gebhart/patrepeval huggingface dataset:
Mining and summarizing customer reviews (2004)

Merchants selling products on the Web often ask their customers to review the products that they have purchased and the associated services. As e-commerce is becoming more and more popular, the number of customer reviews that a product receives grows rapidly. For a popular product, the number of reviews can be in hundreds or even thousands. This makes it difficult for a potential customer to read them to make an informed decision on whether to purchase the product. It also makes it difficult for the manufacturer of the product to keep track and to manage customer opinions. For the manufacturer, there are additional difficulties because many merchant sites may sell the same product and the manufacturer normally produces many kinds of products. In this research, we aim to mine and to summarize all the customer reviews of a product. This summarization task is different from traditional text summarization because we only mine the features of the product on which the customers have expressed their opinions and whether the opinions are positive or negative. We do not summarize the reviews by selecting a subset or rewrite some of the original sentences from the reviews to capture the main points as in the classic text summarization. Our task is performed in three steps: (1) mining product features that have been commented on by customers; (2) identifying opinion sentences in each review and deciding whether each opinion sentence is positive or negative; (3) summarizing the results. This paper proposes several novel techniques to perform these tasks. Our experimental results using reviews of a number of products sold online demonstrate the effectiveness of the techniques.
Bruton's Tyrosine Kinase-mediated Interleukin-2 Gene Activation in Mast Cells (1998)

Cross-linking of the high affinity IgE receptor (FcepsilonRI) on mast cells induces secretion of cytokines, including interleukin (IL)-2, through transcriptional activation of cytokine genes. Previously, defects in the gene coding for Bruton's tyrosine kinase (Btk) were shown to result in defective cytokine production in mast cells, and thereby mice carrying btk mutations exhibited diminished anaphylactic reactions in response to IgE and antigen. In this study, we provide evidence that the transcription factors involved in the IL-2 gene expression in T cells are also required for maximal activation of the IL-2 gene in FcepsilonRI-stimulated mast cells. Among them, AP-1 (Jun/Fos) and NF-AT were identified as candidate transcription factors that are regulated by Btk. Consistent with our previous data indicating that Btk regulates stress-activated protein kinases, c-Jun N-terminal kinase (JNK), c-Jun and other JNK-regulatable transcription factors are activated by FcepsilonRI cross-linking in a Btk-dependent manner. Further, FcepsilonRI-induced IL-2 gene activation is dependent on c-Jun and a component, SEK1, of its upstream activation pathway. Collectively, these data demonstrate that Btk regulates the transcription of the IL-2 gene through the JNK-regulatable transcription factors in FcepsilonRI-stimulated mast cells.
[A short term study on the efficacies of intratympanic prednisolone and dexamethasone injection for subjective tinnitus]. (2008)

Intratympanic steroid injection has a positive effect on subjective tinnitus and may be considered to be an alternative treatment to subjective tinnitus.
Phasenbeziehungen zwischen Imidazolylketonen und Hydroxypyrazinen (1964)

Abstract Die isomeren, strukturell aber so unterschiedlichen 2‐Aroyl‐4(5)‐aryl‐imidazole und 3‐Hydroxy‐2,5‐diaryl‐pyrazine sind im gesamten Konzentrationsbereich lückenlos mischbar.
Pattern Based Sequence Classification (2015)

Sequence classification is an important task in data mining. We address the problem of sequence classification using rules composed of interesting patterns found in a dataset of labelled sequences and accompanying class labels. We measure the interestingness of a pattern in a given class of sequences by combining the cohesion and the support of the pattern. We use the discovered patterns to generate confident classification rules, and present two different ways of building a classifier. The first classifier is based on an improved version of the existing method of classification based on association rules, while the second ranks the rules by first measuring their value specific to the new data object. Experimental results show that our rule based classifiers outperform existing comparable classifiers in terms of accuracy and stability. Additionally, we test a number of pattern feature based models that use different kinds of patterns as features to represent each sequence as a feature vector. We then apply a variety of machine learning algorithms for sequence classification, experimentally demonstrating that the patterns we discover represent the sequences well, and prove effective for the classification task.
Molecular cloning of the human thyrotropin‐β subunit gene (1985)

Genomic DNA fragments that carried a gene for human thyrotropin-beta (hTSH beta) subunit were isolated. Nucleotide sequence analysis of the gene showed that the hTSH beta subunit precursor consists of 138 amino acid residues. There is an N-terminal sequence of 20 amino acids as a signal peptide, followed by 112 amino acids, whose sequence is in agreement with that known for the secretory form of hTSH beta subunit. This is followed by an additional stretch of 6 hydrophobic amino acids, which may be eliminated post-translationally. The coding region is separated by an intron of about 460 bp. Genomic Southern blot hybridization analysis suggested that the hTSH beta gene is a unique single copy gene.
The Phosphatidylinositol 3-Kinase/mTor Pathway as a Therapeutic Target for Brain Aging and Neurodegeneration (2011)

Many pathological conditions are associated with phosphatidylinositol 3-kinase (PI3K) dysfunction, providing an incentive for the study of the effects of PI3K modulation in different aspects of diabetes, cancer, and aging. The PI3K/AKT/mTOR pathway is a key transducer of brain metabolic and mitogenic signals involved in neuronal proliferation, differentiation, and survival. In several models of neurodegenerative diseases associated with aging, the PI3K/AKT pathway has been found to be dysregulated, suggesting that two or more initiating events may trigger disease formation in an age-related manner. The search for chemical compounds able to modulate the activity of the PI3K/AKT/mTOR pathway is emerging as a potential therapeutic strategy for the treatment and/or prevention of some metabolic defects associated with brain aging. In the current review, we summarize some of the critical actions of PI3K in brain function as well as the evidence of its involvement in aging and Alzheimer’s disease.
Alkali-Metal-Mediated Zincation of Anisole:  Synthesis and Structures of Three Instructive Ortho-Zincated Complexes (2006)

The new concept of alkali-metal-mediated zincation (AMMZ), formally a zinc-hydrogen exchange reaction but one that requires the participation of an alkali metal, is applied here to the alkyl aryl ether anisole, an important molecule for studying directed ortho-metalation (DoM) chemistry. Treating one molar equivalent of anisole with the lithium dialkyl-TMP zincate reagent [THF.Li(mu-TMP)(mu-tBu)Zn(tBu)] (1) in hexane solution affords the mono-ortho-zincated complex [THF.Li(mu-TMP)(mu-o-C6H4OMe)Zn(tBu)] (2), which establishes that 1 functions as an alkyl base although previously it was regarded as an amido (TMP) base in other DoM applications. Treating two molar equivalents of anisole with 1, and increasing the reaction time, affords the bis-ortho-zincated complex [THF.Li(mu-TMP)(mu-o-C6H4OMe)Zn(o-C6H4OMe)] (3), which establishes that 1 can also function as a dual alkyl base. Omitting THF and rerunning the reaction with one or two molar equivalents of anisole affords [Ph(Me)O.Li(mu-TMP)(mu-o-C6H4OMe)Zn(tBu)] (4), which remarkably contains a combination of neutral and ortho-deprotonated anisole ligands. On isolating crystalline 4 from solution and adding THF, it converts to 2 and then to 3 on further stirring of the solution, as determined by NMR studies. This fact, along with other observations, would suggest that a complex-induced proximity effect does not need to be invoked to explain the observed zincation of anisole. The crystal structures of 2-4 are presented, as are their 1H, 13C, and 7Li NMR spectra recorded in C6D6 solution.
A strong mutator effect caused by an amino acid change in the alpha subunit of DNA polymerase III of Escherichia coli. (1991)

Most potent mutators heretofore detected in Escherichia coli are associated with defects in epsilon subunit of DNA polymerase III, encoded by the dnaQ gene. To elucidate the role of the alpha subunit, the catalytic subunit of the polymerase, in maintaining the high fidelity of DNA replication, we isolated a mutator mutant, the mutation (dnaE173) of which resides on the dnaE gene, encoding the alpha subunit. The dnaE173 mutant was unable to grow in salt-free L broth at temperatures exceeding 44.5 degrees C and exhibited an increased frequency of spontaneous mutations, 1,000 to 10,000-fold the wild type level, at permissive temperatures. The mutator effect of dnaE173 mutation is dominant over the wild type allele. These phenotypes are caused by a single base substitution, resulting in one amino acid change, Glu612 (GAA)----Lys(AAA), in the alpha subunit molecule. DNA polymerase III purified from the dnaE173 mutant contained both alpha and epsilon subunits, in a normal molar ratio. We found no differences between wild type and mutant polymerases in the Vmax, thermolabilities, and salt sensitivities. However, the apparent Km for the substrate nucleotide of the mutant polymerase was 1/6 of that determined with the wild type polymerase. Although the mutant polymerase retained a normal level of 3'----5' exonuclease activity, the proofreading capacity determined by "turnover assay" was significantly lower in the mutant polymerase, as compared with findings in the normal enzyme. It seems likely that the enhanced mutability in the dnaE173 strain results from, at least in part, a defect in the editing function of DNA polymerase III, and further suggests that a portion of the alpha subunit in which the amino acid change resides may be important for the proper setting of the two subunits at the replication fork so as to facilitate efficient editing during the DNA replication.
Microtubule‐Binding Proteins as Promising Biomarkers of Paclitaxel Sensitivity in Cancer Chemotherapy (2015)

Microtubules, tirelessly animated and highly dynamic structures, are vital for most cellular processes and their intricacies are still being revealed even after a century since their discovery. The importance of microtubules as chemotherapeutic targets cannot be overstated, and their clinical role is unlikely to abate in the near future. Indeed, improved understanding of microtubule biology could herald a new epoch of anticancer drug design by permitting fine-tuning of microtubule-targeting agents, the clinical utility of which is presently often limited by primary or acquired resistance. Paclitaxel, one such agent belonging to the taxane family, has proven a resoundingly successful treatment for many cancer patients; however, for too many others with paclitaxel-refractory tumors, the drug has offered nothing but side effects. Accumulating evidence suggests that microtubule-binding proteins (MBPs) can regulate paclitaxel sensitivity in a wide range of cancer types. Improved understanding of how these proteins can be assayed to predict treatment responses or manipulated pharmacologically to improve clinical outcomes could transform modern chemotherapy and is urgently awaited.
Intracoronary Adenovirus-Mediated Delivery and Overexpression of the β 2 -Adrenergic Receptor in the Heart (2000)

Percutaneous adenovirus-mediated intracoronary delivery of a potentially therapeutic transgene is feasible, and acute global LV function can be enhanced by LV-specific overexpression of the beta(2)AR. Thus, genetic modulation to enhance the function of the heart may represent a novel therapeutic strategy for congestive heart failure and can be viewed as molecular ventricular assistance.
Early retinoic acid-induced F9 teratocarcinoma stem cell gene ERA-1: alternate splicing creates transcripts for a homeobox-containing protein and one lacking the homeobox. (1988)

Retinoic acid (RA), the natural acidic derivative of vitamin A, can modulate the expression of specific genes and can induce some cell types, such as the murine F9 teratocarcinoma stem cell line, to differentiate in culture. As an initial step toward understanding the molecular mechanism(s) by which RA exerts these effects, we previously isolated cDNA clones for a gene, ERA-1, which has the characteristics of an early, direct target for RA. We demonstrated that RA causes a rapid, dose-dependent, and protein synthesis-independent expression of the ERA-1 gene (G. J. LaRosa and L. J. Gudas, Proc. Natl. Acad. Sci. USA 85:329-333, 1988). We now report the full-length cDNA sequence and the further characterization of this gene. The data indicate that the RA-induced 2.2- to 2.4-kilobase ERA-1 RNA species that we previously detected consists of two alternately spliced messages. One mRNA encodes a protein with a predicted mass of about 36 kilodaltons (kDa) that possesses the Hox 1.6 homeobox domain. The other mRNA encodes a truncated protein of about 15 kDa which is identical to the 36-kDa protein for 114 amino acids at the amino-terminal end but which lacks the homeobox amino acid sequence. The RA-associated increase in the ERA-1 mRNA level does not appear to be due to message stabilization, suggesting that the response is at the level of transcription. By Northern (RNA) blot analysis, the usual 2.2- to 2.4-kilobase mRNA species was also rapidly expressed in P19 teratocarcinoma cells during their differentiation to fibroblastic cells in response to RA and was detected in day 10.5 and day 13.5 mouse embryos. This result indicates that the expression of this gene is not limited to the endodermal differentiation of F9 cells.
High yield preparation of isolated human adult hepatocytes by enzymatic perfusion of the liver (1982)

Abstract We have developed experimental conditions allowing the isolation of as many as 1–10 × 10 8 human adult hepatocytes by perfusing the left lobe of the liver. About 70–85% cells were viable with the trypan blue exclusion test; they attached to substrates and formed monolayers which survived for up to 8 days in culture.
Ulex europaeus I lectin as a marker for vascular endothelium in human tissues. (1982)

Ulex europaeus I agglutinin, a lectin specific for some alpha-L-fucose-containing glycocompounds, was used in fluorescence microscopy to stain cryostat sections of human tissues. The endothelium of vessels of all sizes was stained ubiquitously in all tissues studied as judged by double staining with a known endothelial marker, antibodies against human clotting factor VIII. Cultured human umbilical vein endothelial cells, but not fibroblasts, also bound Ulex lectin. The staining was not affected by the blood group type of the tissue donor. In some tissues Ulex lectin presented additional binding to epithelial structures. Also, this was independent on the blood group or the ability of the tissue donor to secrete soluble blood group substances. Lotus tetragonolobus agglutinin, another lectin specific for some alpha-L-fucose-containing moieties failed to react with endothelial cells. Our results suggest that Ulex europaeus I agglutinin is a good histologic marker for endothelium in human tissues.
Swollenin, a Trichoderma reesei protein with sequence similarity to the plant expansins, exhibits disruption activity on cellulosic materials (2002)

Plant cell wall proteins called expansins are thought to disrupt hydrogen bonding between cell wall polysaccharides without hydrolyzing them. We describe here a novel gene with sequence similarity to plant expansins, isolated from the cellulolytic fungus Trichoderma reesei. The protein named swollenin has an N-terminal fungal type cellulose binding domain connected by a linker region to the expansin-like domain. The protein also contains regions similar to mammalian fibronectin type III repeats, found for the first time in a fungal protein. The swollenin gene is regulated in a largely similar manner as the T. reesei cellulase genes. The biological role of SWOI was studied by disrupting the swo1 gene from T. reesei. The disruption had no apparent effect on the growth rate on glucose or on different cellulosic carbon sources. Non-stringent Southern hybridization of Trichoderma genomic DNA with swo1 showed the presence of other swollenin-like genes, which could substitute for the loss of SWOI in the disruptant. The swollenin gene was expressed in yeast and Aspergillus niger var. awamori. Activity assays on cotton fibers and filter paper were performed with concentrated SWOI-containing yeast supernatant that disrupted the structure of the cotton fibers without detectable formation of reducing sugars. It also weakened filter paper as assayed by an extensometer. The SWOI protein was purified from A. niger var. awamori culture supernatant and used in an activity assay with Valonia cell walls. It disrupted the structure of the cell walls without producing detectable amounts of reducing sugars.
Antisense oligonucleotides for the treatment of spinocerebellar ataxia type 2 (SCA2) (S32.002) (2015)

OBJECTIVE: To demonstrate that lowering ATXN2 expression using antisense oligonucleotides (ASOs) modifies molecular, motor, and neurophysiological phenotypes of SCA2 mice. BACKGROUND: SCA2 is a heritable neurodegenerative disorder resulting from CAG repeat expansion mutations in the ATXN2 gene. The ATXN2 gene protein product ataxin-2 is characterized by gains of function upon ATXN2 mutation, caused by expansion of the CAG-encoded polyglutamine tract in ataxin-2. We hypothesize that treatments using ASOs targeting the expression of ATXN2 will result in delayed onset of molecular, motor, and neurophysiological phenotypes characteristic of our SCA2 transgenic mice. Utility of ASOs for treating SCA2 is supported by the lack of neurodegeneration in ATXN2 knockout mice, and inducible reversibility of polyQ disease mouse phenotypes of HD and SCA1. DESIGN/METHODS: We screened >100 ASOs designed to lower ATXN2 expression in vitro in HepG2 cells, and then identified the most efficacious ASOs for lowering ATXN2 expression in vivo using multiple SCA2 mouse models. ATXN2-Q127 transgenic mice were treated by intracerebroventricular (ICV) injection of ASOs and rotarod phenotype was determined. Cerebellar molecular phenotypes were determined by qPCR and Purkinje cell firing frequencies were studied for a subset of mice. RESULTS: Three ASOs lowered ATXN2 expression in ATXN2-Q172 transgenic mice, the best by >80[percnt] after 7 d, without evidence of toxicity (Iba1 activation). ATXN2 remained significantly reduced after 7 wks. Immunohistochemical staining of ASOs using anti-ASO antibody demonstrated ASO localization in Purkinje cells. ATXN2-Q172 mice treated 13 weeks with ATXN2 ASO had delayed motor phenotype onset (rotarod), and normal pacemaking Purkinje cell firing frequencies determined by extracellular recordings, unlike saline treated control mice. CONCLUSIONS: We identified ASOs that potently lower ATXN2 expression resulting in delayed progression of SCA2 phenotypes in ATXN2 transgenic mice. Ongoing studies include screens for more efficacious ASOs toward developing a treatment for SCA2. Study Supported by: R01NS033123, R21NS081182, RC4NS073009.
Enzymes: An integrated view of structure, dynamics and function (2006)

Microbes utilize enzymes to perform a variety of functions. Enzymes are biocatalysts working as highly efficient machines at the molecular level. In the past, enzymes have been viewed as static entities and their function has been explained on the basis of direct structural interactions between the enzyme and the substrate. A variety of experimental and computational techniques, however, continue to reveal that proteins are dynamically active machines, with various parts exhibiting internal motions at a wide range of time-scales. Increasing evidence also indicates that these internal protein motions play a role in promoting protein function such as enzyme catalysis. Moreover, the thermodynamical fluctuations of the solvent, surrounding the protein, have an impact on internal protein motions and, therefore, on enzyme function. In this review, we describe recent biochemical and theoretical investigations of internal protein dynamics linked to enzyme catalysis. In the enzyme cyclophilin A, investigations have lead to the discovery of a network of protein vibrations promoting catalysis. Cyclophilin A catalyzes peptidyl-prolyl cis/trans isomerization in a variety of peptide and protein substrates. Recent studies of cyclophilin A are discussed in detail and other enzymes (dihydrofolate reductase and liver alcohol dehydrogenase) where similar discoveries have been reported are also briefly discussed. The detailed characterization of the discovered networks indicates that protein dynamics plays a role in rate-enhancement achieved by enzymes. An integrated view of enzyme structure, dynamics and function have wide implications in understanding allosteric and co-operative effects, as well as protein engineering of more efficient enzymes and novel drug design.
Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean (2012)

The rhg1-b allele of soybean is widely used for resistance against soybean cyst nematode (SCN), the most economically damaging pathogen of soybeans in the United States. Gene silencing showed that genes in a 31-kilobase segment at rhg1-b, encoding an amino acid transporter, an α-SNAP protein, and a WI12 (wound-inducible domain) protein, each contribute to resistance. There is one copy of the 31-kilobase segment per haploid genome in susceptible varieties, but 10 tandem copies are present in an rhg1-b haplotype. Overexpression of the individual genes in roots was ineffective, but overexpression of the genes together conferred enhanced SCN resistance. Hence, SCN resistance mediated by the soybean quantitative trait locus Rhg1 is conferred by copy number variation that increases the expression of a set of dissimilar genes in a repeated multigene segment.
Synthesis of Asynchronous VLSI Circuits (1991)

No abstract available.
HOP-1, a Caenorhabditis elegans presenilin, appears to be functionally redundant with SEL-12 presenilin and to facilitate LIN-12 and GLP-1 signaling (1997)

Mutant presenilins have been found to cause Alzheimer disease. Here, we describe the identification and characterization of HOP-1, a Caenorhabditis elegans presenilin that displays much more lower sequence identity with human presenilins than does the other C. elegans presenilin, SEL-12. Despite considerable divergence, HOP-1 appears to be a bona fide presenilin, because HOP-1 can rescue the egg-laying defect caused by mutations in sel-12 when hop-1 is expressed under the control of sel-12 regulatory sequences. HOP-1 also has the essential topological characteristics of the other presenilins. Reducing hop-1 activity in a sel-12 mutant background causes synthetic lethality and terminal phenotypes associated with reducing the function of the C. elegans lin-12 and glp-1 genes. These observations suggest that hop-1 is functionally redundant with sel-12 and underscore the intimate connection between presenilin activity and LIN-12/Notch activity inferred from genetic studies in C. elegans and mammals.
Porphyrins, Phthalocyanines, and Naphthalocyanines for Various Processes of Visible Light Driven Conversion Processes (1991)

Phthalocyanines, naphthalocyanines, tetraphenylporphyrins, and perylenebis(dicarboximides) are interesting compounds for the conversion of visible light. For photon-induced reactions in solution or in thin films of photoelectrochemical or photovoltaic cells some examples are given. It is shown that the position of energy levels or energy bands is a prerequisite for these visible-light-driven processes.