gebhart/patrepeval huggingface dataset:
Monoclonal Antibodies to the Multienzyme Enniatin Synthetase. Production and Use in Structural Studies (1987)

Monoclonal antibodies have been prepared against the multifunctional enzyme enniatin synthetase, which catalyses the biosynthesis of the cyclodepsipeptide antibiotic enniatin. Five different antibodies (designated 1.56, 21.1, 25.91, 28.7 and 28.34) were characterized. 1.56, 21.1 and 25.91 were of IgG1 and 28.7 and 28.34 of IgM subclass. Binding studies showed that 21.1 and 25.91 are obviously directed against determinants based on the primary structure of the enzyme, whereas 28.7, 28.34 and 1.56 bind to the native enzyme. All antibodies inhibited enniatin formation. Based on their ability to inhibit different partial reactions of the multienzyme the antibodies could be divided into three groups: 21.1 and 25.91 inhibit valyl thioester formation, 1.56 additionally inhibits D-2-hydroxyisovaleric acid thioesterification, and 28.7 and 28.34 block both thioester sites as well as the N-methylation step. None of the antibodies affected the formation of L-valyl or D-hydroxyisovaleryl adenylate by the enzyme. The results indicate that there must be distinct thioester activation sites for valine and D-hydroxyisovalerate close to each other and in the neighbourhood of the methyltransferase site. The adenylation sites for D-hydroxy-isovalerate and L-valine are obviously located at some distance.
Properties and structure (2005)

Ionic Liquids III will complete the trilogy of Symposium Series books Ionic Liquids: Industrial Applications for Green Chemistry, SS 818 and Ionic Liquids as Green Solvents: Progress and Prospects, SS 856 edited by Robin Rogers and Ken Seddon. Ionic Liquids III will include the latest advances in the field of ionic liquids (IL).
Structural Studies of a Neuropeptide Precursor Protein with an RGD Proteolytic Site (2001)

The snail Lymnaea stagnalis produces a neuropeptide precursor protein that contains seven Arg-Gly-Asp (RGD) sites. These sites are recognized and cleaved by one or more prohormone convertases in the first processing step to yield mature neuropeptides in the secretory pathway. Conformations of two synthetic RGD-containing peptides derived from the L. stagnalis precursor protein were determined by NMR spectroscopy. The peptides were tested in a platelet aggregation assay for RGD activity and were processed in vitro by PC2 and furin. The native peptide with a proline following the RGD site has minimal structure around the RGD region, does not inhibit platelet aggregation, and is properly processed by the enzymes PC2 and furin. A variant of the native fragment with a serine following the RGD sequence has a significant amount of a reverse turn around the RGD region, is a potent inhibitor of platelet aggregation, and is processed with the same specificity as the native fragment. The large conformational differences between the two peptides provide a molecular mechanism for effects of proline residues following the RGD site and suggest that precursor processing is influenced more by flexibility than by the conformation of the processing site.
Muscle: a source of progenitor cells for bone fracture healing (2011)

Bone repair failure is a major complication of open fracture, leading to non-union of broken bone extremities and movement at the fracture site. This results in a serious disability for patients. The role played by the periosteum and bone marrow progenitors in bone repair is now well documented. In contrast, limited information is available on the role played by myogenic progenitor cells in bone repair. In a recent article published in BMC Musculoskeletal Disorders, Liu et al. compared the presence of myogenic progenitor (MyoD lineage cells) in closed and open fractures. They showed that myogenic progenitors are present in open, but not closed fractures, suggesting that muscle satellite cells may colonize the fracture site in the absence of intact periosteum. Interestingly, these progenitors sequentially expressed a chondrogenic and, thereafter, an osteoblastic phenotype, suggestive of a functional role in the repair process. This finding opens up new perspectives for the research of orthopedic surgical methods, which could maximize myogenic progenitor access and mobilization to augment bone repair. Please see related article: http://www.biomedcentral.com/1471-2474/12/288.
Characterization of cDNAs for Human Estradiol 17β-Dehydrogenase and Assignment of the Gene to Chromosome 17: Evidence of two mRNA Species with Distinct 5′-Termini in Human Placenta (1989)

Human placental estradiol 17β-dehydrogenase (E2DH) cDNA clones were isolated from a λgt11 expression library by screening with 33 mer synthetic oligonucleotides derived from the amino acid sequence of the catalytic site of E2DH and with polyclonal antibodies raised against the enzyme purified from human placenta. Using 32P-labeled fragments from the coding and 5′-untranslated regions, two mRNA species have been identified in poly(A)+ RNA from human placenta, a major species migrating at 1.3 kilobases (kb) while a minor one is found at 2.2 kb. Primer extension analysis identifies the major mRNA as starting 9–10 nucleotides upstream from the in-frame ATG initiating codon while the longer mRNA has at least 814 noncoding nucleotides at its 5′-terminus. Sequence analysis of the longest cDNA clone (2092 base pairs) shows that this clone possesses identical coding and noncoding sequences in the regions of overlap with the shorter cDNA clones. The 32P-labeled 5′-noncoding fragment hybridized only to the 2.2 kb band, thus providing additional evidence for the existence of two distinct mRNA species which differ only in their 5′- noncoding regions. Using hpE2DH36 cDNA as a probe for in situ hybridization, the human E2DH gene was localized to the q11-q12 region of chromosome 17. The cloned cDNAs encode E2DH, a 327-amino acid protein having a calculated molecular weight of 34,853. Since E2DH is the enzyme required for the formation of 17β-estradiol, the availability of the cDNA encoding the enzyme should permit a detailed investigation of the factors regulating the expression and activity of this crucial enzyme in both normal and malignant tissues, especially breast cancer.
The Human Cytomegalovirus UL116 Glycoprotein Is a Chaperone to Control gH-Based Complexes Levels on Virions (2021)

Human cytomegalovirus (HCMV) relies in large part upon the viral membrane fusion glycoprotein B and two alternative gH/gL complexes, gH/gL/gO (Trimer) and gH/gL/UL128/UL130/UL131A (Pentamer) to enter into cells. The relative amounts of Trimer and Pentamer vary among HCMV strains and contribute to differences in cell tropism. Although the viral ER resident protein UL148 has been shown to interact with gH to facilitate gO incorporation, the mechanisms that favor the assembly and maturation of one complex over another remain poorly understood. HCMV virions also contain an alternative non-disulfide bound heterodimer comprised of gH and UL116 whose function remains unknown. Here, we show that disruption of HCMV gene UL116 causes infectivity defects of ∼10-fold relative to wild-type virus and leads to reduced expression of both gH/gL complexes in virions. Furthermore, gH that is not covalently bound to other viral glycoproteins, which are readily detected in wild-type HCMV virions, become undetectable in the absence of UL116 suggesting that the gH/UL116 complex is abundant in virions. We find evidence that UL116 and UL148 interact during infection indicating that the two proteins might cooperate to regulate the abundance of HCMV gH complexes. Altogether, these results are consistent with a role of UL116 as a chaperone for gH during the assembly and maturation of gH complexes in infected cells.
EMF genes regulate Arabidopsis inflorescence development. (1997)

Mutations in EMBRYONIC FLOWER (EMF) genes EMF1 and EMF2 abolish rosette development, and the mutants produce either a much reduced inflorescence or a transformed flower. These mutant characteristics suggest a repressive effect of EMF activities on reproductive development. To investigate the role of EMF genes in regulating reproductive development, we studied the relationship between EMF genes and the genes regulating inflorescence and flower development. We found that APETALA1 and AGAMOUS promoters were activated in germinating emf seedlings, suggesting that these genes may normally be suppressed in wild-type seedlings in which EMF activities are high. The phenotype of double mutants combining emf1-2 and apetala1, apetala2, leafy1, apetala1 cauliflower, and terminal flower1 showed that emf1-2 is epistatic in all cases, suggesting that EMF genes act downstream from these genes in mediating the inflorescence-to-flower transition. Constitutive expression of LEAFY in weak emf1, but not emf2, mutants increased the severity of the emf phenotype, indicating an inhibition of EMF activity by LEAFY, as was deduced from double mutant analysis. These results suggest that a mechanism involving a reciprocal negative regulation between the EMF genes and the floral genes regulates Arabidopsis inflorescence development.
A Variant of Recombinant Factor VIIa with Enhanced Procoagulant and Antifibrinolytic Activities in a Model of Hemophilia. (2006)

Abstract Recombinant factor VIIa (rFVIIa, NovoSeven; Novo Nordisk A/S, Copenhagen, Denmark) has proven efficacy in treating bleeding in hemophilia patients with inhibitors. We have shown that high concentrations of rFVIIa improve parameters of thrombin generation and fibrin clot formation and stability in an in vitro model of hemophilia (Wolberg et al. 2005 Brit J Haem 131:645–55). Recently, new rFVIIa analogs with increased procoagulant activity have been described. One of these analogs, rFVIIa with mutations V158D/E296V/M298Q (NN1731), exhibits increased activity in in vitro and in vivo models. In the present study, we compared the abilities of rFVIIa and NN1731 to specifically modulate factor X activation, platelet activation, thrombin generation, and fibrin clot formation and stability in an in vitro model of hemophilia. RFVIIa and NN1731 similarly increased factor X activation on tissue factor−bearing monocytes; however, NN1731 exhibited 30−fold higher factor Xa generation rates on activated platelets than similar concentrations of rFVIIa. We employed a complete, cell−based, reconstituted model of coagulation to compare the activities of rFVIIa and NN1731 in hemophilic conditions. The model system consists of tissue−factor bearing monocytes, purified pro− and anti−coagulant proteins (XI, X, IX, VIII, VIIa, V, II, AT, TFPI), and freshly−isolated, unactivated platelets. Fibrinogen is included in certain wells to examine clot formation. “Hemophilia” is simulated by omitting factors VIII and IX. In this assay, NN1731 produced 4 – 10−fold higher maximal thrombin generation rates than equal concentrations of rFVIIa. In contrast to even very high concentrations of rFVIIa (up to 500 nM), NN1731 was able to normalize the rate of thrombin generation. NN1731 did not directly activate platelets and thrombin generation was not detected prior to platelet activation, suggesting that the presence of NN1731 would not lead to thrombin generation in the absence of injury. Both rFVIIa and NN1731 shortened clotting times in the absence of factors IX and VIII; however, NN1731 did so at lower concentrations than were required of rFVIIa. In a plasmin challenge assay, in which clot formation is initiated in the presence of plasmin, both rFVIIa and NN1731 increased fibrin formation and the length of time that fibrin was present in the absence of factors IX and VIII; however, NN1731 was effective at lower concentrations than were required of rFVIIa. Our results indicate that NN1731 increases factor Xa and thrombin generation and promotes clot formation and stability to a greater degree than equal concentrations of rFVIIa. For these reasons, NN1731 may be especially efficacious in situations in which rapid formation of a firm fibrin clot with increased resistance to fibrinolysis is necessary to achieve hemostasis.
Dynamic charge storage in 6H silicon carbide (1992)

pn-junction storage capacitors have been fabricated in 6H silicon carbide. The charge decay is dominated by surface generation at the mesa edges, and the storage time strongly depends on the method of surface passivation. Charge recovery is thermally activated. Devices passivated by dry oxidation and by wet oxidation exhibit activation energies of 0.66 and 1.48 eV, respectively. As a figure of merit, extrapolation of the dry-oxide data gives a room-temperature storage time of 106 s, while extrapolation of the wet-oxide data gives a room-temperature storage time of 1014 s.
Nucleotide Sequence of the Simian Virus 40 HindII + III Restriction Fragment D and the Total Amino Acid Sequence of the Late Proteins VP2 and VP3 (1978)

Earlier papers from our laboratory reported the nucleotide sequence of the beginning of the simian virus 40 HindII + III fragment D (Hind-D, which contains the information for the presumed initiation codon for the VP2 protein), HindII + III fragment E (HindII + III fragment K (Hind-K, which contains the information for the termination signal for the VP2 and VP3 proteins and the initiation signal for the VP1 protein). We report here the nucleotide sequence of the remainder of fragment Hind-D as determined by the partial, chemical degradation procedure of Maxam and Gilbert [Proc. Natl Acad. Sci. U.S.A. (1977) 74, 560–564]. As the aforementioned restriction fragments cover the total of the overlapping VP2 and VP3 genes, the entire nucleotide sequence of these genes, as well as the derived amino acid sequence of the VP2 and VP3 proteins, is now known. Assuming that eukaryotic protein synthesis always starts with an AUG codon (and not with a GUG) and considering various evidence about the position of the VP3 gene within the VP2 gene, we conclude that the second AUG codon in phase coded by fragment Hind-D serves as the initiation codon for the translation of VP3. The first part of VP2 (98 residues), which is not present in VP3, is very hydrophobic and contains no cysteine or basic amino acids; possibly it serves for binding to, or penetrating through, membranes. The very basic carboxyl terminus of both VP2 and VP3 may possibly be involved in attachment to the DNA.
Sequencing and genotypic analysis of the triosephosphate isomerase (TPI1) locus in a large sample of long-lived Germans (2008)

This study marks the TPI1 locus as extraordinarily conserved, even when analyzing intronic and non-coding regions of the gene. None of the identified sequence variations affected the amino acid composition of the TPI protein and hence, are unlikely to impact the catalytic activity of the enzyme. Thus, TPI variants occur less frequent than expected and inactive alleles are not enriched in German centenarians.
Bone grafts in hip replacement surgery. The pelvic side. (1993)

Replacement arthroplasty of the hip may require restoration of bone stock to provide support for the acetabular implant and to restore anatomy and leg lengths. This article discusses the indications, surgical technique, results, and controversies of using bulk autograft bone to provide cup support for primary hip replacement in hip dysplasia. In addition, the use of allograft bone to restore bone stock in the revision situation is covered. The indications, surgical technique, and results of the use of both morsellized and bulk allograft bone are presented.
Encoding First Order Proofs in SMT (2008)

We present a method for encoding first order proofs in SMT. Our implementation, called ChewTPTP-SMT, transforms a set of first order clauses into a propositional encoding (modulo theories) of the existence of a rigid first order connection tableau and the satisfiability of unification constraints, which is then fed to Yices. For the unification constraints, terms are represented as recursive datatypes, and unification constraints are equations on terms. The finiteness of the tableau is encoded by linear real arithmetic inequalities. We compare our implementation with our previous implementation ChewTPTP-SAT, encoding rigid connection tableau in SAT, and show that for Horn clauses many fewer propositional clauses are generated by ChewTPTP-SMT, and ChewTPTP-SMT is much faster than ChewTPTP-SAT. This is not the case for our non-Horn clause encoding. We explain this, and we conjecture a rule of thumb on when to use theories in encoding a problem.
Stopped-flow kinetic analysis of long-chain fatty acid dissociation from bovine serum albumin (2002)

The kinetics of the interaction of long-chain fatty acids (referred to as fatty acids) with albumin is critical to understanding the role of albumin in fatty acid transport. In this study we have determined the kinetics of fatty acid dissociation from BSA and the BSA-related fatty acid probe BSA-HCA (BSA labelled with 7-hydroxycoumarin-4-acetic acid) by stopped-flow methods. Fatty acid—albumin complexes of a range of natural fatty acid types and albumin molecules (donors) were mixed with three fatty acid-binding acceptor proteins. Dissociation of fatty acids from the donor was monitored by either the time course of donor fluorescence/absorbance or the time course of acceptor fluorescence. The results of these measurements indicate that fatty acid dissociation from BSA as well as BSA-HCA is well described by a single exponential function over the entire range of fatty acid/albumin molar ratios used in these measurements, from 0.5:1 to 6:1. The observed rate constants (kobs) for the dissociation of each fatty acid type reveal little or no dependence on the initial fatty acid/albumin ratio. However, dissociation rates were dependent upon the type of fatty acid. In the case of native BSA with an initial fatty acid/BSA molar ratio of 3:1, the order of kobs values was stearic acid (1.5s−1)<oleic acid<palmitic acid≅linoleic acid<arachidonic acid (8s−1) at 37°C. The corresponding values for BSA-HCA were about half the values for BSA. The results of this study show that the rate of fatty acid dissociation from native BSA is more than 10-fold faster than reported previously and that the off-rate constants for the five primary fatty acid-binding sites differ by less than a factor of 2. We conclude that for reported rates of fatty acid transport across cell membranes, dissociation of fatty acids from the fatty acid—BSA complexes used in the transport studies should not be rate-limiting.
Optimum Bit-Level Distribution Matching with at most O(N3) Implementation Complexity (2019)

An algorithm of distribution matching which could be effectively implemented for short block lengths of around 100 bit or less is proposed, enabling better performance than the constant composition schemes with the same block lengths.
Cardiac troponin biosensors: where are we now? (2018)

Abstract: Acute myocardial infarction (AMI) is one of the leading causes of death among the cardiovascular diseases. Of several biomarkers used for detection, increased levels of cardiac troponins have proved to be significant in diagnosing AMI. This has motivated researchers in the field to develop point-of-care biosensors for rapid detection of an episode of AMI. Over the years, various detection techniques have emerged for the estimation of cardiac troponins. This review focuses on summarizing various biosensing methods, including optical, electrochemical, and acoustic techniques, for the detection of cardiac troponins. Keywords: cardiac troponin, acute myocardial infarction, optical, electrochemical, SPR, SERS
Inactivation of the p16 Cyclin-Dependent Kinase Inhibitor in High-Grade Canine Non-Hodgkin's T-Cell Lymphoma (2007)

The significance of p16/Rb tumor suppressor pathway inactivation in T-cell non-Hodgkin's lymphoma (NHL) remains incompletely understood. We used naturally occurring canine NHL to test the hypothesis that p16 inactivation has specific pathologic correlates. Forty-eight samples (22 T-cell NHL and 26 B-cell NHL) were included. As applicable, metaphase- or array-based comparative genomic hybridization, Southern blotting, promoter methylation, and Rb phosphorylation were used to determine the presence, expression, and activity of p16. Fisher's exact test was used to test for significance. Deletion of p16 (or loss of dog chromosome 11) was restricted to high-grade T-cell NHL (lymphoblastic T-cell lymphoma and peripheral T-cell lymphoma, not otherwise specified). These were characterized by a concomitant increase of tumor cells with Rb phosphorylation at canonical CDK4 sites. Rb phosphorylation also was seen in high-grade B-cell NHL (diffuse large B-cell lymphoma and Burkitt-type lymphoma), but in those cases, it appeared to be associated with c-Myc overexpression. The data show that p16 deletion or inactivation occurs almost exclusively in high-grade T-cell NHL; however, alternative pathways can generate functional phenotypes of Rb deficiency in low-grade T-cell NHL and in high-grade B-cell NHL. Both morphologic classification according to World Health Organization criteria and assessment of Rb phosphorylation are prognostically valuable parameters for canine NHL.
TO-SYN-FUEL, The Demonstration of Waste Biomass to Synthetic Fuels and Green Hydrogen, European Commission Horizon2020 programme (2018)

TO-SYN-FUEL will demonstrate the conversion of organic waste biomass (Sewage Sludge) into biofuels. The project implements a new integrated process combining Thermo-Catalytic Reforming (TCR'), with hydrogen separation through pressure swing adsorption (PSA), and hydro deoxygenation (HDO), to produce a fully equivalent gasoline and diesel substitute (compliant with EN228 and EN590 European Standards) and green hydrogen for use in transport . The TO-SYN-FUEL project consortium has undoubtedly bought together the leading researchers, industrial technology providers and renewable energy experts from across Europe, in a combined, committed and dedicated research effort to deliver the overarching ambition. Building and extending from previous framework funding this project is designed to set the benchmark for future sustainable development and growth within Europe and will provide a real example to the rest of the world of how sustainable energy, economic, social and environmental needs can successfully be addressed. This project will be the platform for deployment of a subsequent commercial scale facility. This will be the first of its kind to be built anywhere in the world, processing organic industrial wastes directly into transportation grade biofuels fuels which will be a demonstration showcase for future sustainable investment and economic growth across Europe. This project will mark the first pre-commercial scale deployment of the technology processing up to 2100 tonnes per year of dried sewage sludge into 210,000 litres per year of liquid biofuels and up to 30,000 kg of green hydrogen. The scale up of 100 of such plants installed throughout Europe would be sufficient to convert up to 32 million tonnes per year of organic wastes into sustainable biofuels, contributing towards 35 million tonnes of GHG savings and diversion of organic wastes from landfill. This proposal is responding to the European Innovation Call LCE-19.
Workflow Complexity for Collaborative Interactions: Where are the Metrics? -- A Challenge (2017)

In this paper, we introduce the problem of denoting and deriving the complexity of workflows (plans, schedules) in collaborative, planner-assisted settings where humans and agents are trying to jointly solve a task. The interactions -- and hence the workflows that connect the human and the agents -- may differ according to the domain and the kind of agents. We adapt insights from prior work in human-agent teaming and workflow analysis to suggest metrics for workflow complexity. The main motivation behind this work is to highlight metrics for human comprehensibility of plans and schedules. The planning community has seen its fair share of work on the synthesis of plans that take diversity into account -- what value do such plans hold if their generation is not guided at least in part by metrics that reflect the ease of engaging with and using those plans?