gebhart/patrepeval huggingface dataset:
Fourteen and counting: unraveling trinucleotide repeat diseases (2000)

The pathological expansion of unstable trinucleotide repeats currently is known to cause 14 neurological diseases. Over the past several years, researchers have concentrated on the challenging task of identifying the mechanism by which the expanded trinucleotide repeat leads to abnormal cellular function. As a consequence, the trinucleotide repeat field has grown dramatically since the initial discovery of dynamic mutations less than a decade ago. Trinucleotide repeat expansions may prove to cause pathology through a variety of mechanisms including interference with DNA structure, transcription, RNA-protein interaction and altered protein conformations/interactions. The goal of this review is to provide a brief description of the genes harboring expanded repeats, coupled with new insights into the molecular pathways most likely to be disrupted by these expansions. Data from studies of patient material, cell culture and animal models demonstrate the complexity of the pathogenic mechanisms in each of the diseases.
Staphylococcal Coagulase: Mode of Action and Antigenicity (1952)

Summary: Different strains of staphylococci vary in ability to produce free coagulase. Methods are given for the selection of suitable strains and for the production and concentration of coagulase from one of them. Of animal plasmas examined, cow, sheep, dog, guinea-pig and mouse showed a relative deficiency in coagulase activator, while plasma of man, monkey, horse, cat, pig, fowl and rabbit contained the most. Coagulase activator resembles prothrombin closely in physical properties such as thermolability, behaviour during salting out and removal by adsorbents. They are both partly lost in blood clotting and in dicumarol poisoning, but while prothrombin is apparently removed from plasma by repeated Seitz filtration there is no loss of activator. The question of probable identity is discussed. Antibody to coagulase is present in the sera many normal individuals and in those suffering from chronic staphylococcal infections. The intramuscular injection of coagulase adsorbed on aluminium phosphate produces similar antibodies in the sera of rabbits.
The production and analysis of microcellular foam (1981)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1981.
Competition in the British Electricity Spot Market (1992)

Most of the British electricity supply industry has been privatized. Two dominant generators supply bulk electricity to an unregulated "pool." They submit a supply schedule of prices for generation and receive the market-clearing price, which varies with demand. Despite claims that this should be highly competitive, the authors show that the Nash equilibrium in supply schedules implies a high markup on marginal cost and substantial deadweight losses. Further simulations, to show the effect of entry by 1994, produce somewhat lower prices at the cost of excessive entry; subdividing the generators into five firms would produce better results. Copyright 1992 by University of Chicago Press.
Mice deficient in CD23 reveal its modulatory role in IgE production but no role in T and B cell development. (1994)

To assess roles of CD23 in lymphocyte development and immune function in vivo, CD23-deficient mice (CD23-/-) were generated. Mice heterozygous with respect to the defective allele (CD23+/-) display 50% reduced levels of CD23 expression on CD23+ cell types. This pattern is consistent with a lack of parental or tissue-specific imprinting of the CD23 gene. Neither a 50% reduced level nor a complete lack of CD23 caused profound changes in lymphocyte compartments (thymocytes, peripheral T cells, and B-1 and B-2 B cells). The lack of CD23 also did not significantly alter in vitro the proliferative response of B cells triggered via the Ag receptor in combination with CD40 ligand, IL-2, and/or IL-4. Effects on polyclonal Ig production were tested in a Th2 cell-driven immune response in vivo after infection with Nippostrongylus brasiliensis, a parasite that dramatically enhances CD23 expression on B cells. In both primary and secondary immune responses, heterozygous CD23+/- mice developed slightly higher and CD23-/- mice similar serum IgE and IgG1 levels as compared with CD23+/+ (wild-type) mice. The increase in blood eosinophil counts was similar in all three types of mice. These findings show that after N. brasiliensis infection 1) a complete lack of CD23 in vivo neither prohibits nor significantly alters quantitatively polyclonal IgE levels in serum, and 2) a 50% reduction in cell-surface CD23 expression (CD23+/- mice) correlates with slightly increased serum IgE levels.
Is the CO Adduct of Myoglobin Bent, and Does It Matter? (2000)

Early reports of a severely bent CO adduct in myoglobin inspired the idea that heme proteins discriminate against CO, relative to O(2), via steric hindrance imposed by a distal histidine residue. Recent results showing that the bound CO is only slightly distorted do not by themselves overthrow the steric hypothesis, because the steric energy could be stored in displacements of the protein. However, experimental data on site-directed mutants show that the main determinant of ligand affinity changes is the polarity of the binding pocket and that H-bonding by the distal histidine accounts for about 85% of the O(2)/CO discrimination while steric hindrance accounts for the remaining 15%.
Classification of non-Hodgkin lymphoma in Central and South America: a review of 1028 cases (2012)

The distribution of non-Hodgkin lymphoma (NHL) subtypes differs around the world but a systematic study of Latin America has not been done. Therefore, we evaluated the relative frequencies of NHL subtypes in Central and South America (CSA). Five expert hematopathologists classified consecutive cases of NHL from 5 CSA countries using the WHO classification and compared them to 400 cases from North America (NA). Among the 1028 CSA cases, the proportions of B- and T-cell NHL and the sex distribution were similar to NA. However, the median age of B-cell NHL in CSA (59 years) was significantly lower than in NA (66 years; P < .0001). The distribution of high-grade (52.9%) and low-grade (47.1%) mature B-cell NHL in CSA was also significantly different from NA (37.5% and 62.5%; P < .0001). Diffuse large B-cell lymphoma was more common in CSA (40%) than in NA (29.2%; P < .0001), whereas the frequency of follicular lymphoma was similar in Argentina (34.1%) and NA (33.8%), and higher than the rest of CSA (17%; P < .001). Extranodal NK/T-cell NHL was also more common in CSA (P < .0001). Our study provides new objective evidence that the distribution of NHL subtypes varies significantly by geographic region and should prompt epidemiologic studies to explain these differences.
The chemistry of signal transduction. (1995)

Several disciplines, including chemical ecology, seek to understand the molecular basis of information transfer in biological systems, and general molecular strategies are beginning to emerge. Often these strategies are discovered by a careful analysis of natural products and their biological effects. Cyclosporin A, FK506, and rapamycin are produced by soil microorganisms and are being used or considered as clinical immunosuppressive agents. They interrupt the cytoplasmic portion of T-cell signaling by forming a complex with a binding protein--FKBP12 in the case of FK506 and rapamycin and cyclophilin A (CyPA) in the case of cyclosporin A (CsA). This complex in turn inhibits a protein target, and the best understood target is calcineurin, which is inhibited by FK506-FKBP12 and CyPA-CsA. Mutational and structural studies help define how FK506-FKBP12 interacts with calcineurin, and the results of these studies are summarized. The existence of strong FK506-FKBP12 binding suggests that FK506 is mimicking some natural ligand for FKBP12. Synthetic and structural studies to probe this mimicry are also described.
Inactivation of Human White Blood Cells in Red Blood Cell Products Using the MIRASOL® System for Whole Blood. (2007)

Abstract Transfusion of blood products containing white blood cells (WBC) can result in the induction of immune responses that can negatively impact the recipient. An approach that would mitigate these consequences would be beneficial. Previous studies had shown that exposure of platelet concentrates to light in the presence of riboflavin was able to inhibit immune responses mediated by WBC. To make this protocol more widely applicable the effect of treating whole blood units with riboflavin and varying amounts of light was tested. Human peripheral blood mononuclear cells were purified by Ficoll-Hypaque discontinuous centrifugation from aliquots of nonleukoreduced whole blood units that were untreated or exposed to Mirasol treatment using varying light dosages. Viability and phenotype of treated cells was unchanged compared to untreated controls. The results showed that exposure of whole blood units to 33J/mL red blood cells (RBC) UV light in the presence of riboflavin completely inhibited proliferation of WBC in response to polyclonal stimulators such as phytohemagglutinin, and anti-CD3/CD28 or to allogeneic stimulator cells in a mixed lymphocyte culture (MLC). Additional assays showed that treated WBC were unable to induce proliferation of normal responder cells in an MLC. Treated cells did not produce inflammatory or TH1/TH2 cytokines when stimulated with lipopolysaccharide for 24 hours or anti-CD3/CD28 for 72 hours. In addition, treatment was found to inhibit T cell activation as evidenced by the lack of CD69 expression in treated compared to untreated control cells when incubated with phorbol 12-myristate 13-acetate. These treatment conditions did not induce crossmatch incompatibility. Methemoglobin levels and hemolysis in RBC units stayed below 1% during storage for 42 days in AS-3. Platelet and plasma units separated from whole blood after treatment showed acceptable cell and protein quality over 5 days in storage or as fresh frozen plasma, respectively. In summary, Mirasol treatment was able to functionally inactivate WBC in whole blood products without adversely affecting the quality of the RBC, platelets and plasma. This technique offers potential means to achieve inactivation of WBC in whole blood units that can subsequently be separated into RBC, platelet and plasma components.
A Collaborative Multiagent Taxi-Dispatch System (2009)

This paper presents a novel multiagent approach to automating taxi dispatch that services current bookings in a distributed fashion. The existing system in use by a taxi operator in Singapore and elsewhere, attempts to increase customer satisfaction locally, by sequentially dispatching nearby taxis to service customers. The proposed dispatch system attempts to increase customer satisfaction more globally, by concurrently dispatching multiple taxis to the same number of customers in the same geographical region, and <b xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">vis-à-vis</b> human driver satisfaction. To realize the system, a multiagent architecture is proposed, populated with software collaborative agents that can actively negotiate on behalf of taxi drivers in groups of size N for available customer bookings. Theoretically, an analysis of the boundary and optimal multiagent taxi-dispatch situations is presented along with a discussion of their implications. Experimentally, the operational efficiency of the existing and proposed dispatch systems was evaluated through computer simulations. The empirical results, obtained for a 1000-strong taxi fleet over a discrete range of N , show that the proposed system can dispatch taxis with reduction in customer waiting and empty taxi cruising times of up to 33.1% and 26.3%, respectively; and up to 41.8% and 41.2% reduction when a simple negotiation speedup heuristic was applied.
Epitope mapping of human thyroid peroxidase defined seven epitopes recognized by sera from patients with thyroid pathologies. (1993)

Human thyroid peroxidase (hTPO) is the major component of the microsomal antigen. In almost cases, antibodies against this protein are found in sera from patients with autoimmune thyroid diseases. Overlapping cDNAs which correspond to the complete hTPO mRNA obtained from a thyroid library or by polymerase chain reaction were cloned and expressed as fusion proteins in a prokaryotic vector. Seven antigenic determinants between 21 and 49 amino acids were defined by cloning, subcloning of the immunoreactive regions and screenings with the two rabbit polyclonal anti hTPO antibodies. This study confirms the antigenic nature of the sequences 70-160 and 590-675 but above all refines the localization of three shorter distinct antigenic peptides corresponding to the sequences 68-105, 106-126 and 574-621. Moreover, four other determinants were characterized on the sequences 233-277, 467-515, 641-685 and 701-730. Analysis of sera from patients with autoimmune thyroid diseases (AITD) against the seven immunoreactive peptides confirms the heterogeneous nature of autoantibodies to hTPO.
A comparative study of image retargeting (2010)

The numerous works on media retargeting call for a methodological approach for evaluating retargeting results. We present the first comprehensive perceptual study and analysis of image retargeting. First, we create a benchmark of images and conduct a large scale user study to compare a representative number of state-of-the-art retargeting methods. Second, we present analysis of the users' responses, where we find that humans in general agree on the evaluation of the results and show that some retargeting methods are consistently more favorable than others. Third, we examine whether computational image distance metrics can predict human retargeting perception. We show that current measures used in this context are not necessarily consistent with human rankings, and demonstrate that better results can be achieved using image features that were not previously considered for this task. We also reveal specific qualities in retargeted media that are more important for viewers. The importance of our work lies in promoting better measures to assess and guide retargeting algorithms in the future. The full benchmark we collected, including all images, retargeted results, and the collected user data, are available to the research community for further investigation at http://people.csail.mit.edu/mrub/retargetme.
Phosphorescent Organic Light-Emitting Devices: Working Principle and Iridium Based Emitter Materials (2008)

Even though organic light-emitting device (OLED) technology has evolved to a point where it is now an important competitor to liquid crystal displays (LCDs), further scientific efforts devoted to the design, engineering and fabrication of OLEDs are required for complete commercialization of this technology. Along these lines, the present work reviews the essentials of OLED technology putting special focus on the general working principle of single and multilayer OLEDs, fluorescent and phosphorescent emitter materials as well as transfer processes in host materials doped with phosphorescent dyes. Moreover, as a prototypical example of phosphorescent emitter materials, a brief discussion of homo- and heteroleptic iridium(III) complexes is enclosed concentrating on their synthesis, photophysical properties and approaches for realizing iridium based phosphorescent polymers.
A time-domain differential solver for electromagnetic scattering problems (1989)

The authors' objective is to extend computational fluid dynamics (CFD) based upwind schemes to solve numerically the Maxwell equations for scattering from objects with layered non-metallic sections. After a discussion on the character of the Maxwell equations it is shown that they represent a linearly degenerate set of hyperbolic equations. To show the feasibility of applying CFD-based algorithms, first the transverse magnetic (TM) and the transverse electric (TE) waveforms of the Maxwell equations are considered. A finite-volume scheme is developed with appropriate representations for the electric and magnetic fluxes at a cell interface, accounting for variations in material properties in both space and time. This process involves a characteristic subpath integration known as the 'Riemann solver'. An explicit-Lax-Wendroff upwind scheme, which is second-order accurate in both space and time, is employed to solve the TM and TE equations. A body-fitted coordinate transformation is introduced to treat arbitrary cross-sectioned bodies with computational grids generated using an elliptic grid solver procedure. For treatment of layered media, a multizonal representation is employed satisfying appropriate zonal boundary conditions in terms of flux conservation. The computational solution extending from the object to a far-field boundary located a few wavelengths away constitutes the near-field solution. A Green's function based near-field-to-far-field transformation is employed to obtain the bistatic radar cross section (RCS) information.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Kallikrein-related peptidase 7 (KLK7) is a proliferative factor that is aberrantly expressed in human colon cancer (2014)

Emerging evidence indicates that serine proteases of the tissue kallikrein-related peptidases family (KLK) are implicated in tumorigenesis. We recently reported the ectopic expression of KLK4 and KLK14 in colonic cancers and their signaling to control cell proliferation. Human tissue kallikrein-related peptidase 7 (KLK7) is often dysregulated in many cancers; however, its role in colon tumorigenesis has not yet been established. In the present study, we analyzed expression of KLK7 in 15 colon cancer cell lines and in 38 human colonic tumors. In many human colon cancer cells, KLK7 mRNA was observed, which leads to KLK7 protein expression and secretion. Furthermore, KLK7 was detected in human colon adenocarcinomas, but it was absent in normal epithelia. KLK7 overexpression in HT29 colon cancer cells upon stable transfection with a KLK7 expression plasmid resulted in increased cell proliferation. Moreover, subcutaneous inoculation of transfected cells into nude mice led to increased tumor growth that was associated with increased tumor cell proliferation as reflected by a positive Ki-67 staining. Our results demonstrate the aberrant expression of KLK7 in colon cancer cells and tissues and its involvement in cell proliferation in vitro and in vivo. Thus, KLK7 may represent a potential therapeutic target for human colon tumorigenesis.
Embryonic stem cell-like cells established by culture of adult ovarian cells in mice (2010)

Coculture of adult ovarian cells with somatic fibroblasts can yield colony-forming cells having ESC-like activity, which may provide an alternative for establishing autologous stem cells from adults that can be obtained without genetic manipulation.
Update on Bioabsorbable Stents: From Bench to Clinical (2006)

Permanent metallic stents are associated with limitations such as continued mechanical stress, transfer to the tissue, and continued biological interaction with the surrounding tissue. They are also associated with late stent thrombosis and artifacts when non-invasive technologies such as MRI and MSCT are used. The potential advantages of bioabsorbable polymeric or metallic stents are to leave no stent behind, they are fully compatible with MRI and MSCT imaging, and are not associated with late stent thrombosis. This review covers the different stent programs as they move from bench to bed and clinical trials. Bioabsorbable stents are considered the next frontier of stenting and we will discuss their potential to fulfill this promise in interventional cardiology.
Full 2-D photonic bandgaps in silica/air structures (1995)

Full 2-D photonic bandgaps are demonstrated for all polarisations in structures with refractive index contrast as small as that of silica and air. They occur for light propagating out of the transverse plane, with a longitudinal component of wave vector. A new type of optical fibre based on these structures is proposed.
DNA Methylation in Peripheral Blood: A Potential Biomarker for Cancer Molecular Epidemiology (2012)

Aberrant DNA methylation is associated with cancer development and progression. There are several types of specimens from which DNA methylation pattern can be measured and evaluated as an indicator of disease status (from normal biological process to pathologic condition) and even of pharmacologic response to therapy. Blood-based specimens such as cell-free circulating nucleic acid and DNA extracted from leukocytes in peripheral blood may be a potential source of noninvasive cancer biomarkers. In this article, we describe the characteristics of blood-based DNA methylation from different biological sources, detection methods, and the factors affecting DNA methylation. We provide a comprehensive literature review of blood-based DNA methylation as a cancer biomarker and focus on the study of DNA methylation using peripheral blood leukocytes. Although DNA methylation patterns measured in peripheral blood have great potential to be useful and informative biomarkers of cancer risk and prognosis, large systematic and unbiased prospective studies that consider biological plausibility and data analysis issues will be needed in order to develop a clinically feasible blood-based assay.
Optimization of the Bosch CO2 Reduction Process (1991)

&lt;div class="htmlview paragraph"&gt;Extensive development testing to support the design of the Space Station Freedom (SSF) Carbon Dioxide (CO&lt;sub&gt;2&lt;/sub&gt;) Reduction Assembly (CReA) has been conducted. Both dual and single reactor eight-person capacity systems, supported by experimental test setups, have been used to broaden the design data base. Multiple catalysts were evaluated. Of significant importance was data that showed that operation of the Bosch reaction at elevated pressure 150-205 kPa (7-15 psig) provides significant increases in process efficiency. These improvements significantly reduce the recycle gas rate necessary to achieve a 99%+ CO&lt;sub&gt;2&lt;/sub&gt; reduction efficiency. Data presented illus-trates the improvements realized and defines the benefits that the new technology offers in terms of savings in power, weight and volume as illustrated by the SSF CReA.&lt;/div&gt;
Design, Synthesis, and Characterization of a Series of Cytochrome P4503A-Activated Prodrugs (HepDirect Prodrugs) Useful for Targeting Phosph(on)ate-Based Drugs to the Liver§ (2004)

A new class of phosphate and phosphonate prodrugs, called HepDirect prodrugs, is described that combines properties of rapid liver cleavage with high plasma and tissue stability to achieve increased drug levels in the liver. The prodrugs are substituted cyclic 1,3-propanyl esters designed to undergo an oxidative cleavage reaction catalyzed by a cytochrome P(450) (CYP) expressed predominantly in the liver. Reported herein is the discovery of a prodrug series containing an aryl substituent at C4 and its use for the delivery of nucleoside-based drugs to the liver. Prodrugs of 5'-monophosphates of vidarabine, lamivudine (3TC), and cytarabine as well as the phosphonic acid adefovir were shown to cleave following exposure to liver homogenates and exhibit good stability in blood and other tissues. Prodrug cleavage required the presence of the aryl group in the cis-configuration, but was relatively independent of the nucleoside and absolute stereochemistry at C4. Mechanistic studies suggested that prodrug cleavage proceeded via an initial CYP3A-catalyzed oxidation to an intermediate ring-opened monoacid, which subsequently was converted to the phosph(on)ate and an aryl vinyl ketone by a beta-elimination reaction. Studies in primary rat hepatocytes and normal rats comparing 3TC and the corresponding HepDirect prodrug demonstrated the ability of these prodrugs to effectively bypass the rate-limiting nucleoside kinase step and produce higher levels of the biologically active nucleoside triphosphate.