gebhart/patrepeval huggingface dataset:
Disposition and Metabolism of Adriamycin in the Rat (1980)

Adriamycin (ADR) is extensively excreted in bile and moderately in urine following its administration to anesthetized rats. At intravenous doses ranging from 5 to 20 mg/kg, approximately 34% of the injected ADR is excreted in bile as total drug equivalents and 6-8% in urine over a 10-hour period. Thin-layer chromatography of bile, urine and tissue extracts revealed the presence of three major metabolic products in addition to the parent drug. In either bile or urine, unchanged ADR was the predominant form excreted and accounted for about 70% of the total drug equivalents. Adriamycinol and ADR conjugates were the major metabolites, were excreted at comparable rates and together accounted for most of the remaining fluorescence or radioactivity in either body fluid. ADR itself was the main form found in all tissues examined. ADR conjugates were not detected in any tissue whereas adriamycinol was observed in kidney, heart and spleen, but not in the liver. ADR aglycones could not be detected in the heart. They appeared preferentially in the liver where, 3 h after ADR was injected, they accounted for about 40% of total tissue fluorescence or radioactivity. The low rate of ADR conversion observed in the present studies supports the hypothesis of species difference in the metabolism of the drug.
Cell encapsulation with alginate and α-phenoxycinnamylidene-acetylated poly(allylamine) (2000)

In general, microcapsules prepared from alginate and polycations lack mechanical strength because the interaction between alginate and polycations is ionic instead of covalent, which represents a much stronger bond. To increase the mechanical strength of the capsule, we prepared photosensitive microcapsules that could form covalent bonds between polymers in the capsular membrane by light irradiation. Two types of photosensitive poly(allylamine), with 5% and 10% of amino groups modified by alpha-phenoxycinnamylidene acetylchloride, were synthesized. Both photopolymers exhibited an absorption maximum at 325 nm and were capable of crosslinking upon light exposure. These photosensitive polymers were used for the preparation of microcapsules. The capsules formed from this photosensitive poly(allylamine) and alginate were strengthened significantly by light irradiation. Only 28% of the microcapsules prepared from the 5%-modified photopolymer fractured after 48 h of shaking at 150 rpm. This fracture percentage is much lower when compared with the 60% of capsules fractured when prepared from the untreated poly(allylamine). By using poly(allylamine) at 10% modification, the mechanical strength was improved only slightly, with 26% of capsules fractured. Analysis of the permeability test indicated that the photo-crosslinked capsular membrane was freely permeable to cytochrome c and myoglobin, but less permeable to serum albumin. The encapsulation method was used to entrap and culture IW32 mouse leukemia cells. The cells proliferated to a density of about 1.1 x 10(7) cells/mL in the capsules after 7 days of cultivation. Concurrently, the concentration of erythropoietin in the microcapsules increased to 800 mU/mL. This new encapsulation technique has great potential in the application of a bioindustrial cell-culturing process.
Fecal microbiota transplantation (2013)

There is increasing interest in the role of altered microbiota in the development of a myriad of diseases. Together with new insights comes an interest in influencing this altered microbiota as a potential target for therapy. FMTs are effective against recurrent CDI, a disorder caused by disruption of the normal microbiota. Restoration of intestinal flora and thereby restoration of colonization resistance is thought to be the mechanism responsible for cure. With the developments in FMT and the extension of this treatment modality to both intestinal and extra-intestinal diseases, a new field of targeted therapy awaits. The ultimate goal is the development of powerful probiotic regimens that can replace FMT. Currently, FMT should only be given in a strict experimental setting for other conditions than CDI.
T-kininogen gene expression is induced during aging. (1989)

We have constructed a cDNA library from senescent (24-month-old) rat liver mRNA and, by differential screening, have selected clones corresponding to mRNA species with increased abundance in aging rats. Direct sequencing of the inserts indicated that most of the clones (9 of 10) contained sequences coding for T-kininogen, also called major acute-phase protein, cysteine protease inhibitor, or thiostatin. Nuclear elongation experiments showed that the increase in mRNA concentration was controlled at the transcriptional level. RNase mapping and S1 analysis indicated that the age-dependent induction operated preferentially at one of the three transcriptional start sites of the gene(s). The acute-phase reaction (inflammation) is known to also induce these genes at the level of transcription; however, two of the three start sites are induced by inflammation. Transcription from one of these sites was induced by both phenomena, aging and inflammation.
Examination of the Kinetics of Herpes Simplex Virus Glycoprotein D Binding to the Herpesvirus Entry Mediator, Using Surface Plasmon Resonance (1998)

Previously, we showed that truncated soluble forms of herpes simplex virus (HSV) glycoprotein D (gDt) bound directly to a truncated soluble form of the herpesvirus entry mediator (HveAt, formerly HVEMt), a cellular receptor for HSV. The purpose of the present study was to determine the affinity of gDt for HveAt by surface plasmon resonance and to compare and contrast the kinetics of an expanded panel of gDt variants in binding to HveAt in an effort to better understand the mechanism of receptor binding and virus entry. Both HveAt and gDt are dimers in solution and interact with a 2:1 stoichiometry. With HveAt, gD1(306t) (from the KOS strain of HSV-1) had a dissociation constant (KD) of 3.2 x 10(-6) M and gD2(306t) had a KD of 1.5 x 10(-6) M. The interaction between gDt and HveAt fits a 1:1 Langmuir binding model, i.e., two dimers of HveAt may act as one binding unit to interact with one dimer of gDt as the second binding unit. A gD variant lacking all signals for N-linked oligosaccharides had an affinity for HveAt similar to that of gD1(306t). A variant lacking the bond from cysteine 1 to cysteine 5 had an affinity for HveAt that did not differ from that of the wild type. However, variants with double cysteine mutations that eliminated either of the other two disulfide bonds showed decreased affinity for HveAt. This result suggests that two of the three disulfide bonds of gD are important for receptor binding. Four nonfunctional gDt variants, each representing one functional domain of gD, were also studied. Mutations in functional regions I and II drastically decreased the affinity of gDt for HveAt. Surprisingly, a variant with an insertion in functional region III had a wild-type level of affinity for HveAt, suggesting that this domain may function in virus entry at a step other than receptor binding. A variant with a deletion in functional region IV [gD1(Delta290-299t)] exhibited a 100-fold enhancement in affinity for HveAt (KD = 3.3 x 10(-8) M) due mainly to a 40-fold increase in its kinetic on rate. This agrees with the results of other studies showing the enhanced ability of gD1(Delta290-299t) to block infection. Interestingly, all the variants with decreased affinities for HveAt exhibited decreased kinetic on rates but only minor changes in their kinetic off rates. The results suggest that once the complex between gDt and HveAt forms, its stability is unaffected by a variety of changes in gD.
Primary Structures and Chain Dominance of Anti-DNA Antibodies (2001)

Using several anti-DNA autoantibodies, we analyzed the relative involvement of heavy and light chains in their interactions with DNA. We previously obtained eight hybridomas producing monoclonal anti-DNA autoantibodies by fusing spleen cells from an MRL-lpr/lpr mouse with myeloma cells. The chain dominance was analyzed by UV cross-linking experiments, in which the antibodies were covalently cross-linked with radioisotope-labeled oligonucleotides by short-wavelength UV-light, and the cross-linked H and L chains were analyzed by SDS-PAGE and densitometric scanning. Among these, three were found to be heavy chain dominant antibodies in which heavy chains are dominantly involved in DNA binding. The other five were co-dominant antibodies in which both heavy and light chains are involved in DNA binding. To determine the factor(s) that can explain the chain dominance in DNA binding, we determined the amino acid sequences of the variable regions of both heavy (VH) and light (VL) chains of all eight monoclonal antibodies. By analyzing the data, we were able to draw the following conclusions: (1) The arginine residues are found in the CDR3 regions of both VH and VL of the co-dominant antibodies; whereas, the same residues are found only in the CDR3s of VH, but not in VL, of the heavy chain dominant antibodies. (2) The net charges of the V regions affect the chain dominance. From the results of this study it is suggested that the presence of arginine residue in CDR3 is a critical factor in determining chain-dominance, as well as DNA binding of anti-DNA antibodies in general.
TORC-Specific Phosphorylation of Mammalian Target of Rapamycin (mTOR): Phospho-Ser2481 Is a Marker for Intact mTOR Signaling Complex 2 (2009)

The mammalian target of rapamycin (mTOR) serine/threonine kinase is the catalytic component of two evolutionarily conserved signaling complexes. mTOR signaling complex 1 (mTORC1) is a key regulator of growth factor and nutrient signaling. S6 kinase is the best-characterized downstream effector of mTORC1. mTOR signaling complex 2 (mTORC2) has a role in regulating the actin cytoskeleton and activating Akt through S473 phosphorylation. Herein, we show that mTOR is phosphorylated differentially when associated with mTORC1 and mTORC2 and that intact complexes are required for these mTORC-specific mTOR phosphorylations. Specifically, we find that mTORC1 contains mTOR phosphorylated predominantly on S2448, whereas mTORC2 contains mTOR phosphorylated predominantly on S2481. Using S2481 phosphorylation as a marker for mTORC2 sensitivity to rapamycin, we find that mTORC2 formation is in fact rapamycin sensitive in several cancer cell lines in which it had been previously reported that mTORC2 assembly and function were rapamycin insensitive. Thus, phospho-S2481 on mTOR serves as a biomarker for intact mTORC2 and its sensitivity to rapamycin.
Model‐Based Quality Assessment and Base‐Calling for Second‐Generation Sequencing Data (2009)

Second-generation sequencing (sec-gen) technology can sequence millions of short fragments of DNA in parallel, making it capable of assembling complex genomes for a small fraction of the price and time of previous technologies. In fact, a recently formed international consortium, the 1000 Genomes Project, plans to fully sequence the genomes of approximately 1200 people. The prospect of comparative analysis at the sequence level of a large number of samples across multiple populations may be achieved within the next five years. These data present unprecedented challenges in statistical analysis. For instance, analysis operates on millions of short nucleotide sequences, or reads-strings of A,C,G, or T's, between 30 and 100 characters long-which are the result of complex processing of noisy continuous fluorescence intensity measurements known as base-calling. The complexity of the base-calling discretization process results in reads of widely varying quality within and across sequence samples. This variation in processing quality results in infrequent but systematic errors that we have found to mislead downstream analysis of the discretized sequence read data. For instance, a central goal of the 1000 Genomes Project is to quantify across-sample variation at the single nucleotide level. At this resolution, small error rates in sequencing prove significant, especially for rare variants. Sec-gen sequencing is a relatively new technology for which potential biases and sources of obscuring variation are not yet fully understood. Therefore, modeling and quantifying the uncertainty inherent in the generation of sequence reads is of utmost importance. In this article, we present a simple model to capture uncertainty arising in the base-calling procedure of the Illumina/Solexa GA platform. Model parameters have a straightforward interpretation in terms of the chemistry of base-calling allowing for informative and easily interpretable metrics that capture the variability in sequencing quality. Our model provides these informative estimates readily usable in quality assessment tools while significantly improving base-calling performance.
Erythroid differentiation in cultured Friend leukemia cells treated with metabolic inhibitors. (1976)

The induction of erythroid differentiation in the T3-C12 clone of Friend leukemia cells by dimethyl sulfoxide is accompanied by reduction in viral RNA-dependent DNA polymerase activity with increased cellular delta-aminolevulinic acid synthetase activity and hemoglobin synthesis. These cells were treated with a variety of compounds to determine whether other durgs are capable on inducing erythroid differentiation. While several hormones, inhibitors of RNA synthesis, organic solvents, inhibitors of DNA polymerase, sulfhydryl inhibitors, and inducers of delta-aminolevulinic acid synthetase administered singly did not stimulate hemoglobin synthesis like dimethyl sulfoxide, inhibitors of DNA and RNA synthesis such as adriamycin, mitomycin C, and hydroxyurea:mithramycin were synergistic in stimulating erythroid differentiation.
A method to determine shear adhesive strength of fibrin sealants (1992)

The adhesive strength of fibrin sealants has not been rigorously evaluated to date. The adhesive strength of six different concentrations of cryoprecipitated fibrinogen as well as the commercially available fibrin tissue adhesive Tissucol was tested under controlled conditions utilizing split-thickness skin grafts as the test adherand. This test configuration permitted the modeling of bonding strength for attachment of skin grafts as well as incorporate established engineering test standards for adhesives. An increase in fibrin concentration corresponded with an increase in shear adhesive strength. No significant increases in adhesive strength were attained after 5 min of bonding for all tested concentrations, except for the commercial adhesive, which attained the adhesive strength of an equivalent concentration of cryoprecipitated adhesive after 90 min. The adhesive strength, however, was an order of magnitude less than reported values of the tensile strength of fibrin material for similar concentrations. Therefore, it is important that the surgeon use a sufficiently high fibrinogen concentration for the specific clinical indication. The method of fibrin sealant preparation and/or the compounding adjuncts appear to have an effect on the development of adhesive strength.
Deep Relative Distance Learning: Tell the Difference between Similar Vehicles (2016)

The growing explosion in the use of surveillance cameras in public security highlights the importance of vehicle search from a large-scale image or video database. However, compared with person re-identification or face recognition, vehicle search problem has long been neglected by researchers in vision community. This paper focuses on an interesting but challenging problem, vehicle re-identification (a.k.a precise vehicle search). We propose a Deep Relative Distance Learning (DRDL) method which exploits a two-branch deep convolutional network to project raw vehicle images into an Euclidean space where distance can be directly used to measure the similarity of arbitrary two vehicles. To further facilitate the future research on this problem, we also present a carefully-organized largescale image database "VehicleID", which includes multiple images of the same vehicle captured by different realworld cameras in a city. We evaluate our DRDL method on our VehicleID dataset and another recently-released vehicle model classification dataset "CompCars" in three sets of experiments: vehicle re-identification, vehicle model verification and vehicle retrieval. Experimental results show that our method can achieve promising results and outperforms several state-of-the-art approaches.
Chip-Based Capillary Electrophoresis/Mass Spectrometry Determination of Carnitines in Human Urine (2001)

A chip-based capillary electrophoresis/mass spectrometry (CE/MS) system is described for the CE separation and on-line electrospray detection of carnitine and selected acylcarnitines from mixtures of analytical standards as well as extracts of fortified human urine. Chip-based CE/MS experiments in two different laboratories were carried out using a triple-quadrupole mass spectrometer and a quadrupole time-of-flight (QTOF) mass spectrometer, respectively. The glass chips used with both systems were comparably equipped with a microfabricated capillary electrophoresis (CE) channel but with different electrosprayers. The quadrupole chip-based CE/MS experiments employed a miniature coupled microsprayer, which allowed coupling of the microelectrospray process via a micro liquid junction at the exit of the CE capillary channel. Selected ion monitoring (SIM) CE/MS experiments were employed for all of the quadrupole CE/MS work. The QTOF CE/MS full-scan single MS and MS/MS experiments were carried out in another laboratory using accurate mass measurement TOF mass spectrometry techniques. The electrospray process that was employed with the QTOF system differed in that an inserted nanoelectrospray capillary needle was carefully affixed into a flat-bottomed hole that was aligned with the CE channel exit orifice. SIM CE/MS using the described quadrupole system provided acceptable ion current electropherograms from fmole levels from analytical standard solutions of carnitine and acylcarnitines that were manually injected (loaded) onto the chip. In addition, the corresponding electropherograms for human urine fortified with the target carnitine and acylcarnitines at a 10-20 microg/mL (35-124 microM) level were obtained via SIM CE/MS techniques. The measured CE separation efficiency for the SIM CE/MS electropherograms was determined to be 2860 plates (peak width at half-height method or N = 5.54(T/WO.5(2)), and carnitine and three acylcarnitines were separated in less than 48 s. In contrast, using quadrupole-TOF technologies, the same samples could be diluted by a factor of 2-4 to obtain a comparable detector response for the target compounds. In the full-scan, single mass analyzer mode (m/z 150-500), the CE separation efficiency was measured to be 2600 plates, but mass measurement accuracy was less than 5.0 ppm for the quaternary cations. In the CE/MS/MS mode, full-scan collision-induced dissociation (CID) mass spectra were obtained with a mass accuracy of < or =10 ppm for the higher mass ions and < or =27 ppm for the lower mass product ions. These results demonstrate the feasibility for on-chip CE separation and electrospray mass spectrometric detection for these important compounds in synthetic mixtures, as well as in human urine extracts.
Funktionsszintigraphie: Eine einheitliche Methode zur Quantifizierung von Stoffwechsel und Funktion in Organen (1985)

Zusammenfassung Die Funktionsszintigraphie ist eine quantitative Methode, mit welcher Stoffwechselgrößen eines Organs durch die Messung des zeitlichen Aktivitätsverlaufs eines Tracers im Gewebe bestimmt werden können. Ihre quantitative Aussage wird jedoch durch inhärente Fehlerquellen wie Absorption der Strahlung im Organ und Überlagerung von Vorder- und Hintergrundaktivität eingeschränkt. Bisherige Verfahren zur Berechnung von Funktionsparametern orientierten sich mehr an den gegebenen technischen Möglichkeiten als an gemeinsamen theoretischen Grundlagen. Sie fallen durch Vielfalt in ihren methodischen Ansätzen mit oft empirischem Charakter auf. Quantitative Ergebnisse verschiedener Institute und Kliniken sind deshalb selten vergleichbar. In der vorliegenden Arbeit wird ein methodischer Ansatz zur Vereinheitli-chung nuklearmedizinischer Auswertemethoden beschrieben. Grundlage ist die Einbeziehung der Pharmakokinetik eines Tracers im Blut. Dies führt zur Compartmentanalyse (deterministischen) oder zur stochastischen (nicht deterministischen) Beschreibung der kinetischen Vorgänge im Organ. Die stochastische Beschreibung setzt die Berechnung der Linear-Response-Funktion aus einem Fal-tungsintegral voraus. Mit Hilfe funktionalanalytischer Methoden wurde ein mathematisches Verfahren entwickelt, das es erlaubt, die Linear-Response-Funktion erstmals in jedem Bildpunkt und zu jedem Zeitpunkt zu berechnen. An einfach lesbaren Funktionsbildern wird gezeigt, wie relevante Parameter aus dem Funktionsverlauf der Linear-Response-Funktion berechnet werden können. Da diese Funktion modellunabhängig ist, ergibt sich die Möglichkeit, bestehende oder neue Modellvorstellungen der Tracer-kinetik im betreffenden Organ auch regional zuüberprüfen.
A covalently bound photoisomerizable agonist: comparison with reversibly bound agonists at Electrophorus electroplaques. (1980)

After disulphide bonds are reduced with dithiothreitol, trans-3- (alpha-bromomethyl)-3'-[alpha- (trimethylammonium)methyl]azobenzene (trans-QBr) alkylates a sulfhydryl group on receptors. The membrane conductance induced by this "tethered agonist" shares many properties with that induced by reversible agonists. Equilibrium conductance increases as the membrane potential is made more negative; the voltage sensitivity resembles that seen with 50 [mu]M carbachol. Voltage- jump relaxations follow an exponential time-course; the rate constants are about twice as large as those seen with 50 muM carbachol and have the same voltage and temperature sensitivity. With reversible agonists, the rate of channel opening increases with the frequency of agonist-receptor collisions: with tethered trans-Qbr, this rate depends only on intramolecular events. In comparison to the conductance induced by reversible agonists, the QBr-induced conductance is at least 10-fold less sensitive to competitive blockade by tubocurarine and roughly as sensitive to "open-channel blockade" bu QX-222. Light-flash experiments with tethered QBr resemble those with the reversible photoisomerizable agonist, 3,3',bis-[alpha-(trimethylammonium)methyl]azobenzene (Bis-Q): the conductance is increased by cis {arrow} trans photoisomerizations and decreased by trans {arrow} cis photoisomerizations. As with Bis-Q, ligh-flash relaxations have the same rate constant as voltage-jump relaxations. Receptors with tethered trans isomer. By comparing the agonist-induced conductance with the cis/tans ratio, we conclude that each channel's activation is determined by the configuration of a single tethered QBr molecule. The QBr-induced conductance shows slow decreases (time constant, several hundred milliseconds), which can be partially reversed by flashes. The similarities suggest that the same rate-limiting step governs the opening and closing of channels for both reversible and tethered agonists. Therefore, this step is probably not the initial encounter between agonist and receptor molecules.