gebhart/patrepeval huggingface dataset:
Graph2Seq: Graph to Sequence Learning with Attention-based Neural Networks (2018)

The celebrated Sequence to Sequence learning (Seq2Seq) technique and its numerous variants achieve excellent performance on many tasks. However, many machine learning tasks have inputs naturally represented as graphs; existing Seq2Seq models face a significant challenge in achieving accurate conversion from graph form to the appropriate sequence. To address this challenge, we introduce a novel general end-to-end graph-to-sequence neural encoder-decoder model that maps an input graph to a sequence of vectors and uses an attention-based LSTM method to decode the target sequence from these vectors. Our method first generates the node and graph embeddings using an improved graph-based neural network with a novel aggregation strategy to incorporate edge direction information in the node embeddings. We further introduce an attention mechanism that aligns node embeddings and the decoding sequence to better cope with large graphs. Experimental results on bAbI, Shortest Path, and Natural Language Generation tasks demonstrate that our model achieves state-of-the-art performance and significantly outperforms existing graph neural networks, Seq2Seq, and Tree2Seq models; using the proposed bi-directional node embedding aggregation strategy, the model can converge rapidly to the optimal performance.
SNJ‐1945, a calpain inhibitor, protects SH‐SY5Y cells against MPP+ and rotenone (2013)

Complex pathophysiology of Parkinson's disease involves multiple CNS cell types. Degeneration in spinal cord neurons alongside brain has been shown to be involved in Parkinson's disease and evidenced in experimental parkinsonism. However, the mechanisms of these degenerative pathways are not well understood. To unravel these mechanisms SH-SY5Y neuroblastoma cells were differentiated into dopaminergic and cholinergic phenotypes, respectively, and used as cell culture model following exposure to two parkinsonian neurotoxicants MPP(+) and rotenone. SNJ-1945, a cell-permeable calpain inhibitor was tested for its neuroprotective efficacy. MPP(+) and rotenone dose-dependently elevated the levels of intracellular free Ca(2+) and induced a concomitant rise in the levels of active calpain. SNJ-1945 pre-treatment significantly protected cell viability and preserved cellular morphology following MPP(+) and rotenone exposure. The neurotoxicants elevated the levels of reactive oxygen species more profoundly in SH-SY5Y cells differentiated into dopaminergic phenotype, and this effect could be attenuated with SNJ-1945 pre-treatment. In contrast, significant levels of inflammatory mediators cyclooxygenase-2 (Cox-2 and cleaved p10 fragment of caspase-1) were up-regulated in the cholinergic phenotype, which could be dose-dependently attenuated by the calpain inhibitor. Overall, SNJ-1945 was efficacious against MPP(+) or rotenone-induced reactive oxygen species generation, inflammatory mediators, and proteolysis. A post-treatment regimen of SNJ-1945 was also examined in cells and partial protection was attained with calpain inhibitor administration 1-3 h after exposure to MPP(+) or rotenone. Taken together, these results indicate that calpain inhibition is a valid target for protection against parkinsonian neurotoxicants, and SNJ-1945 is an efficacious calpain inhibitor in this context. SH-SY5Y cells, differentiated as dopaminergic (TH positive) and cholinergic (ChAT positive), were used as in vitro models for Parkinson's disease. MPP+ and rotenone induced up-regulation of calpain, expression, and activity as a common mechanism of neurodegeneration. SNJ-1945, a novel calpain inhibitor, protected both the cell phenotypes against MPP+ and rotenone.
Control of oskar mRNA translation by Bruno in a novel cell-free system from Drosophila ovaries (2000)

The coupled regulation of oskar mRNA localization and translation in time and space is critical for correct anteroposterior patterning of the Drosophila embryo. Localization-dependent translation of oskar mRNA, a mechanism whereby oskar RNA localized at the posterior of the oocyte is selectively translated and the unlocalized RNA remains in a translationally repressed state, ensures that Oskar activity is present exclusively at the posterior pole. Genetic experiments indicate that translational repression involves the binding of Bruno protein to multiple sites, the Bruno Response Elements (BRE), in the 3' untranslated region (UTR) of oskar mRNA. We have established a cell-free translation system derived from Drosophila ovaries, which faithfully reproduces critical features of mRNA translation in vivo, namely cap structure and poly(A) tail dependence. We show that this ovary extract, containing endogenous Bruno, is able to recapitulate oskar mRNA regulation in a BRE-dependent way. Thus, the assembly of a ribonucleoprotein (RNP) complex leading to the translationally repressed state occurs in vitro. Moreover, we show that a Drosophila embryo extract lacking Bruno efficiently translates oskar mRNA. Addition of recombinant Bruno to this extract establishes the repressed state in a BRE-dependent manner, providing a direct biochemical demonstration of the critical role of Bruno in oskar mRNA translation. The approach that we describe opens new avenues to investigate translational regulation in Drosophila oogenesis at a biochemical level.
Urokinase infusion of chronically occluded femoropopliteal gortex™ bypass grafts via the popliteal approach (1991)

Thrombolysis of two occluded above-knee femoropopliteal Gortex bypass grafts utilizing the popliteal approach for catheter placement was successfully performed without complication. In both cases, the proximal anastomoses of the graft could not be identified. A percutaneous popliteal approach was used for catheter placement and delivery of urokinase. Angioplasty was performed on the unveiled stenoses that, presumptively, led to graft closure. Selective thrombolysis via catheter placed from popliteal approach is a new technique for recanalization of occluded femoropopliteal bypass grafts and warrants further investigation.
Clustering of Microarray Data Reveals Transcript Patterns Associated with Somatic Embryogenesis in Soybean, (2003)

Globular somatic embryos can be induced from immature cotyledons of soybean (Glycine max L. Merr. cv Jack) placed on high levels of the auxin 2,4-dichlorophenoxyacetic acid (2,4-D). Somatic embryos develop from the adaxial side of the cotyledon, whereas the abaxial side evolves into a callus. Using a 9,280-cDNA clone array, we have compared steady-state RNA from the adaxial side from which embryos develop and from the abaxial callus at five time points over the course of the 4 weeks necessary for the development of globular embryos. In a second set of experiments, we have profiled the expression of each clone in the adaxial side during the same period. A total of 495 genes differentially expressed in at least one of these experiments were grouped according to the similarity of their expression profiles using a nonhierarchical clustering algorithm. Our results indicate that the appearance of somatic embryos is preceded by dedifferentiation of the cotyledon during the first 2 weeks on auxin. Changes in mRNA abundance of genes characteristic of oxidative stress and genes indicative of cell division in the adaxial side of the cotyledons suggest that the arrangement of the new cells into organized structures might depend on a genetically controlled balance between cell proliferation and cell death. Our data also suggest that the formation of somatic globular embryos is accompanied by the transcription of storage proteins and the synthesis of gibberellic acid.
Derivatives of imidazole. III. Synthesis and pharmacological activities of nitriles, amides, and carboxylic acid derivatives of imidazo[1,2-a]pyridine (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDerivatives of imidazole. III. Synthesis and pharmacological activities of nitriles, amides, and carboxylic acid derivatives of imidazo[1,2-a]pyridineLuigi Almirante, Alfonso Mugnaini, Pierluigi Rugarli, Afro Gamba, Enzo Zefelippo, Nicola De Toma, and Walter MurmannCite this: J. Med. Chem. 1969, 12, 1, 122–126Publication Date (Print):January 1, 1969Publication History Published online1 May 2002Published inissue 1 January 1969https://pubs.acs.org/doi/10.1021/jm00301a031https://doi.org/10.1021/jm00301a031research-articleACS PublicationsRequest reuse permissionsArticle Views842Altmetric-Citations26LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Antibody-Drug Conjugates of Calicheamicin Derivative: Gemtuzumab Ozogamicin and Inotuzumab Ozogamicin (2011)

Antibody-drug conjugates (ADC) are an attractive approach for the treatment of acute myeloid leukemia and non-Hodgkin lymphomas, which in most cases, are inherently sensitive to cytotoxic agents. CD33 and CD22 are specific markers of myeloid leukemias and B-cell malignancies, respectively. These endocytic receptors are ideal for an ADC strategy because they can effectively carry the cytotoxic payload into the cell. Gemtuzumab ozogamicin (GO, Mylotarg) and inotuzumab ozogamicin consist of a derivative of calicheamicin (a potent DNA-binding cytotoxic antibiotic) linked to a humanized monoclonal IgG4 antibody directed against CD33 or CD22, respectively. Both of these ADCs have a target-mediated pharmacokinetic disposition. GO was the first drug to prove the ADC concept in the clinic, specifically in phase II studies that included substantial proportions of older patients with relapsed acute myeloid leukemia. In contrast, in phase III studies, it has thus far failed to show clinical benefit in first-line treatment in combination with standard chemotherapy. Inotuzumab ozogamicin has shown remarkable clinical activity in relapsed/refractory B-cell non-Hodgkin lymphoma, and it has started phase III evaluation. The safety profile of these ADCs includes reversible myelosuppression (especially neutropenia and thrombocytopenia), elevated hepatic transaminases, and hyperbilirubinemia. There have been postmarketing reports of hepatotoxicity, especially veno-occlusive disease, associated with GO. The incidence is ~2%, but patients who undergo hematopoietic stem cell transplantation have an increased risk. As we steadily move toward the goal of personalized medicine, these kinds of agents will provide a unique opportunity to treat selected patient subpopulations based on the expression of their specific tumor targets.
Evaluation ofSalmonella-VectoredCampylobacterPeptide Epitopes for Reduction ofCampylobacter jejuniin Broiler Chickens (2010)

Campylobacter is a leading cause of bacterial gastroenteritis in humans and is often linked to contaminated poultry products. Live Salmonella vectors expressing three linear peptide epitopes from Campylobacter proteins Cj0113 (Omp18/CjaD), Cj0982c (CjaA), and Cj0420 (ACE393) were administered to chicks by oral gavage on the day of hatch, and the chicks were challenged with Campylobacter jejuni on day 21. All three candidate vaccines produced consistent humoral immune responses with high levels of serum IgG and mucosal secretory IgA (sIgA), with the best response from the Cj0113 peptide-expressing vector. Campylobacter challenge following vaccination of three candidate vaccine groups decreased Campylobacter recovery from the ileum compared to that for controls on day 32. The Cj0113 peptide-expressing vector reduced Campylobacter to below detectable levels. The Salmonella-vectored Cj0113 subunit vaccine appears to be an excellent candidate for further evaluation as a tool for the reduction of Campylobacter in poultry for improved food safety.
Resolution of high and low affinity progesterone receptors from human breast carcinoma T47D cells. (1988)

Each of four independent experimental approaches showed that human breast carcinoma T47D cells contain both high and low affinity progesterone receptors. (i) Equilibrium-specific [3H]progesterone binding to adherent cultured cells revealed dissociation constants (Kd) of 1.5 and 60 nM and 0.33 and 2.4 X 10(6) sites/cell, respectively. Both the high and low affinity receptors were specific for progestins as demonstrated by steroid binding competition studies conducted at 5 and 50 nM [3H]progesterone. (ii) Equilibrium [3H]progesterone binding to the resolved soluble and particulate fractions from a cell homogenate sedimented at 40,000 X g.min revealed Kd = 1.4 nM high affinity binding sites exclusively in the supernatant fraction and Kd = 24 nM low affinity sites exclusively in the particulate fraction. Extraction of the particulate fraction with a high ionic strength buffer solubilized the low affinity receptors stoichiometrically; but once solubilized, they displayed Kd = 2.4 nM high affinity progesterone binding. Characterizations of 3H-ligand bound specifically to progesterone receptors in intact cells or resolved subcellular fractions revealed no [3H]progesterone metabolites that could account for the low affinity binding. (iii) Calculations based on the rate constants of [3H] progesterone association with or dissociation from adherent cells revealed the same dissociation constants for both high and low affinity binding as those determined by equilibrium measurements. (iv) Nonionic detergent extraction of cells incubated with a wide range of [3H]progesterone concentrations revealed high affinity progesterone binding to receptors in the detergent-soluble fraction and low affinity binding associated primarily with the particulate residue, consistent with the data on equilibrium progesterone binding to resolved cell homogenate fractions. The rate of extraction of the high affinity receptor-progesterone complex with nonionic detergent (t1/2 = 1 min at 0 degrees C) equaled the rate of extraction of a representative lysosomal enzyme, beta-acetylglucosaminidase.
Sindbis virus mutations which coordinately affect glycoprotein processing, penetration, and virulence in mice (1989)

Rapid penetration of baby hamster kidney cells was used as a selective pressure for the isolation of pathogenesis mutants of the S.A.AR86 strain of Sindbis virus. Unlike most Sindbis virus strains, S.A.AR86 is virulent in adult as well as neonatal mice. Two classes of mutants were defined. One class was attenuated in adult mice inoculated intracerebrally as well as in neonatal mice inoculated either intracerebrally or subcutaneously. Sequence analysis of the glycoprotein genes of the parent virus and three such mutant strains revealed a single point mutation which resulted in an amino acid change at position 1 in the E2 glycoprotein. The change from a serine in S.A.AR86 to an asparagine in the mutants created a new site for N-linked glycosylation which appeared to be utilized. This mutation did not retard release of infectious particles; however, mutant virions contained the E2 precursor protein (PE2) rather than the E2 glycoprotein itself. The mutants also lost the ability to bind two E2-specific monoclonal antibodies, R6 and R13. A second class of mutants was attenuated in neonatal mice upon subcutaneous inoculation but remained virulent in adults and in neonates when inoculated intracerebrally. Sequence analysis of three such strains revealed the substitution of an arginine residue for a serine at position 114 in the E2 glycoprotein. Reactivity with monoclonal antibodies R6 and R13 was reduced, yet members of this mutant class were more susceptible than S.A.AR86 to neutralization by these antibodies.
Multi-training sensor networks with bipartite conflict graphs (2006)

Due to their potential applications in various situations such as battlefield communications, emergency relief, environmental monitoring, and other special-purpose operations, wireless sensor networks have recently emerged as a new and exciting research area that has attracted a good deal of well-deserved attention in the literature. In this work we take the view that a sensor network consists of a set of tiny sensors, massively deployed over a geographical area. The sensors are capable of performing processing, sensing and communicating with each other by radio links. Alongside, with the tiny sensors, more powerful devices referred as Aggregating and Forwarding Nodes, (AFN, for short) are also deployed. In support of their mission, the AFNs are endowed with a special radio interface for long distance communications, miniaturized GPS, and appropriate networking tools for data collection and aggregation. As a fundamental prerequisite for self-organization, the sensors need to acquire some form of location awareness. Since fine-grain location awareness usually assumes that the sensors are GPS-enabled, in the case of tiny sensors the best we can hope for is to endow them with coarse-grain location awareness. This task is referred to as training and its responsibility lies with the AFNs. However, due to the random deployment, some of the sensors fall under the coverage area of several AFNs, in which case the goal is for these sensors to acquire location information relative to all the covering AFNs. The corresponding task is referred to as multi-training.The main contribution of this work is to show that in case the conflict graphs of the AFN coverage is bipartite, multi-training can be completed very fast by a simple algorithm.
CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes (2015)

Genome editing tools such as the clustered regularly interspaced short palindromic repeat (CRISPR)-associated system (Cas) have been widely used to modify genes in model systems including animal zygotes and human cells, and hold tremendous promise for both basic research and clinical applications. To date, a serious knowledge gap remains in our understanding of DNA repair mechanisms in human early embryos, and in the efficiency and potential off-target effects of using technologies such as CRISPR/Cas9 in human pre-implantation embryos. In this report, we used tripronuclear (3PN) zygotes to further investigate CRISPR/Cas9-mediated gene editing in human cells. We found that CRISPR/Cas9 could effectively cleave the endogenous β-globin gene (HBB). However, the efficiency of homologous recombination directed repair (HDR) of HBB was low and the edited embryos were mosaic. Off-target cleavage was also apparent in these 3PN zygotes as revealed by the T7E1 assay and whole-exome sequencing. Furthermore, the endogenous delta-globin gene (HBD), which is homologous to HBB, competed with exogenous donor oligos to act as the repair template, leading to untoward mutations. Our data also indicated that repair of the HBB locus in these embryos occurred preferentially through the non-crossover HDR pathway. Taken together, our work highlights the pressing need to further improve the fidelity and specificity of the CRISPR/Cas9 platform, a prerequisite for any clinical applications of CRSIPR/Cas9-mediated editing.
Corneal cross-linking treatment of keratoconus (2015)

Keratoconus as the most common cause of ectasia is one of the leading cause of corneal transplants worldwide. The current available therapies do not modify the underlying pathogenesis of the disease, and none of the available approaches but corneal transplant hinder the ongoing ectasia. Several studies document Crosslink defect between collagen fibrils in the pathogenesis of keratoconus. Collagen cross link is a relatively new approach that with the application of the riboflavin and ultraviolet A, new covalent bands reform. Subjective and objective results following this method seem to be promising. Endothelial damage besides other deep structural injury, which is the major concern of this technique have not yet been reported, when applying the standard method.
Exergy Analysis of Metal Oxide Carbothemic Reduction under Vacuum – Sustainability prospects (2012)

Normal 0 false false false EL X-NONE X-NONE MicrosoftInternetExplorer4 Based on the fundamental Le Chatellier principle, gas producing reactions can be pushed at lower temperatures if an appropriate vacuum is applied. A basic thermodynamic analysis is used to predict the effect of pressure decrease on the temperature and exergy cost of a reaction with gaseous products. The energy analysis of 11 different metal producing carbothermic reductions revealed that the pumping work substitutes relatively the same amount of heat in all 11 reactions, despite the fact that the volume of gases evolved in each case differs significantly. The exergy analysis for conducting these reactions with non-renewable resources showed that due to the high exergy cost of fossil fuel generated electricity the application of vacuum would increase the overall exergy cost of these reductions. If the heat needed for the reactions could be produced through renewable resources, such as concentrated solar radiation, then the use of vacuum would have a positive effect in the cases of high temperature reductions of Al 2 O 3 , MgO and CaO, where a significant decrease in reaction temperature is observed as more exergy is spent in pumping work.
Part I.—Einstein's law of photochemical equivalence. Introductory address to Part I (1926)

A. J. Allmand, Trans. Faraday Soc., 1926, 21, 438 DOI: 10.1039/TF9262100438
The development of a ‘process map’ for the growth of carbon nanomaterials from ferrocene by injection CVD (2013)

Ferrocene was used as a catalyst in a hydrocarbon solution to carry out injection chemical vapour deposition (CVD) growth of carbon nanomaterials in a horizontal tube furnace. The presence and quality of various carbon materials was determined using Raman spectroscopy, thermogravimetric analysis, and electron microscopy. Products ranged from amorphous carbon (a-C), multi walled carbon nanotubes (MWNTs) and vapour grown fibers (VGFs). Catalyst concentration, growth temperature, injection rate, carrier gas flow rate, and the choice of hydrocarbon were found to influence the product outcome. Slower injection rates gave higher isolated yield. High catalyst concentrations were found to produce less pure carbon materials with iron oxides impurities. Higher temperatures were favourable to nanotube formation. The use of benzene was found to increase yield compared with the other hydrocarbons. In this work we developed a process map to chart the various carbon nanomaterial allotropes that were created according to reaction parameters.