicin-induced Ca(2+) influx, with an IC50 value of 4.6 nM. In the complete Freund's adjuvant- and carrageenan-induced thermal hypersensitivity models, 4 exhibited full efficacy, with ED80 values of 7.8 and 0.5 mg/kg, respectively, corresponding to plasma levels of 270.8 and 9.2 ng/mL, respectively. On the basis of its superior pharmacologic and safety profile, 4 (mavatrep) was selected for clinical development for the treatment of pain.
Multiple-Instance Pruning For Learning Efficient Cascade Detectors (2007)

Cascade detectors have been shown to operate extremely rapidly, with high ac-curacy, and have important applications such as face detection. Driven by this success, cascade learning has been an area of active research in recent years. Nev-ertheless, there are still challenging technical problems during the training process of cascade detectors. In particular, determining the optimal target detection rate for each stage of the cascade remains an unsolved issue. In this paper, we propose the multiple instance pruning (MIP) algorithm for soft cascades. This algorithm computes a set of thresholds which aggressively terminate computation with no re-duction in detection rate or increase in false positive rate on the training dataset. The algorithm is based on two key insights: i) examples that are destined to be rejected by the complete classifier can be safely pruned early; ii) face detection is a multiple instance learning problem. The MIP process is fully automatic and re-quires no assumptions of probability distributions, statistical independence, or ad hoc intermediate rejection targets. Experimental results on the MIT+CMU dataset demonstrate significant performance advantages. 1
Convergence test for inversion of frequency-resolved optical gating spectrograms (2000)

We describe a new and simple method to aid in the analysis of retrieved pulses from inverted frequency-resolved optical gating (FROG) traces. The analysis can separate noise from distortion and shows that distortion is more deleterious to the retrieved pulse than is pure noise. The analysis relies on the fact that FROG traces can be constructed from a single outer product of two vectors, whereas distortion and noise require the sum of a series of outer products.
High Cumulative Risk of Lung Cancer Death among Smokers and Nonsmokers in Central and Eastern Europe (2006)

The authors have calculated cumulative risks of lung cancer from a case-control study conducted between 1998 and 2002 involving 2,633 lung cancer cases and 2,884 controls in Hungary, Poland, the Czech Republic, Slovakia, Romania, and Russia. The odds ratios for smoking history were combined with national lung cancer mortality rates to obtain the cumulative risk of lung cancer. The cumulative risk of death from lung cancer by the age of 75 years among current male smokers was 14.6% in Romania and Russia and 15.8% in Poland, similar to levels reported in Western Europe, although higher risks were found in the Czech Republic (19.8%), Hungary (21.9%), and Slovakia (28.2%). Cumulative risks of lung cancer death among never smokers of over 1% were observed in Hungary among both men and women and among men in Poland. The effect of quitting smoking on the lifetime cumulative risk was substantial, with between 67% and 83% of lung cancer risk among men being avoided by quitting before the age of 50 years. This substantial reduction in risk among former smokers confirms that lung cancer mortality in Central Europe over the next three decades will be determined by the extent to which current smokers can successfully quit smoking.
Heat shock factor‐4 (HSF‐4a) is a repressor of HSF‐1 mediated transcription* (2001)

Heat shock transcription factors (HSFs) regulate the expression of heat shock proteins and other molecular chaperones that are involved in cellular processes from higher order assembly to protein degradation and apoptosis. Among the human HSFs, HSF-4 is expressed as at least two splice variants. One isoform (HSF-4b) possesses a transcriptional activation domain, but this region is absent in the other isoform (HSF-4a). We have recently shown that the HSF-4a isoform represses basal transcription from heterologous promoters both in vitro and in vivo. Here we show that HSF-4a and HSF-4b have dramatically different effects on HSF-1-containing nuclear bodies, which form after heat shock. While the expression of HSF-4b colocalizes with nuclear granules, the expression of HSF-4a prevents their formation. In addition, there is a concurrent reduction of HSF-1 in the nucleus, and there is reduction in its DNA binding activity and in HSE-dependent transcription of a reporter gene. To better understand the mechanism by which HSF-4a represses transcription, we inducibly expressed HSF-4a in cells and found that HSF-4a binds to the heat shock element (HSE) during attenuation of the heat shock response. Thus HSF-4a is an active repressor of HSF-1-mediated transcription. This repressor function makes the HSF-4a isoform unique within the HSF family.
Adenine Nucleosides in Solution: Circular Dichroism Studies and Base Conformation (1975)

Adenosine, AMP, S-adenosylhomocysteine, S-adenosylmethionine, aristeromycin and 25 other synthetic adenosine analogs modified in the 4' or 5' positions show certain groups of different circular dichroism (CD) spectra. Both positive and negative Cotton effects can occur in the long-wavelength part (250-270 nm) of the spectra. Molar ellipticities [theta] range from -6000 (in adenosine 5'-carboxylate) to +4000 deg. cm2 dmol-1 (in 5'-deoxy-5'iodoadenosine), including some compounds with small, polar 5'-substituents in which low-intensity bands are found in signed pairs. Most of these adenosine derivatives that have the same adenine chromophore and a ribofuranose moiety unsubstituted in the 2' and 3' positions prefer an anti-conformation of the adenine base, as evidenced by proton magnetic resonance spectroscopy. In the majority of cases, electronic perturbations of the chromophore or major alterations of the assymmetric sugar residue can be excluded as sources of the CD variations. Therefore a correlation of the long-wavelength CD bands with the glycosyl torsion angle phiCN is suggested, where the gauche, gauche/anti combination which is typical of AMP in the crystal and in solution (phiCN approximately -40degrees, [theta] negative) is one reference point and a region for phiCN = 0degrees ([theta] positive) is assigned to compounds with space-filling substituents such as S-adenosylmethionine. Both negative and positive Cotton effects can be associated with the anti conformation range. Within this series, the base conformation of novel nucleoside structures could be predicted from CD measurements. The CD spectrum gives no indication, however, of whether a certain torsion angle is the result of a rigid structure (as in AMP) or the average value of a molecule with high rotational freedom (as in 5'-deoxyadenosine). The conformations of aristeromycin and 4'-thioadenosine are discussed in relation to adenosine, and a structure-determining effect of the 4' bridge atom is noted.
Toll-like receptor 2 controls expansion and function of regulatory T cells (2006)

Tregs play a central role in the suppression of immune reactions and prevention of autoimmune responses harmful to the host. During acute infection, however, Tregs might hinder effector T cell activity directed toward the elimination of the pathogenic challenge. Pathogen recognition receptors from the TLR family expressed by innate immune cells are crucial for the generation of effective immunity. We have recently shown the CD4CD25 Treg subset in TLR2 mice to be significantly reduced in number compared with WT littermate control mice, indicating a link between Tregs and TLR2. Here, we report that the TLR2 ligand Pam3Cys, but not LPS (TLR4) or CpG (TLR9), directly acts on purified Tregs in a MyD88-dependent fashion. Moreover, when combined with TCR stimulation, TLR2 triggering augmented Treg proliferation in vitro and in vivo and resulted in a temporal loss of the suppressive Treg phenotype in vitro by directly affecting Tregs. Importantly, WT Tregs adoptively transferred into TLR2 mice were neutralized by systemic administration of TLR2 ligand during the acute phase of a Candida albicans infection, resulting in a 100-fold reduced C. albicans outgrowth. This demonstrates that in vivo TLR2 also controls the function of Tregs and establishes a direct link between TLRs and the control of immune responses through Tregs.
Parkinson's disease in 65 pairs of twins and in a set of quadruplets (1983)

Among 43 monozygotic (MZ) and 19 dizygotic (DZ) pairs in which an index case had definite Parkinson's disease (PD), only one MZ pair was definitely concordant for PD. When pairs with questionable clinical features were included, 4 of 48 MZ and 1 of 19 DZ pairs were concordant. The frequency of PD in MZ cotwins of index cases with PD was similar to that expected in an unrelated control group matched for age and sex. Although we were unable to identify a single environmental agent, we conclude that the major factors in the etiology of PD are nongenetic.
Principles of quasi-equivalence and Euclidean geometry govern the assembly of cubic and dodecahedral cores of pyruvate dehydrogenase complexes (1999)

The pyruvate dehydrogenase multienzyme complex (Mr of 5-10 million) is assembled around a structural core formed of multiple copies of dihydrolipoyl acetyltransferase (E2p), which exhibits the shape of either a cube or a dodecahedron, depending on the source. The crystal structures of the 60-meric dihydrolipoyl acyltransferase cores of Bacillus stearothermophilus and Enterococcus faecalis pyruvate dehydrogenase complexes were determined and revealed a remarkably hollow dodecahedron with an outer diameter of approximately 237 A, 12 large openings of approximately 52 A diameter across the fivefold axes, and an inner cavity with a diameter of approximately 118 A. Comparison of cubic and dodecahedral E2p assemblies shows that combining the principles of quasi-equivalence formulated by Caspar and Klug [Caspar, D. L. & Klug, A. (1962) Cold Spring Harbor Symp. Quant. Biol. 27, 1-4] with strict Euclidean geometric considerations results in predictions of the major features of the E2p dodecahedron matching the observed features almost exactly.
A Practical Video Database Based on Language and Image Analysis (1997)

We integrated a practical digital video database system based on language and image analysis with components from digital video processing, still image search, information retrieval, dosed captioning processing. The attempt is to utilize the multiple modalities of information in video and implement data fusion among the multiple modalities. Keyframes are extracted to represent shots based on video content. Logical structure of video is discovered and represented as Scene Transition Diagram. Storyboard and STG, and catalog information provide means to browse video content non-linearly. Text information from dosed captioning is extracted and associated with shots. Text information search and image similarity search are provided to get direct access to video shots. We integrated a practical digital video database system based on language and image analysis with components from digital video processing, still image search, information retrieval, closed captioning processing, and Intemet and Web page programming. The research and development project currently has digitized video programs of total 13 hours and 50 minutes long, among which one hour and 5 minutes are stored at Advance Inc. and 12.75 hours are stored at Princeton University. These MPEG video stories take up about 8.4 GB disk space. The contents are focused on two areas: US military operation in Bosnia and US presidential politics.
MEK Kinase 1, a Substrate for DEVD-Directed Caspases, Is Involved in Genotoxin-Induced Apoptosis (1998)

MEK kinase 1 (MEKK1) is a 196-kDa protein that, in response to genotoxic agents, was found to undergo phosphorylation-dependent activation. The expression of kinase-inactive MEKK1 inhibited genotoxin-induced apoptosis. Following activation by genotoxins, MEKK1 was cleaved in a caspase-dependent manner into an active 91-kDa kinase fragment. Expression of MEKK1 stimulated DEVD-directed caspase activity and induced apoptosis. MEKK1 is itself a substrate for CPP32 (caspase-3). A mutant MEKK1 that is resistant to caspase cleavage was impaired in its ability to induce apoptosis. These findings demonstrate that MEKK1 contributes to the apoptotic response to genotoxins. The regulation of MEKK1 by genotoxins involves its activation, which may be part of survival pathways, followed by its cleavage, which generates a proapoptotic kinase fragment able to activate caspases. MEKK1 and caspases are predicted to be part of an amplification loop to increase caspase activity during apoptosis.