gebhart/patrepeval huggingface dataset:
The PACAP Ligand/Receptor System Regulates Cerebral Cortical Neurogenesisa (1998)

The PACAP ligand/type I receptor system is expressed throughout the embryonic nervous system, suggesting roles in regulating neural patterning and neurogenesis. In the forebrain, precursors of the six-layered cerebral cortex cease dividing in a highly reproducible spatiotemporal sequence. The time of cell cycle exit in fact determines neuron laminar fate. Our studies indicate that PACAP signaling may elicit cortical precursor withdrawal from the cell cycle, antagonizing mitogenic stimulators. PACAP inhibited embryonic day 13.5 rat cortical precursor [3H]thymidine incorporation, decreasing the proportion of mitotic cells. PACAP promoted morphological and biochemical differentiation, indicating that PACAP-induced cell cycle withdrawal was accompanied by neuronal differentiation. In vivo, embryonic cortex contains PACAP. In culture, 85% of cells expressed PACAP while 64% exhibited receptor. Co-localization studies indicated that PACAP ligand and receptor were expressed by the mitotic precursors that divided in response to bFGF, suggesting that precursors integrate mitogenic and anti-mitogenic signals to determine the timing of cell cycle exit. The expression of PACAP ligand and receptor in precursors raised the possibility of autocrine function. Indeed, peptide antagonists increased proliferation, suggesting that the PACAP system is expressed to elicit cell cycle exit. During ontogeny, an inhibitory signal, such as PACAP, may be required to counter the stimulatory activity of mitogenic bFGF and IGFI whose expression during cortical neurogenesis is sustained. The dynamic interplay of positive and negative regulators would regulate the timing of cell cycle withdrawal, and thus neuronal phenotype and laminar position.
Finding your friends and following them to where you are (2012)

Location plays an essential role in our lives, bridging our online and offline worlds. This paper explores the interplay between people's location, interactions, and their social ties within a large real-world dataset. We present and evaluate Flap, a system that solves two intimately related tasks: link and location prediction in online social networks. For link prediction, Flap infers social ties by considering patterns in friendship formation, the content of people's messages, and user location. We show that while each component is a weak predictor of friendship alone, combining them results in a strong model, accurately identifying the majority of friendships. For location prediction, Flap implements a scalable probabilistic model of human mobility, where we treat users with known GPS positions as noisy sensors of the location of their friends. We explore supervised and unsupervised learning scenarios, and focus on the efficiency of both learning and inference. We evaluate Flap on a large sample of highly active users from two distinct geographical areas and show that it (1) reconstructs the entire friendship graph with high accuracy even when no edges are given; and (2) infers people's fine-grained location, even when they keep their data private and we can only access the location of their friends. Our models significantly outperform current comparable approaches to either task.
lon gene product of Escherichia coli is a heat-shock protein (1984)

The product of the pleiotropic gene lon is a protein with protease activity and has been tentatively identified as protein H94.0 on the reference two-dimensional gel of Escherichia coli proteins. Purified Lon protease migrated with the prominent cellular protein H94.0 in E. coli K-12 strains. Peptide map patterns of Lon protease and H94.0 were identical. A mutant form of the protease had altered mobility during gel electrophoresis. An E. coli B/r strain that is known to be defective in Lon function contained no detectable H94.0 protein under normal growth conditions. Upon a shift to 42 degrees C, however, the Lon protease was induced to high levels in K-12 strains and a small amount of protein became detectable at the H94.0 location in strain B/r. Heat induction of Lon protease was dependent on the normal allele of the regulatory gene, htpR, establishing lon as a member of the high-temperature-production regulon of E. coli.
Purification of glycoside hydrolases from Bacteroides fragilis (1980)

Six glycoside hydrolases in the culture medium of Bacteroides fragilis--alpha-glucosidase, beta-glucosidase, alpha-galactosidase, beta-galactosidase, beta-N-acetylglucosaminidase, and alpha-L-fucosidase-were systematically purified by ammonium sulfate precipitation, gel filtration chromatography, and density gradient isoelectric focusing. The isoelectric focusing resolved the glycosidases into distinct, well-separated fractions and revealed three differently charged forms of beta-N-acetylglucosaminidase and of alpha-L-fucosidase. Furthermore, alpha-glucosidase and beta-N-acetylglucosaminidase were shown to possess dual affinities for the respective galactoside substrates, and beta-galactosidase also hydrolyzed beta-D-fucoside. alpha-Glucosidase was purified to homogeneity, as indicated by a thin-layer isoelectric focusing zymogram technique. The glycosidases, with exception of beta-glucosidase and the acid alpha-L-fucosidase, were each separated from other glycosidic activities to 99%. The molecular weights varied between 58,000 and 125,000. The pH optima ranged from 4.8 to 6.9.
Venous Thromboembolic Disease in Congestive Heart Failure (2010)

Congestive heart failure (CHF) is a medical condition associated with a relatively high risk of venous thromboembolism (VTE). Without thromboprophylaxis, venographically proven deep vein thrombosis occurs in 10% to 22% of hospitalized patients with CHF. Although the elevated VTE risk associated with CHF has been attributed to a variety of abnormalities in the context of Virchow's triad, newer information suggests that an associated chronic inflammatory state may be culpable. Both traditional VTE risk factors and cardiac-specific risk factors further increase the risk of VTE in patients with CHF. Severe left ventricular dysfunction, clinical instability (New York Heart Association class III-IV), young age, and/or right ventricular dysfunction appear to enhance the VTE risk associated with CHF. Grade IA pharmacologic thromboprophylactic recommendations for the hospitalized CHF patient include low molecular weight-heparin, fondaparinux, and low-dose unfractionated heparin. Regrettably, a variance in societal guidelines on the importance of VTE in hospitalized CHF patients may lead to underutilization of thromboprophylaxis.
The molecular basis for differential type I interferon signaling (2017)

Type I interferons (IFN-1) are cytokines that affect the expression of thousands of genes, resulting in profound cellular changes. IFN-1 activates the cell by dimerizing its two-receptor chains, IFNAR1 and IFNAR2, which are expressed on all nucleated cells. Despite a similar mode of binding, the different IFN-1s activate a spectrum of activities. The causes for differential activation may stem from differences in IFN-1-binding affinity, duration of binding, number of surface receptors, induction of feedbacks, and cell type-specific variations. All together these will alter the signal that is transmitted from the extracellular domain inward. The intracellular domain binds, directly or indirectly, different effector proteins that transmit signals. The composition of effector molecules deviates between different cell types and tissues, inserting an additional level of complexity to the system. Moreover, IFN-1s do not act on their own, and clearly there is much cross-talk between the activated effector molecules by IFN-1 and other cytokines. The outcome generated by all of these factors (processing step) is an observed phenotype, which can be the transformation of the cell to an antiviral state, differentiation of the cell to a specific immune cell, senescence, apoptosis, and many more. IFN-1 activities can be divided into robust and tunable. Antiviral activity, which is stimulated by minute amounts of IFN-1 and is common to all cells, is termed robust. The other activities, which we term tunable, are cell type-specific and often require more stringent modes of activation. In this review, I summarize the current knowledge on the mode of activation and processing that is initiated by IFN-1, in perspective of the resulting phenotypes.
Synthesis and structural, electrochromic characterization of pulsed laser deposited vanadium oxide thin films (2001)

Vanadium oxide thin films with different stoichiometry have been deposited on In2O3:SnO2 (ITO) glass and Si wafer by pulsed laser deposition technique at different substrate heating or annealing temperatures and oxygen pressure. The structural properties of as-deposited and annealed VOx thin films were analyzed by using a scanning accessory of transmission electron microscope, x-ray diffraction, Fourier transform infrared spectrum, and Raman spectrum. The as-deposited thin film on the Si(111) wafer showed lower orientation with polycrystalline structure but those annealed at 300 °C above showed highly c-axis oriented growth. Highly c-axis oriented growth nanocrystalline V2O5 thin films with orthorhombic polycrystalline structure were successfully synthesized on ITO glass by using the scanning laser ablation technique at deposition temperature as low as 200 °C. Cyclic voltammograms at sweep rate of 50 mV/s shows that the no-long-term degradation was noticed at least up to 1000 cycles, and durability was verified to 8000 cycles in the voltage range between −1.2 and 1.4 V. It is demonstrated that these c-axis oriented V2O5 thin films on ITO are good candidates for cathode thin films for rechargeable batteries and electrochromic devices.
On the relationship between sequence and structure similarities in proteomics (2007)

Statistical analysis of multiple and pairwise structural alignments of protein structures within SCOP folds is performed. The results indicate that multiple conservation of residue identity is not common and that relationship between sequence and structure may be explained by a model based on the assumption that protein structure is tolerant to residue substitutions preserving hydropathic profile of the sequence. This model also explains the origin and specific value of the sequence similarity threshold, noticed in many previous studies, below which structural resemblance is not statistically expected.
Total and High-Molecular-Weight Adiponectin in Breast Cancer:In Vitroandin VivoStudies (2006)

These studies suggest that adiponectin may act as a biomarker of carcinogenesis and may constitute a molecular link between obesity and breast cancer.
One-step purification of recombinant human papillomavirus type 16 E7 oncoprotein and its binding to the retinoblastoma gene product. (1993)

Six derivatives of the human papillomavirus type 16 E7 gene were constructed, each of which encoded a peptide at the amino terminus of the E7 protein capable of chelating metal ions, for use in subsequent purification of the proteins by chelating peptide-immobilized metal ion affinity chromatography (CP-IMAC). Five of the six chelating peptides examined contained six amino acids, and each varied in the number of histidine and tryptophan residues. The CP-E7 proteins were expressed in Escherichia coli, and the cysteine residues were blocked in the form of S-sulfonate groups. This series of CP-E7 proteins was purified in a single chromatographic step using CP-IMAC. The efficiency of purification correlated with the number of histidine and tryptophan residues present in the CP. The purified CP-E7 proteins bound to the human retinoblastoma gene product, pRB, in in vitro co-immunoprecipitation assays and immobilized CP-E7 binding assays. The efficiency of E7-pRB binding was not altered by the presence of a CP at the N-terminus of E7 nor by the S-sulfonate groups within E7.
Physiological role of a novel neuropeptide, apelin, and its receptor in the rat brain (2001)

Apelin, a peptide recently isolated from bovine stomach tissue extracts, has been identified as the endogenous ligand of the human orphan APJ receptor. We established a stable Chinese hamster ovary (CHO) cell line expressing a gene encoding the rat apelin receptor fused to the enhanced green fluorescent protein, to investigate internalization and the pharmacological profile of the apelin receptor. Stimulation of this receptor by the apelin fragments K17F (Lys1‐Phe‐Arg‐Arg‐Gln‐Arg‐Pro‐Arg‐Leu‐Ser‐His‐Lys‐Gly‐Pro‐Met‐Pro‐Phe17) and pE13F (pGlu5‐Arg‐Pro‐Arg‐Leu‐Ser‐His‐Lys‐Gly‐Pro‐Met‐Pro‐Phe17) resulted in a dose‐dependent inhibition of forskolin‐induced cAMP production and promoted its internalization. In contrast, the apelin fragments R10F (Arg8‐Leu‐Ser‐His‐Lys‐Gly‐Pro‐Met‐Pro‐Phe17) and G5F (Gly13‐Pro‐Met‐Pro‐Phe17) were inactive. The physiological role of apelin and its receptor was then investigated by showing for the first time in rodent brain: (i) detection of apelin neurons in the supraoptic and paraventricular nuclei by immunohistochemistry with a specific polyclonal anti‐apelin K17F antibody; (ii) detection of apelin receptor mRNA in supraoptic vasopressinergic neurons by in situ hybridization and immunohistochemistry; and (iii) a decrease in vasopressin release following intracerebroventricular injection of K17F, or pE13F, but not R10F. Thus, apelin locally synthesized in the supraoptic nucleus could exert a direct inhibitory action on vasopressinergic neuron activity via the apelin receptors synthesized in these cells. Furthermore, central injection of pE13F significantly decreased water intake in dehydrated normotensive rats but did not affect blood pressure. Together, these results suggest that neuronal apelin plays an important role in the central control of body fluid homeostasis.
Role of surface in surface-dependent activation of Hageman factor (blood coagulation Factor XII) (1978)

The mechanism by which negatively charged substances such as celite, kaolin, or ellagic acid contribute to the surface-dependent activation of Hageman factor (Factor XII) was studied. Kinetic studies of the proteolytic activation of (125)I-labeled human Hageman factor by human plasma kallikrein, plasma, activated Factor XI, and trypsin were performed in the presence and absence of high molecular weight kininogen and surface materials such as celite, kaolin, or ellagic acid. The results showed that surface-bound Hageman factor was 500 times more susceptible than soluble Hageman factor to proteolytic activation by kallikrein in the presence of high molecular weight kininogen. Surface binding of Hageman factor enhanced its cleavage by plasmin, activated Factor XI, and trypsin by 100-fold, 30-fold, and 5-fold, respectively. On a molar basis, trypsin was twice as potent as kallikrein in the cleavage of the surface-bound Hageman factor, while plasmin and activated Factor XI were an order of magnitude less potent than kallikrein. Kallikrein even at concentrations as low as 0.5 nM (i.e., 1/1000th of the concentration of prekallikrein in plasma) was very potent in the limited proteolysis of the surface-bound Hageman factor. These results suggest that substances classically known as "activating surfaces" promote the activation of Hageman factor indirectly by altering its structure such that it is much more susceptible to proteolytic activation by other plasma or cellular proteases.
Three‐dimensional hippocampal atrophy maps distinguish two common temporal lobe seizure–onset patterns (2008)

The HS-like distribution of atrophy and the restriction of HA to the ipsilateral hippocampus in HYP patients are consistent with focal hippocampal onsets, and suggest a mechanism utilizing intrahippocampal circuitry. In contrast, the bilateral distribution of nonspecific atrophy in the LVF group may reflect mechanisms involving both hippocampal and extrahippocampal networks.
A Statistics-based Fundamental Model for Side-channel Attack Analysis. (2014)

Abstract. Side-channel attacks (SCAs) exploit leakage from the physi-cal implementation of cryptographic algorithms to recover the otherwise secret information. In the last decade, popular SCAs like differential power analysis (DPA) and correlation power analysis (CPA) have been invented and demonstrated to be realistic threats to many critical em-bedded systems. However, there is still no sound and provable theoretical model that illustrates precisely what the success of these attacks depends on and how. Based on the maximum likelihood estimation (MLE) theory, this paper proposes a general statistical model for side-channel attack analysis that takes characteristics of both the physical implementation and cryptographic algorithm into consideration. The model establishes analytical relations between the success rate of attacks and the crypto-graphic system. For power analysis attacks, the side-channel character-istic of the physical implementation is modeled as signal-to-noise ratio (SNR), which is the ratio between the single-bit unit power consumption
Three-Dimensional Vibrational Imaging by Coherent Anti-Stokes Raman Scattering (1999)

A multiphoton microscopy based on coherent anti-Stokes Raman scattering is accomplished with near-infrared ultrashort laser pulses. We demonstrate vibrational imaging of chemical and biological samples with high sensitivity, high spatial resolution, noninvasiveness, and three-dimensional sectioning capability.
NT-702, a Selective Phosphodiesterase 3 Inhibitor, Dilates Rabbit Spinal Arterioles via Endothelium-Dependent and Endothelium-Independent Mechanisms (2008)

We investigated the effects of NT-702, a selective phosphodiesterase (PDE) 3 inhibitor, on arterioles isolated from rabbit lumbar spinal cords. NT-702 caused a dose-dependent dilation of the isolated spinal arterioles. The disruption of endothelium produced a significant reduction of higher concentrations (10(-7) and 10(-6) M), but not lower concentrations (less than 10(-8) M), of NT-702-induced vasodilation. The NT-702-induced vasodilation of the arterioles with endothelium was not affected by pretreatment with an inhibitor of nitric oxide, cyclooxygenase, or cytochrome P-450 monooxygenase. In contrast, catalase reduced significantly the higher concentrations of NT-702-induced vasodilation only. Tetraethylammonium (TEA) completely reduced the lower concentrations of NT-702-induced vasodilation, but decreased only partially the higher concentrations of NT-702-induced vasodilation of the arterioles with endothelium. Hydrogen peroxide dilated significantly the isolated arterioles with endothelium, the response of which was reduced significantly by TEA. KT5720 (a selective protein kinase inhibitor) significantly decreased both the lower and higher concentrations of NT-702-induced vasodilation of the arterioles with endothelium. The findings suggest that NT-702 dose-dependently dilated the isolated spinal arterioles of rabbits via endothelium-dependent and endothelium-independent mechanisms. Protein kinase A (PKA)- and TEA-sensitive K(+) channels may be involved in the NT-702-induced vasodilation. Moreover, hydrogen peroxide may contribute in part to the endothelium-dependent higher concentrations of NT-702-induced vasodilation.
Characterization of the mouse lymphotoxin-beta gene. (1995)

Lymphotoxin-beta (LT-beta) is a member of the TNF family of ligands which when expressed with lymphotoxin-alpha (LT-alpha, i.e., the original LT or TNF-beta) forms a heteromeric complex with LT-alpha on the cell surface. The mouse gene structure was determined by both cDNA cloning and analysis of a genomic DNA fragment encompassing the TNF/LT locus in the H-2 region of chromosome 17. The mouse and human genomic structures were found to be similar in terms of location in the class III region of the MHC; however, the mouse gene lacks one intron found in most members of the family. Both the cDNA and the genomic sequences revealed an altered splice donor in the conventional intron 2 position, rendering it nonfunctional. The altered gene retains an open reading frame such that an additional 66 amino acids are inserted into the stalk region connecting the transmembrane domain with the receptor binding domain encoded by exon 4 in this type II membrane protein. Northern analysis showed that this gene is expressed predominantly in lymphoid organs. The outlining of the complete mouse TNF locus will further studies of the relationship between these genes and immune function.
Haemophilus ducreyi Is Susceptible to Protegrin (1998)

Protegrins, potent antimicrobial peptides found in porcine leukocytes, have activity against the sexually transmitted pathogens Neisseria gonorrhoeae, Chlamydia trachomatis, and human immunodeficiency virus type 1. We tested synthetic protegrin 1 (PG-1) for activity against nine isolates of Haemophilus ducreyi, the etiologic agent of chancroid. The test organisms included CIP 542 (the type strain), 35000HP (a human-passaged variant of 35000), 35000HP-RSM2 (an isogenic D-glycero-D-manno-heptosyltransferase mutant of 35000HP), and six clinical isolates. The isolates were epidemiologically unrelated, represented three HindIII ribotypes, and had varying antimicrobial resistance patterns. In bactericidal assays, five isolates were rapidly killed by synthetic PG-1. In radial diffusion assays, all nine isolates were exquisitely sensitive to PG-1. These data highlight the potential of protegrins for development as topical agents to prevent many sexually transmitted diseases, including chancroid.
Broadband ac conductivity of conductor-polymer composites (1998)

The electrical conductivity of a composite model system formed by highly structured carbon black (CB) filled, within an amorphous polymer, poly(ethylene terephtalate) composite is studied. The dc conductivity as a function of CB content follows a scaling law of the type $\ensuremath{\sigma}\ensuremath{\propto}(p\ensuremath{-}{p}_{c}{)}^{t}$ yielding for the percolation concentration, ${p}_{c}=0.011$ and for the exponent, $t=2.17$. The analysis of the temperature dependence of the conductivity suggests that for temperatures larger than 45 K, conduction can be ascribed to thermal fluctuation induced tunneling of the charge carriers through the insulating layer of polymer separating two CB aggregates. At lower temperatures, conductivity becomes temperature independent, which is typical of conventional tunneling. The frequency dependence of the conductivity is also studied between dc and ${10}^{9}$ Hz. By the introduction of a shift factor ${a}_{p},$ a procedure for the construction of a master curve based on a ``time-length equivalence principle'' is proposed. Finally, a model is introduced to describe the frequency dependence of the conductivity of CB-filled composites based on the behavior of charge carriers placed in a fractal object.