gebhart/patrepeval huggingface dataset:
Activity of <i>Candida rugosa</i> Lipase Immobilized on γ-Fe<sub>2</sub>O<sub>3</sub> Magnetic Nanoparticles (2003)

We report the stability and enzymatic activity of Candida rugosa Lipase (E.C.3.1.1.3) immobilized on gamma-Fe2O3 magnetic nanoparticles. The immobilization strategies were either reacting the enzyme amine group with a nanoparticle surface acetyl, or amine groups. In the former, the enzyme was attached through a C=N bond, while in the latter it was connected using glutaraldehyde. AFM images show an average particle size of 20 +/- 10 nm after deconvolution. The enzymatic activity of the immobilized lipase was determined by following the ester cleavage of p-nitrophenol butyrate. The covalently immobilized enzyme was stabile and reactive over 30 days.
Fibrin Affinity and Clearance of t-PA Deletion and Substitution Analogues (1990)

To investigate structure-function relationships in tissue-type plasminogen activator (t-PA) we deleted the following domains in the heavy chain: a) The epidermal growth factor domain (t-PA del. G), b) the finger domain, and the epidermal growth factor domain (t-PA del. FG), and c) the finger, the epidermal growth factor and Kringle 1 (t-PA del. FGK1). To study specifically the function of the growth factor domain we made two substitutions of d) 8 amino acids (consensus sequence) in the growth factor domain (t-PA G-CS) and e) the whole domain with factor IX growth factor domain (t-PA G-IX). Finally, f) an analogue with substitution in the finger domain (fibronectin consensus sequence) was constructed (t-PA F-CS). A reduced fibrin binding of all the analogues was found. The fibrin stimulated activity of all analogues was also reduced and correlated to the fibrin binding. In contrast, the activity of the analogues in the clot lysis assay and the plate assay were only slightly reduced as compared to authentic t-PA. This suggested that at high fibrin concentrations the decreased fibrin affinity was less critical for obtaining a high fibrinolytic activity. All analogues had a prolonged half-life in vivo as compared to authentic t-PA. The assumption of clearance mechanism involving mainly the growth factor region (or Kringle 1) was not challenged by the observation of a prolonged half-life for the substitution analogue t-PA F-CS.2+off
Synthesis and Antiviral Activities of Methylenecyclopropane Analogs with 6-Alkoxy and 6-Alkylthio Substitutions That Exhibit Broad-Spectrum Antiviral Activity against Human Herpesviruses (2013)

Methylenecyclopropane nucleosides have been reported to be active against many of the human herpesviruses. The most active compound of this class is cyclopropavir (CPV), which exhibits good antiviral activity against human cytomegalovirus (HCMV), Epstein-Barr virus, both variants of human herpesvirus 6, and human herpesvirus 8. CPV has two hydroxymethyl groups on the methylenecyclopropane ring, but analogs with a single hydroxymethyl group, such as the prototypical (S)-synguanol, are also active and exhibit a broader spectrum of antiviral activity that also includes hepatitis B virus and human immunodeficiency virus. Here, a large set of monohydroxymethyl compounds with ether and thioether substituents at the 6 position of the purine was synthesized and evaluated for antiviral activity against a range of human herpesviruses. Some of these analogs had a broader spectrum of antiviral activity than CPV, in that they also inhibited the replication of herpes simplex viruses 1 and 2 and varicella-zoster virus. Interestingly, the antiviral activity of these compounds appeared to be dependent on the activity of the HCMV UL97 kinase but was relatively unaffected by the absence of thymidine kinase activity in HSV. These data taken together indicate that the mechanism of action of these analogs is distinct from that of CPV. They also suggest that they might be useful as broad-spectrum antiherpesvirus agents and may be effective in the treatment of resistant virus infections.
Cloning, expression and chromosomal localization of Wnt-13, a novel member of the Wnt gene family. (1996)

The Wnt genes, encoding structurally-related secreted glycoproteins, are implicated in mammary carcinogenesis induced by mouse mammary tumor virus. In search of the Wnt gene(s) expressed in human gastric cancer, a WTGC1 cDNA fragment sharing 66.9% amino-acid homology with human and mouse Wnt-2 was isolated by degenerate polymerase chain reaction. The human gene corresponding to WTGC1 was designated as Wnt-13 and overlapping Wnt-13 cDNAs were cloned. Nucleotide sequence analysis indicated that the Wnt-13 gene encodes the protein of 372 amino acids, including a signal peptide, two potential N-glycosylation sites and 24 cystein residues highly conserved among members of the Wnt gene family. The Wnt-13 mRNA of 2.5 kb in size was detected in heart, brain, placenta, lung, prostate, testis, ovary, small intestine and colon of adult human and also in brain, lung and kidney of fetal human. Among various cancer cell lines, the Wnt-13 mRNA was detected in HeLa (cervical cancer), MKN28 and MKN74 (gastric cancer). The Wnt-13 gene has been mapped to human chromosome 1p13. These results suggest that the Wnt-13 gene may be involved in normal human development or differentiation as well as in human carcinogenesis.
Erythropoietin mediates tissue protection through an erythropoietin and common β-subunit heteroreceptor (2004)

The cytokine erythropoietin (Epo) is tissue-protective in preclinical models of ischemic, traumatic, toxic, and inflammatory injuries. We have recently characterized Epo derivatives that do not bind to the Epo receptor (EpoR) yet are tissue-protective. For example, carbamylated Epo (CEpo) does not stimulate erythropoiesis, yet it prevents tissue injury in a wide variety of in vivo and in vitro models. These observations suggest that another receptor is responsible for the tissue-protective actions of Epo. Notably, prior investigation suggests that EpoR physically interacts with the common beta receptor (betacR), the signal-transducing subunit shared by the granulocyte-macrophage colony stimulating factor, and the IL-3 and IL-5 receptors. However, because betacR knockout mice exhibit normal erythrocyte maturation, betacR is not required for erythropoiesis. We hypothesized that betacR in combination with the EpoR expressed by nonhematopoietic cells constitutes a tissue-protective receptor. In support of this hypothesis, membrane proteins prepared from rat brain, heart, liver, or kidney were greatly enriched in EpoR after passage over either Epo or CEpo columns but covalently bound in a complex with betacR. Further, antibodies against EpoR coimmunoprecipitated betacR from membranes prepared from neuronal-like P-19 cells that respond to Epo-induced tissue protection. Immunocytochemical studies of spinal cord neurons and cardiomyocytes protected by Epo demonstrated cellular colocalization of Epo betacR and EpoR. Finally, as predicted by the hypothesis, neither Epo nor CEpo was active in cardiomyocyte or spinal cord injury models performed in the betacR knockout mouse. These data support the concept that EpoR and betacR comprise a tissue-protective heteroreceptor.
Expression of the Apoptosis-Mediator Fas Is Enhanced by Dysfunctional Mitochondria (1996)

We applied an antibody against an apoptosis mediator, Fas/APO-1/CD95, to HeLa-derived cells that completely lack mitochondrial DNA (mtDNA) or have mutant mtDNAs. The anti-Fas antibody killed the cells completely lacking mtDNA (EB8), at concentrations as low as 1 ng/ml, but not control cells harboring wild-type mtDNA (Ft2-11). TUNEL (terminal deoxynucleotidyl transferase mediated dUTP-biotin nick end-labeling) and analysis of fragmented DNA indicated that the cell death of EB8 was due to apoptosis. The antibody was cytotoxic to other two cell lines harboring mutant mtDNA with a point mutation or a large-scale deletion. RT-PCR (reverse transcriptase-polymerase chain reaction) showed that the mRNA content of the Fas gene was 2 to 19-fold higher in the cells with deficient mtDNA than in the control cells. In addition, the expressed Fas protein was detected by immunohistochemical staining in the cells without mtDNA but not in the control cells. Incubating the cells containing wild-type mtDNA with the respiratory inhibitors rotenone and antimycin A enhanced the content of mRNA of the Fas gene 2 to 4-fold and sensitized cells to the antibody. Thus, defects in mitochondria caused apoptotic cell death by anti-Fas antibody and enhanced Fas gene expression.
Direct Binding Assay for the Detection of Type IV Allosteric Inhibitors of Abl (2012)

Abelson (Abl) tyrosine kinase is an important cellular enzyme that is rendered constitutively active in the breakpoint cluster region (BCR)-Abl fusion protein, contributing to several forms of leukemia. Although inhibiting BCR-Abl activity with imatinib shows great clinical success, many patients acquire secondary mutations that result in resistance to imatinib. Second-generation inhibitors such as dasatinib and nilotinib can overcome the majority of these mutations but fail to treat patients with an especially prevalent T315I mutation at the gatekeeper position of the kinase domain. However, a combination of nilotinib with an allosteric type IV inhibitor was recently shown to overcome this clinically relevant point mutation. In this study, we present the development of a direct binding assay that enables the straightforward detection of allosteric inhibitors which bind within the myristate pocket of Abl. The assay is amenable to high-throughput screening and exclusively detects the binding of ligands to this unique allosteric site.
Application of atomic force microscopy in the characterization of cell morphology of bacillus cereus bacteria in the biosorption process of heavy metal ions (2004)

Atomic force microscopy (AFM) has been used to investigate the morphology of the cell surfaces of Bacillus Cereus in the biosorption process of heavy metal ions. Changes in the cell surface structures including the size, shape and properties of the bacteria under different media conditions and the Pb(Ⅱ) ion exposure as well are probed and characterized through sectional analysis. While newly cultivated Bacillus cereus cells usually have a smooth surface and may have a variety in their cell dimensions from different bacterial colonies, cells after treated in 0.1?mol·L~(-1) HNO_3 or EDTA for overnight become more rough in their cell surface, but remain to preserve the integrity of their cell structure such as the shape and size, implying that the treatment with 0.1?mol·L~(-1) HNO_3 or EDTA does not cause any major change in the cell structure and probably can release only the acidic or binding sites occupied by the metal ions on the cell surface. The morphology of Bacillus Cereus bacteria in the control blank without Pb(Ⅱ) is rod-like in shape with a smooth surface, the size dimension of which is about 3.3?μm in length with a section profile of 1.9?μm in width and 0.3-0.4?μm in height. The bacteria cells are usually found to form a larger rod-like ultra-structure with internal cells connected from end to end. With the Pb(Ⅱ) ion exposure the larger ultra-structures of the bacteria cells are mostly disconnected, and the size dimensions of the bacteria cells are enlarged. The length of the bacteria cells is 3.9?μm, the width and height in the section profile are 3.1?μm and 1.15?μm, respectively. Further more, the surfaces of the bacteria cells are more roughened, and the cells are more likely to adhere to each other randomly. Through the use of section analysis, one interesting phenomenon in the morphological observation of Bacillus Cereus bacteria has been found, i.e. the distortion of section profile in the vertical direction relative to the lateral direction. The cross section shape is far from a circle or a semi-circle, but like an arch. This is attributed to the morphological changes of the soft sample itself when adsorbed onto mica substances, and is believed to be due to the different interaction forces between the bacteria and substrate surfaces, such as the surface charges (both sample and substrate surfaces) in cooperation with internal forces of the bacteria sample etc. This type of change has no range limit and varies quite a lot, depending on sample and surface properties in the particular environment. Nevertheless, it can be characterized by the ratio of vertical vs. lateral distances in the sectional profile, through which the morphological changes of the bacteria cells with Pb(Ⅱ) exposure in relation to the control blank without Pb(Ⅱ) are found, the R value varying from 0.165 to 0.416.
Regional and strain-specific gene expression mapping in the adult mouse brain (2000)

To determine the genetic causes and molecular mechanisms responsible for neurobehavioral differences in mice, we used highly parallel gene expression profiling to detect genes that are differentially expressed between the 129SvEv and C57BL/6 mouse strains at baseline and in response to seizure. In addition, we identified genes that are differentially expressed in specific brain regions. We found that approximately 1% of expressed genes are differentially expressed between strains in at least one region of the brain and that the gene expression response to seizure is significantly different between the two inbred strains. The results lead to the identification of differences in gene expression that may account for distinct phenotypes in inbred strains and the unique functions of specific brain regions.
Cap-independent translation of encephalomyocarditis virus RNA: structural elements of the internal ribosomal entry site and involvement of a cellular 57-kD RNA-binding protein. (1990)

Translation of encephalomyocarditis virus (EMCV) mRNA occurs by ribosomal internal entry into the 5'-nontranslated region (5' NTR) rather than by ribosomal scanning. The internal ribosomal entry site (IRES) in the EMCV 5' NTR was determined by in vitro translation with RNAs that were generated by in vitro transcription of EMCV cDNAs containing serial deletions from either the 5' or 3' end of the EMCV 5' NTR. Regions downstream of nucleotide 403 and upstream of nucleotide 811 of EMCV were required for efficient translation. Site-directed mutagenesis revealed that a stem-loop structure (400 nucleotides upstream of the initiation codon) was essential for IRES function. We discovered a 57-kD cellular protein whose specific interaction with this stem-loop appears to be prerequisite for IRES function. A A pyrimidine-rich stretch proximal to the initiation codon was also crucial for efficient translation of EMCV mRNA. We propose that ribosomes bind directly to the initiating AUG without scanning.
Differences in the Human and Mouse Amino-Terminal Leader Peptides of Ornithine Transcarbamylase Affect Mitochondrial Import and Efficacy of Adenoviral Vectors (2001)

Mouse models of ornithine transcarbamylase (OTC) deficiency are being used to test the efficacy of viral vectors as possible vehicles for gene therapy. However, it has been demonstrated that virus containing the human OTC cDNA failed to express functional OTC enzyme in the recipient animals. Because functional OTC is assembled as a homotrimer in the mitochondria, there are at least two possible explanations for these results. Either endogenous mutant protein coassembles with the human OTC and has a "dominant-negative effect," or the human version of the protein is not appropriately imported or processed in the mouse mitochondria. To test the importance of processing, which in rodents is thought to depend on the leader peptide, adenoviral vectors containing chimeric OTC cDNAs were prepared. These vectors were evaluated in the OTC-deficient sparse fur mouse models. Although comparable levels of transgene expression were observed in all groups of mice, the only mice that had high levels of OTC activity and mitochondrial OTC immunoreactivity were those mice injected with the vectors containing the mouse leader peptide (mouse OTC and a mouse-human chimera of OTC). To address possible dominant-negative effects, adenoviruses containing mutant human or mouse OTC cDNAs were prepared and evaluated in cell lines or normal C3H mice, respectively. No inhibition of normal OTC activity was observed in either model system. Together, these studies provide no evidence of a dominant-negative effect and suggest that the human and rodent enzymes responsible for transporting of OTC and possibly other mitochondrial proteins have different specificity.
An experimental model for peripheral neuropathy produced by segmental spinal nerve ligation in the rat (1992)

We attempted to develop an experimental animal model for peripheral neuropathic pain. Under sodium pentobarbital anesthesia, both the L5 and L6 spinal nerves (group 1) or the L5 spinal nerve alone (group 2) of one side of the rat were tightly ligated. For comparison, a parallel study was conducted with another group of rats (group 3) which received a partial tight sciatic nerve ligation, a paradigm developed previously as a neuropathy model. Withdrawal latencies to application of radiant heat to the foot were tested for the next 16 weeks in all 3 groups. Sensitivity of the hind paw to mechanical stimulation was tested with von Frey filaments. The general behavior of each rat was noted during the entire test period. Results suggested that the surgical procedure in all 3 groups produced a long-lasting hyperalgesia to noxious heat (at least 5 weeks) and mechanical allodynia (at least 10 weeks) of the affected foot. In addition, there were behavioral signs of the presence of spontaneous pain in the affected foot. Therefore, we believe we have developed an experimental animal model for peripheral neuropathy using tight ligations of spinal nerves. The model manifests the symptoms of human patients with causalgia and is compatible with a previously developed neuropathy model. The present model has two unique features. First, the surgical procedure is stereotyped. Second, the levels of injured and intact spinal segments are completely separated, allowing independent experimental manipulations of the injured and intact spinal segments in future experiments to answer questions regarding mechanisms underlying causalgia.
Strategy for applying genome‐wide selection in dairy cattle (2006)

Animals can be genotyped for thousands of single nucleotide polymorphisms (SNPs) at one time, where the SNPs are located at roughly 1-cM intervals throughout the genome. For each contiguous pair of SNPs there are four possible haplotypes that could be inherited from the sire. The effects of each interval on a trait can be estimated for all intervals simultaneously in a model where interval effects are random factors. Given the estimated effects of each haplotype for every interval in the genome, and given an animal's genotype, a 'genomic' estimated breeding value is obtained by summing the estimated effects for that genotype. The accuracy of that estimator of breeding values is around 80%. Because the genomic estimated breeding values can be calculated at birth, and because it has a high accuracy, a strategy that utilizes these advantages was compared with a traditional progeny testing strategy under a typical Canadian-like dairy cattle situation. Costs of proving bulls were reduced by 92% and genetic change was increased by a factor of 2. Genome-wide selection may become a popular tool for genetic improvement in livestock.
Order Matters: Sequence to sequence for sets (2015)

Sequences have become first class citizens in supervised learning thanks to the resurgence of recurrent neural networks. Many complex tasks that require mapping from or to a sequence of observations can now be formulated with the sequence-to-sequence (seq2seq) framework which employs the chain rule to efficiently represent the joint probability of sequences. In many cases, however, variable sized inputs and/or outputs might not be naturally expressed as sequences. For instance, it is not clear how to input a set of numbers into a model where the task is to sort them; similarly, we do not know how to organize outputs when they correspond to random variables and the task is to model their unknown joint probability. In this paper, we first show using various examples that the order in which we organize input and/or output data matters significantly when learning an underlying model. We then discuss an extension of the seq2seq framework that goes beyond sequences and handles input sets in a principled way. In addition, we propose a loss which, by searching over possible orders during training, deals with the lack of structure of output sets. We show empirical evidence of our claims regarding ordering, and on the modifications to the seq2seq framework on benchmark language modeling and parsing tasks, as well as two artificial tasks -- sorting numbers and estimating the joint probability of unknown graphical models.
Combining Tag and Value Similarity for Data Extraction and Alignment (2011)

Web databases generate query result pages based on a user's query. Automatically extracting the data from these query result pages is very important for many applications, such as data integration, which need to cooperate with multiple web databases. We present a novel data extraction and alignment method called CTVS that combines both tag and value similarity. CTVS automatically extracts data from query result pages by first identifying and segmenting the query result records (QRRs) in the query result pages and then aligning the segmented QRRs into a table, in which the data values from the same attribute are put into the same column. Specifically, we propose new techniques to handle the case when the QRRs are not contiguous, which may be due to the presence of auxiliary information, such as a comment, recommendation or advertisement, and for handling any nested structure that may exist in the QRRs. We also design a new record alignment algorithm that aligns the attributes in a record, first pairwise and then holistically, by combining the tag and data value similarity information. Experimental results show that CTVS achieves high precision and outperforms existing state-of-the-art data extraction methods.
4E-Binding Protein 1: A Key Molecular “Funnel Factor” in Human Cancer with Clinical Implications (2007)

In an attempt to identify molecules that clearly reflect the oncogenic role of cell signaling pathways in human tumors, we propose a concept we term "funnel factor", a factor where several oncogenic signals converge and drive the proliferative signal downstream. In studies done in various tumor types, the expression of key cell signaling factors, including Her1 and Her2 growth factor receptors, as well as the RAS-RAF-mitogen-activated protein kinase and the phosphatidylinositol 3-kinase-AKT-mammalian target of rapamycin pathways was correlated with the associated clinicopathologic characteristics of these tumors. The downstream factors p70, S6, 4E-binding protein 1 (4E-BP1), and eukaryotic translation initiation factor 4E, which play a critical role in the control of protein synthesis, survival, and cell growth, were also analyzed. We found that phosphorylated 4E-BP1 (p-4E-BP1) expression in breast, ovary, and prostate tumors is associated with malignant progression and an adverse prognosis regardless of the upstream oncogenic alterations. Thus, p-4E-BP1 seems to act as a funnel factor for an essential oncogenic capability of tumor cells, self-sufficiency in growth signals, and could be a highly relevant molecular marker of malignant potential. Further investigation into this concept may identify additional funnel factors in the oncogenic pathways and provide potential therapeutic targets.