gebhart/patrepeval huggingface dataset:
Innovations in optical microfluidic technologies for point-of-care diagnostics (2008)

Despite a growing focus from the academic community, the field of microfluidics has yet to produce many commercial devices for point-of-care (POC) diagnostics. One of the main reasons for this is the difficulty in producing low-cost, sensitive, and portable optical detection systems. Although electrochemical methods work well for certain applications, optical detection is generally regarded as superior and is the method most widely employed in laboratory clinical chemistry. Conventional optical systems, however, are costly, require careful alignment, and do not translate well to POC devices. Furthermore, many optical detection paradigms such as absorbance and fluorescence suffer at smaller geometries because the optical path length through the sample is shortened. This review examines the innovative techniques which have recently been developed to address these issues. We highlight microfluidic diagnostic systems which demonstrate practical integration of sample preparation, analyte enrichment, and optical detection. We also examine several emerging detection paradigms involving nanoengineered materials which do not suffer from the same miniaturization disadvantages as conventional measurements.
A Case of Foul Genital Odor Treated with Botulinum Toxin A (2004)

BACKGROUND Genital odor is an uncommon condition characterized by an offensive and malodorous smell in the genital area. Although the etiology of foul genital odor is multifactorial, an important cause is sweat secretion and decomposition of sweat components by bacteria. Different methods are effective in reducing body odor secondary to bromhidrosis. Conservative methods only act for a short period of time, and more invasive surgical methods carry risk of complications or are inapplicable for the genital region. METHODS A patient with localized foul odor in the genital hair bearing area was treated with botulinum toxin A. RESULTS Botulinum toxin A was effective in creating an odorless and anhydrous response in the genital region, and no major adverse effects were noted during a follow-up of 9 months after injection. CONCLUSION Local injection of botulinum toxin A appears to be a useful treatment for foul genital odor related to sweat glands activity.
NOBOX Deficiency Disrupts Early Folliculogenesis and Oocyte-Specific Gene Expression (2004)

Primordial ovarian follicles in mice form when somatic cells surround individual oocytes. We show that lack of Nobox, an oocyte-specific homeobox gene, accelerates postnatal oocyte loss and abolishes the transition from primordial to growing follicles in mice. Follicles are replaced by fibrous tissue in female mice lacking Nobox in a manner similar to nonsyndromic ovarian failure in women. Genes preferentially expressed in oocytes, including Oct4 and Gdf9, are down-regulated in Nobox-/- mice, whereas ubiquitous genes such as Bmp4, Kit, and Bax remain unaffected. Therefore, Nobox is critical for specifying an oocyte-restricted gene expression pattern essential for postnatal follicle development.
Integration of speech recognition and natural language processing in the MIT VOYAGER system (1991)

The MIT VOYAGER speech understanding system is an urban exploration and navigation system that interacts with the user through spoken dialogue, text, and graphics. The authors describe recent attempts at improving the integration between the speech recognition and natural language components. They used the generation capability of the natural language component to produce a word-pair language model to constrain the recognizer's search space, thus improving the coverage of the overall system. They also implemented a strategy in which the recognizer generates the top N word strings and passes them along to the natural language component for filtering. Results on performance evaluation are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Enhancing major histocompatibility complex class I antigen presentation by targeting antigen to centrosomes. (2003)

Several strategies that increase proteasomal degradation of antigen have been shown to improve MHC class I presentation of antigen. Because recent studies have demonstrated that the centrosome is a subcellular compartment rich in proteasomes, we hypothesized that targeting a tumor antigen to centrosomal compartments would enhance both the MHC class I presentation of antigen and the vaccine potency. We, therefore, created a chimera of gamma-tubulin, an established centrosomal marker, with a model tumor antigen, human papillomavirus type 16 (HPV-16) E7, in a DNA vaccine. The linkage of gamma-tubulin to E7-targeted antigen to centrosomal compartments, resulted in enhanced MHC class I presentation of E7, and led to a marked increase in the number of E7-specific CD8(+) T-cell precursors as well as a potent CD4-independent antitumor effect against an E7-expressing tumor cell line, TC-1. In addition, vaccination with gamma-tubulin/E7 DNA in transporter associated with antigen presentation (TAP)-1-knockout mice revealed that the enhancement of E7-specific CD8(+) T-cell immune responses is TAP-1-dependent. Our data suggest that the centrosome may be an important locus for MHC class I antigen processing and that targeting antigen to the centrosome can improve DNA vaccine potency.
Biosynthetic Incorporation and Chemical Modification of Alkene Functionality in Genetically Engineered Polymers (1997)

Abstract Repetitive polypeptides of sequence [(AlaGly)3ProGluGly]16 3a, have been prepared in Escherichia coli as overexpressed recombinant proteins. Replacement of more than 90% of the naturally occurring proline (Pro) residues with 3,4-dehydroproline (Dhp) in sequence 3a was achieved by in vivo expression of the target protein in medium containing Dhp and lacking Pro. The resulting material (3b) was treated with H2O2 or Br2 to yield polymers containing 3,4-dihydroxyproline (Dhy, 3c) and 3,4-dibromoproline (Dbr, 3d), respectively, in place of the Dhp residue. These results represent the first demonstration of the incorporation and modification of alkene functionality in recombinant proteins.
Entrapment of an Ionic Liquid in a Metallic Silver Matrix through Precipitation (2008)

Entrapment of an ionic liquid within metallic silver by means of physical caging is described. Thermal analysis of this new silver-based composite material allows estimation of the 1-butyl-3-methylimidazolium nitrate entrapment efficiency at 98%.
Hepsin, a putative cell-surface serine protease, is required for mammalian cell growth. (1993)

Hepsin was previously identified as a putative cell-surface serine protease. When hepatoma cells were treated with anti-hepsin antibodies, their growth was substantially arrested, suggesting the requirement of hepsin molecules present at the cell surface for normal cell growth. This was further supported by a gross inhibition of cell growth with hepsin-specific antisense oligonucleotides. Upon treatment of cells with antisense oligonucleotides, rapid reduction in cellular hepsin was observed. This reduction in cellular hepsin levels was accompanied by drastic morphological changes. Various tissues in the developing mouse embryo showed greatly elevated hepsin levels in regions of active proliferation. These results indicate that hepsin plays an essential role in cell growth and maintenance of cell morphology.
Factors Controlling the Fluorine Content and the Electrochemical Performance of Spinel Oxyfluoride Cathodes (2007)

An investigation of spinel (, ) cathodes synthesized by firing the cation-substituted oxide analogs with the fluorinating agent at reveals that the amount of fluorine that could be incorporated into the spinel lattice is limited by the Mn valence in the spinel lattice; it is difficult to incorporate fluorine as the Mn valence lowers to around . Although fluorine substitution increases the capacity, spinel cathodes with a Mn valence of encounters a larger lattice mismatch between the two cubic phases formed during the charge-discharge process and higher Mn dissolution, resulting in a degradation of the electrochemical properties. For example, with an initial Mn valence of exhibits a combination of high capacity, excellent cyclability with graphite anode at , good storage characteristics, high rate capability, and low irreversible capacity compared to .
Stereospecific Synthesis of 1,6-Dioxadecalins and 2,2‘-Linked Ditetrahydrofurans by Rearrangement of Steroidal Spiroacetals (1998)

The reduction of steroidal spiroacetal methanesulfonate derivatives, containing the 1,6-dioxaspiro[4.5]decan-10-yl ring system, with DIBALH promotes a new rearrangement to give steroidal 1,6-dioxadecalin (octahydropyrano[3,2-b]pyran) or 2,2'-linked ditetrahydrofuran (octahydro[2,2']bifuranyl) derivatives. To study the scope and selectivity of the reaction, several steroidal spiroacetals such as (23R,25R)-3beta-methoxy-5alpha-spirostan-23-yl methanesulfonate (2) and its 23S-isomer (5) and (22R,23R,25R)-3beta-acetoxy-16beta,23:23,26-diepoxycholest-5-en-22-yl methanesulfonate (15) and its 22S-isomer (19) have been synthesized. Compound 2 was rearranged with absolute regio- and stereoselectivity to give (22S,23S,25R)-3beta-methoxy-16beta,23:22,26-diepoxy-5alpha-cholestane (3) which possesses a cis-fused 1,6-dioxadecalin ring system. The reaction of compound 5 gave exclusively (22S,23R,25R)-3beta-methoxy-23,26-epoxy-5alpha-furostane (6) in which the spiroacetal was converted into a ditetrahydrofuran subunit. The two other isomeric spiroacetals 15 and 19 were also mainly transformed into (22S,23S,25R)-3beta-acetoxy-16beta,23:22,26-diepoxycholest-5-ene (16) and (22R,23R,25R)-3beta-acetoxy-23,26-epoxyfurost-5-ene (20), respectively. A mechanism is proposed to explain the regio- and sterospecificity observed in the rearrangement.
Planning and control of Electric Vehicles using dynamic energy capacity models (2013)

This paper focuses on energy management for a large population of Plug-in Electric Vehicles (PEVs) for demand response applications. We consider both real time charging control as well as energy planning optimizations. The main contribution of the paper lies in the development of a novel dynamic energy capacity model in which the energy variation range of the aggregated loads available at each time step is a function of the past energy management decisions. Such a model enables systematic yet simple design of planning strategies that minimize energy costs while respecting the dynamic energy shifting capacity of the load aggregation. A further contribution is on the development of a novel stochastic hybrid system model that can fully characterizes the dynamics and stochasticity of individual charging demands for real time implementation of the planning decisions. Simulation results show that the proposed energy capacity model closely captures the capabilities of the real system. Additionally, we show how the model could be used to achieve a specific objective: minimization of daily energy costs.
Global behavior of two competitive rational systems of difference equations in the plane (2014)

We investigate the global dynamics of solutions of two distinct competitive rational systems of difference equations in the plane. We show that the basins of attraction of different locally asymptotically stable equilibrium points are separated by the global stable manifolds of either saddle points or of non-hyperbolic equilibrium points. Our results give
[Functionalization of aminomodified probes for atomic force microscopy]. (2006)

Probes for atomic force microscopy functionalized by bovine serum albumin were obtained, which may be used for molecular recognition studies. The procedure of the modification and functionalization of probes includes three stages. First, amino probes are obtained by modification in vapors of amino silane derivative. Then a homobifunctional amino reactive cross-linker is covalently linked to surface amino groups of the amino probe. And finally, the probe with the covalently attached cross-linker is functionalized by bovine serum albumin molecules. The probes obtained were characterized at different stages of the modification by atomic force microscopy: the adhesion force and the work of adhesion force were determined from histograms. The modification of probe surface was confirmed by visualization of bovine serum albumin and supercoiled pGEMEX DNA molecules immobilized on the amino mica and amino mica modified by cross-linker.
Epoxy/SiO2 Interpenetrating Polymer Networks (1996)

We demonstrate a potentially useful method of generating an SiO2 morphology, in situ, with interpenetrating polymer networks (IPN) chemistry. Organic/inorganic IPNs were synthesized with an organic phase made of epoxy resin and an SiO2 phase made by sol—gel chemistry. The two types of polymerization used were sequential and simultaneous with SiO2 content ranging from 0.02 to 0.43 g SiO2/g total weight. The resultant morphologies were examined by small angle X-ray scattering and transmission electron microscopy. The sequential IPNs were strongly phase separated into a finely divided SiO2 phase of ∼10 nm size scale. The simultaneous IPNs were weakly phase separated with considerable mixing in the phases. Thermal studies showed increased thermal stability for the IPNs, compared with unfilled epoxies or physically mixed silica filled epoxies.
Mild acid hydrolysis of sulfated fucans: a selective 2-desulfation reaction and an alternative approach for preparing tailored sulfated oligosaccharides (2005)

Sulfated fucans from marine invertebrates have simple, linear structures, composed of repeating units of oligosaccharides. Most of these polysaccharides contain 3-linked fucosyl units, but each species of invertebrate has a specific pattern of sulfation. No specific enzyme able to cleave or to desulfate these polysaccharides has been described yet. Therefore, we employed an alternative approach, based on mild acid hydrolysis, in an attempt to obtain low molecular-weight derivatives from sulfated fucans. Surprisingly, we observed that sulfated fucans from Lytechinus variegatus and Strongylocentrotus pallidus (but not the sulfated fucans from other species) yield by mild acid hydrolysis oligosaccharides with well-defined molecular size as shown by narrow bands in polyacrylamide gel electrophoresis (PAGE). The sulfated oligosaccharides obtained by mild acid hydrolysis were purified by gel-filtration chromatography, and their structures were identified by (1)H-nuclear magnetic resonance (NMR) spectroscopy, revealing an identical chemical composition for all oligosaccharides. When we followed the acid hydrolysis by (1)H-NMR spectroscopy, we found that a selective 2-desulfation occurs in the fucans from S. pallidus and from L. variegatus. The reaction has two stages. Initially, 2-sulfate esters at specific sites are removed. Then the desulfated units are cleaved, yielding oligosaccharides with well-defined molecular size. The apparent requirement for the selective 2-desulfation is the occurrence of an exclusively 2-sulfated fucosyl unit linked to or preceded by a 4-sulfated residue. Thus, a homofucan from Strongylocentrotus franciscanus resists desulfation by mild acid hydrolysis, because it lacks the neighboring 4-sulfated unit. Overall, our results show a new approach for desulfating sulfated fucans at specific sites and obtaining tailored sulfated oligosaccharides.
2-O, 3-O-Desulfated Heparin Inhibits Neutrophil Elastase–Induced HMGB-1 Secretion and Airway Inflammation (2014)

Neutrophil elastase (NE) is a major inflammatory mediator in cystic fibrosis (CF) that is a robust predictor of lung disease progression. NE directly causes airway injury via protease activity, and propagates persistent neutrophilic inflammation by up-regulation of neutrophil chemokine expression. Despite its key role in the pathogenesis of CF lung disease, there are currently no effective antiprotease therapies available to patients with CF. Although heparin is an effective antiprotease and anti-inflammatory agent, its anticoagulant activity prohibits its use in CF, due to risk of pulmonary hemorrhage. In this report, we demonstrate the efficacy of a 2-O, 3-O-desulfated heparin (ODSH), a modified heparin with minimal anticoagulant activity, to inhibit NE activity and to block NE-induced airway inflammation. Using an established murine model of intratracheal NE-induced airway inflammation, we tested the efficacy of intratracheal ODSH to block NE-generated neutrophil chemoattractants and NE-triggered airway neutrophilic inflammation. ODSH inhibited NE-induced keratinocyte-derived chemoattractant and high-mobility group box 1 release in bronchoalveolar lavage. ODSH also blocked NE-stimulated high-mobility group box 1 release from murine macrophages in vitro, and inhibited NE activity in functional assays consistent with prior reports of antiprotease activity. In summary, this report suggests that ODSH is a promising antiprotease and anti-inflammatory agent that may be useful as an airway therapy in CF.
Sphingosylphosphocholine is a naturally occurring lipid mediator in blood plasma: a possible role in regulating cardiac function via sphingolipid receptors (2001)

Blood plasma and serum contain factors that activate inwardly rectifying GIRK1/GIRK4 K+ channels in atrial myocytes via one or more non-atropine-sensitive receptors coupled to pertussis-toxin-sensitive G-proteins. This channel is also the target of muscarinic M2 receptors activated by the physiological release of acetylcholine from parasympathetic nerve endings. By using a combination of HPLC and TLC techniques with matrix-assisted laser desorption ionization–time-of-flight MS, we purified and identified sphingosine 1-phosphate (SPP) and sphingosylphosphocholine (SPC) as the plasma and serum factors responsible for activating the inwardly rectifying K+ channel (IK). With the use of MS the concentration of SPC was estimated at 50nM in plasma and 130nM in serum; those concentrations exceeded the 1.5nM EC50 measured in guinea-pig atrial myocytes. With the use of reverse-transcriptase-mediated PCR and/or Western blot analysis, we detected Edg1, Edg3, Edg5 and Edg8 as well as OGR1 sphingolipid receptor transcripts and/or proteins. In perfused guinea-pig hearts, SPC exerted a negative chronotropic effect with a threshold concentration of 1µM. SPC was completely removed after perfusion through the coronary circulation at a concentration of 10µM. On the basis of their constitutive presence in plasma, the expression of specific receptors, and a mechanism of ligand inactivation, we propose that SPP and SPC might have a physiologically relevant role in the regulation of the heart.
Structure-Function Relationships of a Novel Bacterial Toxin, Hemolysin E (2000)

The novel pore-forming toxin hemolysin E (HlyE, ClyA, or SheA) consists of a long four-helix bundle with a subdomain (beta tongue) that interacts with target membranes at one pole and an additional helix (alpha(G)) that, with the four long helices, forms a five-helix bundle (tail domain) at the other pole. Random amino acid substitutions that impair hemolytic activity were clustered mostly, but not exclusively, within the tail domain, specifically amino acids within, adjacent to, or interacting with alpha(G). Deletion of amino acids downstream of alpha(G) did not affect activity, but deletions encompassing alpha(G) yielded insoluble and inactive proteins. In the periplasm Cys-285 (alpha(G)) is linked to Cys-87 (alpha(B)) of the four-helix bundle via an intramolecular disulfide. Oxidized HlyE did not form spontaneously in vitro but could be generated by addition of Cu(II) or mimicked by treatment with Hg(II) salts to yield inactive proteins. Such treatments did not affect binding to target membranes nor assembly into non-covalently linked octameric complexes once associated with a membrane. However, gel filtration analyses suggested that immobilizing alpha(G) inhibits oligomerization in solution. Thus once associated with a membrane, immobilizing alpha(G) inhibits HlyE activity at a late stage of pore formation, whereas in solution it prevents aggregation and consequent inactivation.
[The clinical course and laboratory data of hemorrhagic colitis caused by Escherichia coli O157:H7]. (1997)

An outbreak of E. coli O157 infection occurred in July 1996 in Sakai City, apparently associated with school lunches. About 5000 children were infected and more than 600 were hospitalized. In our hospital, we treated 13 patients of hemorrhagic colitis(HC) including 4 hemolytic uremic syndrome(HUS) patients then. First, a typical patient developed HUS was presented. A case was 8 years' old girl. She was developed HUS on the 6th day after the onset of HC. We treated her with plasma exchange. She was recovered on the 14th day from HUS without any sequela. In this report, I discussed about pathophysiology of HUS according to her clinical course. Secondly, I reported that analysis of the clinical courses and laboratory data of 818 patients hospitalized from the questionnaires sent by Osaka Prefecture Medical Association. One One hundred twenty two patients developed HUS. Patients with HUS produced bloody stools longer than the others, on the average(6.7 vs. 3.4 day). Mean serum C-reactive protein levels was 4.8mg/dl in patients with HUS but 1.5mg/dl in the other patients; the WBC count also was higher in HUS(17,780 vs. 9,700mm3). The mean serum Na level was lower in patients of HUS. Almost all patients were given antibiotics. The incidence of HUS among patients treated with new quinolones was lower than that of all patients. On the contrary, the higher incidence among patients with cephalosporins was observed.
Flow cytometric analysis of the DNA content of non-small cell lung cancer ploidy as a significant prognostic indicator in squamous cell carcinoma of the lung (1990)

To assess the prognostic value of DNA ploidy in non-small cell lung cancer (NSCLC), we performed a flow cytometric study using paraffin-embedded archival material from 158 patients who underwent surgical resection between 1980 and 1982. Single-variable histograms were examined and the results of these histograms were correlated with clinicopathologic characteristics and outcome. Histograms that could be analyzed were obtained in 146 cases, of which 85 (58%) were aneuploid and 61 (42%) were diploid. Survival analysis showed that patients with diploid squamous cell carcinomas (SCC) survived significantly longer than those with aneuploid SCC (a 5-year survival rate of 70% as compared with 26% [P = 0.002], respectively), and the results were independent of stage. However, DNA ploidy was not a significant prognostic factor in non-SCC (P = 0.337). Ploidy did not correlate with other clinicopathologic variables such as stage, nodal status, degree of differentiation, nuclear grade, and mitotic rate. These results suggest that DNA ploidy, as determined by flow cytometric analysis, provides an independent prognostic variable for patients with SCC and that it should be considered in treatment planning. However, non-SCC of lung may have different biologic variables, and their prognostic variables should be evaluated separately.