gebhart/patrepeval huggingface dataset:
Transactional Memory Coherence and Consistency (2004)

In this paper, we propos a new shared memory model: Transactionalmemory Coherence and Consistency (TCC).TCC providesa model in which atomic transactions are always the basicunit of parallel work, communication, memory coherence, andmemory reference consistency.TCC greatly simplifies parallelsoftware by eliminating the need for synchronization using conventionallocks and semaphores, along with their complexities.TCC hardware must combine all writes from each transaction regionin a program into a single packet and broadcast this packetto the permanent shared memory state atomically as a large block.This simplifies the coherence hardware because it reduces theneed for small, low-latency messages and completely eliminatesthe need for conventional snoopy cache coherence protocols, asmultiple speculatively written versions of a cache line may safelycoexist within the system.Meanwhile, automatic, hardware-controlledrollback of speculative transactions resolves any correctnessviolations that may occur when several processors attemptto read and write the same data simultaneously.The cost of thissimplified scheme is higher interprocessor bandwidth.To explore the costs and benefits of TCC, we study the characterisitcsof an optimal transaction-based memory system, and examinehow different design parameters could affect the performanceof real systems.Across a spectrum of applications, the TCC modelitself did not limit available parallelism.Most applications areeasily divided into transactions requiring only small write buffers,on the order of 4-8 KB.The broadcast requirements of TCCare high, but are well within the capabilities of CMPs and small-scaleSMPs with high-speed interconnects.
Clinical course of a loxosceles spider bite in Turkey. (2004)

We report the first case from Turkey of a dermonecrotic wound associated with possible Loxosceles spider bite and offer the complete clinical course that resulted in a permanent scar. Emergency physicians in western Turkey should be aware of Loxosceles spider bites as a cause of necrotizing wounds.
Byproduct Cross Feeding and Community Stability in an In Silico Biofilm Model of the Gut Microbiome (2017)

The gut microbiome is a highly complex microbial community that strongly impacts human health and disease. The two dominant phyla in healthy humans are Bacteroidetes and Firmicutes, with minor phyla such as Proteobacteria having elevated abundances in various disease states. While the gut microbiome has been widely studied, relatively little is known about the role of interspecies interactions in promoting microbiome stability and function. We developed a biofilm metabolic model of a very simple gut microbiome community consisting of a representative bacteroidete (Bacteroides thetaiotaomicron), firmicute (Faecalibacterium prausnitzii) and proteobacterium (Escherichia coli) to investigate the putative role of metabolic byproduct cross feeding between species on community stability, robustness and flexibility. The model predicted coexistence of the three species only if four essential cross-feeding relationships were present. We found that cross feeding allowed coexistence to be robustly maintained for large variations in biofilm thickness and nutrient levels. However, the model predicted that community composition and short chain fatty acid levels could be strongly affected only over small ranges of byproduct uptake rates, indicating a possible lack of flexibility in our cross-feeding mechanism. Our model predictions provide new insights into the impact of byproduct cross feeding and yield experimentally testable hypotheses about gut microbiome community stability.
Synthesis and Structure−Activity Studies on N-[5-(1H-Imidazol-4-yl)-5,6,7,8-tetrahydro-1-naphthalenyl]methanesulfonamide, an Imidazole-Containing α1A-Adrenoceptor Agonist (2004)

Structure-activity studies were performed on the alpha(1A)-adrenoceptor (AR) selective agonist N-[5-(1H-imidazol-4-yl)-5,6,7,8-tetrahydro-1-naphthalenyl]methanesulfonamide (4). Compounds were evaluated for binding activity at the alpha(1A), alpha(1b), alpha(1d), alpha(2a), and alpha(2B) subtypes. Functional activity in tissues containing the alpha(1A) (rabbit urethra), alpha(1B) (rat spleen), alpha(1D) (rat aorta), and alpha(2A) (rat prostatic vas deferens) was also evaluated. A dog in vivo model simultaneously measuring intraurethral pressure (IUP) and mean arterial pressure (MAP) was used to assess the uroselectivity of the compounds. Many of the compounds that were highly selective in vitro for the alpha(1A)-AR subtype were also more uroselective in vivo for increasing IUP over MAP than the nonselective alpha(1)-agonists phenylpropanolamine (PPA) (1) and ST-1059 (2, the active metabolite of midodrine), supporting the hypothesis that greater alpha(1A) selectivity would reduce cardiovascular side effects. However, the data also support a prominent role of the alpha(1A)-AR subtype in the control of MAP.
Gene Therapy for Immunodeficiency Due to Adenosine Deaminase Deficiency (2009)

Gene therapy, combined with reduced-intensity conditioning, is a safe and effective treatment for SCID in patients with ADA deficiency. (ClinicalTrials.gov numbers, NCT00598481 and NCT00599781.)
Safety and Efficacy of Recombinant Human α-Galactosidase A Replacement Therapy in Fabry's Disease (2001)

Recombinant alpha-galactosidase A replacement therapy cleared microvascular endothelial deposits of globotriaosylceramide from the kidneys, heart, and skin in patients with Fabry's disease, reversing the pathogenesis of the chief clinical manifestations of this disease.
D2 Dopamine Receptor Homodimerization Is Mediated by Multiple Sites of Interaction, Including an Intermolecular Interaction Involving Transmembrane Domain 4 (2003)

In this study, we examined the mechanisms of intermolecular interaction involved in D2 dopamine receptor dimer formation to develop an understanding of the quaternary structure of G protein-coupled receptors. The potential role of two mechanisms was investigated: disulfide bridges and hydrophobic interactions between transmembrane domains. D2 dopamine receptor oligomers were unaffected by treatment with a reducing agent; however, oligomers of the D1 dopamine receptor dissociated following a similar treatment. This observation suggested that other forces such as hydrophobic interactions were more robust in the D2 receptor than in the D1 receptor in maintaining oligomerization. To elucidate which transmembrane domains were involved in the intermolecular hydrophobic interactions, truncation mutants were generated by successive deletion of transmembrane domains from amino and/or carboxyl portions of the D2 dopamine receptor. Immunoblot analyses revealed that all the fragments were well expressed but only fragments containing transmembrane domain 4 were able to self-associate, suggesting that critical areas for receptor dimerization resided within this transmembrane domain. Disruption of the helical structure of transmembrane domain 4 in a truncated receptor capable of forming dimers interfered with its ability to self-associate; however, a similar disruption of the transmembrane domain 4 helix structure in the full-length receptor did not significantly affect dimerization. These results indicated that there are other sites of interaction involved in D2 receptor oligomer assembly in addition to transmembrane domain 4.
Theory and design of high-index-contrast microphotonic circuits (2008)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2008.
Forward with Osmosis: Emerging Applications for Greater Sustainability (2011)

Many conventional practices in the production and use of water, energy, and food are unsustainable. Existing technologies and concepts can be improved with the integration of forward osmosis, a membrane-based technology that uses osmosis as its driving force. This Feature highlights five emerging applications of forward osmosis that elegantly bypass the difficult step of draw solution regeneration and make common processes more sustainable. These applications enhance the efficiency of the production and use of water, energy, and food; utilize wastes and abundant, low value resources; and better protect the environment.
Synthesis and Utilization of Monodisperse Superparamagnetic Colloidal Particles for Magnetically Controllable Photonic Crystals (2001)

We demonstrate fabrication of novel magnetically controllable photonic crystals formed through the self-assembly of highly charged, monodisperse superparamagnetic colloidal spheres. These superparamagnetic monodisperse charged polystyrene particles containing nanoscale iron oxide nanoparticles were synthesized through emulsion polymerization. They self-assemble into crystalline colloidal arrays (CCAs) in deionized water and Bragg diffract visible light. The diffraction from these superparamagnetic CCAs can be controlled by imposition of magnetic fields, which readily alter the CCA lattice constant. We also observe magnetically induced self-assembly of these superparamagnetic particles into CCAs in media such as NaCl aqueous solutions and organic polar solvents, which normally do not permit spontaneous CCA self-assembly. We also find that magnetic fields can strain the face-centered cubic lattice of superparamagnetic CCAs polymerized within hydrogels.The lattice symmetry of this photonic crystal becomes tetragonal. The observed magnetically induced CCA self-assembly enables the development of novel photonic crystal materials and devices.
Extreme Diversity, Conservation, and Convergence of Spider Silk Fibroin Sequences (2001)

Spiders (Araneae) spin high-performance silks from liquid fibroin proteins. Fibroin sequences from basal spider lineages reveal mosaics of amino acid motifs that differ radically from previously described spider silk sequences. The silk fibers of Araneae are constructed from many protein designs. Yet, the repetitive sequences of fibroins from orb-weaving spiders have been maintained, presumably by stabilizing selection, over 125 million years of evolutionary history. The retention of these conserved motifs since the Mesozoic and their convergent evolution in other structural superproteins imply that these sequences are central to understanding the exceptional mechanical properties of orb weaver silks.
1,25-Dihydroxyvitamin D3 modulates bone marrow macrophage precursor proliferation and differentiation. Up-regulation of the mannose receptor. (1987)

1,25-Dihydroxyvitamin D3 (1,25-(OH)2D3), the biologically active form of vitamin D3, has been shown to inhibit proliferation and promote monocytic differentiation of leukemic cell lines. In the present communication, we extend these observations to normal bone marrow macrophage precursors, and 1) identify the stage of monocytic maturation wherein the steroid exerts its antiproliferative effect, and 2) demonstrate that 1,25-(OH)2D3 promotes bone marrow macrophage differentiation as manifest by specific up-regulation of the lineage-specific membrane protein, the mannose-fucose receptor. In these experiments, the 1,25-(OH)2D3-mediated inhibitory effect on colony formation was shown to be independent of attendant levels of colony stimulating factor-1 and targeted through the adherent bone marrow macrophage precursor. Examination of this steroid-sensitive adherent precursor population demonstrates that its specific binding of 125I-mannose bovine serum albumin spontaneously and progressively increases with time in culture. Whereas adherent bone marrow macrophages cultured for 2 days express 3 X 10(4) mannose receptors/cell, the number of binding sites increases to 7 X 10(4)/cell by day 4. When bone marrow macrophage precursors are exposed to 1,25-(OH)2D3, an additional stepwise enhancement of 125I-mannose bovine serum albumin obtains with time. Four days of culture with the steroid results in 1.6 X 10(5) mannose receptors/cell, a 100% increase as compared to control cells. Neither duration of culture nor exposure to 1,25-(OH)2D3 alters the KD of 125I-mannose bovine serum albumin which approximates 3-5 X 10(-9) ml-1. Finally, the "specificity" of vitamin D-mediated up-regulation of the mannose receptor was established by demonstrating that the steroid does not alter binding of 125I-alpha-thrombin by bone marrow-derived macrophage precursors.
Endomysial Fibrosis in Duchenne Muscular Dystrophy: A Marker of Poor Outcome Associated With Macrophage Alternative Activation (2009)

There is considerable interindividual variability in motor function among patients with Duchenne muscular dystrophy (DMD); moreover, pathogenetic mechanisms of motor dysfunction in DMD are not understood. Using multiparametric analysis, we correlated initial histologic alterations in quadriceps muscle biopsies from 25 steroid therapy-free patients with DMD with 13 relevant clinical features assessed by a single clinical team during a long-term period (mean, >10 years). There was no residual muscle dystrophin by immunohistochemistry and Western blot analysis in the biopsies. Myofiber size, hypercontracted fibers, necrotic/basophilic fibers, endomysial and perimysial fibrosis, and fatty degeneration were assessed by morphometry. Endomysial fibrosis was the only myopathologic parameter that significantly correlated with poor motor outcome as assessed by quadriceps muscle strength, manual muscle testing of upper and lower limbs at 10 years, and age at ambulation loss (all p<0.002). Motor outcome and fibrosis did not correlate with genotype. Myofibers exhibited oxidative stress-induced protein alterations and became separated from capillaries by fibrosis that was associated with both increase of CD206+ alternatively activated macrophages and a relative decrease of CD56+ satellite cells (both p<0.0001). This study provides a strong rationale for antifibrotic therapeutic strategies in DMD and supports the view that alternatively activated macrophages that are known to inhibit myogenesis while promoting cellular collagen production play a key role in myofibrosis.
Enhanced Multiple Transform for Video Coding (2016)

The Discrete Cosine Transform (DCT), and in particular the DCT type II, has been widely used for image and video compression. Although DCT efficiently approximates the optimal Karhunen–Loève transform under first-order Markov conditions with low complexity, the energy packing efficiency is still limited since a fixed transform cannot always capture the highly dynamic statistics of natural video content. In this paper, to further improve the transform efficiency, an Enhanced Multiple Transform (EMT) scheme is proposed. In the proposed EMT, a few sinusoidal transforms, other than DCT, have also been utilized for coding both Intra and Inter prediction residuals. The best transform, as selected from a pre-defined transform subset specified by prediction mode, is explicitly signaled in a joint coding block level manner. Moreover, to accelerate encoding process, fast methods have also been proposed by skipping unnecessary transform rate-distortion evaluations using previously encoding statistics. The proposed method has been implemented on top of High-Efficiency Video Coding (HEVC) reference software, and significant coding gain has been verified.
Effect of Osmotic Stress on Carbon Metabolism in Chlamydomonas reinhardtii (1986)

NaCl, KCl, and sucrose at equiosmolar concentrations had similar inhibitory effects on photosynthetic carbon metabolism by the freshwater green alga, Chlamydomonas reinhardtii. Inhibitory concentrations of these solutes altered the products of photosynthetic (14)CO(2) incorporation, resulting in reduced incorporation into starch, sugar phosphates, lactate, and glycolate, but caused an accumulation of glycerol both intracellularly and in the medium.
Effect of l acY Expression on Homogeneity of Induction from the P t ac and P trc Promoters by Natural and Synthetic Inducers (2002)

The role of the Escherichia coli lactose permease (LacY) in the homogeneous induction of the lactose-inducible promoters P(tac) and P(trc) by the natural inducer lactose and the synthetic inducer isopropyl-beta-D-thiogalactopyranoside (IPTG) was investigated. Lactose requires active transport by LacY, whereas IPTG can freely penetrate the cell wall. In E. coli strains lacking a functional LacY, IPTG is required for induction of P(tac) and P(trc). In E. coli strains carrying a functional LacY, induction of P(trc) and P(tac) with intermediate concentrations of lactose gave rise to two subpopulations, one fully induced and one uninduced, whereas a single, fully induced population resulted when high inducer concentrations were used. In contrast, induction with IPTG gave rise to a single population of cells at all inducer concentrations in both lacY and lacY(+) strains.
Molecules and materials for the optical detection of explosives and toxic chemicals (2006)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2006.
Simvastatin protects against the development of monocrotaline-induced pulmonary hypertension in rats via a heme oxygenase-1–dependent pathway (2011)

Heme oxygease-1 (HO-1) is the rate-limiting enzyme in heme catabolism. Induction of HO-1 has been shown to have vasodilatory, anti-inflammatory, and proapoptotic effects. More recently, experimental studies suggested the potential of simvastatin as a novel therapy for pulmonary hypertension (PH); however, the underlying mechanism remains to be investigated. The aim of this study was to evaluate whether HO-1 is required for the pulmonary vascular protective effects of simvastatin. Simvastatin (2 mg/kg/day) was administered once daily to rats for 4 weeks after monocrotaline (MCT) injection. Zn-protoporphyrin (Znpp), a potent inhibitor of HO, was used to confirm the role of HO-1. The hemodynamic changes, right heart hypertrophy, interleukin-6 (IL-6) level, and HO-1 protein expression in lungs were measured at day 28. Simvastatin significantly ameliorated mean pulmonary arterial hypertension (20.6 mm Hg). In addition, perivascular infiltration of inflammatory cells and the level of IL-6 were decreased in simvastatin treatment group. Simvastatin also increased significantly lung HO-1 protein expression. Inhibiting HO-1 using Znpp resulted in a loss of the effect of simvastatin in MCT rats. These results suggest that HO-1 expression is critical for the vascular protective effects of simvastatin in MCT-induced PH rats.
Nonlinear structured-illumination microscopy with a photoswitchable protein reveals cellular structures at 50-nm resolution (2011)

Using ultralow light intensities that are well suited for investigating biological samples, we demonstrate whole-cell superresolution imaging by nonlinear structured-illumination microscopy. Structured-illumination microscopy can increase the spatial resolution of a wide-field light microscope by a factor of two, with greater resolution extension possible if the emission rate of the sample responds nonlinearly to the illumination intensity. Saturating the fluorophore excited state is one such nonlinear response, and a realization of this idea, saturated structured-illumination microscopy, has achieved approximately 50-nm resolution on dye-filled polystyrene beads. Unfortunately, because saturation requires extremely high light intensities that are likely to accelerate photobleaching and damage even fixed tissue, this implementation is of limited use for studying biological samples. Here, reversible photoswitching of a fluorescent protein provides the required nonlinearity at light intensities six orders of magnitude lower than those needed for saturation. We experimentally demonstrate approximately 40-nm resolution on purified microtubules labeled with the fluorescent photoswitchable protein Dronpa, and we visualize cellular structures by imaging the mammalian nuclear pore and actin cytoskeleton. As a result, nonlinear structured-illumination microscopy is now a biologically compatible superresolution imaging method.
Protein trafficking in kinetoplastid protozoa (1995)

The kinetoplastid protozoa infect hosts ranging from invertebrates to plants and mammals, causing diseases of medical and economic importance. They are the earliest-branching organisms in eucaryotic evolution to have either mitochondria or peroxisome-like microbodies. Investigation of their protein trafficking enables us to identify characteristics that have been conserved throughout eucaryotic evolution and also reveals how far variations, or alternative mechanisms, are possible. Protein trafficking in kinetoplastids is in many respects similar to that in higher eucaryotes, including mammals and yeasts. Differences in signal sequence specificities exist, however, for all subcellular locations so far examined in detail--microbodies, mitochondria, and endoplasmic reticulum--with signals being more degenerate, or shorter, than those of their higher eucaryotic counterparts. Some components of the normal array of trafficking mechanisms may be missing in most (if not all) kinetoplastids: examples are clathrin-coated vesicles, recycling receptors, and mannose 6-phosphate-mediated lysosomal targeting. Other aspects and structures are unique to the kinetoplastids or are as yet unexplained. Some of these peculiarities may eventually prove to be weak points that can be used as targets for chemotherapy; others may turn out to be much more widespread than currently suspected.
Selecting antagonistic antibodies that control differentiation through inducible expression in embryonic stem cells (2013)

Antibodies that modulate receptor function have great untapped potential in the control of stem cell differentiation. In contrast to many natural ligands, antibodies are stable, exquisitely specific, and are unaffected by the regulatory mechanisms that act on natural ligands. Here we describe an innovative system for identifying such antibodies by introducing and expressing antibody gene populations in ES cells. Following induced antibody expression and secretion, changes in differentiation outcomes of individual antibody-expressing ES clones are monitored using lineage-specific gene expression to identify clones that encode and express signal-modifying antibodies. This in-cell expression and reporting system was exemplified by generating blocking antibodies to FGF4 and its receptor FGFR1β, identified through delayed onset of ES cell differentiation. Functionality of the selected antibodies was confirmed by addition of exogenous antibodies to three different ES reporter cell lines, where retained expression of pluripotency markers Oct4, Nanog, and Rex1 was observed. This work demonstrates the potential for discovery and utility of functional antibodies in stem cell differentiation. This work is also unique in constituting an example of ES cells carrying an inducible antibody that causes a functional protein "knock-down" and allows temporal control of stable signaling components at the protein level.
TESTOSTERONE UNDECANOATE: A NEW ORALLY ACTIVE ANDROGEN (1975)

Oral testosterone undecanoate (TU) in arachis oil has been evaluated with a view to its possible use as a means of androgen replacement therapy. A single 100 mg dose was found to elevate plasma androgen levels and urinary 17-ketosteroid excretion in 6 normal men. Ninety mg/day and 60 mg/day doses taken by a hypogonadal man resulted in sustained levels of androgen which appeared physiological when measured by radioimmunoassay without chromatography. However, upon separation of the steroids by chromatography it was found that much of the androgen present was in fact dihydrotestosterone not testosterone. Both TU and dihydrotestosterone undecanoate were detected in plasma by gas chromatography and it is suggested that the ester is absorbed as such from the intestine and the unesterified steroid subsequently released by hydrolysis. The convenience of oral administration, the resulting prolonged elevated plasma androgen levels and the probable lack of deleterious effects on the liver may render oral TU of value where androgen replacement therapy is indicated.