gebhart/patrepeval huggingface dataset:
A New Theory of Enterorecirculation of Amino Acids and its use for Depleting Unwanted Amino Acids Using Oral Enzyme-Artificial Cells, as in Removing Phenylalanine in Phenylketonuria (1995)

Oral binders remove intestinal bile acid and prevent its reabsorption and recycling thereby lowering systemic cholesterol levels. The results in this paper demonstrate the presence of another extensive enterorecirculation for amino acids. Pancreatic and other glandular secretions into the intestine contain large amounts of proteins, enzymes and polypeptides. Tryptic digestion converts these into amino acids which are then reabsorbed back into the body as they pass down the intestine. This paper shows that this forms a large enterorecirculation of amino acids between the body and intestine. The dietary protein source of amino acids is negligible when compared to the endogenous source, since this paper shows that protein-free diet did not alter the intestinal amino acid concentration. This raises the possibility of using this for the selective depletion of specific body amino acids. In this paper we use a phenylketonuria (PKU) model in rats to test the use of this hypothesis. In PKU rats, artificial cells microencapsulated phenylalanine ammonia lyase (PAL) given orally is more effective than a phenylalanine-free diet. The enzyme artificial cells are more efficient in lowering PHE in the intestine, plasma and cerebrospinal fluid. Compared to PKU on PHE-free diet, this has resulted in better weight gain and general physical condition. Preliminary studies also show that artificial cells microencapsulated asparaginase, glutaminase and tyrosinase given orally can deplete the corresponding amino acid from the intestine.
RNAi-mediated silencing of hepaticAlas1effectively prevents and treats the induced acute attacks in acute intermittent porphyria mice (2014)

The acute hepatic porphyrias are inherited disorders of heme biosynthesis characterized by life-threatening acute neurovisceral attacks. Factors that induce the expression of hepatic 5-aminolevulinic acid synthase 1 (ALAS1) result in the accumulation of the neurotoxic porphyrin precursors 5-aminolevulinic acid (ALA) and porphobilinogen (PBG), which recent studies indicate are primarily responsible for the acute attacks. Current treatment of these attacks involves i.v. administration of hemin, but a faster-acting, more effective, and safer therapy is needed. Here, we describe preclinical studies of liver-directed small interfering RNAs (siRNAs) targeting Alas1 (Alas1-siRNAs) in a mouse model of acute intermittent porphyria, the most common acute hepatic porphyria. A single i.v. dose of Alas1-siRNA prevented the phenobarbital-induced biochemical acute attacks for approximately 2 wk. Injection of Alas1-siRNA during an induced acute attack significantly decreased plasma ALA and PBG levels within 8 h, more rapidly and effectively than a single hemin infusion. Alas1-siRNA was well tolerated and a therapeutic dose did not cause hepatic heme deficiency. These studies provide proof-of-concept for the clinical development of RNA interference therapy for the prevention and treatment of the acute attacks of the acute hepatic porphyrias.
Semiconductor laser optical amplifiers for use in future fiber systems (1988)

The application of semiconductor laser amplifiers to long-wavelength optical fiber systems is discussed. The basic equations defining laser amplifier characteristics are presented together with experimental results. Linear and nonlinear modes of operation are considered; the former includes use as an optical gain block, a linear repeater, and a preamplifier, while the latter includes use as a bistable element, an electrically controlled optical switch, and an injection-locked amplifier.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Fast variable window for stereo correspondence using integral images (2003)

We develop a fast and accurate variable window approach. The two main ideas for achieving accuracy are choosing a useful range of window sizes/shapes for evaluation and developing a new window cost which is particularly suitable for comparing windows of different sizes. The speed of our approach is due to the integral image technique, which allows computation of our window cost over any rectangular window in constant time, regardless of window size. Our method ranks in the top four on the Middlebury stereo database with ground truth, and performs best out of methods which have comparable efficiency.
Glare aware photography (2008)

Glare arises due to multiple scattering of light inside the camera's body and lens optics and reduces image contrast. While previous approaches have analyzed glare in 2D image space, we show that glare is inherently a 4D ray-space phenomenon. By statistically analyzing the ray-space inside a camera, we can classify and remove glare artifacts. In ray-space, glare behaves as high frequency noise and can be reduced by outlier rejection. While such analysis can be performed by capturing the light field inside the camera, it results in the loss of spatial resolution. Unlike light field cameras, we do not need to reversibly encode the spatial structure of the ray-space, leading to simpler designs. We explore masks for uniform and non-uniform ray sampling and show a practical solution to analyze the 4D statistics without significantly compromising image resolution. Although diffuse scattering of the lens introduces 4D low-frequency glare, we can produce useful solutions in a variety of common scenarios. Our approach handles photography looking into the sun and photos taken without a hood, removes the effect of lens smudges and reduces loss of contrast due to camera body reflections. We show various applications in contrast enhancement and glare manipulation.
Elevation of IgE-binding factors in serum of patients with B cell- derived chronic lymphocytic leukemia (1988)

One hundred nineteen sera from patients with various lymphoproliferative diseases and normal sera were tested by a solid-phase radioimmunoassay (RIA) for their content in IgE-binding factor (IgE-BF), a soluble glycoprotein binding to IgE and derived from low-affinity IgE receptors (Fc epsilon R). Fc epsilon R, recently identified as CD23, are known to be expressed on the surface of B cells at the intermediate stage of differentiation. The results indicate that in all cases of chronic lymphocytic leukemia (CLL) tested (n = 40), IgE-BF levels (45 to 8,656 U/mL) were 3-fold to 500-fold higher than in 24 controls (15.5 +/- 2 U/mL). With a few exceptions, serum IgE-BF levels could differentiate patients with CLL from those with other leukemias or lymphomas. In vitro studies indicated that B lymphocytes isolated from CLL patients produced 8 to 50 times more IgE-BF than did normal B cells (P less than 0.001). IgE-BF level was correlated with the Rai stage of the disease (P = 0.002) and the lymphocyte count (P = 0.041). IgE-BF was purified to homogeneity from one CLL serum sample by a combination of affinity chromatography and reverse-phase high-performance liquid chromatography (HPLC). this IgE-BF proved identical to IgE-BF isolated from the culture supernatant of RPMI 8866 cells, a B lymphoblastoid cell line bearing Fc epsilon R and secreting IgE-BF. Indeed, the two molecules had the same mol wt (25 to 27 kd), the same isoelectric point, and the same tryptic map. We suggest that determination of serum IgE-BF might prove useful for clinical monitoring of CLL.
Specific binding of concanavalin A to glycolipid monolayers on gold electrodes (1992)

Formation of monolayers of disulfide-containing glycolipids by spontaneous adsorption onto gold electrodes and their specific binding properties to a lectin are described.
NAD+-Dependent (S)-Specific Secondary Alcohol Dehydrogenase Involved in Stereoinversion of 3-Pentyn-2-ol Catalyzed byNocardia fuscaAKU 2123 (1999)

An NAD(+)-dependent alcohol dehydrogenase was purified to homogeneity from Nocardia fusca AKU 2123. The enzyme catalyzed (S)-specific oxidation of 3-pentyn-2-ol (PYOH), i.e., part of the stereoinversion reaction for the production of (R)-PYOH, which is a valuable chiral building block for pharmaceuticals, from the racemate. The enzyme used a broad variety of secondary alcohols including alkyl alcohols, alkenyl alcohols, acetylenic alcohols, and aromatic alcohols as substrates. The oxidation was (S)-isomer specific in every case. The K(m) and Vmax for (S)-PYOH and (S)-2-hexanol oxidation were 1.6 mM and 53 mumol/min/mg, and 0.33 mM and 130 mumol/min/mg, respectively. The enzyme also catalyzed stereoselective reduction of carbonyl compounds. (S)-2-Hexanol and ethyl (R)-4-chloro-3-hydroxybutanoate in high optical purity were produced from 2-hexanone and ethyl 4-chloro-3-oxobutanoate by the purified enzyme, respectively. The K(m) and Vmax for 2-hexanone reduction were 2.5 mM and 260 mumol/min/mg. The enzyme has a relative molecular mass of 150,000 and consists of four identical subunits. The NH2-terminal amino acid sequence of the enzyme shows similarity with those of the carbonyl reductase from Rhodococcus erythropolis and phenylacetaldehyde reductase from Corynebacterium sp.
Size-Selective Synthesis of Nanostructured Transition Metal Clusters (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSize-Selective Synthesis of Nanostructured Transition Metal ClustersManfred T. Reetz and Wolfgang HelbigCite this: J. Am. Chem. Soc. 1994, 116, 16, 7401–7402Publication Date (Print):August 1, 1994Publication History Published online1 May 2002Published inissue 1 August 1994https://pubs.acs.org/doi/10.1021/ja00095a051https://doi.org/10.1021/ja00095a051research-articleACS PublicationsRequest reuse permissionsArticle Views4820Altmetric-Citations716LEARN 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-Alertsclose Get e-Alerts
Multiway analysis of preconcentrator-sampled surface acoustic wave chemical sensor array data (1998)

New data processing methods for preconcentrator-sampled surface acoustic wave (SAW) sensor arrays are described. The preconcentrator-sampling procedure is used to collect and concentrate analyte vapors on a porous solid sorbent. Subsequent thermal desorption provides a crude chromatographic separation of the collected vapors prior to exposure to the SAW array. This article describes experiments to test the effects of incorporating retention information into the pattern-recognition procedures and to explore the feasibility of multiway classification methods. Linear discriminant analysis (LDA) and nearest-neighbor (NN) pattern-recognition models are built to discriminate between SAW sensor array data for four toxic organophosphorus chemical agent vapors and one agent simulant collected under a wide variety of conditions. Classification results are obtained for three types of patterns: (a) first-order patterns; (b) first-order patterns augmented with the time of the largest peak; and (c) second-order patterns with the use of the SAW frequency for each sensor over a broad time window. Classification models for the second-order patterns are also developed with the use of unfolded and multiway partial least-squares discriminants (uPLSD and mPLSD) and NN and LDA of the scores from unfolded and multiway principal-component analysis (uPCA and mPCA). It is determined that classification performance improves when information about the desorption time is included. Treating the preconcentrator-sampled SAW sensor array as a second-order analytical instrument and using a classification model based upon either uPLSD, uPCA-LDA, or NN results in the correct identification of 100% of the patterns in the prediction set. With the second-order patterns, the other pattern-recognition algorithms only do slightly worse. © 1998 John Wiley & Sons, Inc. Field Analyt Chem Technol 2: 179–192, 1998
Dietary Protein Affects Gene Expression and Prevents Lipid Accumulation in the Liver in Mice (2012)

Feeding a HP diet prevented the development of NAFLD by enhancing lipid secretion into VLDL particles and a less efficient use of ingested calories.
IL-23/IL-17 immunity as a hallmark of Crohnʼs disease (2008)

Our findings suggest that activation of the IL-23/IL-17 axis is fundamentally connected to the etiology of CD and may represent the basis for the relapsing nature of the disease by increasing the sensitivity of epithelium to microbial LPS.
Micromachined microbial and photosynthetic fuel cells (2006)

This paper presents two types of fuel cells: a miniature microbial fuel cell (µMFC) and a miniature photosynthetic electrochemical cell (µPEC). A bulk micromachining process is used to fabricate the fuel cells, and the prototype has an active proton exchange membrane area of 1 cm2. Two different micro-organisms are used as biocatalysts in the anode: (1) Saccharomyces cerevisiae (baker's yeast) is used to catalyze glucose and (2) Phylum Cyanophyta (blue-green algae) is used to produce electrons by a photosynthetic reaction under light. In the dark, the µPEC continues to generate power using the glucose produced under light. In the cathode, potassium ferricyanide is used to accept electrons and electric power is produced by the overall redox reactions. The bio-electrical responses of µMFCs and µPECs are characterized with the open-circuit potential measured at an average value of 300–500 mV. Under a 10 ohm load, the power density is measured as 2.3 nW cm−2 and 0.04 nW cm−2 for µMFCs and µPECs, respectively.
Epigenetic modulation of endogenous tumor suppressor expression in lung cancer xenografts suppresses tumorigenicity (2006)

Epigenetic changes involved in cancer development, unlike genetic changes, are reversible. DNA methyltransferase and histone deacetylase inhibitors show antiproliferative effects in vitro, through tumor suppressor reactivation and induction of apoptosis. Such inhibitors have shown activity in the treatment of hematologic disorders but there is little data concerning their effectiveness in treatment of solid tumors. FHIT, WWOX and other tumor suppressor genes are frequently epigenetically inactivated in lung cancers. Lung cancer cell clones carrying conditional FHIT or WWOX transgenes showed significant suppression of xenograft tumor growth after induction of expression of the FHIT or WWOX transgene, suggesting that treatments to restore endogenous Fhit and Wwox expression in lung cancers would result in decreased tumorigenicity. H1299 lung cancer cells, lacking Fhit, Wwox, p16(INK4a) and Rassf1a expression due to epigenetic modifications, were used to assess efficacy of epigenetically targeted protocols in suppressing growth of lung tumors, by injection of 5-aza-2-deoxycytidine (AZA) and trichostatin A (TSA) in nude mice with established H1299 tumors. High doses of intraperitoneal AZA/TSA suppressed growth of small tumors but did not affect large tumors (200 mm(3)); lower AZA doses, administered intraperitoneally or intratumorally, suppressed growth of small tumors without apparent toxicity. Responding tumors showed restoration of Fhit, Wwox, p16(INKa), Rassf1a expression, low mitotic activity, high apoptotic fraction and activation of caspase 3. These preclinical studies show the therapeutic potential of restoration of tumor suppressor expression through epigenetic modulation and the promise of re-expressed tumor suppressors as markers and effectors of the responses.
Melanosis of the choroid plexus (1976)

A unique case of melanosis of the choroid plexus in a 74-year-old man who died of hypertensive cardiovascular disease is described. The cerebral lesion did not cause symptoms. The proposed pathogenesis is the conversion of choroidal epithelial lipofuscin into melanin. Our findings also may explain the origin of a previously reported primary malignant melanoma of the choroid plexus and of black cortical adenomas of the adrenal gland.
The role of cell-extracellular matrix interactions in neural crest cell migration (1989)

The formation of the embryo involves intricate cell movements, cell proliferation, and differentiation. The neural crest has long served as a model for the study of these processes because these cells: 1. migrate extensively along characteristic pathways during embryogenesis. 2. give rise to diverse and numerous derivatives, including pigment cells, adrenal chromaffin cells, and the ganglia of the peripheral nervous system; and 3. are accessible to surgical, immunological, and biochemical manipulations during both initial and certain later stages in their development. We are in the process of identifying factors that influence cell migration and differentiation in the neural crest system. Neural crest cells follow two primary migratory pathways in the trunk: a dorsolateral route underneath the skin, and a ventral route through the somite. Within the somites, neural crest cells preferentially migrate through the rostral half of each sclerotome but are absent from the caudal sclerotome. The regions through which neural crest cells migrate are lined with extracellular matrix (ECM) molecules. Because of the intimate relationship between neural crest cells and the surrounding matrix, it has been proposed that the ECM plays an important role in the initiation, guidance, and cessation of neural crest cell movement.
Cost-Effective Condition Monitoring for Wind Turbines (2009)

Cost-effective wind turbine (WT) condition monitoring assumes more importance as turbine sizes increase and they are placed in more remote locations, for example, offshore. Conventional condition monitoring techniques, such as vibration, lubrication oil, and generator current signal analysis, require the deployment of a variety of sensors and computationally intensive analysis techniques. This paper describes a WT condition monitoring technique that uses the generator output power and rotational speed to derive a fault detection signal. The detection algorithm uses a continuous-wavelet-transform-based adaptive filter to track the energy in the prescribed time-varying fault-related frequency bands in the power signal. The central frequency of the filter is controlled by the generator speed, and the filter bandwidth is adapted to the speed fluctuation. Using this technique, fault features can be extracted, with low calculation times, from direct- or indirect-drive fixed- or variable-speed WTs. The proposed technique has been validated experimentally on a WT drive train test rig. A synchronous or induction generator was successively installed on the test rig, and both mechanical and electrical fault like perturbations were successfully detected when applied to the test rig.
Cryptosporidium parvumSporozoite Pellicle Antigen Recognized by a Neutralizing Monoclonal Antibody Is a β-Mannosylated Glycolipid (1999)

The protozoan parasite Cryptosporidium parvum is an important cause of diarrhea in humans, calves, and other mammals worldwide. No approved vaccines or parasite-specific drugs are currently available for the control of cryptosporidiosis. To effectively immunize against C. parvum, identification and characterization of protective antigens are required. We previously identified CPS-500, a conserved, neutralization-sensitive antigen of C. parvum sporozoites and merozoites defined by monoclonal antibody 18.44. In the present study, the biochemical characteristics and subcellular location of CPS-500 were determined. CPS-500 was chloroform extractable and eluted with acetone and methanol in silicic acid chromatography, consistent with being a polar glycolipid. Following chloroform extraction and silicic acid chromatography, CPS-500 was isolated by high-pressure liquid chromatography for glycosyl analysis, which indicated the presence of mannose and inositol. To identify which component of CPS-500 comprised the neutralization-sensitive epitope recognized by 18.44, the ability of the monoclonal antibody to bind CPS-500 treated with proteases, or with alpha- or beta-glycosidases, was determined. Monoclonal antibody 18.44 did not bind antigen treated with beta-D-mannosidase but did bind antigen treated with alpha-D-mannosidase, other alpha- or beta-glycosidases, or a panel of proteases. These data indicated that the target epitope was dependent on terminal beta-D-mannopyranosyl residues. By immunoelectron microscopy, 18.44 binding was localized to the pellicle and an intracytoplasmic tubulovesicular network in sporozoites. Monoclonal antibody 18.44 also bound to antigen deposited and released onto substrate over the course travelled by gliding sporozoites and merozoites. Surface localization, adhesion and release during locomotion, and neutralization sensitivity suggest that CPS-500 may be involved in motility and invasion processes of the infective zoite stages.
High-Resolution Genome-Wide Mapping of Transposon Integration in Mammals (2005)

The Sleeping Beauty (SB) transposon is an emerging tool for transgenesis, gene discovery, and therapeutic gene delivery in mammals. Here we studied 1,336 SB insertions in primary and cultured mammalian cells in order to better understand its target site preferences. We report that, although widely distributed, SB integration recurrently targets certain genomic regions and shows a small but significant bias toward genes and their upstream regulatory sequences. Compared to those of most integrating viruses, however, the regional preferences associated with SB-mediated integration were much less pronounced and were not significantly influenced by transcriptional activity. Insertions were also distinctly nonrandom with respect to intergenic sequences, including a strong bias toward microsatellite repeats, which are predominantly enriched in noncoding DNA. Although we detected a consensus sequence consistent with a twofold dyad symmetry at the target site, the most widely used sites did not match this consensus. In conjunction with an observed SB integration preference for bent DNA, these results suggest that physical properties may be the major determining factor in SB target site selection. These findings provide basic insights into the transposition process and reveal important distinctions between transposon- and virus-based integrating vectors.
High-Q microring resonator for biochemical sensors (2005)

The large refractive index difference between silicon nitride and silicon dioxide allows silicon nitride/dioxide waveguides to have a small mode size and low radiation bending loss. Low radiation bending loss enables high quality (Q) factor microring resonators. In this paper, we will present a record high quality factor microring resonator using silicon nitride and silicon dioxide on a silicon wafer. The microring resonator was fabricated using a deep UV photolithography and etching process. The microring resonator was critically coupled to a straight waveguide. An intrinsic quality factor of 240,000 has been measured. We will also present our result of using on-chip high-Q microring resonators for liquid phase chemical sensing application.