gebhart/patrepeval huggingface dataset:
Software Assisted Transact Cache to Support Efficient Unbounded Transactional Memory (2008)

Transactional memory (TM) provides efficient, easy, deadlock-free parallel programming model for today's multicore-ubiquitous hardware platform. Implementation of TM needs to guarantee that the transaction is executed atomically and in isolation. Our paper proposes an efficient and unbounded hybrid-mode TM system with strong isolation guarantee, called HybridTCache. HybridTCache optimizes the common case by executing small transactions completely by hardware, and triggers operating system (OS) support with low overhead for the uncommon case when transaction size exceeds the hardware capacity. HybridTCache adds a new L1 cache, named TCache, to buffer transactional data for the active transaction executed by the processor. Compared with traditional log based approach, TCache provides fast bookkeeping which eliminates software logging overhead for the un-overflowed blocks, thus making both transaction commit and abort fast. A key design point of hardware TM is to support unbounded transactions. HybridTCache achieves this by introducing TCache overflow exceptions and resorting to OS to handle the overflowed blocks.
Infrared Absorption of Reduced Rutile TiO2Single Crystals (1959)

Rutile Ti${\mathrm{O}}_{2}$ single crystal plates have been reduced in hydrogen at about 700\ifmmode^\circ\else\textdegree\fi{}C for several minutes to make them semiconducting. The concentration of oxygen vacancies was controlled by variations of time and temperature. The infrared absorption of a series of plane parallel plates having electrical resistivities ranging from 3 to 0.01 ohm-m has been examined. It is postulated that the electrical conductivity arises from the ionization of either one or two trapped electrons from each oxygen vacancy.In samples with electrical resistivity (\ensuremath{\perp} to the $c$ axis) greater than 0.04 ohm-m, the optical absorption at room temperature peaks at about 0.75 ev. For samples with electrical resistivity less than 0.03 ohm-m, the optical absorption shows a new maximum at 1.18 ev. The decrease of thermal activation energy with increasing oxygen vacancy concentration is expected to explain the "optical transition" from 0.75 to 1.18 ev. The ionization energies agree reasonably well with those calculated for a helium atom model of a doubly ionizable donor immersed in a dielectric medium [${K}_{e}={{n}_{o}}^{2}={(2.40)}^{2}$], namely 0.73 ev and 1.64 ev. A modification of this theory is also indicated which predicts the second ionization energy as 1.41 ev in better agreement with the experimental value of 1.18 ev.
In vivo documentation of photochemical internalization, a novel approach to site specific cancer therapy (2001)

Photochemical internalization (PCI) is a unique procedure for site-specific delivery of several types of membrane-impermeable molecules to the cytosol of target cells. The technology is based on photochemical-induced release of endocytosed macromolecules from endosomes and lysosomes into the cytosol. The purpose of this study was to evaluate the therapeutic potential of PCI of the type I ribosomal-inactivating protein gelonin in an animal model. The photosensitizer aluminum phthalocyanine disulfonate (AlPcS(2a)) was injected intraperitoneally (10 mg/kg) into athymic female BALB/c (nu/nu) nude mice (8-9 mice per group) with subcutaneously growing human adenocarcinoma (WiDr) tumors 48 hr before exposure to 135 J/cm(2) of red light focused on the tumor. Six hours before light exposure a single dose of 50 microg gelonin was administrated intratumorally. Tumor growth was measured at least twice a week. After immunomagnetic separation of in vivo growing tumor cells the subcellular localization of the photosensitizer was evaluated by fluorescence microscopy. The photosensitizer localized in endocytic vesicles in in vivo growing WiDr cells. Furthermore, it was found that in vitro gelonin treatment of WiDr cells isolated from photosensitizer-treated mice potentiated a light-induced decrease of clonal survival. Complete remission in 6 of 9 (67%) of the treated mice were induced. Our findings indicate that photochemical treatment with the photosensitizer AlPcS(2a) activates the cytotoxic potential of gelonin in vivo. These results demonstrate that the synergistic effect of combining photoactivation of photosensitizer located in endocytic vesicles and gelonin is indeed a result of PCI of gelonin.
Drug-induced mild therapeutic hypothermia obtained by administration of a transient receptor potential vanilloid type 1 agonist (2010)

Our data support the hypothesis that infusion of dihydrocapsaicin is a candidate for testing as a primary or adjunct method of inducing and maintaining therapeutic hypothermia.
Optimization and analysis of lipid nanoparticles for in vivo mRNA delivery (2017)

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2017.
Developing Visible Fluorogenic ‘Click-On’ Dyes for Cellular Imaging (2011)

New fluorogenic dyes were designed and synthesized based on Cu(I)-catalyzed 'click' reaction. Conjugating weakly fluorescent benzothiazole derivatives with an electron-deficient alkyne group at the 2-position with azide-containing molecules in aqueous solution form 'click-on' fluorescent adducts. Model reactions and cell culture experiment indicated that the developed 'click-on' dye could be applied to labeling various biomolecules, such as nucleic acids, proteins, and other molecules, in cells.
UMSCC38 cells amplified at 11q13 for the folate receptor synthesize a mutant nonfunctional folate receptor. (1994)

Some cells accumulate folate via a receptor-coupled process termed potocytosis. The folate receptor, a glycosyl phosphatidylinositol anchored M(r) 38,000-39,000 glycoprotein, is coded for by at least two genes (FR alpha and FR beta) at 11q13. The karyotype of UMSCC38, a human squamous cell carcinoma cell line, suggests that it may contain multiple copies of the folate receptor gene(s). Southern blot analysis confirms the presence of four to six copies. Using polymerase chain reaction methodology, Northern blot analysis, immunoblotting, and immunofluorescence, we find relatively limited expression of FR alpha and no FR beta in UMSCC38 cells when compared to nonamplified lines. Antigen is observed on the cell surface in a punctate pattern, and the protein is anchored via a glycosyl phosphatidylinositol anchor. Transport of 5-[methyl-3H]tetrahydrofolic acid is blocked by 5-methyltetrahydrofolic acid and probenecid, which suggests anion transport. Monensin, an inhibitor of potocytosis, and folic acid, a high-affinity ligand for the receptor, do not effectively block 5-methyltetrahydrofolic acid transport. Taken together, the results suggest that UMCSCC38 cells, although gene amplified, synthesize surprisingly small amounts of receptor and that receptor is nonfunctional. In order to establish further the nature of the receptor, 16 clones were obtained, and the complementary DNA was sequenced. Three mutations were found.
Differential Scatter of Left and Right Circularlay Polarized Light by Optically Active Particulate Systems (1970)

Because of the many heterogeneous systems which are of interest to the chemist and biochemist, the problems of distortions in circular dichroism patterns have been investigated. Specifically in this communication it is shown with a relatively well-characterized particular system (a suspension of alpha-helical poly-L-glutamic acid) that there is a measurable differential scatter of left and right circularly polarized light by suspensions of the optically active particles. This is a specific example of Perrin's assertion in 1942 (Perrin, F., J. Chem. Phys., 10, 415 (1942)) that the polarization characteristics of scattered light would differ depending on whether or not the scattering particle was optically active. Differential scatter is included with the concentration obscuring effects to demonstrate that distorted circular dichroism spectra on poly-L-glutamic acid suspension can be calculated with satisfying accuracy. The approach should be applicable to correcting the circular dichroism spectra for the many particles of biological interest, e.g., membranes, viruses, mitochondria, and insoluble proteins and polypeptides, and for small crystals in an effort to answer the crystal solution problem.
In Vitro and In Vivo Isotope Effects with Hepatitis C Protease Inhibitors: Enhanced Plasma Exposure of Deuterated Telaprevir versus Telaprevir in Rats (2009)

Telaprevir 2 (VX-950), an inhibitor of the hepatitis C virus (HCV(a)) NS3-4A protease, is in phase 3 clinical trials. One of the major metabolites of 2 is its P1-(R)-diastereoisomer, 3 (VRT-394), containing an inversion at the chiral center next to the alpha-ketoamide on exchange of a proton with solvent. Compound 3 is approximately 30-fold less active against HCV protease. In an attempt to suppress the epimerization of 2 without losing activity against the HCV protease, the proton at that chiral site was replaced with deuterium (d). The compound 1 (d-telaprevir) is as efficacious as 2 in in vitro inhibition of protease activity and viral replication (replicon) assays. The kinetics of in vitro stability of 1 and 2 in buffered pH solutions and plasma samples, including human plasma, suggest that 1 is significantly more stable than 2. Oral administration (10 mg/kg) in rats resulted in a approximately 13% increase of AUC for 1.
Oxytocin Induces the Migration of Prostate Cancer Cells: Involvement of the Gi-Coupled Signaling Pathway (2010)

Expression of genes that encode oxytocin (OXT) and vasopressin (AVP) and their cognate receptors in normal and diseased prostates are only partially characterized. Reverse transcription and PCR were used to examine the expression of these genes in normal prostate epithelial and stromal cell lines, k-ras-transformed prostate epithelial cell lines, and in four prostate cancer cell lines. Secreted and cell-associated OXT peptide was measured by an enzyme immunoassay. OXT and its receptor (OXTR) were expressed in all eight prostate cell lines. Cell-associated OXT peptide was also found in all prostate epithelial cell lines except in DU145 cells. Neither AVP nor its cognate receptors (V1a receptor and V2 receptor) were expressed in any prostate cell line examined. These data point to the OXTR as the primary target of OXT and AVP, and suggest that OXT might be an autocrine/paracrine regulator in human prostate. We found that OXT induces the migration of PC3 and PC3M, but not DU145 prostate cancer cells. The effect of OXT is distinct from the epidermal growth factor (EGF)-induced migration of prostate cancer cells, in which ERK1/2 and EGF receptor kinase activities were required. When cells were pretreated with pertussis toxin, the effect of OXT, but not EGF, on cell migration was abolished. Pretreatment with the cyclic AMP analogue, 8-Br-cAMP, did not affect OXT-induced cell migration, which eliminated the nonspecific effect of pertussis toxin. We conclude that a Gi-dependent mechanism is involved in OXTR-mediated migration of prostate cancer cells, and indicates a role for OXTR in prostate cancer metastasis.
[Plasma catecholamines, free and conjugated, in the hemodialyzed chronic renal failure patient]. (1986)

Free, sulfo and glucuro-conjugated catecholamines (dopamine, noradrenaline and adrenaline) were measured to study their metabolism in 35 non-selected patients with chronic renal failure, and under hemodialysis for various periods of time. Our data demonstrate a statistically significant increase of free dopamine, and free noradrenaline concentration in these patients, while that of free adrenaline was not different from controls. However a careful scrutiny of 35 individual data suggests that sub-groups of patients with either high normal or low plasma free noradrenaline concentration could exist; this likely heterogeneity could be a good explanation for conflicting conclusions provided by previous reports. Suspecting that conjugated catecholamines might be altered in these patients, plasma sulfo and glucuro-conjugated amines were measured. We have found a predictable and highly significant increase of sulfo-conjugated catecholamines; glucuroconjugated dopamine and noradrenaline were unchanged, while glucuroconjugated adrenaline was significantly increased. The physiological meaning, if any, of these new observations on conjugated catecholamines cannot be assessed at the moment.
AKT2, a putative oncogene encoding a member of a subfamily of protein-serine/threonine kinases, is amplified in human ovarian carcinomas. (1992)

We isolated cDNA clones containing the entire coding region of the putative oncogene AKT2. Sequence analysis and in vitro translation demonstrated that AKT2 encodes a 56-kDa protein with homology to serine/threonine kinases; moreover, this protein contains a Src homology 2-like domain. AKT2 was shown to be amplified and overexpressed in 2 of 8 ovarian carcinoma cell lines and 2 of 15 primary ovarian tumors. AKT2 was mapped to chromosome region 19q13.1-q13.2 by fluorescence in situ hybridization. In the two ovarian carcinoma cell lines exhibiting amplification of AKT2, the amplified sequences were localized within homogeneously staining regions. We conclude that AKT2 belongs to a distinct subfamily of protein-serine/threonine kinases containing Src homology 2-like domains and that alterations of AKT2 may contribute to the pathogenesis of ovarian carcinomas.
Tumor necrosis factor: Receptor binding and mitogenic action in fibroblasts (1987)

Until about two years ago, the only known function of tumor necrosis factor (TNF) was inhibition of tumor growth. Since then it has become apparent that many types of normal and transformed cells express specific high-affinity TNF receptors (Kd 200 pM) and that the presence of receptors does not correlate with susceptibility to the cytotoxic/cytostatic action of TNF. Recent evidence shows that TNF exerts a variety of other important biological activities on cells in culture and in the intact organism. Among the newly recognized activities is a potent mitogenic effect in fibroblasts. Many of the activities of TNF overlap the actions of interleukin-1 (IL-1).
In situ formation of palisade bodies in calcium, aluminum‐rich refractory inclusions (1997)

Abstract— It has been suggested that palisade bodies—shells of spinel found within some calcium, aluminum‐rich inclusions (CAIs) and the phases the shells enclose—are intact mini‐CAIs that predate and were captured by their current hosts while the latter were still molten. We present new data and observations that indicate that most palisade bodies formed instead in situ while their host inclusions were crystallizing. The evidence includes observations of spinel‐lined cavities and glass‐filled, circular structures outlined by spinel in experimental run products crystallized from melts; a partially formed palisade body in an inclusion; a fassaite crystal that is optically continuous across a palisade wall; and similarity of unusual mineral compositions in some palisade bodies and their hosts. Our observations can be used to refute arguments for exotic origin and are most consistent with a model for in situ formation involving: (1) formation of vesicles in a largely molten inclusion; (2) nucleation of spinel upon and/or adherence to vapor‐melt interfaces, forming spinel shells around vesicles; (3)leakage of vesicles and filling with melt while spinel shells remain largely intact; and (4) crystallization of melt inside shells. This model is similar to one proposed for formation of segregation vesicles, which are partially‐ to completely‐filled vesicles found in some terrestrial basalts. In addition, we interpret framboids ( i.e. , dense clusters of spinel with little material between grains, found in most inclusions that contain palisade bodies) as polar or near‐polar sections through palisade bodies and therefore do not make a genetic distinction between the two features.
The A.H.E.A.D. method: a quantitative automated measurement of the hematotoxicity of anticancer drugs. (1990)

Among the limiting side-effects of anticancer drugs, hematological toxicity is the most frequent. Hematological analysis focuses on nucleated blood cells from mouse peripheral blood or hematopoietic organs (bone marrow, spleen, thymus). We have developed an automated method called A.H.E.A.D. (Automated Hematotoxicological Evaluation of Anticancer Drugs) allowing us routinely to screen chemical products for hematotoxicity, simultaneously with in vivo and in vitro antitumoral assays. Data are collected after a simple dilution of biological samples without any additional isolation, enrichment or purification process. The measurements are performed through an electronic Coulter counter and a slightly modified pulse-height model C1000 analyzer connected on-line to a computer. In addition to nucleated cell counts, this method allows us to get information about cell volume distribution within a given population of leukocytes. In bone marrow, a single assay provides simultaneous information on the relative contents of red, lymphoid, polymorphonuclear and blast cells. We present results obtained with this method during the hematological toxicity studies of some standard anticancer drugs. Besides drug induced alterations, the A.H.E.A.D. method allows monitoring of the recovery of hematological tissues characterization of growing populations of precursors renewing the hematopoietic organs.
In vitro Tomato Fruit Cultures Demonstrate a Role for Indole-3-acetic Acid in Regulating Fruit Ripening (1996)

An in vitro system was used for the production of tomato ( Lycopersicon esculentum ) fruit in culture starting from immature flowers. This system produced small parthenocarpic (seedless) fruit in response to 10 -4 m indole-3-acetic acid (IAA) supplied in the medium. Other auxins, auxin conjugates and antiauxins tested were not effective or produced markedly fewer fruit. Additional IAA supplied to the fruit culture media before breaker stage resulted in an increase in the time period between breaker and red-ripe stages from 7 days without additional IAA to 12 days when 10 -5 m IAA was added. These results suggest that significant changes in the ripening period could be obtained by alteration of auxin relationships in tomato fruit.
Secretion of functional human enzymes by Tetrahymena thermophila (2006)

The ciliate expression system has the potential to become an excellent expression system. However, additional optimisation steps including host strain improvement as wells as measures to increase the yield of expression are necessary to be able to provide an alternative to the common E. coli and yeast-based systems as well as to transformed mammalian cell lines.
34. Tautomerism in the solid state. Part I. Thermochromism of heterocyclic phenols (1961)

A. G. Cairns-Smith, J. Chem. Soc., 1961, 182 DOI: 10.1039/JR9610000182
Multiplex gene regulation: a two-tiered approach to transgene regulation in transgenic mice. (1989)

Transgenic mice have been used to study gene function and regulation by introducing inducible or tissue-specific transgenes. This approach is generally limited to studying gene function in adult mice since ectopic expression of many interesting genes is disease causing or may be lethal to the developing embryo. To extend the utility of the transgenic mouse system to the early stages of embryogenesis, we have developed a two-tiered method of gene regulation to control transgene expression. Our multiplex gene regulatory system (MGR) allows the establishment of transgenic lines that harbor inducible potentially lethal transgenes. These inducible transgenes are activated only when mated to a second transgenic animal. Induction in the MGR system provides a high degree of temporal and spatial control over transgene expression and should be suitable for engineering "gain of function mutations" for many developmental genes.
Aza-Tricyclic Substance P Antagonists (1994)

The synthesis and structure-activity relationships of a series of aza-tricyclic analogs of the quinuclidine substance P (SP) antagonist 1 are described. The SP receptor affinity of these compounds was found to vary according to the size of the new ring fused to the quinuclidine and the mode of fusion. Correlations between receptor affinity and (1) the steric bulk of the newly introduced ring fusion and (2) the dihedral angle between the benzhydryl and benzylamino substituents of these aza-tricyclic compounds were explored.
Self‐crosslinkable hydrogels composed of partially oxidized hyaluronan and gelatin: In vitro and in vivo responses (2007)

Self-crosslinkable hydrogels had been formulated from two precursors, partially oxidized hyaluronan (oHA) and gelatin. The physicochemical properties of the resulting hydrogels have been elucidated by instrumental analyses (FTIR, SEM, and rheometry). These hydrogels were highly porous with an average pore size of 60 microm, and evidently, accommodative to cell infiltration. Increasing the oxidation degree of oHA resulted in corresponding increases in hydrogels' storage moduli and decreases in water uptake. Dermal fibroblasts were used to study the cell-hydrogel interactions in vitro. Both the hydrogels and their degradation byproducts are biocompatible as indicated by long-term cell viability assay. In addition, significant amount of cells migrated into the hydrogels and they aligned into highly organized arrays. When cultured with cells, the hydrogels underwent degradation within 4 weeks depending on composition with obvious loss of cohesiveness over time. The good biocompatibility and biodegradability of oHA/gelatin hydrogel were further demonstrated in mice subdermal implantations. Lastly, in vitro and in vivo depositions of extracellular matrix in hydrogels by cells were demonstrated by SEM analyses.
What Yelp Fake Review Filter Might Be Doing? (2021)

Online reviews have become a valuable resource for decision making. However, its usefulness brings forth a curse ‒ deceptive opinion spam. In recent years, fake review detection has attracted significant attention. However, most review sites still do not publicly filter fake reviews. Yelp is an exception which has been filtering reviews over the past few years. However, Yelp’s algorithm is trade secret. In this work, we attempt to find out what Yelp might be doing by analyzing its filtered reviews. The results will be useful to other review hosting sites in their filtering effort. There are two main approaches to filtering: supervised and unsupervised learning. In terms of features used, there are also roughly two types: linguistic features and behavioral features. In this work, we will take a supervised approach as we can make use of Yelp’s filtered reviews for training. Existing approaches based on supervised learning are all based on pseudo fake reviews rather than fake reviews filtered by a commercial Web site. Recently, supervised learning using linguistic n-gram features has been shown to perform extremely well (attaining around 90% accuracy) in detecting crowdsourced fake reviews generated using Amazon Mechanical Turk (AMT). We put these existing research methods to the test and evaluate performance on the real-life Yelp data. To our surprise, the behavioral features perform very well, but the linguistic features are not as effective. To investigate, a novel information theoretic analysis is proposed to uncover the precise psycholinguistic difference between AMT reviews and Yelp reviews (crowdsourced vs. commercial fake reviews). We find something quite interesting. This analysis and experimental results allow us to postulate that Yelp’s filtering is reasonable and its filtering algorithm seems to be correlated with abnormal spamming behaviors.