gebhart/patrepeval huggingface dataset:
Conserved RNA secondary structures in Flaviviridae genomes (2004)

Presented here is a comprehensive computational survey of evolutionarily conserved secondary structure motifs in the genomic RNAs of the family Flaviviridae: This virus family consists of the three genera Flavivirus, Pestivirus and Hepacivirus and the group of GB virus C/hepatitis G virus with a currently uncertain taxonomic classification. Based on the control of replication and translation, two subgroups were considered separately: the genus Flavivirus, with its type I cap structure at the 5' untranslated region (UTR) and a highly structured 3' UTR, and the remaining three groups, which exhibit translation control by means of an internal ribosomal entry site (IRES) in the 5' UTR and a much shorter less-structured 3' UTR. The main findings of this survey are strong hints for the possibility of genome cyclization in hepatitis C virus and GB virus C/hepatitis G virus in addition to the flaviviruses; a surprisingly large number of conserved RNA motifs in the coding regions; and a lower level of detailed structural conservation in the IRES and 3' UTR motifs than reported in the literature. An electronic atlas organizes the information on the more than 150 conserved, and therefore putatively functional, RNA secondary structure elements.
THE EFFECT OF CHRONIC RESTRAINT STRESS ON SPATIAL LEARNING AND MEMORY: RELATION TO OXIDANT STRESS (2004)

The aim of this study was to investigate the effect of chronic restraint stress (RS) on spatial learning and memory. Fifty healthy male Wistar rats, aged three months were used. They were equally divided into five groups--C: Control, W: Water Maze, CS-1: Restrained for 21 days (1 h/day) + water maze protocol following stress period, CS-2: Restrained for 28 days (1 h/day) + water maze protocol during last 7 days of stress period, CS-3: Restrained for 21 days and allowed to recovery for 7 days (1 h/day). Corticosterone levels were higher in all stress groups than in C and W groups. Nitrite levels of frontal cortex and hippocampus were found to be elevated in chronic stress groups with respect to C and W groups. Thiobarbituric acid reactive substances (TBARS) of both tissues were increased significantly in CS1 and CS2 groups compared with C, W, and CS3 groups. Escape latencies of CS1 and CS2 groups were longer than those of the W group on each day of acquisition. In transfer test, CS1 and CS2 groups stayed significantly shorter in target quadrant according to the W group. Significant correlations between corticosterone and either nitrite or TBARS of hippocampus and frontal cortex were found. Both acquisition and memory performances were negatively correlated with plasma corticosterone level, nitrite, and TBARS levels of hippocampus and frontal cortex. The results of this study suggest that stress-induced lipid peroxidation may affect the acquisition and memory performances.
Electromagnetic contributions to single-molecule sensitivity in surface-enhanced Raman scattering (2000)

We examine whether single molecule sensitivity in surface-enhanced Raman scattering (SERS) can be explained in the framework of classical electromagnetic theory. The influence of colloid particle shape and size, composition (Ag or Au) and interparticle separation distance on the wavelength-dependent SERS enhancement factor is reported. Our calculations indicate that the maximum enhancement factor achievable through electromagnetics is of the order 10(11). This is obtained only under special circumstances, namely at interstitial sites between particles and at locations outside sharp surface protrusions. The comparative rarity of such sites, together with the extreme spatial localization of the enhancement they provide, can qualitatively explain why only very few surface sites seem to contribute to the measured signal in single-molecule SERS experiments. Enhancement factors of the order 10(14)-10(15), which have been reported in recent experiments, are likely to involve additional enhancement mechanisms such as chemisorption induced resonance Raman effects.
Stacks of convolutional Restricted Boltzmann Machines for shift-invariant feature learning (2009)

In this paper we present a method for learning class-specific features for recognition. Recently a greedy layer-wise procedure was proposed to initialize weights of deep belief networks, by viewing each layer as a separate restricted Boltzmann machine (RBM). We develop the convolutional RBM (C-RBM), a variant of the RBM model in which weights are shared to respect the spatial structure of images. This framework learns a set of features that can generate the images of a specific object class. Our feature extraction model is a four layer hierarchy of alternating filtering and maximum subsampling. We learn feature parameters of the first and third layers viewing them as separate C-RBMs. The outputs of our feature extraction hierarchy are then fed as input to a discriminative classifier. It is experimentally demonstrated that the extracted features are effective for object detection, using them to obtain performance comparable to the state of the art on handwritten digit recognition and pedestrian detection.
High efficiency single dopant white electrophosphorescent light emitting diodesElectronic supplementary information (ESI) available: emission spectra as a function of doping concentration for 3 in CBP, as well as the absorption and emission spectra of Irppz, CBP and mCP. See http://www.rsc.org/suppdata/nj/b2/b204301g/ (2002)

Efficient white electrophosphorescence has been achieved with a single emissive dopant. The dopant in these white organic light emitting diodes (WOLEDs) emits simultaneously from monomer and aggregate states, leading to a broad spectrum and high quality white emission. The dopant molecules are based on a series of platinum(II) [2-(4,6-difluorophenyl)pyridinato-N,C2′] β-diketonates. All of the dopant complexes described herein have identical photophysics in dilute solution with structured blue monomer emission (λmax = 468, 500, 540 nm). A broad orange aggregate emission (λmax ≈ 580 nm) is also observed, when doped into OLED host materials. The intensity of the orange band increases relative to the blue monomer emission, as the doping level is increased. The ratio of monomer to aggregate emission can be controlled by the doping concentration, the degree of steric bulk on the dopant and by the choice of the host material. A doping concentration for which the monomer and excimer bands are approximately equal gives an emission spectrum closest to standard white illumination sources. WOLEDs have been fabricated with doped CBP and mCP luminescent layers (CBP = N,N′-dicarbazolyl-4,4′-biphenyl, mCP = N,N′-dicarbazolyl-3,5-benzene). The best efficiencies and color stabilities were achieved when an electron/exciton blocking layer (EBL) is inserted into the structure, between the hole transporting layer and doped CBP or mCP layer. The material used for an EBL in these devices was fac-tris(1-phenylpyrazolato-N,C2′)iridium(III). The EBL material effectively prevents electrons and excitons from passing through the emissive layer into the hole transporting NPD layer. CBP based devices gave a peak external quantum efficiency of 3.3 ± 0.3% (7.3 ± 0.7 lm W−1) at 1 cd m−2, and 2.3 ± 0.2% (5.2 ± 0.3 lm W−1) at 500 cd m−2. mCP based devices gave a peak external quantum efficiency of 6.4% (12.2 lm W−1, 17.0 cd A−1), CIE coordinates of 0.36, 0.44 and a CRI of 67 at 1 cd m−2 (CIE = Commission Internationale de l'Eclairage, CRI = color rendering index). The efficiency of the mCP based device drops to 4.3 ± 0.5% (8.1 ± 0.6 lm W−1, 11.3 cd A−1) at 500 cd m−2, however, the CIE coordinates and CRI remain unchanged.
A soluble gradient of endogenous monocyte chemoattractant protein-1 promotes the transendothelial migration of monocytes in vitro (1995)

Abstract Chemokines secreted by endothelium may promote diapedesis of leukocytes by a gradient-dependent chemotactic mechanism or by stimulating random motility so that leukocytes transmigrate in a gradient-independent manner. Alternatively, chemokines may bind to endothelium and extracellular matrix to stimulate haptotactic migration. We first analyzed the role of the chemokine monocyte chemoattractant protein-1 (MCP-1) in the migration of human monocytes across untreated or IL-1-stimulated HUVEC monolayers cultured on human amnion. Then we further examined whether MCP-1-dependent transmigration occurred through a chemokinetic, chemotactic, or haptotactic mechanism. A neutralizing mAb against MCP-1 inhibited passage of monocytes across untreated or IL-1-stimulated HUVEC by 74 +/- 3% and 45 +/- 4%, respectively. Addition of MCP-1 itself to the apical compartment of unstimulated HUVEC/amnion cultures also reduced the transmigration of monocytes, in this instance by 73 +/- 9%. MCP-1 suppressed diapedesis only when present above the endothelium at a concentration equal to or greater than that endogenously deposited beneath the endothelium, and its inhibitory action could be overcome by addition of more concentrated MCP-1 below the HUVEC cultures. As much as 90% of the MCP-1 secreted into the underlying basement membrane and connective tissue could be washed out of HUVEC/amnion cultures; this procedure decreased transmigration by 69 +/- 4%. These data indicate that MCP-1 promotes transmigration of monocytes, but only when present in a gradient across endothelial monolayers. They further suggest that this gradient is predominantly soluble, rather than haptotactic.
Kinetics of Tethering Quaternary Ammonium Compounds to K+ Channels (2002)

Polymeric maleimido-quaternary ammonium (QA) compounds have been shown to function as molecular tape measures when covalently tethered to external cysteine residues of a Shaker K(+) channel (Blaustein R.O., P.A. Cole, C. Williams, and C. Miller. 2000. Nat. Struct. Biol. 7:309-311). For sufficiently long compounds, the cysteine-maleimide tethering reaction creates a high concentration, at the channel's pore, of a TEA-like moiety that irreversibly blocks current. This paper investigates a striking feature of the maleimide-cysteine tethering kinetics. Strong blockers-those that induce substantial levels (>80%) of irreversible inhibition of current-react with channel cysteines much more rapidly than weak blockers and, when delivered to channels with four cysteine targets, react with multiexponential kinetics. This behavior is shown to arise from the ability of a strong blocker to concentrate its maleimide end near a channel's cysteine target by exploiting the reversible pore-blocking affinity of its QA headgroup.
<title>Culture of bone-marrow-derived cells in microfabricated pit arrays</title> (2001)

Tissue cells cannot survive without the attachment to extracellular matrix (ECM). Furthermore, the geometry of ECM is known to play an essential role in the regulation for these cells to proliferate and differentiate so that tissues with normal morphologies can be formed or maintained. We have introduced microfabricated surface structures coated with ECM protein collagen into cell culture studies to examine a possibility of 3D patterning of ECM.
Realizing Quantum Boltzmann Machines Through Eigenstate Thermalization (2019)

Quantum Boltzmann machines are natural quantum generalizations of Boltzmann machines that are expected to be more expressive than their classical counterparts, as evidenced both numerically for small systems and asymptotically under various complexity theoretic assumptions. However, training quantum Boltzmann machines using gradient-based methods requires sampling observables in quantum thermal distributions, a problem that is NP-hard. In this work, we find that the locality of the gradient observables gives rise to an efficient sampling method based on the Eigenstate Thermalization Hypothesis, and thus through Hamiltonian simulation an efficient method for training quantum Boltzmann machines on near-term quantum devices. Furthermore, under realistic assumptions on the moments of the data distribution to be modeled, the distribution sampled using our algorithm is approximately the same as that of an ideal quantum Boltzmann machine. We demonstrate numerically that under the proposed training scheme, quantum Boltzmann machines capture multimodal Bernoulli distributions better than classical restricted Boltzmann machines with the same connectivity structure. We also provide numerical results on the robustness of our training scheme with respect to noise.
Printing 2-Dimentional Droplet Array for Single-Cell Reverse Transcription Quantitative PCR Assay with a Microfluidic Robot (2015)

This paper describes a nanoliter droplet array-based single-cell reverse transcription quantitative PCR (RT-qPCR) assay method for quantifying gene expression in individual cells. By sequentially printing nanoliter-scale droplets on microchip using a microfluidic robot, all liquid-handling operations including cell encapsulation, lysis, reverse transcription, and quantitative PCR with real-time fluorescence detection, can be automatically achieved. The inhibition effect of cell suspension buffer on RT-PCR assay was comprehensively studied to achieve high-sensitivity gene quantification. The present system was applied in the quantitative measurement of expression level of mir-122 in single Huh-7 cells. A wide distribution of mir-122 expression in single cells from 3061 copies/cell to 79998 copies/cell was observed, showing a high level of cell heterogeneity. With the advantages of full-automation in liquid-handling, simple system structure, and flexibility in achieving multi-step operations, the present method provides a novel liquid-handling mode for single cell gene expression analysis, and has significant potentials in transcriptional identification and rare cell analysis.
Clonal analysis of the differentiation potential of human adipose‐derived adult stem cells (2005)

Pools of human adipose-derived adult stem (hADAS) cells can exhibit multiple differentiated phenotypes under appropriate in vitro culture conditions. Because adipose tissue is abundant and easily accessible, hADAS cells offer a promising source of cells for tissue engineering and other cell-based therapies. However, it is unclear whether individual hADAS cells can give rise to multiple differentiated phenotypes or whether each phenotype arises from a subset of committed progenitor cells that exists within a heterogeneous population. The goal of this study was to test the hypothesis that single hADAS are multipotent at a clonal level. hADAS cells were isolated from liposuction waste, and ring cloning was performed to select cells derived from a single progenitor cell. Forty-five clones were expanded through four passages and then induced for adipogenesis, osteogenesis, chondrogenesis, and neurogenesis using lineage-specific differentiation media. Quantitative differentiation criteria for each lineage were determined using histological and biochemical analyses. Eighty one percent of the hADAS cell clones differentiated into at least one of the lineages. In addition, 52% of the hADAS cell clones differentiated into two or more of the lineages. More clones expressed phenotypes of osteoblasts (48%), chondrocytes (43%), and neuron-like cells (52%) than of adipocytes (12%), possibly due to the loss of adipogenic ability after repeated subcultures. The findings are consistent with the hypothesis that hADAS cells are a type of multipotent adult stem cell and not solely a mixed population of unipotent progenitor cells. However, it is important to exercise caution in interpreting these results until they are validated using functional in vivo assays.
The evolution of viruses and worms (2004)

Computer viruses and network worms have evolved through a continuous series of innovations, leading to the recent wave of fast-spreading and dangerous worms. A review of their historical development and recent outbreaks leads to a number of observations. First, while viruses were more common than worms initially, worms have become the predominant threat in recent years, coinciding with the growth of computer networking. Second, despite widespread use of firewalls and other network security equipment, worm outbreaks still occur and will likely continue to be a threat for the near future. Third, recent worms are appearing as a series of quick successive variants. Unlike the independent efforts of early viruses, these variants suggest an increasing level of coordination among worm creators. Fourth, recent worms have shown capabilities to spread faster and exploit more infection vectors. This trend implies a more urgent need for automated, coordinated protection measures. Finally, more dangerous payloads are becoming commonplace. This suggests that worm creators are using worms for other objectives than simply infection, such as data theft and setting up denial of service networks.
Chitin and Chitinases (1999)

Native, industrial and fossil chitins.- Chitin synthesis.- Biochemistry of chitin synthase.- Chitin biosynthesis and structural organizationin vivo.- Chitin synthases in yeast and fungi.- Function of chitin oligosaccharides in plant and animal development.- Molecular and biochemical aspects of chitin synthesis inhibition.- Characteristics of chitin-binding proteins from streptomycetes.- Chitinases.- Biochemistry of chitinases.- The structure and action of chitinases.- Classification of chitinase modules.- Aggressive and defensive roles for chitinases.- Chitinases in biological control.- Host-parasite interactions: elicitation of defense responses in plants with chitosan.- Inhibitors of chitinases.- Mammalian chitinase-like proteins.- Chitinases of human parasites and their implications as antiparasitic targets.- Analytical biochemistry and clinical significance of N-acetyl-ss-D-glucosaminidase and related enzymes.- Exogenous chitosans.- Biochemistry, histology and clinical uses of chitins and chitosans in wound healing.- Veterinary practice with chitin and chitosan.- Immunological aspects of chitin and chitin derivatives administered to animals.- Clinical and biochemical evaluation of chitosan for hypercholesterolemia and overweight control.- Microparticulate drug delivery systems.- Antimicrobial action of exogenous chitosan.
Threading analysis suggests that the obese gene product may be a helical cytokine (1995)

The ob gene encodes a protein that, in mutant form, is associated with obesity and type II diabetes in mice. Sequence analysis has revealed no similarities to other proteins, however, and no clues as to possible functions. The possibility nonetheless remains that ob is functionally or ancestrally related to other proteins, whose sequences are divergent to the point that only a comparison of three-dimensional structures might detect relationship. To explore this possibility, we conduct a 'threading' search of a 3-dimensional structure database, to determine whether the ob protein might adopt a fold similar to any known structure. This search reveals that the ob sequence is compatible, at a significance level of P < 0.05, with structures from the family of helical cytokines that includes interleukin-2 and growth hormone. A structural model of ob based upon these results is physically and biologically plausible and leads to testable predictions, including the prediction that ob may activate the JAK-STAT pathway, via binding to a receptor resembling those of the cytokine family.
Microarray Analysis of Papillary Thyroid Cancers in Korean (2010)

These findings demonstrate both similarities and differences between our results and previous reports. In Korean cases of PTC, Foxa2 activity was reduced with its cytoplasmic accumulation. Further studies are needed to confirm the relationship between FOXA2 and BRAF mutations in Korean cases of PTC.
Evidence for cytokine-inducible nitric oxide synthesis from L-arginine in patients receiving interleukin-2 therapy. (1992)

An interferon-gamma, tumor necrosis factor, and interleukin-1-inducible, high-output pathway synthesizing nitric oxide (NO) from L-arginine was recently identified in rodents. High-dose interleukin-2 (IL-2) therapy is known to induce the same cytokines in patients with advanced cancer. Therefore, we examined renal cell carcinoma (RCC; n = 5) and malignant melanoma (MM; n = 7) patients for evidence of cytokine-inducible NO synthesis. Activity of this pathway was evaluated by measuring serum and urine nitrate (the stable degradation product of NO) during IL-2 therapy. IL-2 administration caused a striking increase in NO generation as reflected by serum nitrate levels (10- and 8-fold increase [P less than 0.001, P less than 0.003] for RCC and MM patients, respectively) and 24-h urinary nitrate excretion (6.5- and 9-fold increase [both P less than 0.001] for RCC and MM patients, respectively). IL-2-induced renal dysfunction made only a minor contribution to increased serum nitrate levels. Metabolic tracer studies using L-[guanidino-15N2]arginine demonstrated that the increased nitrate production was derived from a terminal guanidino nitrogen atom of L-arginine. Our results showing increased endogenous nitrate synthesis in patients receiving IL-2 demonstrate for the first time that a cytokine-inducible, high-output L-arginine/NO pathway exists in humans.
Enzymatic Glycoprotein Synthesis:  Preparation of Ribonuclease Glycoforms via Enzymatic Glycopeptide Condensation and Glycosylation (1997)

In order to study the effects carbohydrates have on glycoprotein structure and function, it is imperative to be able to synthesize the appropriate natural and non-natural glycoprotein variants in a single form. Because the available in vivo techniques provide only heterogeneous mixtures of different glycoforms, enzymatic in vitro methodologies have been pursued. Using the N-glycoprotein RNase B as a model system, the oligosaccharide was removed leaving only the N-acetylglucosamine as a “tag” to the site of glycosylation. Glycosyltransferases were then used to build a unique carbohydrate moiety. A new RNase glycoform containing the branched oligosaccharide, sialyl Lewis X or the Hg derivative, was synthesized enzymatically to demonstrate the feasibility of the method. In addition, the monoglycosylated protein was digested into several smaller pieces by subtilisin BPN‘. These fragments were religated by subtilisin 8397 to the full length RNase by addition of glycerol; this method points to a new chemical-enzymatic process for the synthesis of glycoproteins using synthetic peptides and glycopeptides as substrates for enzymatic ligation followed by further enzymatic glycosylations.
Sugar transport. The crr mutation: its effect on repression of enzyme synthesis. (1976)

The accompanying report describes phosphotransferase system-mediated repression in mutants of Salmonella typhimurium and Escherichia coli defective in Enzyme I and histidine-containing phosphate carrier protein (HPr), the general proteins of the phosphotransferase system (PTS). Such repression prevented the cells from synthesizing the catabolic systems required for utilization of the non-PTS compounds glycerol, maltose, melibiose, mannose 6-phosphate, and alpha-glycerol phosphate. This defect can be overcome by introducing a single mutation, designated crr, into the pts mutants. The pts crr double mutants can be induced to synthesize the non-PTS catabolic systems and can therefore grow on the non-PTS sugars. The crr gene is closely linked to but not part of the pts operon, and may be a regulatory gene for the operon. Assay of the PTS proteins in crr mutants showed that the only component detectably affected was a sugar-specific protein of the PTS, Factor IIIG1c, involved in the phsophorylation of glucose (and methyl alpha-glucoside). In some crr mutants Factor IIIG1c was not detected, whereas in others it was present at reduced levels. Thus the crr gene appears to code for or regulate the synthesis of this protein. In addition to the general crr mutants, several classes of sugar-specific crr mutants were isolated. For example, maltose-, melibiose-, and glycerol-specific crr mutants were isolated, each being inducible for the corresponding catabolic enzyme system but not for the others. Unlike the general crr gene, the sugar-specific crr genes do not map near the pts operon.