gebhart/patrepeval huggingface dataset:
A kepstrum approach to filtering, smoothing and prediction (2002)

The kepstrum (or complex cepstrum) method is revisited and applied to the problem of spectral factorization &#13;\nwhere the spectrum is directly estimated from observations. The solution to this problem in turn leads to a new &#13;\napproach to optimal filtering, smoothing and prediction using the Wiener theory. Unlike previous approaches to &#13;\nadaptive and self-tuning filtering, the technique, when implemented, does not require a priori information on the &#13;\ntype or order of the signal generating model. And unlike other approaches - with the exception of spectral &#13;\nsubtraction - no state-space or polynomial model is necessary. In this first paper results are restricted to &#13;\nstationary signal and additive white noise.
Biofilm accumulation model that predicts antibiotic resistance of Pseudomonas aeruginosa biofilms (1994)

A computer model of biofilm dynamics was adapted to incorporate the activity of an antimicrobial agent on bacterial biofilm. The model was used to evaluate the plausibility of two mechanisms of biofilm antibiotic resistance by qualitative comparison with data from a well-characterized experimental system (H. Anwar, J. L. Strap, and J. W. Costerton, Antimicrob. Agents Chemother. 36:1208-1214, 1992). The two mechanisms involved either depletion of the antibiotic by reaction with biomass or physiological resistance due to reduced bacterial growth rates in the biofilm. Both mechanisms predicted the experimentally observed resistance of 7-day-old Pseudomonas aeruginosa biofilms compared with that of 2-day-old ones. A version of the model that incorporated growth rate-dependent killing predicted reduced susceptibility of thicker biofilms because oxygen was exhausted within these biofilms, leading to very slow growth in part of the biofilm. A version of the model that incorporated a destructive reaction of the antibiotic with biomass likewise accounted for the relative resistance of thicker biofilms. Resistance in this latter case was due to depletion of the antibiotic in the bulk fluid rather than development of a gradient in the antibiotic concentration within the biofilm. The modeling results predicted differences between the two cases, such as in the survival profiles within the biofilm, that could permit these resistance mechanisms to be experimentally distinguished.
A mechanism for neutrophil-mediated lysis of human neuroblastoma cells. (1993)

Neutrophils mediate the lysis of human neuroblastoma cells coated with human/mouse chimeric anti-GD2 ganglioside antibody ch14.18. This study examined the mechanism(s) by which this occurs. Neutrophil degranulation was found to be a required step for lysis, since release of granular enzymes from neutrophils correlated with the lysis of antibody-coated neuroblastoma cells. In addition, agents which block degranulation specifically inhibited this process. Antibody-dependent lysis of neuroblastoma cells was enhanced by exposing neutrophils to granulocyte-macrophage colony stimulatory factor. An increased release of lytic granular molecules was found to be responsible for this lymphokine-mediated phenomenon. Among the molecules released from neutrophil granules that were shown to be involved in neuroblastoma cell lysis were defensins, M(r) 3000-4000 neutrophil granular proteins which are known to bind and permeabilize tumor cells. In addition, cathepsin-G, a neutrophil granular protease, was demonstrated for the first time to mediate the lysis of human neuroblastoma cells. The enzymatic activity of cathepsin-G was found to be required for the lysis of these tumor cells, since phenylmethylsulfonyl fluoride blocks the lytic ability of this protein.
Structural and Functional Repetition in a Marine Mussel Adhesive Protein (1990)

The DOPA-rich polyphenolic protein secreted by the marine mussel Mytilus edulis establishes key chemical linkages in a water-resistant adhesive. Molecular cloning of the gene for this remarkable protein reveals its primary structure as one of the most repetitive proteins identified in the animal kingdom. Expression and purification of polyphenolic proteins from recombinant yeast have provided sufficient material to demonstrate adhesivity of these polypeptides in the laboratory. Adhesive tests reveal a water-resistant bonding capacity of the protein that is dependent on in vitro modification of tyrosine residues to DOPA and the subsequent oxidation to quinone.
Science with no fiction: measuring the veracity of scientific reports by citation analysis (2017)

Abstract The current crisis of veracity in biomedical research is enabled by the lack of publicly accessible information on whether the reported scientific claims are valid. One approach to solve this problem is to replicate previous studies by specialized reproducibility centers. However, this approach is costly or unaffordable and raises a number of yet to be resolved concerns that question its effectiveness and validity. We propose to use an approach that yields a simple numerical measure of veracity, the R-factor, by summarizing the outcomes of already published studies that have attempted to test a claim. The R-factor of an investigator, a journal, or an institution would be the average of the R-factors of the claims they reported. We illustrate this approach using three studies recently tested by a replication initiative, compare the results, and discuss how using the R-factor can help improve the veracity of scientific research.
Biosynthesis of the Allylmalonyl-CoA Extender Unit for the FK506 Polyketide Synthase Proceeds through a Dedicated Polyketide Synthase and Facilitates the Mutasynthesis of Analogues (2010)

The allyl moiety of the immunosuppressive agent FK506 is structurally unique among polyketides and critical for its potent biological activity. Here, we detail the biosynthetic pathway to allylmalonyl-coenzyme A (CoA), from which the FK506 allyl group is derived, based on a comprehensive chemical, biochemical, and genetic interrogation of three FK506 gene clusters. A discrete polyketide synthase (PKS) with noncanonical domain architecture presumably in coordination with the fatty acid synthase pathway of the host catalyzes a multistep enzymatic reaction to allylmalonyl-CoA via trans-2-pentenyl-acyl carrier protein. Characterization of this discrete pathway facilitated the engineered biosynthesis of novel allyl group-modified FK506 analogues, 36-fluoro-FK520 and 36-methyl-FK506, the latter of which exhibits improved neurite outgrowth activity. This unique feature of FK506 biosynthesis, in which a dedicated PKS provides an atypical extender unit for the main modular PKS, illuminates a new strategy for the combinatorial biosynthesis of designer macrolide scaffolds as well as FK506 analogues.
PCR Protocols (1993)

PCR has been successfully utilized in every facet of basic, cli- cal, and applied studies of the life sciences, and the impact that PCR has had on life science research is already staggering. C- comit
Purification of H gene-encoded beta-galactoside alpha 1—-2 fucosyltransferase from human serum. (1990)

The human serum enzyme, beta-galactoside alpha 1----2 fucosyltransferase, presumably blood group H gene-encoded, was purified to homogeneity from serum of AB and mixed secretor phenotype individuals. The purification procedure involved chromatography on phenyl-Sepharose, S-Sepharose, GDP-hexanolamine-Sepharose, and high pressure liquid chromatography gel filtration. The enzyme was purified 10 x 10(6)-fold, with a final specific activity of 23.6 units/mg for the phenyl-beta-O-galactoside acceptor. The apparent Mr of the H gene-encoded beta-galactoside alpha 1----2 fucosyltransferase was determined as 200,000 and 50,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis in nonreducing and reducing conditions, respectively. The Mr of native enzyme was found by gel filtration chromatography to be 148,000. The subunit structure as well as the sensitivity of the enzymatic activity to beta-mercaptoethanol suggest that the native enzyme exists in polymeric form of covalently bound subunits. Lectin binding properties of the purified molecule indicate that the enzyme is glycosylated. Another human serum beta-galactoside alpha 1----2 fucosyltransferase, presumably Se gene-encoded, was separated from the H enzyme by adsorption on S-Sepharose cation exchange matrix. A comparison of the kinetic parameters of the initial rate data of both alpha 1----2 fucosyltransferases revealed differences between Km values for various oligosaccharide acceptors. Higher Km values for the phenyl-beta-O-galactoside acceptor and a lower Km for the lacto-N-tetraose-beta-O-PA8 type 1 acceptor for the enzyme that adsorbed to S-Sepharose compared with nonadsorbed enzyme were observed. The two enzymes also were differentiated by binding properties to S-Sepharose and electrophoretic mobilities on native gel electrophoresis. We, therefore, postulate that the enzyme which does not adsorb to S-Sepharose and adsorbed enzyme are structurally different molecules and they represent the H and Se gene-encoded beta-galactoside alpha 1----2 fucosyltransferases, respectively.
Surface Modification of Silicone Elastomer Using Perfluorinated Ether (1999)

The surface properties of a poly(dimethylsiloxane) elastomer have been modified by reacting an allyl amide functional perfluorinated ether (PFE) to the siloxane network by a hydrosilation reaction. Examination of the surface by contact angle and X-ray photoelectron spectroscopy revealed that the perfluorinated ether migrates to the surface of the polymer, thus reducing its surface energy from 22 to about 8 mJ/m2 without affecting its bulk material properties. The resultant surface however exhibits higher contact angle hysteresis than that seen with the PFE-free elastomer. These results indicate that the higher energy amide functionalities of the perfluorinted ether are available for interfacial interaction, even though they are buried below the PFE layer. This study demonstrates that a high-energy group can be pulled to the free surface of a polymer by the driving forces of the lower energy groups segregating to the surface. The high-energy groups are available for further chemical interactions when the surface reconstructs in contact with a high-energy environment.
Evidence for evolution of canine parvovirus type 2 in Italy (2001)

Two isolates of canine parvovirus (CPV) were obtained from dogs affected with severe haemorrhagic diarrhoea. Type 2b antigenic specificity was predicted by both antigenic analysis with monoclonal antibodies and PCR characterization with type-specific primers. Nevertheless, sequence analysis of the capsid protein-encoding gene revealed two amino acid changes. One of the changes affected position 426 (Asp to Glu), in a major antigenic site of the viral capsid, determining the replacement of a residue unique to CPV type 2b. The failure of established typing methods to distinguish this antigenic variant was overcome by the development of an RFLP assay.
Advanced turbine cooling, heat transfer, and aerodynamic studies (1995)

The contractual work is in three parts: Part I - Effect of rotation on enhanced cooling passage heat transfer, Part II - Effect of Thermal Barrier Coating (TBC) spallation on surface heat transfer, and Part III - Effect of surface roughness and trailing edge ejection on turbine efficiency under unsteady flow conditions. Each section of this paper has been divided into three parts to individually accommodate each part. Part III is further divided into Parts IIIa and IIIb.
An Intronic Splicing Silencer Causes Skipping of the IIIb Exon of Fibroblast Growth Factor Receptor 2 through Involvement of Polypyrimidine Tract Binding Protein (2000)

Alternative splicing of fibroblast growth factor receptor 2 (FGF-R2) transcripts involves the mutually exclusive usage of exons IIIb and IIIc to produce two different receptor isoforms. Appropriate splicing of exon IIIb in rat prostate cancer DT3 cells requires a previously described cis element (ISAR, for "intronic splicing activator and repressor") which represses the splicing of exon IIIc and activates the splicing of exon IIIb. This element is nonfunctional in rat prostate AT3 cells, which repress exon IIIb inclusion and splice to exon IIIc. We have now identified an intronic element upstream of exon IIIb that causes repression of exon IIIb splicing. Deletion of this element abrogates the requirement for ISAR in order for exon IIIb to be spliced in DT3 cells and causes inappropriate inclusion of exon IIIb in AT3 cells. This element consists of two intronic splicing silencer (ISS) sequences, ISS1 and ISS2. The ISS1 sequence is pyrimidine rich, and in vitro cross-linking studies demonstrate binding of polypyrimidine tract binding protein (PTB) to this element. Competition studies demonstrate that mutations within ISS1 that abolish PTB binding in vitro alleviate splicing repression in vivo. Cotransfection of a PTB-1 expression vector with a minigene containing exon IIIb and the intronic splicing silencer element demonstrate PTB-mediated repression of exon IIIb splicing. Furthermore, all described PTB isoforms were equally capable of mediating this effect. Our results support a model of splicing regulation in which exon IIIc splicing does not represent a default splicing pathway but rather one in which active repression of exon IIIb splicing occurs in both cells and in which DT3 cells are able to overcome this repression in order to splice exon IIIb.
Tumor lysate-pulsed dendritic cells can elicit an effective antitumor immune response during early lymphoid recovery (2002)

Dendritic cells (DC) can serve to immunize the newborn immune system to foreign antigen. In a lymphopenic environment, naive T cells undergoing homeostasis-driven proliferation can acquire increased sensitivity to antigen stimulation. Here, we evaluated the capacity of DC to effectively prime the host immune system to elicit antitumor effects in the setting of early lymphoid reconstitution after bone marrow transplantation (BMT). Indeed, bone marrow-derived, cytokine-driven DC pulsed with whole tumor lysates (TP-DC) could, early on, prime a specific and long-lasting antitumor immune response, which mediated the rejection of a lethal challenge of a weakly immunogenic breast tumor. In the therapeutic setting, TP-DC could also inhibit the growth of preexisting breast tumor metastases by repetitive immunizations initiated early after BMT. Spleen T cells obtained from mice immunized with TP-DC early after BMT showed a substantial increase in tumor-specific IFN-gamma production. Our findings demonstrate that it is possible to promote effective antitumor immunity in a defined lymphopenic environment through DC-based immunization.
Identification of bitmap compression history: jpeg detection and quantizer estimation (2003)

Sometimes image processing units inherit images in raster bitmap format only, so that processing is to be carried without knowledge of past operations that may compromise image quality (e.g., compression). To carry further processing, it is useful to not only know whether the image has been previously JPEG compressed, but to learn what quantization table was used. This is the case, for example, if one wants to remove JPEG artifacts or for JPEG re-compression. In this paper, a fast and efficient method is provided to determine whether an image has been previously JPEG compressed. After detecting a compression signature, we estimate compression parameters. Specifically, we developed a method for the maximum likelihood estimation of JPEG quantization steps. The quantizer estimation method is very robust so that only sporadically an estimated quantizer step size is off, and when so, it is by one value.
Attaching Silica Nanoparticles from Suspension onto Surface Charge Patterns Generated by a Conductive Atomic Force Microscope Tip (2001)

A conductive atomic force microscope (AFM) tip acts as a nanopencilto write positive or negative charge patterns into a fluorocarbon film. Silica nanobeads (with a positive surface charge) can be attached to negative patterns by Coulombic interaction. While the resolution of the writing process is up to 100 nm, coagulation of the silica beads makes 1 μm a realistic minimum width for structures thus formed (see Figure and also cover).
Two membrane protein fractions from rat central myelin with inhibitory properties for neurite growth and fibroblast spreading. (1988)

Lack of neurite growth in optic nerve explants in vitro has been suggested to be due to nonpermissive substrate properties of higher vertebrate central nervous system (CNS) white matter. We have searched for surface components in CNS white matter, which would prevent neurite growth. CNS, but not peripheral nervous system (PNS) myelin fractions from rat and chick were highly nonpermissive substrates in vitro. We have used an in vitro spreading assay with 3T3 cells to quantify substrate qualities of membrane fractions and of isolated membrane proteins reconstituted in artificial lipid vesicles. CNS myelin nonpermissiveness was abolished by treatment with proteases and was not associated with myelin lipid. Nonpermissive proteins were found to be membrane bound and yielded highly nonpermissive substrates upon reconstitution into liposomes. Size fractionation of myelin protein by SDS-PAGE revealed two highly nonpermissive minor protein fractions of Mr 35 and 250-kD. Removal of 35- and of 250-kD protein fractions yielded a CNS myelin protein fraction with permissive substrate properties. Supplementation of permissive membrane protein fractions (PNS, liver) with low amounts of 35- or of 250-kD CNS myelin protein was sufficient to generate highly nonpermissive substrates. Inhibitory 35- and 250-kD proteins were found to be enriched in CNS white matter and were found in optic nerve cell cultures which contained highly nonpermissive, differentiated oligodendrocytes. The data presented demonstrate the existence of membrane proteins with potent nonpermissive substrate properties. Distribution and properties suggest that these proteins might play a crucial inhibitory role during development and regeneration in CNS white matter.
Study of Unique-Word Based GFDM Transmission Systems (2018)

In this paper, we propose the use of a deterministic sequence, known as unique word (UW), instead of the cyclic prefix (CP) in generalized frequency division multiplexing (GFDM) systems. The UW consists of known sequences that, if not null, can be used advantageously for synchronization and channel estimation purposes. In addition, UW allows the application of a highly efficient linear minimum mean squared error (LMMSE) smoother for noise reduction at the receiver. To avoid the conditions of non-orthogonality caused by the insertion of the UW and performance degradation in time varying frequency-selective channels, we use frequency-shift offset quadrature amplitude modulation (FS-OQAM). We present a signal model of a UW-GFDM system considering a single and multiple UWs. We then develop an LMMSE receive filter for signal reception of the proposed UW-GFDM system. Simulations show that the proposed UW-GFDM system outperforms prior work.
Stereospecific PARP Trapping by BMN 673 and Comparison with Olaparib and Rucaparib (2013)

Anti-PARP drugs were initially developed as catalytic inhibitors to block the repair of DNA single-strand breaks. We recently reported that several PARP inhibitors have an additional cytotoxic mechanism by trapping PARP-DNA complexes, and that both olaparib and niraparib act as PARP poisons at pharmacologic concentrations. Therefore, we have proposed that PARP inhibitors should be evaluated based both on catalytic PARP inhibition and PARP-DNA trapping. Here, we evaluated the novel PARP inhibitor, BMN 673, and compared its effects on PARP1 and PARP2 with two other clinical PARP inhibitors, olaparib and rucaparib, using biochemical and cellular assays in genetically modified chicken DT40 and human cancer cell lines. Although BMN 673, olaparib, and rucaparib are comparable at inhibiting PARP catalytic activity, BMN 673 is ∼100-fold more potent at trapping PARP-DNA complexes and more cytotoxic as single agent than olaparib, whereas olaparib and rucaparib show similar potencies in trapping PARP-DNA complexes. The high level of resistance of PARP1/2 knockout cells to BMN 673 demonstrates the selectivity of BMN 673 for PARP1/2. Moreover, we show that BMN 673 acts by stereospecific binding to PARP1 as its enantiomer, LT674, is several orders of magnitude less efficient. BMN 673 is also approximately 100-fold more cytotoxic than olaparib and rucaparib in combination with the DNA alkylating agents methyl methane sulfonate (MMS) and temozolomide. Our study demonstrates that BMN 673 is the most potent clinical PARP inhibitor tested to date with the highest efficiency at trapping PARP-DNA complexes.
James Cowan and the white quest for the black self (2001)

A literary genre is emerging in which Aborigines are cast as the spiritual saviours of the supposedly alienated Western self. One of the most prolific authors writing in this field is the Australian, James Cowan. Through a series of books Cowan moves further and further into the Aboriginal metaphysical realm until at last, he would have his readers believe, he actually enters the Dreaming and becomes an intrinsic part of it. In this article I critically examine these books, focusing on Cowans construction of Aborigines and the sorts of claims he makes. I also consider some possible consequences of his particular portrayal of Aborigines. Despite his prominence in this field, and publishers claims that he is an internationally respected authority on Australian Aborigines and other indigenous peoples, his work so far has received little critical analysis.
GPFS: A Shared-Disk File System for Large Computing Clusters (2002)

GPFS is IBM&amp;apos;s parallel, shared-disk file system for cluster computers, available on the RS/6000 SP parallel supercomputer and on Linux clusters. GPFS is used on many of the largest supercomputers in the world. GPFS was built on many of the ideas that were developed in the academic community over the last several years, particularly distributed locking and recovery technology. To date it has been a matter of conjecture how well these ideas scale. We have had the opportunity to test those limits in the context of a product that runs on the largest systems in existence. While in many cases existing ideas scaled well, new approaches were necessary in many key areas. This paper describes GPFS, and discusses how distributed locking and recovery techniques were extended to scale to large clusters.
Noninvasive In Vivo Human Coronary Artery Lumen and Wall Imaging Using Black-Blood Magnetic Resonance Imaging (2000)

In vivo high-spatial-resolution BB-MR provides a unique new method to noninvasively image and assess the morphological features of human coronary arteries. This may allow the identification of atherosclerotic disease before it is symptomatic. Further studies are necessary to identify the different plaque components and to assess lesions in asymptomatic patients and their outcomes.