gebhart/patrepeval huggingface dataset:
Safety, Visibility, and Performance in a Wide-Area File System (2002)

As mobile clients travel, their costs to reach home filing ser-vices change, with serious performance implications. Current file systems mask these performance problems by reducing the safety of updates, their visibility, or both. This is the re-sult of combining the propagation and notification of updates from clients to servers. Fluid Replication separates these mechanisms. Client updates are shipped to nearby replicas, called WayStations, rather than remote servers, providing inexpensive safety. WayStations and servers periodically exchange knowledge of updates through reconciliation, providing a tight bound on the time until up-dates are visible. Reconciliation is non-blocking, and update contents are not propagated immediately; propagation is de-ferred to take advantage of the low incidence of sharing in file systems. Our measurements of a Fluid Replication prototype show that update performance is completely independent of wide-area networking costs, at the expense of increased sharing costs. This places the costs of sharing on those who require it, pre-serving common case performance. Furthermore, the benefits of independent update outweigh the costs of sharing for a work-load with substantial sharing. A trace-based simulation shows that a modest reconciliation interval of 15 seconds can elimi-nate 98 % of all stale accesses. Furthermore, our traced clients could collectively expect availability of five nines, even with deferred propagation of updates. 1
A survey of halftoning algorithms and investigation of the error diffusion technique (1984)

Thesis (B.S.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1984.
Thiol-mediated redox regulation of apoptosis. Possible roles of cellular thiols other than glutathione in T cell apoptosis. (1995)

Thiol redox status modulates various aspects of cellular function. We demonstrate that oxidation of cellular sulfhydryl (SH) groups induces apoptosis. In Jurkat T cells and human PBL blasts, the fraction of apoptotic nuclei increased after treatment with an SH-specific oxidant, diamide. Analysis of DNA fragmentation and nuclear morphology also indicated that SH oxidation could induce apoptosis. In the apoptosis induced by SH oxidation, the decrease of cellular glutathione was transient and the increase of glutathione disulfide was observed only after apoptotic changes had occurred. Depletion of cellular glutathione with buthionine sulfoximine failed to induce apoptosis, despite a marked decrease of cellular glutathione, which was greater than that observed in apoptosis induced by diamide. Thus, the changes of cellular glutathione or glutathione disulfide may not be the major cause of apoptosis induced by diamide. Intracellular adult T cell leukemia-derived factor/human thioredoxin, another thiol-related antioxidant protein, was oxidized by incubation with diamide. These results suggest that thiol redox status is one of the key factors of the apoptotic pathway in which thiols other than glutathione may play even more critical roles.
Poly(2-methacryloyloxyethyl phosphorylcholine) for Protein Conjugation (2008)

The water-soluble, biocompatible polymer poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC) was evaluated for protein conjugation. PMPC is a zwitterionic polymer that is able to form a more compact conformation in aqueous solution than poly(ethylene glycol) (PEG). While a terminally functionalized N-hydroxysuccinimide derivative of PMPC was not efficient for conjugation to an amine moiety on interferon-alpha2a (IFN), we found that a bis-thiol specific derivative of PMPC could be conjugated after reduction of the disulfide bonds in IFN. Utilizing PMPC that displayed a similar hydrodynamic volume to 20 kDa PEG, we evaluated the in vitro antiviral and antiproliferative activity and pharmacokinetics of a PMPC-IFN conjugate. As a hygroscopic zwitterionic polymer, PMPC is able to form a compact conformation in aqueous solution, which was found to be more compact than PEG. This suggests that PMPC protein conjugates may display different plasma elimination characteristics than PEG protein conjugates. PMPC-IFN displayed marked resistance to antibody binding in Western blot analysis with a polyclonal anti-IFN antibody while displaying comparable in vitro antiviral and antiproliferative activity to PEG-IFN. During an in vivo pharmacokinetic study, the absorption t(1/2) for PMPC-IFN was considerably extended compared to the native IFN and 20 kDa PEG analogue. This is also consistent with the SDS-PAGE result where an apparent reduction in mobility through a hydrated medium was observed. The elimination t(1/2) was also vastly extended over the native IFN and twice the value of 20 kDa PEG-IFN. This suggests that tissue migration of PMPC-IFN occurs more slowly than the 20 kDa PEG-IFN despite their similarity in hydrodynamic volume, leading to an an improved depot effect, which could explain the longer elimination t(1/2). In this study, we demonstrate a potential use of PMPCylation as a novel tool for enhancing the pharmacokinetic profile of therapeutic proteins in ways that complement PEGylation.
The NF-kappaB transcription factor in oncogenesis. (1996)

The NF-kappaB transcription factor complex is a pleiotropic activator that participates in the induction of a wide variety of cellular and viral genes. The active complex is composed of two subunits designated NFKB1 and RelA (formerly called p50 and p65, respectively). Binding sites for NF-kappaB are present in the promoter region of many cell adhesion molecules, cytokines and growth factors. Antisense inhibition of the individual subunits of NF-kappaB exerted differential effects on cell adhesion. Antisense phosphorothioate oligomers to relA but not NFKB1 caused a rapid inhibition of cell adhesion in diverse cell types. Antisense relA oligomers exerted antigrowth effects on diverse transformed cells in vitro and caused a pronounced inhibition of tumorigenicity in nude mice tumor models. Stable transfectants of a fibrosarcoma cell line expressing dexamethasone-inducible antisense RNA to relA also showed inhibition of in vitro growth and in vivo tumor development. In response to inducible expression of antisense RNA, a pronounced tumor regression was seen in nude mice. Use of a "decoy" approach to inhibit RelA function directly also caused inhibition of tumor cell growth in vitro and in vivo. Our results indicate that key regulatory molecules such as transcription factors can be selectively targeted for therapeutic intervention in cancer.
BRCA1-Associated Protein-1 Is a Tumor Suppressor that Requires Deubiquitinating Activity and Nuclear Localization (2008)

BRCA1-associated protein-1 (BAP1), a deubiquitinating enzyme of unknown cellular function, is mutated in breast and lung cancers. In this study, we have shown for the first time that BAP1 has tumor suppressor activity in vivo by showing that BAP1 can suppress tumorigenicity of lung cancer cells in athymic nude mice. We show that BAP1 fulfills another criterion of a genuine tumor suppressor because cancer-associated BAP1 mutants are deficient in deubiquitinating activity. We show for the first time that one of the two predicted nuclear targeting motifs is required for nuclear localization of BAP1 and that a truncation mutant found in a lung cancer cell line results in BAP1 that fails to localize to the nucleus. Furthermore, we show that deubiquitinating activity and nuclear localization are both required for BAP1-mediated tumor suppression in nude mice. We show that BAP1 exerts its tumor suppressor functions by affecting the cell cycle, speeding the progression through the G(1)-S checkpoint, and inducing cell death via a process that has characteristics of both apoptosis and necrosis. Surprisingly, BAP1-mediated growth suppression is independent of wild-type BRCA1. Because deubiquitinating enzymes are components of the ubiquitin proteasome system, this pathway has emerged as an important target for anticancer drugs. The identification of the deubiquitinating enzyme BAP1 as a tumor suppressor may lead to further understanding of how the ubiquitin proteasome system contributes to cancer and aid in the identification of new targets for cancer therapy.
Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages (2018)

Overall, our data demonstrate P. freudenreichii bacteriophages are distinct from C. acnes phages, as evidenced by their higher genetic diversity, potential for lysogenic growth, and more restricted host ranges. This suggests substantial differences in the evolution of these related species from the Propionibacteriaceae family and their phages, which is potentially related to their distinct environmental niches.
Stem cells in normal and leukemic hemopoiesis (Henry Stratton Lecture, 1982) (1983)

This paper deals with three themes: (1) the nature of differentiation in normal and leukemic processes, (2) stochastic and deterministic control mechanisms that affect differentiation, and (3) the nature of the events that separate self-renewing stem cells from their committed descendants. These all impinge on both myelopoietic and lymphopoietic leukemias. The view is advanced that differentiation continues in these diseases, but new programs are assembled abnormally but with normal components.
Molecular mechanisms of immunosuppression by cyclosporine, FK506, and rapamycin (1995)

The immunosuppressant cyclosporine A revolutionized treatment of graft rejection. Two newer agents, FK506 and rapamycin, show great clinical potential. These drugs suppress the immune system by forming protein-drug complexes that interact with and inhibit key components of the signal transduction pathways required for T-cell activation. The target of the cyclophilin A-cyclosporine A and FKBP12-FK506 complexes is calcineurin, a protein phosphatase required for signaling via the T-cell receptor. Cyclosporine A and FK506 nephrotoxicity may reflect renal-specific functions of calcineurin. The target of the FKBP12-rapamycin complex is TOR, a lipid and protein kinase homolog that is likely to be required for T-cell proliferation in response to interleukin-2. The identification of cyclosporine A, FK506, and rapamycin targets reveals much concerning T-cell signaling and provides the means to design novel immunosuppressants with reduced toxicity.
Stimulant and Anticataplectic Effects of Reboxetine in Patients with Narcolepsy: A Pilot Study (2001)

Our results suggest that reboxetine exerts stimulant and anticataplectic effects in narcolepsy. Contrary to previous thinking, by which stimulant action would require dopaminergic facilitation, noradrenergic mechanisms might be relevant to the control of wakefulness.
Localization of a receptor nonapeptide with a possible role in the binding of the type I interferons. (2000)

Interferons (IFNs) in common with other cytokines activate Janus tyrosine kinases and latent STAT transcription factors upon binding to their cell surface receptor. Type I IFNs bind to a receptor composed of two transmembrane polypeptides, IFNAR1 and IFNAR2, which belong to the class II cytokine receptor family that also includes the cellular receptors for IFN-gamma, interleukin-10 and coagulation protease factor VII (tissue factor). The extracellular domain of the type I IFN receptor chain IFNAR1, has four fibronectin type-III sub-domains. Human IFNAR1 has intrinsic weak affinity for type I IFNs and plays an essential role in transmembrane signaling, formation of a high affinity complex with IFN and the modulation of ligand specificity. In order to characterise the ligand binding site on IFNAR1 we analysed the epitope recognized by the anti-IFNAR1 mAb, 64G12, which inhibits the binding and biological activities of both IFN-alpha and IFN-beta. The target peptide recognized by the 64G12 mAb was determined by screening a set of 48 overlapping peptides covering the first two subdomains (residues 23-229) of the extracellular region of IFNAR1. The results of this study show that the peptide (FSSLKLNVY), localized within the first sub-domain (residues 89-97) of IFNAR1, which is recognized by the 64G12 mAb, most likely overlaps a site to which both IFN-alpha and IFN-beta bind in the ligand-receptor complex. Thus, since the 64G12 mAb can neutralize the biological activities of all the type I IFNs tested, we suggest that the target peptide recognized by the 64G12 mAb, is a possible anchorage point on IFNAR1, common to binding of both IFN-alpha and IFN-beta.
Essential Roles forCaenorhabditis elegansLamin Gene in Nuclear Organization, Cell Cycle Progression, and Spatial Organization of Nuclear Pore Complexes (2000)

Caenorhabditis elegans has a single lamin gene, designated lmn-1 (previously termed CeLam-1). Antibodies raised against the lmn-1 product (Ce-lamin) detected a 64-kDa nuclear envelope protein. Ce-lamin was detected in the nuclear periphery of all cells except sperm and was found in the nuclear interior in embryonic cells and in a fraction of adult cells. Reductions in the amount of Ce-lamin protein produce embryonic lethality. Although the majority of affected embryos survive to produce several hundred nuclei, defects can be detected as early as the first nuclear divisions. Abnormalities include rapid changes in nuclear morphology during interphase, loss of chromosomes, unequal separation of chromosomes into daughter nuclei, abnormal condensation of chromatin, an increase in DNA content, and abnormal distribution of nuclear pore complexes (NPCs). Under conditions of incomplete RNA interference, a fraction of embryos escaped embryonic arrest and continue to develop through larval life. These animals exhibit additional phenotypes including sterility and defective segregation of chromosomes in germ cells. Our observations show that lmn-1 is an essential gene in C. elegans, and that the nuclear lamins are involved in chromatin organization, cell cycle progression, chromosome segregation, and correct spacing of NPCs.
Lewis acid-mediated condensation of alkenols and aldehydes. A selective synthesis of tetrahydropyrans and oxepanes (1988)

A stereoselective synthesis of different oxacycles is reported starting from aldehydes and unsaturated alcohols in the presence of AlCl3 or AlBr3. © 1988, American Chemical Society. All rights reserved.
Design of a Microbreather for Two-Phase Microchannel Devices (2008)

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2008.
Fast tunable diode laser with digital control and multiple line selection (1999)

Tunable diode lasers have become a light source of choice for spectroscopic applications because of their small size, high efficiency, reliability, and low cost. Tuning for a particular wavelength is commonly realized by using the Littman-Metcalf external cavity configuration with a diffractive grating and rotating mirror. Using this approach, mechanical moving parts and a high degree of precision in the rotation mechanism are required for wavelength selection. Because of this mechanical motion, the tuning process is relatively slow. In some spectroscopic applications sample probing at more than one wavelength is desirable, which currently requires two or more lasers. The development of a single laser source with fast selection over a definable set of wavelengths, also capable of simultaneous emission of a multi-line spectrum, is described. Such a laser can be used to match the spectral signature of the sample and would dramatically increase the speed and reliability of a laser spectrometer. The design is based on an external-cavity configuration with fast computer controlled (in the millisecond range) line selection and has no moving parts. The laser is capable of emitting sets of multi-line near infrared spectra, each spectrum stored as a record in a computer database and matching the spectral signature of a particular chemical component, thus facilitating rapid and reliable spectroscopic detection and analysis of compound samples. The laser design and experimental test results are presented and discussed in the paper.
Expression of an intercellular adhesion molecule, ICAM-1, by human thyroid cells (1989)

Intercellular adhesion molecule-1 (ICAM-1), hitherto identified on activated B cells, macrophages, dendritic cells, endothelia and certain epithelial cells, serves as a ligand for the lymphocyte function-associated antigen-1 (LFA-1). ICAM-1 binding by LFA-1 enhances the efficiency of lymphocyte-target cell and lymphocyte-accessory cell interactions. We have investigated the in-vitro expression of ICAM-1 by cultured thyroid cells from five patients with Graves' disease using indirect immunofluorescence analysis, and found that 30 +/- 11% (mean +/- S.D.) of cells were ICAM-1 positive under basal conditions. The proportion of cells which were ICAM-1 positive and the amount of ICAM-1 per cell (assessed by fluorescence intensity) were both increased in all cases by the cytokines gamma-interferon, interleukin-1 and tumour necrosis factor. Immunohistochemical analysis of frozen sections from thyroidectomy specimens demonstrated ICAM-1 on thyroid follicular cells in areas of lymphocytic infiltration in patients with Graves' disease (n = 2) or Hashimoto's thyroiditis (n = 2). ICAM-1 was not found in specimens from a patient with a toxic multinodular goitre or a patient with Graves' disease without focal lymphocytic accumulation. These results suggest that the thyroid epithelium may express ICAM-1 as well as major histocompatibility complex class II antigens, such as HLA-DR, in response to locally synthesized cytokines. The enhanced expression of ICAM-1 may render these cells more susceptible as targets for lymphocyte-mediated cytotoxicity, and together with HLA-DR antigen expression may increase the accessory cell capability of the thyroid follicular cells.
Radiofrequency Catheter Ablation of Ventricular Tachycardia After Myocardial Infarction (1998)

Radiofrequency catheter ablation controls VT that is sufficiently stable to allow mapping in 67% of patients despite failure of antiarrhythmic drug therapy and multiple inducible VTs. However, ablation was largely adjunctive to amiodarone and defibrillators in this referral population.
Comparison of the device physics principles of planar and radial p-n junction nanorod solar cells (2005)

A device physics model has been developed for radial p-n junction nanorod solar cells, in which densely packed nanorods, each having a p-n junction in the radial direction, are oriented with the rod axis parallel to the incident light direction. High-aspect-ratio (length/diameter) nanorods allow the use of a sufficient thickness of material to obtain good optical absorption while simultaneously providing short collection lengths for excited carriers in a direction normal to the light absorption. The short collection lengths facilitate the efficient collection of photogenerated carriers in materials with low minority-carrier diffusion lengths. The modeling indicates that the design of the radial p-n junction nanorod device should provide large improvements in efficiency relative to a conventional planar geometry p-n junction solar cell, provided that two conditions are satisfied: (1) In a planar solar cell made from the same absorber material, the diffusion length of minority carriers must be too low to allow for extraction of most of the light-generated carriers in the absorber thickness needed to obtain full light absorption. (2) The rate of carrier recombination in the depletion region must not be too large (for silicon this means that the carrier lifetimes in the depletion region must be longer than ∼10ns). If only condition (1) is satisfied, the modeling indicates that the radial cell design will offer only modest improvements in efficiency relative to a conventional planar cell design. Application to Si and GaAs nanorod solar cells is also discussed in detail.
First Observation of Phase Transformation of All Four Fe2O3Phases (γ → ε → β → α-Phase) (2009)

Iron oxide (Fe(2)O(3)) has four crystal structures: gamma-, epsilon-, beta-, and alpha-Fe(2)O(3). Until now, routes of the phase transformations among the four Fe(2)O(3) phases have not been clarified because a systematic synthesis that yields all four Fe(2)O(3) phases has yet to be reported. Herein we report the synthesis of a series of Fe(2)O(3) nanoparticles using mesoporous SiO(2). The crystal structures of the Fe(2)O(3) nanoparticles change in the order of gamma-Fe(2)O(3) --> epsilon-Fe(2)O(3) --> beta-Fe(2)O(3) --> alpha-Fe(2)O(3) as the particle size increases. Threshold sizes were estimated as gamma --> epsilon at 8 nm, epsilon --> beta at 30 nm, and beta --> alpha at 50 nm in the synthesis using FeSO(4) as a precursor. The phase transformations among the four Fe(2)O(3) phases have been observed for the first time.
Erythropoietin in liver tissue extracts and in liver perfusates from hypoxic rats (1983)

An attempt to evaluate the role of the liver in extrarenal erythropoietin production was made by measuring the content of erythropoietin in homogenates and perfusates from hypoxic rat livers. Extracts from livers from nephric or anephric animals rendered both anemic and hypoxic showed no detectable erythropoietin despite the fact that both plasma and kidney extracts contained large amounts of erythropoietin. This lack of measurable erythropoietin in the liver is not caused by degradation of erythropoietin during the extraction procedure because exogenously added rat erythropoietin was recovered to the same extent from livers or kidney homogenates. More likely, however, it is caused by the fact that extrarenal erythropoietin production accounts for only one-fifth of total erythropoietin production and that the liver mass is about six times that of both kidneys. Consequently, the erythropoietin content of 1 g of liver should be about one-thirtieth of that of 1 g of kidney, an amount that is below the limit of detection of the assay. On the other hand, the 2-h in situ perfusates of livers from similarly stimulated animals contained significant amounts of secreted erythropoietin. It is concluded that the liver participates actively in extrarenal erythropoietin production in the adult rat. However, the small amount expected to be present in tissue homogenates cannot be detected with our current bioassay.
Characterization of Bacillus thuringiensis and related bacteria by ribosomal RNA gene restriction fragment length polymorphisms (1994)

Ribosomal RNA gene restriction patterns have been determined for 43 strains of Bacillus thuringiensis representing 10 serovars and eight reference strains of B. anthracis, B. cereus and B. mycoides. Strains within a B. thuringiensis serovar produced highly related or identical ribotype patterns: in particular, 12 strains of serovar israelensis, five strains of serovar kurstaki, two strains of serovar galleriae and three strains of serovar aizawa produced ribotype patterns consistent with serotype designations. Moreover, variety tenebrionis (serotype 8a8b), a coleopteran pathogen, could be distinguished from the more common lepidopteran pathogens of this serotype (serovar morrisoni) by ribotyping. The correlation of ribotype patterns with serotype suggests a clonal population structure for B. thuringiensis.
Inhibition of pancreatic lipase in vitro by the covalent inhibitor tetrahydrolipstatin (1988)

Tetrahydrolipstatin inhibits pancreatic lipase from several species, including man, with comparable potency. The lipase is progressively inactivated through the formation of a long-lived covalent intermediate, probably with a 1:1 stoichiometry. The lipase substrate triolein and also a boronic acid derivative, which is presumed to be a transition-state-form inhibitor, retard the rate of inactivation. Therefore, in all probability, tetrahydrolipstatin reacts with pancreatic lipase at, or near, the substrate binding or active site. Tetrahydrolipstatin is a selective inhibitor of lipase; other hydrolases tested were at least a thousand times less potently inhibited.