gebhart/patrepeval huggingface dataset:
Native-oxide-masked Si impurity-induced layer disordering of AlxGa1−xAs-AlyGa1−yAs-AlzGa1−zAs quantum-well heterostructures (1991)

Data are presented showing that the native oxide that can be formed on high Al composition AlxGa1−xAs (x≳0.7) confining layers commonly employed on AlxGa1−xAs-AlyGa1−yAs-AlzGa1−zAs (y≳z) superlattices or quantum-well heterostructures serves as an effective mask against Si diffusion, and thus impurity-induced layer disordering. The high-quality native oxide is produced by the conversion of high-composition AlxGa1−xAs (x≳0.7) confining layers via H2O vapor oxidation (≳400 °C) in N2 carrier gas.
Expression of human chorionic gonadotropin beta subunit genes in superficial and invasive bladder carcinomas. (1995)

Increased serum levels of human chorionic gonadotropin beta subunit (hCG beta) were described previously in patients with bladder cancer. To obtain insight into such production of hCG beta, the expression of hCG beta 7, 8, 5, and 3 genes in bladder carcinomas and normal urothelia was investigated by reverse transcription PCR. Surprisingly, hCG beta mRNAs were detected in both normal urothelial and carcinomatous cells. However, tumor progression was characterized by different patterns of transcription of the hCG beta genes; the beta 7 gene was the only gene transcribed in normal urothelia and Ta tumors included in this study, whereas in addition to beta 7, genes beta 5, 8, and 3 were transcribed in T1 to T4 tumors. Moreover, transcription levels of the latter three genes increased with the stage of the disease. These observations showed that dramatic modifications in the expression of hCG beta genes accompany progression of bladder carcinomas.
Thiopyrophosphoantigens: Solid-phase Synthesis and in Vitro Characterization of a New Class of Vγ9 Vδ2 T Cells Activators (2009)

The Vgamma9 Vdelta2 T cells mediate rapid, innate-like immune responses to pathogens and are important in several key immunoregulatory pathways, including those involved in infections and tumor development. Vgamma9 Vdelta2 T cells respond to low molecular weight isoprenoid phosphoantigens; the prototypic stimulatory compound is isopentenylpyrophosphate (IPP), an alkylphosphate intermediate of mevalonate metabolism that elicits proliferative, cytotoxic, and cytokine secretion responses. We studied the replacement of the pyrophosphate moiety with the thiopyrophosphate bioisostere, synthesizing thioanalogues of IPP and 4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP, the most potent natural antigen known to date). Once their in vitro efficacy and stability had been demonstrated, we synthesized a small library of compounds through the development of an innovative solid-phase strategy. Biological results confirmed thioHMBPP to be the best compound of this first series. Future aims are (i) the exploitation of the parallel solid-phase strategy to further explore structure-activity relationships of this new class of synthetic antigens and (ii) the determination of the PK/PD profile of thioHMBPP.
Preparation of layered double hydroxides and their applications as additives in polymers, as precursors to magnetic materials and in biology and medicine (2005)

In recent years layered double hydroxides (LDHs), also known as hydrotalcite-like materials, have attracted considerable interest from both industry and academia. In this article, we discuss methods of preparing LDHs with an emphasis on the way in which particle size and morphology can be controlled with regard to specific target applications; scale-up of one such preparation procedure is also described. In addition, we review selected applications of LDHs developed by our own and other laboratories.
Large‐scale biodiesel production from microalga Chlorella protothecoides through heterotrophic cultivation in bioreactors (2007)

An integrated approach of biodiesel production from heterotrophic Chlorella protothecoides focused on scaling up fermentation in bioreactors was reported in this study. Through substrate feeding and fermentation process controls, the cell density of C. protothecoides achieved 15.5 g L(-1) in 5 L, 12.8 g L(-1) in 750 L, and 14.2 g L(-1) in 11,000 L bioreactors, respectively. Resulted from heterotrophic metabolism, the lipid content reached 46.1%, 48.7%, and 44.3% of cell dry weight in samples from 5 L, 750 L, and 11,000 L bioreactors, respectively. Transesterification of the microalgal oil was catalyzed by immobilized lipase from Candidia sp. 99-125. With 75% lipase (12,000 U g(-1), based on lipid quantity) and 3:1 molar ratio of methanol to oil batch-fed at three times, 98.15% of the oil was converted to monoalkyl esters of fatty acids in 12 h. The expanded biodiesel production rates were 7.02 g L(-1), 6.12 g L(-1), and 6.24 g L(-1) in 5 L, 750 L, and 11,000 L bioreactors, respectively. The properties of biodiesel from Chlorella were comparable to conventional diesel fuel and comply with the US Standard for Biodiesel (ASTM 6751). These results suggest that it is feasible to expand heterotrophic Chlorella fermentation for biodiesel production at the industry level.
Potential Role of Inhibitors of Neutrophil Elastase in Treating Diseases of the Airway (2004)

The potential therapeutic use of inhibitors of neutrophil elastase (NE) is reviewed with emphasis on diseases of the airway. In addition to its proteolytic properties, NE is a potent secretagogue and may be pro-inflammatory. The properties of natural occurring inhibitors of NE such as alpha-one antitrypsin and secretory leukoprotease inhibitor are reviewed. In addition, recombinant versions of naturally occurring inhibitors and synthetic small molecule inhibitors are potential therapies for respiratory diseases. For recombinant proteins, aerosol administration has been the preferred method of delivery. The inhaled mode of delivery can complicate the determination of dose responsiveness and thus the evaluation of safety and efficacy of these agents. In addition to the aerosolization issue, there remain other significant barriers to the successful deployment of these agents in clinical trials. These include the need for high standards for purification of recombinant proteins, the lack of understanding of interaction with airway secretions, the controversy over role of NE in the pathogenesis of nonhereditary COPD, and asthma, while the need for the safety of new classes of systemically delivered small molecules will need to be established.
Sequences Homologous to Yeast Mitochondrial and Bacteriophage T3 and T7 RNA Polymerases Are Widespread Throughout the Eukaryotic Lineage (1996)

Although mitochondria and chloroplasts are considered to be descendants of eubacteria-like endo- symbionts, the mitochondrial RNA polymerase of yeast is a nucleus-encoded, single-subunit enzyme homologous to bacteriophage T3 and T7 RNA polymerases, rather than a multi-component, eubacterial-type alpha 2 beta beta' enzyme, as encoded in chloroplast DNA. To broaden our knowledge of the mitochondrial transcriptional apparatus, we have used a polymerase chain reaction (PCR) approach designed to amplify an internal portion of phage T3/T7-like RNA polymerase genes. Using this strategy, we have recovered sequences homologous to yeast mitochondrial and phage T3/T7 RNA polymerases from a phylogenetically broad range of multicellular and unicellular eukaryotes. These organisms display diverse patterns of mitochondrial genome organization and expression, and include species that separated from the main eukaryotic line early in the evolution of this lineage. In certain cases, we can deduce that PCR-amplified sequences, some of which contain small introns, are localized in nuclear DNA. We infer that the T3/T7-like RNA polymerase sequences reported here are likely derived from genes encoding the mitochondrial RNA polymerase in the organisms in which they occur, suggesting a phage T3/T7-like RNA polymerase was recruited to act in transcription in the mitochondrion at an early stage in the evolution of this organelle.
A small circular TAR RNA decoy specifically inhibits Tat-activated HIV- 1 transcription (1996)

Linear TAR RNA has previously been used as a decoy to inhibit HIV-1 transcription in vitro and HIV-1 replication in vivo. A 48 nucleotide circular RNA containing the stem, bulge and loop of the HIV-1 TAR element was synthesized using the self-splicing activity of a group I permuted intron-exon and was tested for its ability to function as a TAR decoy in vitro. This small circular TAR molecule was exceptionally stable in HeLa nuclear extracts, whereas a similar linear TAR molecule was rapidly degraded. The TAR circle bound specifically to Tfr38, a peptide containing the TAR-binding region of Tat. The ability of Tat to trans-activate transcription from the HIV-1 promoter in vitro was efficiently inhibited by circular TAR RNA but not by TAR circles that contained either bulge or loop mutations. TAR circles did not inhibit transactivation exclusively by binding to Tat since this inhibition was not reversed by adding excess Tat to the transcription reaction. Together, these data suggest that TAR circles act as decoys that inhibit transactivation by binding to Tat and at least one cellular factor. These data also demonstrate the utility of small circular RNA molecules as tools for biochemical studies.
Metabolic activities of the isolated perfused rat kidney (1967)

1. A technique for perfusing the isolated rat kidney is described. It is primarily designed for the study of renal metabolism but is also suitable for studying some aspects of the secretory function; this was normal with respect to minimal glucosuria. The glomerular filtration rate as measured by creatinine clearance was lower than in vivo and slowly decreased with time. 2. Gluconeogenesis from a variety of precursors was rapid and similar to that in kidney-cortex slices, in contrast with liver where the perfused organ is more effective than slices. Whereas the maximal rates of gluconeogenesis from glycerol and pyruvate were similar in liver and kidney, the rates from succinate, malate and fumarate were 14-20 times, and those from glutamate and aspartate about three times, as high in the kidney. 3. The oxygen consumption of the perfused organ was about twice that of cortex slices, presumably because of the secretory work done in the perfused organ but not in slices. 4. The rate of acetoacetate oxidation was about the same in the perfused organ and in slices but, because of the higher rate of oxygen consumption, the percentage contribution of acetoacetate to the fuel of respiration was lower in the perfused organ. The results suggest that acetoacetate can supply energy for the basal requirements and for gluconeogenesis but not for the secretory work. 5. Glutamine was formed at a high rate from glutamate and at a lower rate from aspartate. The high rates indicate that, in the rat, the kidney is a major source of body glutamine.
Assembly of τ protein into Alzheimer paired helical filaments depends on a local sequence motif ( 306 VQIVYK 311 ) forming β structure (2000)

We have searched for a minimal interaction motif in tau protein that supports the aggregation into Alzheimer-like paired helical filaments. Digestion of the repeat domain with different proteases yields a GluC-induced fragment comprising 43 residues (termed PHF43), which represents the third repeat of tau plus some flanking residues. This fragment self assembles readily into thin filaments without a paired helical appearance, but these filaments are highly competent to nucleate bona fide PHFs from full-length tau. Probing the interactions of PHF43 with overlapping peptides derived from the full tau sequence yields a minimal hexapeptide interaction motif of (306)VQIVYK(311) at the beginning of the third internal repeat. This motif coincides with the highest predicted beta-structure potential in tau. CD and Fourier transform infrared spectroscopy shows that PHF43 acquires pronounced beta structure in conditions of self assembly. Point mutations in the hexapeptide region by proline-scanning mutagenesis prevent the aggregation. The data indicate that PHF assembly is initiated by a short fragment containing the minimal interaction motif forming a local beta structure embedded in a largely random-coil protein.
Sensitive densitometry for the determination of platelet-activating factor and other phospholipids in human tears (1996)

A sensitive TLC method is reported for the determination of the platelet-activating factor (PAF) and other phospholipids in human tears. Tear samples absorbed on filter-paper were subjected to diatomite column extraction with chloroform-methanol. The eluent containing phospholipids was spotted on a silica gel plate. After removing lipids other than phospholipids by pre-development with hexane-diethyl ether (4 + 1 v/v), individual phospholipid separation was carried out by development with chloroform-methanol-water (65 + 35 + 7 v/v). Phospholipase C and then alkaline phosphatase solutions were sprayed on the TLC plate at 45 degrees C to liberate phosphate from each phospholipid. By spray application of a mixture of ammonium molybdate and Malachite Green, the liberated phosphates appeared as blue-green spots of molybdophosphate-Malachite Green aggregate on a yellow-brown background. The absorbance of each spot on the plate was measured at 620 nm with a densitometer. The peak area was found to be linearly related to PAF content in the range 2-100 pmol per spot, the RSD being 2% (n = 7). Approximately 86% of standard PAF added to tears was recovered. By this method, lysophosphatidylcholine (lysoPC), phosphatidylcholine (PC) and phosphatidylethanolamine (PE) in human tears could also be detected with high sensitivity. Each phospholipid in healthy human tears showed a nearly constant content; PAF, lysoPC, PC and PE were present at levels of 26.2, 42.3, 10.0 and 19.7%, respectively.
Stem cell factor induces mast cell adhesion to fibronectin. (1994)

Stem cell factor (SCF) or c-kit ligand is a growth factor cytokine produced by stromal cells that is known to influence mast cell proliferation and differentiation. We hypothesized that SCF may also influence the adhesion of mast cells to connective tissue matrix. To examine this hypothesis, we stimulated MCP5/L mast cells or murine bone marrow-derived cultured mast cells (BMCMC) with either SCF or PMA and observed adhesion to fibronectin (FN). As expected, 80 to 90% of PMA-activated MCP5/L cells or BMCMC adhered to FN. In addition, SCF promoted MCP5/L cell or BMCMC adhesion to FN in a dose-response fashion with 50 to 60% of BMCMC adhering to FN at a concentration 10 ng/ml of SCF. BMCMC adhesion was observed with as little as 200 pg/ml of SCF. Adhesion of SCF stimulated BMCMC to FN did not require IL-3, but was dependent on the concentration of FN used to coat the assay surface. Mast cell adhesion in the presence of SCF appeared to occur through an integrin receptor as adhesion was calcium dependent and could be blocked by an RGD (Ang, Gly, Asp)-containing peptide. SCF did not directly mediate adhesion through interaction with c-kit, as FN-coated surfaces exposed to SCF before initiation of the adhesion assay did not promote adhesion in the absence of soluble SCF. Rather, SCF appeared to stimulate adhesion to FN by activating mast cells through its interaction with c-kit. Thus, antibody to SCF blocked adhesion, and rat and murine SCF stimulated BMCMC adhesion to FN, but human SCF, which does not bind to murine c-kit, did not stimulate adhesion. Genistein, which inhibits tyrosine kinase activity, partially inhibited SCF-induced adhesion. SCF thus stimulates mast cell adhesion and, because SCF is produced normally in tissues, it may be a major factor responsible for the adhesion of mast cells to connective tissue matrix under physiologic conditions.
Residues Glu2181-Val2243 Contain a Major Determinant of the Inhibitory Epitope in the C2 Domain of Human Factor VIII (1998)

The human blood coagulation factor VIII C2 domain (Ser2173-Tyr2332) contains an epitope recognized by most polyclonal inhibitory anti-factor VIII alloantibodies and autoantibodies. We took advantage of the differential reactivity of inhibitory antibodies with human and porcine factor VIII and mapped a major determinant of the C2 epitope by using a series of active recombinant hybrid human/porcine factor VIII molecules. A series of five C2-specific human antibodies and a murine anti-factor VIII monoclonal antibody, NMC-VIII/5, inhibited a hybrid containing a substitution of porcine sequence for Glu2181-Val2243 significantly less than human factor VIII. In contrast, four of the five patient antibodies and NMC-VIII/5 inhibited a hybrid containing a substitution of porcine sequence for Thr2253-Tyr2332 equally well as human factor VIII. Thus, a major factor VIII inhibitor epitope determinant is bounded by Glu2181-Val2243 at the NH2-terminal end of the C2 domain. Because C2 inhibitors block the binding of factor VIII to phospholipid and von Willebrand factor, for which binding sites have been localized to Thr2303-Tyr2332, these results imply that the segment bounded by Glu2181-Val2243 also is involved in these macromolecular interactions.
Antisense targeting of Mcl-1 has therapeutic potential in gastric cancer (2006)

Commentary to:Mcl-1 is a Relevant Molecular Target for Antisense Oligonucleotide Strategies in Gastric Cancer CellsVolker Wacheck, Daniel Cejka, Wolfgang Sieghart, Doris Losert, Sabine Strommer, Richard Crevenna, Brett P Monia and Edgar Selzer
Paraquat elicited neurobehavioral syndrome caused by dopaminergic neuron loss (1999)

The herbicide paraquat, bearing structural similarity to the known dopaminergic neurotoxicant MPTP, has been suggested as a potential etiologic factor in Parkinson's disease. Consideration of paraquat as a candidate neurotoxicant requires demonstration that systemic delivery produces substantia nigra dopaminergic neuron loss and the attendant neurobehavioral syndrome reflecting depletion of dopamine terminals within the striatum. To address these issues paraquat was administered systemically into adult C57 bl/6 mice, ambulatory behavior monitored, substantia nigra dopamine neuron number and striatal dopamine terminal density quantified. The data indicate that paraquat like MPTP elicits a dose-dependent decrease in substantia nigra dopaminergic neurons assessed by a Fluoro-gold prelabeling method, a decline in striatal dopamine nerve terminal density assessed by measurement of tyrosine hydroxylase immunoreactivity; and neurobehavioral syndrome characterized by reduced ambulatory activity. Taken together, these data suggest that systemically absorbed paraquat crosses the blood–brain barrier to cause destruction of dopamine neurons in the substantia nigra, consequent reduction of dopaminergic innervation of the striatum and a neurobehavioral syndrome similar to the well characterized and bona fide dopaminergic toxin MPTP.
Analytical strategies for amperometric biosensors based on chemically modified electrodes (1998)

Various strategies based on the use of chemically modified electrodes for the development of amperometric biosensors are described. Particular emphasis is placed on materials capable of catalyzing the oxidation of NADH and coupling these with enzymatic activities for biosensor construction. In terms of electrocatalysts, the discussion will centre on electrodeposited films of 3,4-dihydroxy benzaldehyde (3,4-DHB) and related analogs as well as on electrodeposited films of transition metal complexes of 1,10-phenanthroline-5,6-dione (phen-dione). Electrodeposited films of these materials have been coupled to the enzymatic activity of aldehyde dehydrogenase and alcohol dehydrogenase for the development of biosensors for aldehydes and ethanol, respectively.
Practical Free-Space Quantum Key Distribution over 1 km (1998)

A working free-space quantum key distribution system has been developed and tested over an outdoor optical path of $\ensuremath{\sim}1\mathrm{km}$ at Los Alamos National Laboratory under nighttime conditions. Results show that free-space quantum key distribution can provide secure real-time key distribution between parties who have a need to communicate secretly. Finally, we examine the feasibility of surface to satellite quantum key distribution.
Evaluation of the adeno-associated virus mediated long-term expression of channelrhodopsin-2 in the mouse retina. (2009)

Expression of Chop2-GFP could be achieved in retinal neurons in vivo for the duration of the lifespan of mice. The expression of Chop2-GFP did not cause any detectable toxicity and cell death to neurons of the ganglion cell layer.
Structural Differences between the Free and Bound States of the DNA-Bisintercalating Peptide YSPTSPSY (1996)

The YSPTSPSY peptide is a DNA-bisintercalator that can adopt nonrandom conformations in solution. Strategies based on random conformational search and energy minimizations have been applied to generate populations of conformers characterizing YSPTSPSY. Subsequent analysis based on statistical methods and clustering allowed to determine the existence of four classes of conformers containing beta- and/or gamma-turns. NMR spectra of YSPTSPSY in solution provide evidence for such structures. Employing a Monte Carlo-based docking procedure, the YSPTSPSY peptide was docked in a DNA double-helical fragment with the sequence [d(GACGTC)]2. The peptide binds on the minor groove of DNA stacking the central CG base pairs, in a manner similar to that observed in complexes of triostin A with DNA. Upon binding, the structure of the C-terminal segment is modified into a type I beta-turn. Five intermolecular hydrogen bonds are observed, but the van der Waals interactions constitute the major stabilization factor for the complex. NMR chemical shifts, coupling constants, and NOESY connectivities are in agreement with the molecular model.
Quantitative susceptibility mapping (QSM): Decoding MRI data for a tissue magnetic biomarker (2014)

In MRI, the main magnetic field polarizes the electron cloud of a molecule, generating a chemical shift for observer protons within the molecule and a magnetic susceptibility inhomogeneity field for observer protons outside the molecule. The number of water protons surrounding a molecule for detecting its magnetic susceptibility is vastly greater than the number of protons within the molecule for detecting its chemical shift. However, the study of tissue magnetic susceptibility has been hindered by poor molecular specificities of hitherto used methods based on MRI signal phase and T2* contrast, which depend convolutedly on surrounding susceptibility sources. Deconvolution of the MRI signal phase can determine tissue susceptibility but is challenged by the lack of MRI signal in the background and by the zeroes in the dipole kernel. Recently, physically meaningful regularizations, including the Bayesian approach, have been developed to enable accurate quantitative susceptibility mapping (QSM) for studying iron distribution, metabolic oxygen consumption, blood degradation, calcification, demyelination, and other pathophysiological susceptibility changes, as well as contrast agent biodistribution in MRI. This paper attempts to summarize the basic physical concepts and essential algorithmic steps in QSM, to describe clinical and technical issues under active development, and to provide references, codes, and testing data for readers interested in QSM.
Plasmid-Mediated Resistance to Vancomycin and Teicoplanin in Enterococcus Faecium (1988)

THE glycopeptide antibiotic agents vancomycin and teicoplanin are useful in the treatment of severe infections due to gram-positive bacteria.1 2 3 Staphylococci, streptococci, and enterococci are almost always susceptible to these agents, which constitute an alternative to the penicillins in cases of resistance or intolerance.Resistance to glycopeptides is extremely common in leuconostoc species4 and pediococcus species and also occurs in lactobacilli.5 , 6 These gram-positive bacteria rarely cause infections and are considered opportunistic pathogens. The emergence of strains of Staphylococcus haemolyticus that became resistant during vancomycin therapy has recently been reported.7 Resistance to vancomycin is rare in streptococci.8 Enterococcal isolates with minimal inhibitory . . .