gebhart/patrepeval huggingface dataset:
Structural Role for Tyr-104 in Escherichia coli Isopentenyl-diphosphate Isomerase (2006)

Isopentenyl-diphosphate (IPP):dimethylallyl diphosphate isomerase is a key enzyme in the biosynthesis of isoprenoids. The mechanism of the isomerization reaction involves protonation of the unactivated carbon-carbon double bond in the substrate, but identity of the acidic moiety providing the proton is still not clear. Multiple sequence alignments and geometrical features observed in crystal structures of complexes with IPP isomerase suggest that Tyr-104 could play an important role during catalysis. A series of mutants was constructed by directed mutagenesis and characterized by enzymology. Crystallographic and thermal denaturation data for Y104A and Y104F mutants were obtained. Those data demonstrate the importance of residue Tyr-104 for proper folding of Escherichia coli type I IPP isomerase.
Influence of nitrogen fertilization on morphological development of indeterminate and determinate soybeans (1990)

Abstract Although large quantities of nitrogen are required for high soybean [Glycine max (L.) Merr.] yields, yield increases with N fertilization are not easily achieved. Along with adverse effects on N‐fixation, N fertilization has been reported to stimulate excessive vegetative growth, especially in soybeans with the indeterminate growth habit. The objective of this study was to compare the influence of N application (150 kg N/ha, applied in irrigation water between growth stages Rl and R5) on morphological development of the indeterminate cultivar Weber and the semi‐dwarf determinate line 172–16. The two genotypes were morphologically similar at growth stage Rl (beginning bloom), but morphological differences were apparent from R3 (beginning pod stage) until maturity, with greater development of main‐stem and: branch lengths for Weber than for 172–16.’ For Weber, N fertilization greatly stimulated branch length; this was apparent at growth stage R3 and was associated with lodging and disease infestation. For the lodging‐resistant 172–16, which had essentially achieved final node numbers by R3, N had little effect on branching or main‐stem development. For Weber, substantial yield decreases have been associated with high inputs of N, whereas yields of 172–16 may be more stable or even enhanced as N availability increases. These results may be related to the differential influence of N on vegetative growth responses of these genotypes.
Bipolar Electrochemical Mechanism for the Propulsion of Catalytic Nanomotors in Hydrogen Peroxide Solutions (2006)

Bimetallic nanorods are propelled in aqueous solutions by the catalytic decomposition of hydrogen peroxide to oxygen and water. Several mechanisms (interfacial tension gradients, bubble recoil, viscous Brownian ratchet, self-electrophoresis) have been proposed for the transduction of chemical to mechanical energy in this system. From Tafel plots of anodic and cathodic hydrogen peroxide reactions at various metal (Au, Pt, Rh, Ni, Ru, and Pd) ultramicroelectrodes, we determine the potential at which the anodic and cathodic reaction rates are equal for each metal. These measurements allow one to predict the direction of motion of all possible bimetallic combinations according to the bipolar electrochemical (or self-electrophoretic) mechanism. These predictions are consistent with the observed direction of motion in all cases studied, providing strong support for the mechanism. We also find that segmented nanorods with one Au end and one poly(pyrrole) end containing catalase, an enzyme that decomposes hydrogen peroxide nonelectrochemically, perform the overall catalytic reaction at a rate similar to that of nanorods containing Au and Pt segments. However, in this case there is no observed axial movement, again supporting the bipolar electrochemical propulsion mechanism for bimetallic nanorods.
Immunogenic Correlation between Cross-Reacting Material (CRM197) Produced by a Mutant of Corynebacterium diphtheriae and Diphtheria Toxoid (1980)

The in vivo immunizing potency of diphtheria toxoid and formalin-treated corss-reacting material (CRM197, a nontoxic mutant protein) was compared in guinea pigs. Major antigenic differences between the two untreated proteins were also tested in rats. The results showed that diphtheria toxoid and CRM197 were equally effective immunogens, but only if the latter was treated with formalin in the same concentration (0.7% vol/vol) was that of the toxoid. Formalin treatment rendered the antigens more resistant to enzymatic proteolysis by trypsin in vitro.
The Warwick Framework: A Container Architecture for Aggregating Sets of Metadata (1996)

We describe a result of the June 1996 Warwick Metadata II Workshop. This Warwick Framework is a container architecture for aggregating logically, and perhaps physically, distinct packages of metadata. This architecture allows separate administration and access to metadata packages, provides for varying syntax in each package in conformance with semantic requirements, and it promotes interoperability and extensibility by allowing tools and agents to selectively access and manipulate individual packages and ignore others. At the conclusion of the paper we propose implementations of the Framework in HTML, MIME, SGML, and distributed objects.
Classification of current anticancer immunotherapies (2014)

During the past decades, anticancer immunotherapy has evolved from a promising therapeutic option to a robust clinical reality. Many immunotherapeutic regimens are now approved by the US Food and Drug Administration and the European Medicines Agency for use in cancer patients, and many others are being investigated as standalone therapeutic interventions or combined with conventional treatments in clinical studies. Immunotherapies may be subdivided into "passive" and "active" based on their ability to engage the host immune system against cancer. Since the anticancer activity of most passive immunotherapeutics (including tumor-targeting monoclonal antibodies) also relies on the host immune system, this classification does not properly reflect the complexity of the drug-host-tumor interaction. Alternatively, anticancer immunotherapeutics can be classified according to their antigen specificity. While some immunotherapies specifically target one (or a few) defined tumor-associated antigen(s), others operate in a relatively non-specific manner and boost natural or therapy-elicited anticancer immune responses of unknown and often broad specificity. Here, we propose a critical, integrated classification of anticancer immunotherapies and discuss the clinical relevance of these approaches.
Genetic Control of Programmed Cell Death in Drosophila (1994)

A gene, reaper (rpr), that appears to play a central control function for the initiation of programmed cell death (apoptosis) in Drosophila was identified. Virtually all programmed cell death that normally occurs during Drosophila embryogenesis was blocked in embryos homozygous for a small deletion that includes the reaper gene. Mutant embryos contained many extra cells and failed to hatch, but many other aspects of development appeared quite normal. Deletions that include reaper also protected embryos from apoptosis caused by x-irradiation and developmental defects. However, high doses of x-rays induced some apoptosis in mutant embryos, and the resulting corpses were phagocytosed by macrophages. These data suggest that the basic cell death program is intact although it was not activated in mutant embryos. The DNA encompassed by the deletion was cloned and the reaper gene was identified on the basis of the ability of cloned DNA to restore apoptosis to cell death defective embryos in germ line transformation experiments. The reaper gene appears to encode a small peptide that shows no homology to known proteins, and reaper messenger RNA is expressed in cells destined to undergo apoptosis.
Characterization of a mammalian smooth muscle myosin heavy chain cDNA clone and its expression in various smooth muscle types. (1988)

A cDNA clone, SMHC-29, encoding the light meromyosin of smooth muscle myosin heavy chain (MHC), was isolated from a rabbit uterus cDNA library constructed in phage lambda gt11. This smooth muscle MHC cDNA demonstrates significant nucleotide and amino acid sequence homologies with known sarcomeric MHC genes from rabbit, rat skeletal, and nematode body wall myosin, and even with nonmuscle MHC gene from a slime mold (Dictyostelium discoideum), suggesting that smooth muscle, striated muscle, and nonmuscle MHC genes diverged from a common ancestor. The deduced amino acid sequences of the smooth muscle light meromyosin show very similar periodic distributions of hydrophobic and charged residues as found for the light meromyosin of striated muscle MHCs together with a high potential for alpha-helical formation, indicating an alpha-helical coiled-coil structure for the smooth muscle light meromyosin sequences. Furthermore, S1 nuclease mapping has revealed that this smooth muscle MHC gene for SMHC-29 is specifically expressed in smooth muscles of vascular and nonvascular types but not in the striated muscles or nonmuscle cells.
Trop2 expression contributes to tumor pathogenesis by activating the ERK MAPK pathway (2010)

Abstract Background Trop2 is a cell-surface glycoprotein overexpressed by a variety of epithelial carcinomas with reported low to restricted expression in normal tissues. Expression of Trop2 has been associated with increased tumor aggressiveness, metastasis and decreased patient survival, but the signaling mechanisms mediated by Trop2 are still unknown. Here, we studied the effects murine Trop2 (mTrop2) exerted on tumor cellular functions and some of the signaling mechanisms activated by this oncogene. Results mTrop2 expression significantly increased tumor cell proliferation at low serum concentration, migration, foci formation and anchorage-independent growth. These in vitro characteristics translated to increased tumor growth in both subcutaneous and orthotopic pancreatic cancer murine models and also led to increased liver metastasis. mTrop2 expression also increased the levels of phosphorylated ERK1/2 mediating cell cycle progression by increasing the levels of cyclin D1 and cyclin E as well as downregulating p27. The activation of ERK was also observed in human pancreatic ductal epithelial cells and colorectal adenocarcinoma cells overexpressing human Trop2. Conclusions These findings demonstrate some of the pathogenic effects mediated by mTrop2 expression on cancer cells and the importance of targeting this cell surface glycoprotein. This study also provides the first indication of a molecular signaling pathway activated by Trop2 which has important implications for cancer cell growth and survival.
Homogeneous CO2 Reduction by Ni(cyclam) at a Glassy Carbon Electrode (2012)

The homogeneous CO2 reduction activity of several nickel cyclam complexes was examined by cyclic voltammetry and controlled potential electrolysis. CO production with high efficiency from unsubstituted Ni(cyclam) was verified, while the activity was found to be attenuated with methyl substitution of the amines on the cyclam ring. Reactivity with CO2 was also probed using density functional theory (DFT) calculations. The relative CO2 binding energies to the NiI state obtained from DFT were found to match well with the experimental results and shed light on the possible importance of the isomeric form of Ni(cyclam) in determining the catalytic activity.
Integrated Carbon-Reduced Battery Chemistries for Safer Alternative Li-Ion Cells (2013)

Abstract not Available.
Human interferon-alpha A, -alpha 2, and -alpha 2(Arg) genes in genomic DNA (1993)

The frequency in human genomic DNA of three human interferon (IFN) alpha genes which differ from each other by a single base substitution was examined in 11 normal individuals. The polymerase chain reaction (PCR) was used to amplify the coding sequence for the Hu-IFN-alpha 2, Hu-IFN-alpha A, and Hu-IFN-alpha 2(Arg) sequences from genomic DNA. The PCR products were then cloned and individual clones were sequenced. PCR products were also analyzed by restriction endonuclease analysis for the IFN-alpha 2 and IFN-alpha A genes by use of a HinfI site which is eliminated by the substitution of an A for a G in IFN-alpha A. The IFN-alpha A gene which was cloned from the myeloblastoid cell line KG-1 was not observed in any of the 201 clones sequenced from normal individuals or in the Namalwa cell line. It was detected in KG-1 cell genomic DNA where it represented 49% of the clones sequenced. Similarly the IFN-alpha 2(Arg) gene was not detected in normal individuals or in the KG-1 cell line but only in the lymphoblastoid cell line from which it was cloned. In Namalwa cells the IFN-alpha 2(Arg) sequence represented 35% of the clones sequenced while the IFN-alpha 2 sequence comprised 59%. Therefore, both the IFN-alpha A and IFN-alpha 2(Arg) sequences represent alleles of the IFN-alpha 2 gene.
Single-Step Recombinase Polymerase Amplification Assay Based on a Paper Chip for Simultaneous Detection of Multiple Foodborne Pathogens (2018)

A paper chip device-based recombinase polymerase amplification (RPA) method was developed for highly sensitive and selective single-step detection of foodborne pathogens. A paper chip was manufactured by simply stacking functional papers. RPA reagents and fluorescent probe were dried on the reaction zone of a patterned poly(ether sulfone) membrane. The RPA reaction was initiated by adding pathogen DNAs into an injection hole. Paper chip-based analysis of pathogens showed optimal performance at 37 °C for 20 min and the results were comparable to those obtained with solution-based RPA reactions. Based on the paper chip-based fluorescence signal, Escherichia coli, Staphylococcus aureus, and Salmonella typhimurium were simultaneously detected with detection limits of 10<sup>2</sup> cfu/mL. The diagnostic utility of the device was demonstrated by the reliable detection of E. coli and S. aureus present in spiked milk. This ready-to-use device could be integrated with simple nucleic acid extraction for food pathogen detection in resource-limited settings.
Cloning and Characterization of Lung-Endothelial Cell Adhesion Molecule-1 Suggest It Is an Endothelial Chloride Channel (1997)

Lung-endothelial cell adhesion molecule-1 (Lu-ECAM-1) is an endothelial cell surface molecule that mediates adhesion of metastatic melanoma cells to lung endothelium. Here we analyze the organization of the Lu-ECAM-1 protein complex, report the sequence of Lu-ECAM-1 cDNAs, and reveal a novel function of the protein. Lu-ECAM-1 immunopurified from bovine aortic endothelial cells (BAEC) consists of tightly associated glycoproteins of 90, 38, and 32 kDa, with minor components of 130 and 120 kDa. We present evidence that all of these protein species are encoded by a single open reading frame whose initial translation product is proteolytically processed to yield the other products. Correct processing in vitro was demonstrated by transfection of the longest cDNA into human embryonic kidney 293 cells; immunoblot analysis showed that the approximately 120-kDa precursor gave rise to 90- and 38-kDa products. RNA blots of BAEC mRNA detected messages in agreement with the sizes of the cDNA clones in addition to several of high molecular weight. DNA blot analysis showed that Lu-ECAM-1 is conserved throughout its length in all mammals tested, usually as a single or low copy gene. In the bovine, Lu-ECAM-1 protein is 88% identical to a calcium-dependent chloride channel described recently in tracheal epithelium, Ca-CC. Probes for Lu-ECAM-1 mRNA and protein confirmed the presence of a homolog in this tissue. We show that messages for both proteins are present in lung while only Ca-CC is present in trachea and only Lu-ECAM-1 is present in BAEC. These results suggest that endothelial cells express a chloride channel that is related to, but distinct from, that expressed in tracheal epithelium. They further suggest that an adhesion molecule can also be a chloride channel.
Botulinum Toxin Infiltration for Pain Control After Mastectomy and Expander Reconstruction (2004)

Muscular infiltration of botulinum toxin for mastectomy and tissue expander placement significantly reduced postoperative pain and discomfort without complications.
Object lens: a “spreadsheet” for cooperative work (1988)

Object Lens allows unsophisticated computer users to create their own cooperative work applications using a set of simple, but powerful, building blocks. By defining and modifying templates for various semistructured objects, users can represent information about people, tasks, products, messages, and many other kinds of information in a form that can be processed intelligently by both people and their computers. By collecting these objects in customizable folders, users can create their own displays which summarize selected information from the objects in table or tree formats. Finally, by creating semiautonomous agents, users can specify rules for automatically processing this information in different ways at different times. The combination of these primitives provides a single consistent interface that integrates facilities for object-oriented databases, hypertext, electronic messaging, and rule-based intelligent agents. To illustrate the power of this combined approach, we describe several simple examples of applications (such as task tracking, intelligent message routing, and database retrieval) that we have developed in this framework.
Sequence of the cDNA and 5′-Flanking Region for Human Acid α-Glucosidase, Detection of an Intron in the 5′ Untranslated Leader Sequence, Definition of 18-bp Polymorphisms, and Differences with Previous cDNA and Amino Acid Sequences (1990)

Acid maltase or acid alpha-glucosidase (GAA) is a lysosomal enzyme that hydrolyzes glycogen to glucose and is deficient in glycogen storage disease type II. Previously, we isolated a partial cDNA (1.9 kb) for human GAA; we have now used this cDNA to isolate and determine sequence in longer cDNAs from four additional independent cDNA libraries. Primer extension studies indicated that the mRNA extended approximately 200 bp 5' of the cDNA sequence obtained. Therefore, we isolated a genomic fragment containing 5' cDNA sequences that overlapped the previous cDNA sequence and extended an additional 24 bp to an initiation codon within a Kozak consensus sequence. The sequence of the genomic clone revealed an intron-exon junction 32 bp 5' to the ATG, indicating that the 5' leader sequence was interrupted by an intron. The remaining 186 bp of 5' untranslated sequence was identified approximately 3 kb upstream. The promoter region upstream from the start site of transcription was GC rich and contained areas of homology to Sp1 binding sites but no identifiable CAAT or TATA box. The combined data gave a nucleotide sequence of 2,856 bp for the coding region from the ATG to a stop codon, predicting a protein of 952 amino acids. The 3' untranslated region contained 555 bp with a polyadenylation signal at 3,385 bp followed by 16 bp prior to a poly(A) tail. This sequence of the GAA coding region differs from that reported by Hoefsloot et al. (1988) in three areas that change a total of 42 amino acids. Direct determination of the amino acid sequence in one of these areas confirmed the nucleotide sequence reported here but also disagreed with the directly determined amino acid sequence reported by Hoefsloot et al. (1988). At two other areas, changes in base pairs predicted new restriction sites that were identified in cDNAs from several independent libraries. The amino acid changes in all three ares increased the homology to rabbit-human isomaltase. Therefore, we believe that our nucleotide sequence for GAA is more precise. We have also identified single base-pair polymorphisms at 18 sites for human GAA, some of which are not silent.
Evaluation of Nanostructured Composite Collagen–Chitosan Matrices for Tissue Engineering (2001)

The development of suitable three-dimensional matrices for the maintenance of cellular viability and differentiation is critical for applications in tissue engineering and cell biology. The structure and composition of the extracellular matrix (ECM) has been shown to modulate cell behavior with respect to shape, movement, proliferation, and differentiation. Although collagen and chitosan have separately been proposed as in vitro ECM materials, the influence of chitosan--collagen composite matrices on cell morphology, differentiation, and function is not well studied. To this end, gel matrices of different proportions of collagen and chitosan were examined ultrastructurally and characterized for their ability to regulate cellular activity. A three-chamber system with circulating hydraulic fluids was used to evaluate the gel stability under fluid force. Results indicated that overall matrix integrity increased with the proportion of chitosan. Scanning electron microscopy indicated that the addition of chitosan greatly influences ultrastructure and changes collagen fiber cross-linking, reinforcing the structure and increasing pore size. K562 cells cultured in three-dimensional gels were examined for cell proliferation and differentiation. Although cell proliferation was inhibited with an increasing proportion of chitosan, cell function based on cytokine-release was greatly augmented. Results suggest that a hybrid chitosan--collagen matrix may have potential biological and mechanical benefits for use as a cellular scaffold.
Phylogenetic Position of Cowdria ruminantium (Rickettsiales) Determined by Analysis of Amplified 16S Ribosomal DNA Sequences (1992)

The 16S ribosomal DNA sequence of Cowdria ruminantium, the causative agent of heartwater disease in ruminants, was determined. An analysis of this sequence showed that C. ruminantium forms a tight phylogenetic cluster with the canine pathogen Ehrlichia canis and the human pathogen Ehrlichia chaffeensis. Although a close relationship between the genus Cowdria and several members of the tribe Ehrlichieae has been suspected previously, the tight phylogenetic cluster with E. canis and E. chaffeensis is surprising in view of known differences in host preference and target cells.
Analysisof Bioheat Transport Through a Dual Layer BiologicalMedia (2009)

Abstract A comprehensive analysis of bioheat transport through a double layer and multilayer biological media is presented in this work. Analytical solutions have been developed for blood and tissue phase temperatures and overall heat exchange correlations, incorporating thermal conduction in tissue and vascular system, blood-tissue convective heat exchange, metabolic heat generation, and imposed heat flux, utilizing both local thermal nonequilibrium and equilibrium models in porous media theory. Detailed solutions as well as Nusselt number distributions are given, for the first time, for two primary conditions, namely, isolated core region and uniform core temperature. The solutions incorporate the pertinent effective parameters for each layer, such as volume fraction of the vascular space, ratio of the blood, and the tissue matrix thermal conductivities, interfacial blood-tissue heat exchange, tissue/organ depth, arterial flow rate and temperature, body core temperature, imposed hyperthermia heat flux, metabolic heat generation, and blood physical properties. Interface temperature profiles are also obtained based on the continuity of temperature and heat flux through the interface and the physics of the problem. Comparisons between these analytical solutions and limiting cases from previous works display an excellent agreement. These analytical solutions establish a comprehensive presentation of bioheat transport, which can be used to clarify various physical phenomena as well as establishing a detailed benchmark for future works in this area.