gebhart/patrepeval huggingface dataset:
An actuated pump on-chip powered by cultured cardiomyocytes (2006)

Cellular functions are frequently exploited as processing components for integrated chemical systems such as biochemical reactors and bioassay systems. Here, we have created a new cell-based microsystem exploiting the intrinsic pulsatile mechanical functions of cardiomyocytes to build a cellular micropump on-chip using cardiomyocyte sheets as prototype bio-microactuators. We first demonstrate cell-based control of fluid motion in a model microchannel without check valves and evaluate the potential performance of the bio-actuation. For this purpose, a poly(dimethylsiloxane) (PDMS) microchip with a microchannel equipped with a diaphragm and a push-bar structure capable of harnessing collective cell fluid mechanical forces was coupled to a cultured pulsating cardiomyocyte sheet, activating cell-based fluid movement in the microchannel by actuating the diaphragm. Cell oscillation frequency and correlated fluid displacement in this system depended on temperature. When culture temperature was increased, collective cell contraction frequency remained cooperative and synchronous but increased, while displacement was slightly reduced. We then demonstrated directional fluid pumping within microchannels using cantilever-type micro-check valves made of polyimide. A directional flow rate of nL min(-1) was produced. This cell micropump system could be further developed as a self-actuated and efficient mechanochemical transducer requiring no external energy sources for various purposes in the future.
Assembly of empty capsids by using baculovirus recombinants expressing human parvovirus B19 structural proteins (1991)

Empty parvovirus B19 capsids were isolated from insect cells infected with a recombinant baculovirus expressing parvovirus B19 VP2 alone and also with a double-recombinant baculovirus expressing both VP1 and VP2. That VP2 alone can assemble to form capsids is a phenomenon not previously observed in parvoviruses. The stoichiometry of the capsids containing both VP1 and VP2 was similar to that previously observed in parvovirus B19-infected cells. The capsids were similar to native capsids in size and appearance, and their antigenicity was demonstrated by immunoprecipitation and enzyme-linked immunosorbent assay with B19-specific antibodies.
Ligand Blot Identification of a Manduca sexta Midgut Binding Protein Specific to Three Bacillus thuringiensis CryIA-Type ICPs (1994)

The CryIA(a), CryIA(b) and CryIA(c) Bacillus thuringiensis insecticidal crystal proteins (ICPs) were used in ligand-blot experiments to detect specific binding proteins in brush-border membrane vesicles (BBMV) of Manduca sexta. We identified a protein which binds these three CryIA-type ICPs. The apparent molecular mass of the protein, estimated on SDS-PAGE, was 210 kDa as was the CryIA(b) binding protein previously described by Vadlamudi and col. We have also demonstrated, in ligand blot experiments, that CryIA(a) and CryIA(c) compete with CryIA(b) for binding this 210 kDa protein. Properties of the binding molecule can be correlated with knowledge previously acquired through radiolabelled binding experiments.
Molecular, antibiogram and serological typing of Staphylococcus aureus isolates recovered from Al‐Makased hospital in East Jerusalem (1998)

Staphylococcus aureus is a major cause of nosocomial infections and a risk in patients who have either undergone surgery or are on haemodialysis. The S. aureus infections in patients admitted to the clinical departments of Al-Makased Charitable Hospital in Jerusalem during a period of one year were investigated. Isolates included were from blood, surgical wounds, or other nonsuperficial sites. Of 63 isolates available for analysis, 46 (73.0%) expressed type 8 capsular polysaccharide; 13 (20.7%), type 5 capsular polysaccharide; only 4 isolates (6.3%) did not express type 5 or type 8 antibodies. The strains fitted in 7 different antibiogram types, with the type showing resistance only to penicillin and ampicillin prevalent in 34 out of 63 isolates (54.0%). Of the 12 methicillin-resistant S. aureus (MRSA) isolates (19.1%), 8(66.7%) possessed the type 8 capsule and 4(33.7%) the type 5 capsule. Pulsed-field gel electrophoresis of all isolates with the restriction-endonuclease enzymes Sma I revealed 34 patterns demonstrating that no single methicillin-sensitive S. aureus strain was endemic in the hospital. However, all MRSA isolates with a type 8 capsule showed identical PFGE patterns using the 2 restriction-endonuclease enzymes Sma I and SST II. Moreover, type 5 isolates showed identical patterns (one isolate differed from the rest with one band only). These data suggest and confirm the clonality of type 5 and type 8 MRSA isolates. Analysing the results of the capsular and antibiogram typing schemes in conjunction proved useful and suggested that such an analysis can be employed as a helpful epidemiological tool in hospitals with limited resources.
ADP‐ribosylation of nucleolar proteins in HeLa tumor cells (1993)

ADP-ribosylation reactions in nucleoli of exponentially growing HeLa cells were studied. Isolated nuclei or nucleoli were labeled with 32P-NAD; then the nucleolar proteins were analyzed by 1-dimensional and 2-dimensional polyacrylamide gel electrophoresis (PAGE) and modified proteins were detected by autoradiography. The labeled nucleolar proteins were also chromatographically fractionated on DEAE-cellulose. Electrophoretic analysis of total nucleolar and chromatographically purified proteins revealed that besides nuclear ADP-ribosyltransferase and histones two characteristic nucleolar phosphoproteins numatrin/B23 and nucleolin/C23 were modified by ADP-ribosylation.
Ultrasonic Determination of the Effect of Casein Phosphopeptide-Amorphous Calcium Phosphate Paste on the Demineralization of Bovine Dentin (2007)

The purpose of this study was to investigate the demineralization of dentin by measuring changes in the velocity of the sonic longitudinal waves transmitted through this substrate. One group of samples was immersed in demineralization solution for 10 min twice a day and then stored in artificial saliva. Two additional groups of samples were treated with a solution of casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) paste or a placebo paste without CPP-ACP before demineralization and a control group was stored in artificial saliva. The sonic velocity of the demineralized specimens was found to decrease significantly over time. No significant increase in sonic velocity was observed in specimens treated with CPP-ACP, suggesting that CPP-ACP acted to prevent demineralization.
Imaging Spectrometry for Earth Remote Sensing (1985)

Imaging spectrometry, a new technique for the remote sensing of the earth, is now technically feasible from aircraft and spacecraft. The initial results show that remote, direct identification of surface materials on a picture-element basis can be accomplished by proper sampling of absorption features in the reflectance spectrum. The airborne and spaceborne sensors are capable of acquiring images simultaneously in 100 to 200 contiguous spectral bands. The ability to acquire laboratory-like spectra remotely is a major advance in remote sensing capability. Concomitant advances in computer technology for the reduction and storage of such potentially massive data sets are at hand, and new analytic techniques are being developed to extract the full information content of the data. The emphasis on the deterministic approach to multispectral data analysis as opposed to the statistical approaches used in the past should stimulate the development of new digital image-processing methodologies.
A general photogrammetric method for determining object position and orientation (1989)

The author presents a general method for determining the three-dimensional position and orientation of an object relative to a camera based on a two-dimensional image of known feature points located on the object. In contrast to the conventional approach, the method does not make use of the collinearity condition. Instead, the algebraic structure of the problem is fully exploited in arriving at a solution which is independent of the configuration of the feature points. Although the method is applicable to any number or distribution of feature points, no more than five points are needed from a numerical standpoint; three or four points will typically suffice. A necessary condition for the existence of the solution is obtained for the first time, and a rigorous proof of uniqueness is presented for the case of four coplanar points. Simulation results have shown that, in the case of four feature points, nonplanar configurations generally outperform coplanar point sets in both accuracy and robustness in the presence of image noise.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
AICAR and metformin, but not exercise, increase muscle glucose transport through AMPK-, ERK-, and PDK1-dependent activation of atypical PKC (2009)

Activators of 5'-AMP-activated protein kinase (AMPK) 5-aminoimidazole-4-carboxamide-1-beta-d-ribofuranoside (AICAR), metformin, and exercise activate atypical protein kinase C (aPKC) and ERK and stimulate glucose transport in muscle by uncertain mechanisms. Here, in cultured L6 myotubes: AICAR- and metformin-induced activation of AMPK was required for activation of aPKC and ERK; aPKC activation involved and required phosphoinositide-dependent kinase 1 (PDK1) phosphorylation of Thr410-PKC-zeta; aPKC Thr410 phosphorylation and activation also required MEK1-dependent ERK; and glucose transport effects of AICAR and metformin were inhibited by expression of dominant-negative AMPK, kinase-inactive PDK1, MEK1 inhibitors, kinase-inactive PKC-zeta, and RNA interference (RNAi)-mediated knockdown of PKC-zeta. In mice, muscle-specific aPKC (PKC-lambda) depletion by conditional gene targeting impaired AICAR-stimulated glucose disposal and stimulatory effects of both AICAR and metformin on 2-deoxyglucose/glucose uptake in muscle in vivo and AICAR stimulation of 2-[(3)H]deoxyglucose uptake in isolated extensor digitorum longus muscle; however, AMPK activation was unimpaired. In marked contrast to AICAR and metformin, treadmill exercise-induced stimulation of 2-deoxyglucose/glucose uptake was not inhibited in aPKC-knockout mice. Finally, in intact rodents, AICAR and metformin activated aPKC in muscle, but not in liver, despite activating AMPK in both tissues. The findings demonstrate that in muscle AICAR and metformin activate aPKC via sequential activation of AMPK, ERK, and PDK1 and the AMPK/ERK/PDK1/aPKC pathway is required for metformin- and AICAR-stimulated increases in glucose transport. On the other hand, although aPKC is activated by treadmill exercise, this activation is not required for exercise-induced increases in glucose transport, and therefore may be a redundant mechanism.
Activation of Coagulation after Administration of Tumor Necrosis Factor to Normal Subjects (1990)

Tumor necrosis factor has been implicated in the activation of blood coagulation in septicemia, a condition commonly associated with intravascular coagulation and disturbances of hemostasis. To evaluate the early dynamics and the route of the in vivo coagulative response to tumor necrosis factor, we performed a controlled study in six healthy men, monitoring the activation of the common and intrinsic pathways of coagulation with highly sensitive and specific radioimmunoassays. Recombinant human tumor necrosis factor, administered as an intravenous bolus injection (50 micrograms per square meter of body-surface area), induced an early and short-lived rise in circulating levels of the activation peptide of factor X, reaching maximal values after 30 to 45 minutes (mean +/- SEM increase after 45 minutes, 34.2 +/- 18.2 percent; tumor necrosis factor vs. saline, P = 0.015). This was followed by a gradual and prolonged increase in the plasma concentration of the prothrombin fragment F1+2, peaking after four to five hours (mean increase after five hours, 348.0 +/- 144.8 percent; tumor necrosis factor vs. saline, P less than 0.0001). These findings signify the formation of factor Xa (activated factor X) and the activation of prothrombin. Activation of the intrinsic pathway could not be detected by a series of measurements of the plasma levels of factor XII, prekallikrein, factor XIIa-C1 inhibitor complexes, kallikrein-C1 inhibitor complexes, and the activation peptide of factor IX. The delay between the maximal activation of factor X and that of prothrombin amounted to several hours, indicating that neutralization of factor Xa activity was slow. We conclude that a single injection of tumor necrosis factor elicits a rapid and sustained activation of the common pathway of coagulation, probably induced through the extrinsic route. Our results suggest that tumor necrosis factor could play an important part in the early activation of the hemostatic mechanism in septicemia.
Complementation of a poliovirus defective genome by a recombinant vaccinia virus which provides poliovirus P1 capsid precursor in trans (1993)

Defective interfering (DI) RNA genomes of poliovirus which contain in-frame deletions in the P1 capsid protein-encoding region have been described. DI genomes are capable of replication and can be encapsidated by capsid proteins provided in trans from wild-type poliovirus. In this report, we demonstrate that a previously described poliovirus DI genome (K. Hagino-Yamagishi and A. Nomoto, J. Virol. 63:5386-5392, 1989) can be complemented by a recombinant vaccinia virus, VVP1 (D. C. Ansardi, D. C. Porter, and C. D. Morrow, J. Virol. 65:2088-2092, 1991), which expresses the poliovirus capsid precursor polyprotein, P1. Stocks of defective polioviruses were generated by transfecting in vitro-transcribed defective genome RNA derived from plasmid pSM1(T7)1 into HeLa cells infected with VVP1 and were maintained by serial passage in the presence of VVP1. Encapsidation of the defective poliovirus genome was demonstrated by characterizing poliovirus-specific protein expression in cells infected with preparations of defective poliovirus and by Northern (RNA) blot analysis of poliovirus-specific RNA incorporated into defective poliovirus particles. Cells infected with preparations of defective poliovirus expressed poliovirus protein 3CD but did not express capsid proteins derived from a full-length P1 precursor. Poliovirus-specific RNA encapsidated in viral particles generated in cells coinfected with VVP1 and defective poliovirus migrated slightly faster on formaldehyde-agarose gels than wild-type poliovirus RNA, demonstrating maintenance of the genomic deletion. By metabolic radiolabeling with [35S]methionine-cysteine, the defective poliovirus particles were shown to contain appropriate mature-virion proteins. This is the first report of the generation of a pure population of defective polioviruses free of contaminating wild-type poliovirus. We demonstrate the use of this recombinant vaccinia virus-defective poliovirus genome complementation system for studying the effects of a defined mutation in the P1 capsid precursor on virus assembly. Following removal of residual VVP1 from defective poliovirus preparations, processing and assembly of poliovirus capsid proteins derived from a nonmyristylated P1 precursor expressed by a recombinant vaccinia virus, VVP1 myr- (D. C. Ansardi, D. C. Porter, and C. D. Morrow, J. Virol. 66:4556-4563, 1992), in cells coinfected with defective poliovirus were analyzed. Capsid proteins generated from nonmyristylated P1 did not assemble detectable levels of mature virions but did assemble, at low levels, into empty capsids.(ABSTRACT TRUNCATED AT 400 WORDS)
Improved amino acid flexibility parameters (2003)

Protein molecules exhibit varying degrees of flexibility throughout their three-dimensional structures, with some segments showing little mobility while others may be so disordered as to be unresolvable by techniques such as X-ray crystallography. Atomic displacement parameters, or B-factors, from X-ray crystallographic studies give an experimentally determined indication of the degree of mobility in a protein structure. To provide better estimators of amino acid flexibility, we have examined B-factors from a large set of high-resolution crystal structures. Because of the differences among structures, it is necessary to normalize the B-factors. However, many proteins have segments of unusually high mobility, which must be accounted for before normalization can be performed. Accordingly, a median-based method from quality control studies was used to identify outliers. After removal of outliers from, and normalization of, each protein chain, the B-factors were collected for each amino acid in the set. It was found that the distribution of normalized B-factors followed a Gumbel, or extreme value distribution, and the location parameter, or mode, of this distribution was used as an estimator of flexibility for the amino acid. These new parameters have a higher correlation with experimentally determined B-factors than parameters from earlier methods.
Biochemical characterization of transgenic tomato plants in which carotenoid synthesis has been inhibited through the expression of antisense RNA to pTOM5 (1992)

Summary Transgenic tomato plants expressing antisense RNA to a ripening‐related cDNA clone (pTOM5) had yellow ripening fruit and pale coloured flowers. Carotenoid levels in fruit of these plants were reduced by up to 97%. In order to determine the step of carotenoid biosynthesis which was blocked, a cell‐free system active in the synthesis of carotenoid intermediates was prepared. Incubations with radiolabelled carotenoid precursors led to the identification of the block between GGDP and phytoene. Analysis of carotenoids in different tissues of transgenic and control plants indicated that although ripe fruit and flower carotenoid levels were reduced in the modified plants, leaf carotenoid levels were not decreased. This implies that the pTOM5 gene product is not involved in carotenoid synthesis in the leaf.
Molecular imprinting science and technology: a survey of the literature for the years up to and including 2003 (2006)

Over 1450 references to original papers, reviews and monographs have herein been collected to document the development of molecular imprinting science and technology from the serendipitous discovery of Polyakov in 1931 to recent attempts to implement and understand the principles underlying the technique and its use in a range of application areas. In the presentation of the assembled references, a section presenting reviews and monographs covering the area is followed by papers dealing with fundamental aspects of molecular imprinting and the development of novel polymer formats. Thereafter, literature describing attempts to apply these polymeric materials to a range of application areas is presented.
Molecular cloning of a gene belonging to the carcinoembryonic antigen gene family and discussion of a domain model. (1987)

Carcinoembryonic antigen (CEA) is a glycoprotein important as a tumor marker for colonic cancer. Immunological and biochemical studies have shown it to be closely related to a number of other glycoproteins, which together make up a gene family. We have cloned a member of this gene family by using long oligonucleotide probes (42-54 nucleotides) based on our protein sequence data for CEA and NCA (nonspecific cross-reacting antigen) and on human codon usage. The clone obtained (lambda 39.2) hybridizes with six probes and has a 15-kilobase insert. The 5' end of the gene is contained within a 2700-base-pair EcoRI fragment, which hybridizes with five of the six synthetic probes. Sequencing of the 5' end region revealed the location and structure of one exon and two putative intron boundaries. The exon encodes part of the leader sequence and the NH2-terminal 107 amino acids of NCA. Southern blot analysis of human normal and tumor DNA, using as probes two lambda 39.2 fragments that contain coding sequences, suggests the existence of 9-11 genes for the CEA family. One of the restriction fragments described here has been used by Zimmermann et al. [Zimmermann, W., Ortlieb, B., Friedrich, R. & von Kleist, S. (1987) Proc. Natl. Acad. Sci. USA 84, 2960-2964] to isolate partial cDNA clones for CEA. The identity of this clone was verified with our protein sequence data [Paxton, R., Mooser, G., Pande, H., Lee, T.D. & Shively, J.E. (1987) Proc. Natl. Acad. Sci. USA 84, 920-924]. We discuss a domain structure for CEA based on the CEA sequence data and the NCA exon sequence data. It is likely that this gene family evolved from a common ancestor shared with neural cell adhesion molecule and alpha 1 B-glycoprotein and is perhaps a family within the immunoglobulin superfamily.
A Tissue Plasminogen Activator/P-Selectin Fusion Protein Is an Effective Thrombolytic Agent (1997)

Chimeric proteins P280IR and P121IR have clot lysis activities that are similar to TPAIR both in vitro and in vivo. These chimeric proteins also bind to P-selectin ligand in vitro. Thus, these proteins may provide an efficient method of targeting TPA to the thrombotic region. Further experimental analysis with the use of larger animal coronary occlusion models should help determine the future value of these proteins as clinical therapeutic agents.
The Perpetual Challenge of Infectious Diseases (2012)

During the past 200 years, our understanding of infectious diseases has radically evolved from the identification of microbes, to defining their genetic structure, to the development of focused antimicrobial therapies, to the realization of vector biology. This article highlights the tremendous advances that have been made in the field.
Conditional Deletion of NF-κB–Inducing Kinase (NIK) in Adult Mice Disrupts Mature B Cell Survival and Activation (2015)

NF-κB-inducing kinase (NIK) is a primary regulator of the noncanonical NF-κB signaling pathway, which plays a vital role downstream of BAFF, CD40L, lymphotoxin, and other inflammatory mediators. Germline deletion or inactivation of NIK in mice results in the defective development of B cells and secondary lymphoid organs, but the role of NIK in adult animals has not been studied. To address this, we generated mice containing a conditional allele of NIK. Deletion of NIK in adult mice results in decreases in B cell populations in lymph nodes and spleen, similar to what is observed upon blockade of BAFF. Consistent with this, B cells from mice in which NIK is acutely deleted fail to respond to BAFF stimulation in vitro and in vivo. In addition, mice with induced NIK deletion exhibit a significant decrease in germinal center B cells and serum IgA, which is indicative of roles for NIK in additional pathways beyond BAFF signaling. Our conditional NIK-knockout mice may be broadly useful for assessing the postdevelopmental and cell-specific roles of NIK and the noncanonical NF-κB pathway in mice.