gebhart/patrepeval huggingface dataset:
TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support (2011)

As the relevant literature and the number of experiments increase at a super linear rate, databases that curate and collect experimentally verified microRNA (miRNA) targets have gradually emerged. These databases attempt to provide efficient access to this wealth of experimental data, which is scattered in thousands of manuscripts. Aim of TarBase 6.0 (http://www.microrna.gr/tarbase) is to face this challenge by providing a significant increase of available miRNA targets derived from all contemporary experimental techniques (gene specific and high-throughput), while incorporating a powerful set of tools in a user-friendly interface. TarBase 6.0 hosts detailed information for each miRNA-gene interaction, ranging from miRNA- and gene-related facts to information specific to their interaction, the experimental validation methodologies and their outcomes. All database entries are enriched with function-related data, as well as general information derived from external databases such as UniProt, Ensembl and RefSeq. DIANA microT miRNA target prediction scores and the relevant prediction details are available for each interaction. TarBase 6.0 hosts the largest collection of manually curated experimentally validated miRNA-gene interactions (more than 65,000 targets), presenting a 16.5-175-fold increase over other available manually curated databases.
Sub-Hertz Optical Frequency Comparisons between Two Trapped<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mmultiscripts><mml:mi>Yb</mml:mi><mml:none/><mml:mo>+</mml:mo><mml:mprescripts/><mml:none/><mml:mn>171</mml:mn></mml:mmultiscripts></mml:math>Ions (2005)

We compare the frequencies of the 6s2S(1/2)(F = 0)-->5d2D(3/2)(F = 2) reference transition in 171Yb+ for two single ions stored in independent traps. The quadrupole moment of the 5d2D(3/2) state is measured to be 9.32(48) x 10(-40) C m2 and from the quadratic Stark shift the relevant scalar and tensor polarizabilities are determined to be alphaS(S(1/2)) - alphaS(D(3/2)) = -6.9(1.4) x 10(-40) J m2/V2 and alphaT(D(3/2)) = -13.6(2.2) x 10(-40) J m2/V2, respectively. In the absence of external perturbations we find a mean frequency difference between the two trapped ions of 0.26(42) Hz, corresponding to a relative difference of 3.8(6.1) x 10(-16). This is comparable to the agreement found in the most accurate comparisons between cesium fountain clocks.
Truncated Structural Variants of Lipoarabinomannan in Ethambutol Drug-resistant Strains of Mycobacterium smegmatis (1996)

The anti-tuberculosis drug, ethambutol (Emb), was previously shown to inhibit the synthesis of arabinans of both the cell wall arabinogalactan (AG) and lipoarabinomannan (LAM) of Mycobacterium tuberculosis and other mycobacteria. However, an Emb-resistant mutant, isolated by consecutive passage of the Mycobacterium smegmatis parent strain in media containing increasing concentrations of Emb, while synthesizing a normal version of AG, produced truncated forms of LAM when maintained on 10 microg/ml Emb (Mikusová, K., Slayden, R. A., Besra, G. S., and Brennan, P. J. (1995) Antimicrob. Agents Chemother. 39, 2482-2489). We have now isolated and characterized the truncated LAMs made by both the resistant mutant and a recombinant strain transfected with a plasmid containing the emb region from Mycobacterium avium which encodes for Emb resistance. By chemical analysis, endoarabinanase digestion, high pH anion exchange chromatography, and mass spectrometry analyses, truncation was demonstrated as primarily a consequence of selective and partial inhibition of the synthesis of the linear arabinan terminal motif, which constitutes a substantial portion of the arabinan termini in LAM but not of AG. However, at higher concentrations, Emb also affected the general biosynthesis of arabinan destined for both AG and LAM, resulting in severely truncated LAM as well as AG with a reduced Ara:Gal ratio. The results suggested that Emb exerts its antimycobacterial effect by inhibiting an array of arabinosyltransferases involved in the biosynthesis of arabinans unique to the mycobacterial cell wall. It was further concluded that the uniquely branched terminal Ara6 motif common to both AG and LAM is an essential structural entity for a functional cell wall and, consequently, that the biosynthetic machinery responsible for its synthesis is the effective target of Emb in its role as a potent anti-tuberculosis drug.
Difunctional Initiators Based on 1,3-Diisopropenylbenzene. 3. Synthesis of a Pure Dilithium Adduct and Its Use as Difunctional Anionic Polymerization Initiator (1996)

The addition reaction of tert-butyllithium (t-BuLi) to 1,3-diisopropenylbenzene (1,3-DIB) has been studied. Under optimized conditions, i.e., reaction in cyclohexane at −20 °C and dropwise addition of 1,3-DIB to a 1:1 t-BuLi−triethylamine (Et3N) complex followed by a 1 h postreaction period, a pure diadduct is formed without concomitant oligomerization of 1,3-DIB. The behavior of this diadduct has been investigated, in apolar and polar solvents; triblock copolymers have been prepared and found to have interesting mechanical properties.
Developing on-line help: a practical approach (2002)

The author describes a pragmatic and simple process for creating on-line help for an Operating System/2 (OS/2) presentation manager (PM) application. He defines on-line help, describes how to create an outline as a roadmap to link help information to an application, provides an example of an outline that illustrates typical help information, and explains how a particular tool was used to create the on-line help.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
In vitro Evaluation of Buffy-Coat-Derived Platelet Concentrates Stored in a Synthetic Medium (1991)

Human blood platelets, prepared by the buffy-coat method, were prepared and stored in different synthetic media. In a synthetic medium based on gluconate, acetate and citrate (GAC), the pH was 6.8 on day 6. This medium was chosen for further evaluation. The total platelet count and the leukocyte contamination were significantly lower in the platelet concentrates (PCs) prepared in GAC compared to PCs prepared in plasma. Platelets stored in plasma or in GAC were equally functional when tested for aggregation and adenosine triphosphate (ATP) secretion. Only stimuli that act through the arachidonic-acid pathway induced a lower platelet response in GAC. Platelet morphology was quantified by measuring the difference in light transmission during stirring at different rates in an aggregometer; no significant differences for platelets stored in GAC as compared to plasma were observed. Activation of platelets was measured by binding of monoclonal antibodies (McAb) against the Gp Ilb/IIIa complex and against activation-dependent antigens (GMP140 from the a-granules and a 53-kD glycoprotein from the lysosomal granules). There was no difference in binding of these McAb between platelets prepared and stored in plasma or GAC. We conclude that platelets prepared by the buffy-coat method and stored in GAC have the same in vitro qualitities as platelets stored in plasma, except for the lower aggregation response by the archidonic-acid pathway. This is probably due to an acetate-induced decrease in intracellular pH.
Inherently safe backup routing with BGP (2002)

The Internet consists of a large number of autonomous systems (ASes) that exchange routing information using the border gateway protocol (BGP). Each AS applies local policies for selecting routes and propagating routes to others, with important implications for the reliability and stability of the global system. In and of itself, BGP does not ensure that every pair of hosts can communicate. In addition, routing policies are not guaranteed be safe, and may cause protocol divergence. Backup routing is often used to increase the reliability of the network under link and router failures, at the possible expense of safety. This paper presents a general model for backup routing that increases network reliability while allowing each AS to apply local routing policies that are consistent with the commercial relationships it has with its neighbors. In addition, our model is inherently safe in the sense that the global system remains safe under any combination of link and router failures. Our model and the proof of inherent safety are cast in terms of the stable paths problem, a static formalism that captures the semantics of interdomain routing policies. Then, we describe how to realize our model in BGP with locally-implementable routing policies. To simplify the specification of local policies, we propose a new BGP attribute that conveys the avoidance level of a route. We also describe how to realize these policies without modification to BGP by using the BGP community attribute.
Disruption of BMP signals in embryonic Xenopus ectoderm leads to direct neural induction. (1995)

Bone morphogenetic proteins (BMPs), which have been implicated in the patterning of mesoderm, are members of the transforming growth factor-beta (TGF-beta) superfamily. We have investigated the roles of Xenopus BMP-7 (XBMP-7) and BMP-4 (XBMP-4), and activin (another TGF-beta-related molecule) in early development by generating dominant-negative versions of these growth factors. Mutations were generated by altering the cleavage sites that are required for maturation of the active dimeric forms of XBMP-7, XBMP-4, and activin. These mutant constructs, designated Cm-XBMP-7, Cm-XBMP-4, and Cm-activin, result in polypeptides that allow for dimerization of the subunits, but are incapable of maturation. Expression of Cm-XBMP-7 and Cm-XBMP-4, but not Cm-activin, in the ventral marginal zone of the Xenopus embryo results in the development of a secondary axis, similar to that seen by ectopic expression of the truncated BMP receptor. These results suggest that the cleavage mutants interfere with BMP signaling during mesodermal patterning. We also found that expression of Cm-XBMP-7 or Cm-XBMP-4 in animal cap ectoderm directly induces neuroectoderm. The neural induction was specific for Cm-XBMP-7 and Cm-XBMP-4 because ectopic expression of Cm-activin or Vg-1 did not mimic the same phenotype. Molecular study of neural patterning by Cm-XBMP-7 and Cm-XBMP-4 revealed that only anterior neuroectodermal markers are expressed in response to these Cm-XBMPs. These results suggest that the BMPs are involved in the specification of ectoderm in Xenopus development, and that neural induction requires the removal of BMP signals in the ectoderm. We propose that neural induction occurs by a default mechanism, whereby the inhibition of BMP signaling is required for the conversion of ectoderm to neuroectoderm in the developing Xenopus embryo.
ERK MAP kinase in G<sub>1</sub> cell cycle progression and cancer (2006)

The extracellular-signal-regulated kinase (ERK) mitogen-activated protein (MAP) kinase signaling pathway plays an important role in various cellular responses, including cell proliferation, cell differentiation and cell survival. Recent studies have identified a number of Ras/ERK signaling-related proteins, such as scaffold proteins and inhibitors. These proteins modulate ERK signaling and thereby could give variations in ERK signaling outputs that regulate cell fate decisions. Here we focus on the role of ERK signaling in cell cycle progression from G0/G1 to S phase and cancer.
Isolation and Characterization of Phenol-Degrading Denitrifying Bacteria (1998)

ABSTRACT Phenol is a man-made as well as a naturally occurring aromatic compound and an important intermediate in the biodegradation of natural and industrial aromatic compounds. Whereas many microorganisms that are capable of aerobic phenol degradation have been isolated, only a few phenol-degrading anaerobic organisms have been described to date. In this study, three novel nitrate-reducing microorganisms that are capable of using phenol as a sole source of carbon were isolated and characterized. Phenol-degrading denitrifying pure cultures were obtained by enrichment culture from anaerobic sediments obtained from three different geographic locations, the East River in New York, N.Y., a Florida orange grove, and a rain forest in Costa Rica. The three strains were shown to be different from each other based on physiologic and metabolic properties. Even though analysis of membrane fatty acids did not result in identification of the organisms, the fatty acid profiles were found to be similar to those of Azoarcus species. Sequence analysis of 16S ribosomal DNA also indicated that the phenol-degrading isolates were closely related to members of the genus Azoarcus . The results of this study add three new members to the genus Azoarcus , which previously comprised only nitrogen-fixing species associated with plant roots and denitrifying toluene degraders.
RISE: Randomized Input Sampling for Explanation of Black-box Models (2018)

Deep neural networks are being used increasingly to automate data analysis and decision making, yet their decision-making process is largely unclear and is difficult to explain to the end users. In this paper, we address the problem of Explainable AI for deep neural networks that take images as input and output a class probability. We propose an approach called RISE that generates an importance map indicating how salient each pixel is for the model's prediction. In contrast to white-box approaches that estimate pixel importance using gradients or other internal network state, RISE works on black-box models. It estimates importance empirically by probing the model with randomly masked versions of the input image and obtaining the corresponding outputs. We compare our approach to state-of-the-art importance extraction methods using both an automatic deletion/insertion metric and a pointing metric based on human-annotated object segments. Extensive experiments on several benchmark datasets show that our approach matches or exceeds the performance of other methods, including white-box approaches. Project page: http://cs-people.bu.edu/vpetsiuk/rise/
Attachment of <i>Helicobacter pylori</i> to Human Gastric Epithelium Mediated by Blood Group Antigens (1993)

Helicobacter pylori is associated with development of gastritis, gastric ulcers, and adenocarcinomas in humans. The Lewis(b) (Le(b)) blood group antigen mediates H. pylori attachment to human gastric mucosa. Soluble glycoproteins presenting the Leb antigen or antibodies to the Leb antigen inhibited bacterial binding. Gastric tissue lacking Leb expression did not bind H. pylori. Bacteria did not bind to Leb antigen substituted with a terminal GalNAc alpha 1-3 residue (blood group A determinant), suggesting that the availability of H. pylori receptors might be reduced in individuals of blood group A and B phenotypes, as compared with blood group O individuals.
Filtration Shell Mediated Power Density Independent Orthogonal Excitations–Emissions Upconversion Luminescence (2016)

Abstract Lanthanide doped core–multishell structured NaGdF 4 :Yb,Er@NaYF 4 :Yb@NaGdF 4 :Yb,Nd@NaYF 4 @NaGdF 4 :Yb,Tm@NaYF 4 nanoparticles with power‐density independent orthogonal excitations‐emissions upconversion luminescence (UCL) were fabricated for the first time. The optical properties of these core–multishell structured nanoparticles were related to the absorption filtration effect of the NaGdF 4 :Yb,Tm layer. By tuning the thickness of the filtration layer, the nanoparticles can exhibit unique two independent groups of UCL: Tm 3+ prominent UV/blue (UV=ultraviolet) UCL under the excitation at 980 nm and Er 3+ prominent green/red UCL under the excitation at 796 nm. The filtration‐shell mediated orthogonal excitations‐emissions UCL are power‐density independent. As a proof of concept, the core–multishell nanoparticles are used in multi‐dimensional security design and imaging‐guided combined photodynamic therapy and chemotherapy.
Silencing the expression of connexin 43 decreases inflammation and joint destruction in experimental arthritis (2012)

The objective of the present study was to determine whether the expression of connexin 43 (Cx43) effected on inflammatory conditions in rat fibroblast-like synoviocytes (FLS) and on rat model of rheumatoid arthritis (RA). The expression of Cx43 in rat FLS stimulated with lipopolysaccharide (LPS) was confirmed by real-time reverse transcriptase polymerase chain reaction (RT-PCR). The effects of small-interfering RNA targeting Cx43 (siCx43) on pro-inflammatory cytokines and chemokine were assessed by real-time RT-PCR and enzyme-linked immunosorbent assay (ELISA). The therapeutic and side effects of siCx43 in a rat model of collagen-induced arthritis (CIA) were examined by in vivo electroporation method. LPS markedly enhanced Cx43 gene expression in rat FLS, with transfection of siCx43 suppressing the over-expression of pro-inflammatory cytokines and the chemokine. Treatment of CIA rats with siCx43 significantly ameliorated paw swelling, and significantly reduced histological arthritis scores and radiographic scores. In histological appearance of rat ankle joints, siCx43 treatment significantly decreased the number of tartrate-resistant acid phosphatase (TRAP)-positive (osteoclast-like) cells. These findings indicated that siCx43 had anti-inflammatory effects in rat FLS and efficiently inhibited the development of CIA. Cx43 may play an important role in the pathophysiology of RA, and may be a potential target molecule for novel RA therapies.
Synthesis and Characterization of Cyanate Ester Functional Benzoxazine and Its Polymer (2015)

The first benzoxazine incorporating cyanate ester group in its structure has been synthesized. The polymerization process investigated by differential scanning calometry (DSC) exhibits two clearly separated exotherm maxima, corresponding to cyanate ester trimerization and benzoxazine, respectively. The nature of each exotherm is studied by Fourier transform infrared spectroscopy (FT-IR). The activation energies for cyanate ester trimerization and benzoxazine ring-opening polymerization are determined by both Kissinger's and Ozawa's methods. Furthermore, both exothermic temperatures observed are lower than those of the published values of benzoxazine and dicyanate ester blends. Thermal properties such as glass transition temperature and char yield are studied by thermogravimetric analysis (TGA) and dynamic mechanical analysis (DMA). Those properties are found to be outstanding compared to the reported properties of general benzoxazine resins and polymerized blends of benzoxazine and dicyanate ester, offering a polymeric matrix for composite satisfying many requirements for such a material.
Pancancer analysis of DNA methylation-driven genes using MethylMix (2015)

Aberrant DNA methylation is an important mechanism that contributes to oncogenesis. Yet, few algorithms exist that exploit this vast dataset to identify hypo- and hypermethylated genes in cancer. We developed a novel computational algorithm called MethylMix to identify differentially methylated genes that are also predictive of transcription. We apply MethylMix to 12 individual cancer sites, and additionally combine all cancer sites in a pancancer analysis. We discover pancancer hypo- and hypermethylated genes and identify novel methylation-driven subgroups with clinical implications. MethylMix analysis on combined cancer sites reveals 10 pancancer clusters reflecting new similarities across malignantly transformed tissues.
"On-the-fly" voxelization for 6 degrees-of-freedom haptic virtual sculpting (2006)

Virtual sculpting allows users to created 3-dimensional artworks and prototypes by using a 3D input device to control a sculpting tool. While existing methods allow a range of sculpting effects, they are limited to simplistic polyhedral tool shapes (usually spherical or point-based) or complex voxel-based tools that can only be applied at fixed orientations.This paper presents a model for real-time voxel-based virtual sculpting that performs on-the-fly voxelization of a polyhedral tool to determine the region of the sculpture to modify. This allows the tool to take on a variety of shapes ranging from simple to complex polyhedra. It also allows the tool to be applied to the sculpture at any orientation. The algorithm for voxelization is a seed-filling algorithm that features several heuristics that enhance the performance, allowing sculpting to occur in real-time. The model provides 6-degrees-of-freedom haptic feedback allowing users to feel what they are sculpting. The scene is visualized using a localized Marching Cues algorithm. A working implementation of the model is presented and discussed along with some images of sculptures produced from this implementation.
Designing and screening of universal drug from neem (Azadirachta indica) and standard drug chemicals against influenza virus nucleoprotein (2016)

The compound Hyperoside from neem leaf extract along with drugs LGH, Naproxen, BMS-885838, and BMS-883559 showed best interactions with conserved residues of nucleoprotein. So these compounds have been identified for their potential against influenza strains to be utilized as a universal drug.
Effects of megestrol acetate in patients with cancer anorexia‑cachexia syndrome – a systematic review and meta‑analysis (2008)

Compared to placebo, MA reduces the symptoms of ACS, with no effect on survival. The beneficial effect of MA on the overall quality of life has not been confirmed. In identified studies the effect of MA and glucocorticosteroids on anorexia and cachexia is similar. The estimation of the treatment utility in ACS depends on the weight attributed to discomfort caused by symptoms, adverse effects of the drugs and the treatment cost. Because of the low quality of the included studies a new randomized controlled trial is needed for valid assessment of the effects of MA.
Nitrous Oxide Decomposition and its Reaction with Atomic Oxygen (1973)

Abstract The thermal decomposition of nitrous oxide (N2 0) was studied in a single-pulse shock tube in the temperature range 1300 to 1950 ° K at a total concentration of 2 x 10− 5 moles/ cc. The Arrhenius rate constant for the reaction N2O + M→ N2 O+ M is given by K1 = 1013.1 exp (-44,100/ RT) a/ mole sec. The ratio of the rate constants for the two competing secondary reactions, N2O + O→ N2 + O2 and N2O + O → NO + NO was also determined and was found to be K3 / K2 The overall rate of N2 O decomposition is also discussed and the results of previous investigators are compared to the findings reported here
An Electric Hygrometer and its Application to Radio-Meteorography* (1938)

*Publication Approved by the Director of the National Bureau of Standards of the U. S. Department of Commerce. Paper read at Washington meeting, A. M. Soc., April, 1938.
Radioimmunoassay of Cannabinoid Compounds (1979)

Radioimmunoassay (or RIA) was first introduced as an ananalytical technique in 1959. Since then it has played an increasingly important role in the quantitative analysis of hormones and drugs. Much of the recent rapid progress in endocrinology may in fact be attributed to the availability of this sensitive and accurate method for quantitation of steroidal and protein/peptide hormones. Since radioimmunoassay has permitted the quantitation of substances present in concentrations as low as a few pg/ml of a biological fluid, and since the inherent selectivity of antibodies often make sample preparation requirements minimal and assay methodology simple, RIA has naturally been considered as a means for measuring blood levels of cannabinoid compounds. A number of investigators have been interested in the development of RIA procedures for the cannabinoids. Before beginning a discussion of the RIA of cannabinoid compounds, let us briefly review some general principles of radioimmunoassay. Figure 1 illustrates the