gebhart/patrepeval huggingface dataset:
Modifying the Surface Properties of Superparamagnetic Iron Oxide Nanoparticles through A Sol−Gel Approach (2002)

This paper describes a sol−gel approach for the coating of superparamagnetic iron oxide nanoparticles with uniform shells of amorphous silica. The coating process has been successfully applied to particles contained in a commercial ferrofluid (e.g., the EMG 304 of Ferrofluidics) and those synthesized through a wet chemical process. The thickness of silica coating could be conveniently controlled in the range of 2−100 nm by changing the concentration of the sol−gel solution. Fluorescent dyes, for example, 7-(dimethylamino)-4-methylcoumarin-3-isothiocyanate (DACITC) and tetramethylrhodamine-5-isothiocyanate (5-TRITC), have also been incorporated into the silica shells by covalently coupling these organic compounds with the sol−gel precursor. These multifunctional nanoparticles are potentially useful in a number of areas because they can be simultaneously manipulated with an externally applied magnetic field and characterized in situ using conventional fluorescence microscopy.
Synthesis and properties of optically active helical metallocene oligomers (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and properties of optically active helical metallocene oligomersThomas J. Katz, Anantha Sudhakar, Mark F. Teasley, Adam M. Gilbert, William E. Geiger, Matthew P. Robben, Martin Wuensch, and Michael D. WardCite this: J. Am. Chem. Soc. 1993, 115, 8, 3182–3198Publication Date (Print):April 1, 1993Publication History Published online1 May 2002Published inissue 1 April 1993https://pubs.acs.org/doi/10.1021/ja00061a018https://doi.org/10.1021/ja00061a018research-articleACS PublicationsRequest reuse permissionsArticle Views1023Altmetric-Citations114LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Failure of desmopressin to lower serum sodium or prevent crisis in patients with sickle cell anemia (1981)

An analogue of arginine vasopressin (desmopressin, DDAVP) was evaluated for production chronic hyponatremia and prevention of sickle cell crisis. With sodium restriction (100 meq Na + / day) and water loading ( greater than 3 liters/day), persistent hyponatremia could not be achieved, nor could crises be prevented or aborted. Patients would not comply with a regimen of lower salt and higher fluid intake. More rigorous treatment might be practical during acute sickle cell crises, and a regimen similar to that used here might be more effective in children, whose renal concentrating mechanisms are still intact.
The animal sialyltransferases and sialyltransferase-related genes: a phylogenetic approach (2005)

The animal sialyltransferases are Golgi type II transmembrane glycosyltransferases. Twenty distinct sialyltransferases have been identified in both human and murine genomes. These enzymes catalyze transfer of sialic acid from CMP-Neu5Ac to the glycan moiety of glycoconjugates. Despite low overall identities, they share four conserved peptide motifs [L (large), S (small), motif III, and motif VS (very small)] that are hallmarks for sialyltransferase identification. We have identified 155 new putative genes in 25 animal species, and we have exploited two lines of evidence: (1) sequence comparisons and (2) exon-intron organization of the genes. An ortholog to the ancestor present before the split of ST6Gal I and II subfamilies was detected in arthropods. An ortholog to the ancestor present before the split of ST6GalNAc III, IV, V, and VI subfamilies was detected in sea urchin. An ortholog to the ancestor present before the split of ST3Gal I and II subfamilies was detected in ciona, and an ortholog to the ancestor of all the ST8Sia was detected in amphioxus. Therefore, single examples of the four families (ST3Gal, ST6Gal, ST6GalNAc, and ST8Sia) have appeared in invertebrates, earlier than previously thought, whereas the four families were all detected in bony fishes, amphibians, birds, and mammals. As previously hypothesized, sequence similarities among sialyltransferases suggest a common genetic origin, by successive duplications of an ancestral gene, followed by divergent evolution. Finally, we propose predictions on these invertebrates sialyltransferase-related activities that have not previously been demonstrated and that will ultimately need to be substantiated by protein expression and enzymatic activity assays.
Measurement of glucose in human blood serum using near-infrared Raman spectroscopy (1998)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1998.
Electromagnetic circuit fingerprints for Hardware Trojan detection (2015)

Integrated circuit counterfeits, relabeled parts and maliciously modified integrated circuits (so-called Hardware Trojan horses) are a recognized emerging threat for embedded systems in safety or security critical applications. We propose a Hardware Trojan detection technique based on fingerprinting the electromagnetic emanations of integrated circuits. In contrast to most previous work, we do not evaluate our proposal using simulations but we rather conduct experiments with an FPGA. We investigate the effectiveness of our technique in detecting extremely small Hardware Trojans located at different positions within the FPGA. In addition, we also study its robustness to the often neglected issue of variations in the test environment. The results show that our method is able to detect most of our test Hardware Trojans but also highlight the difficulty of measuring emanations of unrealistically tiny Hardware Trojans. The results also confirm that our method is sensitive to changes in the test environment.
Interaction of reovirus with cell surface receptors. II. Generation of suppressor T cells by the hemagglutinin of reovirus type 3. (1980)

In studying reovirus interactions with lymphocytes, we have found that reovirus type 3, but not type 1, inhibits the in vitro proliferative response of murine splenic lymphocytes to concanavalin A (Con A). By analyzing recombinant clones containing genes from both reovirus types 1 and 3, we found that the S1 gene, the gene that encodes the viral hemagglutinin, is responsible for the inhibitory effect. In addition we found that type 3, but not type 1, generates suppressor T cells in vitro capable of suppressing Con A proliferation. By analyzing recombinant clones, we also found that the viral hemagglutinin is responsible for the generation of suppressor T cells by reovirus type 3. These effects were observed whether UV-inactivated or live virus was used. Reovirus type 3 inhibition of the proliferative response of murine splenic lymphocytes to Con A was blocked by anti-reovirus type 3 antibody but not by anti-reovirus type 1 antibody. Antiviral antibody had no effect on the ability of reovirus type 3 induced suppressor cells to inhibit Con A proliferation. We have previously demonstrated a receptor on murine lymphocytes for the hemagglutinin of reovirus type 3, and our results suggest that the in vitro suppression of Con A proliferation of murine lymphocytes by reovirus type 3 is secondary to the interaction of the viral hemagglutinin with a receptor on the surface of murine lymphocytes, which results in the generation of functionally active suppressor T cells.
Exportin 4 gene expression and DNA promoter methylation status in chronic hepatitis B virus infection (2013)

Exportin 4 (XPO4) is a novel identified candidate tumour-suppressor gene involved in the pathogenesis of hepatocellular carcinoma (HCC). This study was aimed to determine the clinical features of XPO4 mRNA expression and promoter methylation status in peripheral blood mononuclear cells (PBMCs) of patients with chronic hepatitis B virus (HBV) infection. PBMCs were isolated from 44 HCC, 38 liver cirrhosis (LC), 34 chronic hepatitis B (CHB) patients and 17 healthy controls (HCs). The mRNA level and promoter methylation status of XPO4 were determined by quantitative real-time RT-PCR and methylation-specific PCR, respectively. XPO4 mRNA level of HCC patients was significantly lower compared with LC and CHB patients as well as HCs (all P < 0.01, respectively), and significant differences of the XPO4 mRNA level were found in LC and CHB group than in HCs (LC vs HCs, P < 0.01; CHB vs HCs, P < 0.05). Methylation rate of XPO4 promoter was significantly increased in patients with HCC than in patients with CHB and HCs (both P < 0.05). DNA methylation pattern was responsible for the suppression of XPO4 transcription in the progression of HBV infection (P = 0.000). Furthermore, AFP level was significantly higher in HCC patients with XPO4 methylation than in those without methylation ((8702 ± 15635) μm vs (1052 ± 5370) μm, P < 0.05). In conclusion, transcription of XPO4 gene was gradually decreased and methylation rate of XPO4 promoter was increased with the progression of HBV infection. Methylation status of XPO4 in PBMCs tended to be a noninvasive biomarker to predict HCC and the progression of HBV infection.
Mass Transport in a Micro Flow-Through Vial of a Junction-at-the-Tip Capillary Electrophoresis-Mass Spectrometry Interface (2011)

When coupling capillary electrophoresis with postcolumn detection methods, such as mass spectrometry, the presence of postcolumn band broadening must be considered. The band broadening effects introduced by junction-at-the-tip CE-MS interfaces using a postcolumn micro flow-through vial are investigated by studying the hydrodynamic flow patterns and mass transport process inside the micro vial at the end of the CE separation capillary. Simulation results obtained by solving the Navier-Stokes and mass balance equations provide insights into the velocity field and concentration distribution of the analytes in the micro vial and demonstrate that, with a low flow rate of chemical modifier solution, the laminar flow streams confine the analyte molecules to the central part of the micro vial and thus maintain major features of the peak shapes. Peaks detected by UV and MS under similar experimental conditions were compared to verify the numerical prediction that the main features of the UV peak can be retained in the MS peak. Experiments also show that band broadening can be minimized when an appropriate chemical modifier flow rate is selected.
A high-speed atomic force microscope for studying biological macromolecules (2001)

The atomic force microscope (AFM) is a powerful tool for imaging individual biological molecules attached to a substrate and placed in aqueous solution. At present, however, it is limited by the speed at which it can successively record highly resolved images. We sought to increase markedly the scan speed of the AFM, so that in the future it can be used to study the dynamic behavior of biomolecules. For this purpose, we have developed a high-speed scanner, free of resonant vibrations up to 60 kHz, small cantilevers with high resonance frequencies (450-650 kHz) and small spring constants (150-280 pN/nm), an objective-lens type of deflection detection device, and several electronic devices of wide bandwidth. Integration of these various devices has produced an AFM that can capture a 100 x 100 pixel(2) image within 80 ms and therefore can generate a movie consisting of many successive images (80-ms intervals) of a sample in aqueous solution. This is demonstrated by imaging myosin V molecules moving on mica (see http://www.s.kanazawa-u.ac.jp/phys/biophys/bmv_movie.htm).
Thermodynamic studies on subunit assembly in human hemoglobin. Temperature dependence of the dimer-tetramer association constants for oxygenated and unliganded hemoglobins. (1977)

Equilibrium constants for dimer-tetramer association of oxygenated human hemoglobin have been determined as a function of temperature, by analytical molecular sieve chromatography, yielding a van't Hoff enthalpy of 3.8 +/- 1.6 kcal/mol, and a unitary entropy of 48.4 +/- 5.7 e.u. Under the same conditions (0.1 M Tris/HCl, 0.1 M NaCl, 1 mM Na2EDTA, pH 7.4) the equilibrium constants for dimer-tetramer association of unliganded hemoglobin have been determined as a function of temperature from kinetic studies of the forward and reverse rate constants. The derived enthalpy and unitary entropy for association of unliganded hemoglobin are 0deltaH2 = 28.9 +/- 0.5 kcal/mol and 0deltaS2 = -41.8 +/- 1.7 e.u., respectively. Thus the oxygenation-linked enthalpy of subunit association is 32.7 +/- 1.7 kcal. The corresponding entropic coupling is 90.2 +/- 5.9 e.u. The thermodynamic parameters are consistent with an increased role of hydrophobic interactions within the dimer-dimer contact region upon oxygenation, or a decreased role of hydrogen bonds and ion pair interactions. The opposite signs for association entropies in unliganded and oxygenated states suggest the existence of two distinct subunit interaction processes during the course of oxygenation with a reversal in sign at some particular binding step. The results provide a necessary basis for interpretation of calorimetric results on reconstitution of hemoglobin, described in an accompanying paper.
Completely Superhydrophobic PDMS Surfaces for Microfluidics (2012)

This study presents a straightforward two-step fabrication process of durable, completely superhydrophobic microchannels in PDMS. First, a composite material of PDMS/PTFE particles is prepared and used to replicate a master microstructure. Superhydrophobic surfaces are formed by subsequent plasma treatment, in which the PDMS is isotropically etched and PTFE particles are excavated. We compare the advancing and receding contact angles of intrinsic PDMS samples and composite PTFE/PDMS samples (1 wt %, 8 wt %, and 15 wt % PTFE particle concentration) and demonstrate that both the horizontal and vertical surfaces are indeed superhydrophobic. The best superhydrophobicity is observed for samples with a PTFE particle concentration of 15 wt %, which have advancing and receding contact angles of 159° ± 4° and 158° ± 3°, respectively.
Riluzole prolongs survival time and alters nuclear inclusion formation in a transgenic mouse model of Huntington's disease (2002)

Glutamate excitotoxicity has been suggested to contribute to the pathogenesis of Huntington's disease (HD). Riluzole is a substance with glutamate antagonistic properties that is used for neuroprotective treatment in amyotrophic lateral sclerosis and which is currently tested in clinical trials for treatment of HD. R6/2 transgenic mice, which express exon 1 of the human HD gene with an expanded CAG triplet repeat, serve as a well-characterized mouse model for HD with progressing neurological abnormalities and limited survival. We treated R6/2 HD transgenic mice with riluzole orally beginning at a presymptomatic stage until death to investigate its potential neuroprotective effects in this mouse model and found that survival time in the riluzole group was significantly increased in comparison to placebo-treated transgenic controls. Additionally, the progressive weight loss was delayed and significantly reduced by riluzole treatment; behavioral testing of motor coordination and spontaneous locomotor activity, however, showed no statistically significant differences. We also examined the formation of the HD characteristic neuronal intranuclear inclusions (NII) immunohistologically. At a late disease stage, striatal NII from riluzole-treated transgenic mice showed profound changes in ubiquitination, i.e., NII were less ubiquitinated and surrounded by ubiquitinated micro-aggregates. Staining with antibodies directed against the mutated huntingtin revealed no significant difference in this component of NII. Taken together, these data suggest that riluzole is a promising candidate for neuroprotective treatment in human HD.
Genetic engineering of IgG-glucuronidase fusion proteins (2009)

beta-Glucuronidase (GUSB) is a lysosomal enzyme that could be developed as a brain therapy for Type VII Mucopolysaccharidosis. However, GUSB does not cross the blood-brain barrier (BBB). To enable BBB transport of the enzyme, human GUSB was re-engineered as a fusion protein with the chimeric monoclonal antibody (MAb) to the human insulin receptor (HIR). The HIRMAb crosses the BBB on the endogenous insulin receptor, and acts as a molecular Trojan horse to ferry into brain the GUSB. The 611 amino acid GUSB was fused to either the carboxyl or amino terminus of the heavy chain of the HIRMAb. This study illustrates the differential retention of functionality of IgG-enzyme fusion proteins depending on how the fusion protein is engineered.
Adenosine: a physiological modulator of superoxide anion generation by human neutrophils. (1983)

The effects of adenosine were studied on human neutrophils with respect to their generation of superoxide anion, degranulation, and aggregation in response to soluble stimuli. Adenosine markedly inhibited superoxide anion generation by neutrophils stimulated with N-formyl methionyl leucyl phenylalanine (FMLP), concanavalin A (Con A), calcium ionophore A23187, and zymosan-treated serum; it inhibited this response to PMA to a far lesser extent. The effects of adenosine were evident at concentrations ranging from 1 to 1,000 microM with maximal inhibition at 100 microM. Cellular uptake of adenosine was not required for adenosine-induced inhibition since inhibition was maintained despite the addition of dipyridamole, which blocks nucleoside uptake. Nor was metabolism of adenosine required, since both deoxycoformycin (DCF) and erythro-9-(2-hydroxy-3-nonyl) adenine did not interfere with adenosine inhibition of superoxide anion generation. The finding that 2-chloroadenosine, which is not metabolized, resembled adenosine in its ability to inhibit superoxide anion generation added further evidence that adenosine metabolism was not required for inhibition of superoxide anion generation by neutrophils. Unexpectedly, endogenously generated adenosine was present in supernatants of neutrophil suspensions at 0.14-0.28 microM. Removal of endogenous adenosine by incubation of neutrophils with exogenous adenosine deaminase (ADA) led to marked enhancement of superoxide anion generation in response to FMLP. Inactivation of ADA with DCF abrogated the enhancement of superoxide anion generation. Thus, the enhancement was not due to a nonspecific effect of added protein. Nor was the enhancement due to the generation of hypoxanthine or inosine by deamination of adenosine, since addition of these compounds did not affect neutrophil function. Adenosine did not significantly affect either aggregation or lysozyme release and only modestly affected beta-glucuronidase release by neutrophils stimulated with FMLP. These data indicate that adenosine (at concentrations that are present in plasma) acting via cell surface receptors is a specific modulator of superoxide anion generation by neutrophils.
E. coli MEP Synthase:  Steady-State Kinetic Analysis and Substrate Binding (2001)

2-C-Methyl-D-erythritol-4-phosphate synthase (MEP synthase) catalyzes the rearrangement/reduction of 1-D-deoxyxylulose-5-phosphate (DXP) to methylerythritol-4-phosphate (MEP) as the first pathway-specific reaction in the MEP biosynthetic pathway to isoprenoids. Recombinant E. coli MEP was purified by chromatography on DE-52 and phenyl-Sepharose, and its steady-state kinetic constants were determined: k(cat) = 116 +/- 8 s(-1), K(M)(DXP) = 115 +/- 25 microM, and K(M)(NADPH) = 0.5 +/- 0.2 microM. The rearrangement/reduction is reversible; K(eq) = 45 +/- 6 for DXP and MEP at 150 microM NADPH. The mechanism for substrate binding was examined using fosmidomycin and dihydro-NADPH as dead-end inhibitors. Dihydro-NADPH gave a competitive pattern against NADPH and a noncompetitive pattern against DXP. Fosmidomycin was an uncompetitive inhibitor against NADPH and gave a pattern representative of slow, tight-binding competitive inhibition against DXP. These results are consistent with an ordered mechanism where NADPH binds before DXP.
Identification of In Vivo -Induced Conserved Sequences from Yersinia pestis During Experimental Plague Infection in the Rabbit (2010)

In an effort to identify the novel virulence determinants of Yersinia pestis, we applied the gene “discovery” methodology, in vivo-induced (IVI) antigen technology, to detect genes upregulated during infection in a laboratory rabbit model for bubonic plague. After screening over 70,000 Escherichia coli clones of Y. pestis DNA expression libraries, products from 25 loci were identified as being seroreactive to reductively adsorbed, pooled immune serum. Upon sequence analysis of the predicted IVI gene products, more frequently encountered conserved protein functional categories have emerged, to include type-V autotransporters and components of more complex secretion systems including types III and VI. The recombinant products from eight selected clones were subsequently immunoblotted against pooled immune serum from two naturally infected host species: the prairie dog, and a species refractory to lethal disease, the coyote. Immune prairie dog serum recognized 2–3 of the rabbit-reactive antigens, suggesting at least some overlap in the pathogen's in vivo survival mechanisms between these two hosts. Although the coyote serum failed to recognize most of the IVI antigens, LepA was universally reactive with all three host sera. Collectively, the profiles/patterns of IVI conserved sequences (IVICS) may represent immune “signatures” among different host species, possessing the potential for use as a diagnostic tool for plague. Further, the antigenic nature of IVICS makes them ideal for further evaluation as novel subunit vaccine candidates. The gathering of additional data and analysis of the intact IVI genes and the expressed IVICS products should provide insight into the unique biologic processes of Y. pestis during infection and reveal the genetic patterns of the pathogen's survival strategy in different hosts.