gebhart/patrepeval huggingface dataset:
Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis (2001)

We used 2D protein gel electrophoresis and DNA microarray technologies to systematically analyze genes under glucose repression in B:acillus subtilis. In particular, we focused on genes expressed after the shift from glycolytic to gluconeogenic at the middle logarithmic phase of growth in a nutrient sporulation medium, which remained repressed by the addition of glucose. We also examined whether or not glucose repression of these genes was mediated by CcpA, the catabolite control protein of this bacterium. The wild-type and ccpA1 cells were grown with and without glucose, and their proteomes and transcriptomes were compared. 2D gel electrophoresis allowed us to identify 11 proteins, the synthesis of which was under glucose repression. Of these proteins, the synthesis of four (IolA, I, S and PckA) was under CcpA-independent control. Microarray analysis enabled us to detect 66 glucose-repressive genes, 22 of which (glmS, acoA, C, yisS, speD, gapB, pckA, yvdR, yxeF, iolA, B, C, D, E, F, G, H, I, J, R, S and yxbF ) were at least partially under CcpA-independent control. Furthermore, we found that CcpA and IolR, a repressor of the iol divergon, were involved in the glucose repression of the synthesis of inositol dehydrogenase encoded by iolG included in the above list. The CcpA-independent glucose repression of the iol genes appeared to be explained by inducer exclusion.
Cost Effective Nanofiber Formation: Melt Electrospinning (2005)

A multidisciplinary team has been assembled to develop techniques to melt electrospin polymer nanofibers. Preliminary work directed at constructing and testing a crude apparatus to melt electrospin polypropylene was marginally successful; some nanofibers were produced but the overwhelming mass fraction consisted of microfibers. The apparatus could not be upgraded, so a new unit was built and is being tested. A third generation unit will be designed (and eventually tested) by a new student just joining the project. Goals: Research reports on solution electrospinning abound, largely because a laboratory setup is inexpensive and simple. Work on melt electrospinning is relatively scarce in spite of the fact that the most significant limiting factors to economically produce nanofibers are solvent recycling issues and low productivity. Melt electrospinning solves both problems. Productivity will increase 10-500 fold and costs will drop significantly due to elimination of solvent recovery. Why are few scientists working on melt electrospinning? It’s is a difficult problem that requires a logical solution and grant funding. Within the first 18 months we will have a third generation melt electrospinning apparatus built and tested. Success will be judged by having more than 50 volume percent nanofiber from the melt electrospinning apparatus. If the initial runs are successful, we will begin experiments designed to learn more about electrospinning and how to obtain molecular orientation in electrospun fibers. We will also try to melt electrospin biopolymers as well as synthetic polymers used in high volume. If the first trials are not successful, we will make changes in the apparatus, such as bleeding air into near the nozzle to develop a combined electrospin/melt blow process. We also intend to develop real-time, online diagnostics and control of the melt electrospinning process. We propose to create a process control-oriented model that characterizes the flow dynamics in melt electrospinning by using tools formerly developed for investigating reactive flows. Body: Filters for biological/chemical aerosols, clothing insulation better than Thinsulate ® , home insulation better than meltblown glass fiber - the need for fine fibers is great, yet techniques to economically produce them are nil. As new techniques have been developed – meltblowing, electrospinning, sea-island bicomponents – the market seems to expand without limit. Most of the market is in filtration, but as we learn to control the morphology of these fibers, new applications will certainly arise. Meltblowing can produce fibers with diameters only as small as about 0.5 micron, and then copious amounts of hot air are required, but the other two techniques mentioned above are capable of delivering fibers down to the nanometer range. Seaisland bicomponent fibers have been made for decades, but only recently have manufacturers
Biomarkers of Drug-Induced Skeletal Muscle Injury in the Rat: Troponin I and Myoglobin (2009)

The purpose of this investigation was to determine the utility of fast-twitch skeletal muscle troponin I (fsTnI) and urinary myoglobin (uMB) as biomarkers of skeletal muscle injury in 8-week-old Sprague-Dawley rats. fsTnI and uMB were quantified by enzyme-linked immunosorbent assay and compared with standard clinical assays including creatine kinase, aldolase, aspartate aminotransferase, and histopathological assessments. Detectable levels of uMB were normalized to urinary creatinine to control for differences in renal function. Seven compounds, including those with toxic effects on skeletal muscle, cardiac muscle, or liver, were evaluated. fsTnI was typically nondetectable (< 5.9 ng/ml serum) in vehicle-treated female and male rats but increased in a dose-dependent manner to at least 300 ng/ml in cerivastatin-induced severe fast-twitch specific myotoxicity. Minimal myopathy induced by investigational compounds BMS-600149 and BMS-687453 increased serum fsTnI to about 30-50 ng/ml, suggesting a reasonable dynamic range for detecting mild to severe skeletal muscle toxicity. In direct contrast, fsTnI was only marginally increased relative to population control values in rats treated with triamcinolone acetonide, which produces muscle atrophy or the cardiotoxins isoproterenol and CoCl2. uMB was typically nondetectable (< 1.6 ng/ml urine) in vehicle-treated female and male rats but increased to approximately 140, 300, and 30 ng/mg creatinine in rats treated with cerivastatin, BMS-687453, and triamcinolone acetonide, respectively. Cardiotoxicity also increased uMB in rats treated with isoproterenol and CoCl2 with urine concentrations ranging from 20 to 30 ng/mg creatinine. Severe hepatotoxicity (coumarin) did not significantly affect serum fsTnI or uMB levels. Collectively, these data suggest that fsTnI is specific for skeletal muscle toxicity, whereas uMB is nonspecific, increasing with skeletal muscle and cardiac toxicity. Accordingly, the complement of fsTnI and uMB, in conjunction with standard clinical assays may comprise a useful diagnostic panel for assessing drug-induced myopathy in rats.
Simultaneous Visualization of Both Signaling Cascade Activity and End-Point Gene Expression in Single Cells (2011)

We have developed an approach for simultaneous detection of individual endogenous protein modifications and mRNA molecules in single cells in situ. For this purpose we combined two methods previously developed in our lab: in situ proximity ligation assay for the detection of individual protein interactions and -modifications and in situ detection of single mRNA molecules using padlock probes. As proof-of-principle, we demonstrated the utility of the method for simultaneous detection of phosphorylated PDGFRβ and DUSP6/MKP-3 mRNA molecules in individual human fibroblasts upon PDGF-BB stimulation. Further we applied drugs disrupting the PDGFRβ signaling pathway at various sites to show that this combined method can concurrently monitor the molecular effect of the drugs, i.e. inhibition of downstream signaling from the targeted node in the signaling pathway. Due to its ability to detect different types of molecules in single cells in situ the method presented here can contribute to a deeper understanding of cell-to-cell variations and can be applied to e.g. pinpoint effector sites of drugs in a signaling pathway.
[Phenotypic characteristics of infiltrated inflammatory cells, renal tubular epithelial cells and interstitial cells and their possible roles in the outcome of human drug-associated interstitial nephritis]. (2001)

During the early stage of human drug-associated interstitial nephritis, TEC is activated and highly expresses chemoattractants, inducing the infiltration of monocyte/macrophage into the interstitium. Monocyte/macrophage may be used as marker for the chronicity of interstitial inflammation and poor outcome of renal function.
Relaxin protects against myocardial injury caused by ischemia and reperfusion in rat heart. (1998)

Myocardial injury caused by ischemia and reperfusion comes from multiple pathogenic events, including endothelial damage, neutrophil extravasation into tissue, platelet and mast cell activation, and peroxidation of cell membrane lipids, which are followed by myocardial cell alterations resulting eventually in cell necrosis. The current study was designed to test the possible cardioprotective effect of the hormone relaxin, which has been found to cause coronary vessel dilation and to inhibit platelet and mast cell activation. Ischemia (for 30 minutes) was induced in rat hearts in vivo by ligature of the left anterior descending coronary artery; reperfusion (for 60 minutes or less if the rats died before this predetermined time) was induced by removal of the ligature. Relaxin (100 ng) was given intravenously 30 minutes before ischemia. The results obtained showed that relaxin strongly reduces 1) the extension of the myocardial areas affected by ischemia-reperfusion-induced damage, 2) ventricular arrhythmias, 3) mortality, 4) myocardial neutrophil number, 5) myeloperoxidase activity, a marker of neutrophil accumulation, 6) production of malonyldialdehyde, an end product of lipid peroxidation, 7) mast cell granule release, 8) calcium overload, and 9) morphological signs of myocardial cell injury. This study shows that relaxin can be regarded as an agent with a marked cardioprotective action against ischemia-reperfusion-induced myocardial injury.
Human neutrophil defensins selectively chemoattract naive T and immature dendritic cells (2000)

Defensins, a family of cationic, structurally related, antimicrobial peptides, contribute to host defense by disrupting the cytoplasmic membrane of microbes. Here we show that human neutrophil defensins selectively induce the migration of human CD4+/CD45RA+ naive and CD8+, but not CD4+/CD45RO+ memory, T cells. Moreover, human neutrophil defensins are chemotactic for immature human dendritic cells derived from either CD34+ progenitors or peripheral blood monocytes. Upon maturation induced by treatment with tumor necrosis factor alpha (TNF-alpha), dendritic cells lose their responsiveness to human neutrophil defensins. The chemotactic effect of human neutrophil defensins on both T and dendritic cells is pertussis toxin-sensitive, suggesting that a G(ialpha) protein-coupled receptor is responsible. Human neutrophil defensins are also chemotactic for immature murine dendritic cells. These data suggest that, in addition to their antimicrobial role, human neutrophil defensins also contribute to adaptive immunity by mobilizing T cells and dendritic cells.
Flow cytometer with mass spectrometer detection for massively multiplexed single-cell biomarker assay (2008)

Abstract This paper describes the development and application of new metal-tagging reagents and a novel mass spectrometer (MS) detector for a flow cytometer that enables highly multiplexed measurement of many biomarkers in individual cells. A new class of tagging reagents, based on an acrylic polymer backbone that incorporates a reproducible number of lanthanide elements, has been developed. When linked to antibodies that specifically recognize target proteins of interest, determination of the tag elements is diagnostic for the presence and quantification of the antigen. The use of enriched stable isotope tags provides the opportunity for multiparametric assay. The new instrument uses inductively coupled plasma (ICP) to vaporize, atomize, and ionize individual cells that have been probed using the metal-labeled antibodies. The elemental composition, specifically of the metal tags, is recorded simultaneously using a time-of-flight (TOF)-MS that has been specifically designed for high-speed analysis during the short transient corresponding to the individual cell event. The detector provides for well-resolved atomic fingerprints of many elemental and isotopic tags, with little overlap of neighboring signals (high abundance sensitivity) and wide dynamic range both for a single antigen and between antigens.
Optical Flow and Principal Component Analysis-Based Motion Detection in Outdoor Videos (2010)

We propose a joint optical flow and principal component analysis (PCA) method for motion detection. PCA is used to analyze optical flows so that major optical flows corresponding to moving objects in a local window can be better extracted. This joint approach can efficiently detect moving objects and more successfully suppress small turbulence. It is particularly useful for motion detection from outdoor videos with low quality. It can also effectively delineate moving objects in both static and dynamic background. Experimental results demonstrate that this approach outperforms other existing methods by extracting the moving objects more completely with lower false alarms.
Effect of Fluorescently Labeling Protein Probes on Kinetics of Protein−Ligand Reactions (2008)

We studied the effect of fluorescently labeling proteins on protein-ligand reactions. Unlabeled ligands (streptavidin-binding peptides and rabbit immunoglobulin G (IgG) as antigen targets) are immobilized on epoxy-functionalized glass slides. Unlabeled and Cy3-labeled protein probes from the same batch (streptavidin and goat antibodies) subsequently react with the surface-immobilized targets. By monitoring in situ the surface mass density change using an oblique-incidence reflectivity difference scanning microscope (a label-free detector), we measured k(on) and k(off) for streptavidin-peptide reactions and antibody-antigen reaction. We found that (1) equilibrium dissociation constants, defined as K(D) = k(off)/k(on), for streptavidin-peptide reactions increases by a factor of 3-4 when the solution-phase streptavidin is labeled with Cy3 dye and (2) K(D) for reactions of solution-phase goat anti-rabbit antibodies with rabbit IgG targets also change significantly when the goat antibodies are labeled with Cy3 dye.
Poly(L-lactic acid-co-amino acid) Graft Copolymers: A Class of Functional Biodegradable Biomaterials (1996)

The synthesis of poly(L-lactic acid-co-L-lysine), poly(L-lactic acid-co-β-benzyl-L-aspartate), and poly(L-lactic acid-co-D,L-alanine) comb-like graft copolymers and their characterization by 1H NMR and elemental analysis are presented. The lysine ε-amino groups in linear poly(L-lactic acid-co-L-lysine) copolymers with approximately 1% lysine content were utilized to initiate the ring opening polymerization of the amino acid N-carboxyanhydrides to yield the graft copolymers.
Placental pathology of absent and reversed end-diastolic flow in growth-restricted fetuses (1997)

In FGR, UA Doppler velocity wave forms do not demonstrate a continuum of placental lesions in which reversed end-diastolic flow reflects more severe placental histopathology than absent end-diastolic flow and end-diastolic flow present. As expected, absent end-diastolic flow cases had more occlusive lesions of the intraplacental vasculature. In reversed end-diastolic flow, lesions suggesting vascular remodeling and/or damage by pathologic conditions of intraplacental flow predominated.
Long-Term Safety of Patients with Parkinson's Disease Receiving rAAV2-Neurturin (CERE-120) Gene Transfer (2015)

The objective of this study was to assess the long-term safety of surgically administered recombinant adeno-associated virus serotype-2 (rAAV2)-neurturin (NRTN) to patients with advanced Parkinson's disease. Publications from prior trials reported no unexpected or troubling adverse events related to the vector or transgene comprising rAAV2-NRTN. Because rAAV2-NRTN produces long-term NRTN expression, subjects were enrolled in a long-term safety assessment protocol of rAAV2-NRTN. This article presents safety data for up to 5 years, well beyond that reported in the initial publications. Data from 53 patients are included; 47 received rAAV2-NRTN bilaterally to the putamen, whereas 6 subjects received rAAV2-NRTN bilaterally into putamen-plus-substantia nigra. Patients underwent in-person safety assessments on a quarterly to bi-annual basis, including adverse event monitoring, physical and neurological examinations, brain MRI, and laboratory testing. Parkinsonian status was assessed in an unblinded fashion. Fifty-three subjects completed the long-term safety protocol. Nine nonserious adverse events (non-SAEs) in 6 subjects were deemed "possibly related" to rAAV2-NRTN by the principal investigator, whereas none were deemed "related" to rAAV2-NRTN. Over the course of long-term observation, 33 SAEs were reported in 18 subjects, all of who received rAAV2-NRTN into putamen-only; 31 SAEs were deemed not related to rAAV2-NRTN, and 2 were deemed unlikely related. Safety assessments showed no clinically relevant changes in examination, imaging, or laboratory studies. Motor status, on average, was stable or apparently modestly improved (relative to baseline) over the course of the open-label, long-term follow-up. These findings provide evidence for the long-term safety of neurturin when delivered to the putamen or the putamen-plus-substantia nigra via stereotactic surgery and rAAV2 gene transfer. They therefore supplement the safety results reported in four prior publications from the same subjects, significantly extending the safety data for gene therapy and neurotrophic factor expression targeting the brain and adding to growing evidence that rAAV vector-mediated gene therapy to the CNS can be administered safely.
Ultrasensitive Voltammetric Detection of Underivatized Oligonucleotides and DNA (1997)

Electrochemical detection of nucleotides, ssDNA, and dsDNA was accomplished by using sinusoidal voltammetric detection at copper microelectrodes. Generally, detection of these molecules utilizes the electroactive nature of adenine and guanine residues at most electrode surfaces. The detection approach used in this study is based on the electrocatalytic oxidation of sugars and amines at copper surfaces. All nucleotides and DNA molecules comprise a ribose sugar backbone and primary amines present on the different nucleobases. Consequently, the detection approach is universal to all types of nucleotides. As the number of sugar moieties increases with the length of an oligonucleotide, the detection sensitivity is enhanced for bigger oligonucleotides. Irreversible adsorption of these oligonucleotides and other biomacromolecules like dsDNA on the electrode surface was avoided with sinusoidal voltammetry since it is a scanning electrochemical technique. The sensitivity of the detection strategy is, however, still preserved due to the effective decoupling of the faradaic signal from the capacitive background currents in the frequency domain. The ssDNA and dsDNA were detected in the picomolar concentration range. The electrochemical signal due to dsDNA is actually higher than that due to ssDNA due to the larger number of easily accessible sugars on the outer perimeter of a dsDNA double helix compared to those on a ssDNA of the same size. This is in contrast to the existing electrochemical detections techniques based on the electroactivity of the nucleobase.
Mg2+ Binding and Catalytic Function of Sphingomyelinase from Bacillus cereus (1998)

The modes of Mg2+ binding to SMase from Bacillus cereus were studied on the basis of the changes in the tryptophyl fluorescence intensity. This enzyme was shown to possess at least two binding sites for Mg2+ with low and high affinities. The effects of Mg2+ binding on the enzymatic activity and structural stability of the enzyme molecule were also studied. The results indicated that the binding of Mg2+ to the low-affinity site was essential for the catalysis, but was independent of the substrate binding to the enzyme. It was also indicated that the alkaline denaturation of the enzyme was partly prevented by the Mg2+ binding, whereas no significant protective effect was observed against the denaturation by urea. The pH dependence of the kinetic parameters for the hydrolysis of micellar HNP and mixed micellar SM with Triton X-100 (1:10), catalyzed by SMase from B. cereus, was studied in the presence of a large amount of Mg2+ to saturate both the low- and high-affinity sites. The pH dependence curves of the logarithm of 1/Km for these two kinds of substrates were similar in shape to each other, and showed a single transition. On the other hand, the shapes of the pH dependence curves of the logarithm of kcat for these two kinds of substrates were different from each other. The pH dependence curve for micellar HNP showed three transitions and, counting from the acidic end of the pH region, the first and third transitions having tangent lines with slopes of +1 and -1, respectively. On the other hand, the curve for mixed micellar SM with Triton X-100 showed one large transition with a slope of +1 (the first transition) and a very small transition (the third transition). On the basis of the present results and the three-dimensional structure of bovine pancreatic DNase I, which has a primary structure similar to that of B. cereus SMase, we proposed a catalytic mechanism for B. cereus SMase based on general-base catalysis.
Surveillance for Congenital Cytomegalovirus Disease: A Report from the National Congenital Cytomegalovirus Disease Registry (1995)

A national surveillance program for congenital cytomegalovirus (CMV) disease was initiated in 1990. In 4 years 285 cases were reported without seasonal patterns. Mean birth statistics were as follows: gestational age, 36 weeks; weight, 2,224 g; length, 45 cm; and head circumference, 30 cm. Of the infants 68% had CNS involvement, which was significantly (P < .005) associated with a direct bilirubin level of > or = 3 mg/dL, petechiae, an alanine aminotransferase level of > 100 U/L, a platelet count of < or = 75,000/mm3, hepatomegaly, and splenomegaly (P < .05). Maternal demographics revealed that the mean age was 23 years (range, 13-38 years), 59% were white, 33% were black, 47% had low incomes (receiving Medicaid), and 45% were primiparous. Compared with 1990 birth statistics in the United States, mothers of infants with congenital CMV disease were younger, and a greater percentage of these mothers were black. Two distinct maternal groups were identified on the basis of age, socioeconomic status, and parity. This finding may reflect different modes of transmission and suggest target populations for future CMV vaccine initiatives.
Peptide thioester preparation by Fmoc solid phase peptide synthesis for use in native chemical ligation (2000)

Established methodology for the preparation of peptide thioesters requires the use of t-butoxycarbonyl chemistry owing to the lability of thioester linkers to the nucleophilic reagents used in Fmoc solid phase peptide synthesis. Both the greater ease of use and the broad applicability of the method has led to the development of an Fmoc-based methodology for direct peptide thioester synthesis. It was found that successful preparation of a peptide thioester could be achieved when the non-nucleophilic base, 1,8-diazabicyclo[5.4.0]undec-7-ene, together with 1-hydroxybenzotriazole in dimethylformamide, were used as the Nα-Fmoc deprotection reagent. Native chemical ligation of the resulting thioester product to an N-terminal cysteine-containing peptide was successfully performed in aqueous solution to produce a fragment peptide of human α-synuclein. The formation of aspartimide (cyclic imide) in a base-sensitive hexapeptide fragment of scorpion toxin II was found to be significant under the deprotection conditions used. However, this could be controlled by the judicious protection of sensitive residues using the 2-hydroxy-4-methoxybenzyl group. Copyright © 2000 European Peptide Society and John Wiley & Sons, Ltd.