gebhart/patrepeval huggingface dataset:
Interspecies aminopeptidase-N chimeras reveal species-specific receptor recognition by canine coronavirus, feline infectious peritonitis virus, and transmissible gastroenteritis virus (1997)

We report that cells refractory to canine coronavirus (CCV) and feline infectious peritonitis virus (FIPV) became susceptible when transfected with a chimeric aminopeptidase-N (APN) cDNA containing a canine domain between residues 643 and 841. This finding shows that APN recognition by these viruses is species related and associated with this C-terminal domain. The human/canine APN chimera was also able to confer susceptibility to the porcine transmissible gastroenteritis virus (TGEV), whereas its human/porcine homolog failed to confer susceptibility to CCV and FIPV. A good correlation was observed between the capacity of CCV, FIPV, and TGEV to recognize the different interspecies APN chimeras and their ability to infect cells derived from the relevant species. As an exception, TGEV was found to use a human/bovine APN chimera as a receptor although itself unable to replicate in bovine cells.
Abacus: a 1024 processor 8 ns SIMD array (2002)

Describes the Abacus machine at a number of levels. Presents the microarchitecture of the PE comprising the reconfigurable bit-parallel array, a set of arithmetic and communication primitives, details of the VLSI implementation, and system-level design issues of a high-speed SIMD array. The most concrete goal of the Abacus project was to design and build a machine that could be used by members of the MIT Artificial Intelligence Laboratory for real-time early vision processing. Along the way, we explored several architectural ideas.
Blockade of collagen-induced arthritis post-onset by antibody to granulocyte-macrophage colony-stimulating factor (GM-CSF): requirement for GM-CSF in the effector phase of disease (2001)

There is mounting evidence for a role of the growth factor granulocyte-macrophage colony-stimulating factor (GM-CSF) in inflammatory disease, including arthritis. In the present study, we examined the effectiveness of treatment of collagen-induced arthritis (CIA) with a neutralizing mAb to GM-CSF. DBA/1 mice were immunized for the development of CIA and treated at different times, and with different doses, with neutralizing mAb to GM-CSF or isotype control mAb. Anti-GM-CSF mAb treatment prior to the onset of arthritis, at the time of antigen challenge, was effective at ameliorating the ensuing disease. Modulation of arthritis was seen predominantly as a reduction in overall disease severity, both in terms of the number of limbs affected per mouse and the clinical score of affected limbs. Importantly, anti-GM-CSF mAb treatment ameliorated existing disease, seen both as a reduction in the number of initially affected limbs progressing and lower numbers of additional limbs becoming affected. By histology, both inflammation and cartilage destruction were reduced in anti-GM-CSF-treated mice, and the levels of tumor necrosis factor-a and IL-1beta were also reduced in joint tissue washouts of these mice. Neither humoral nor cellular immunity to type II collagen, however, was affected by anti-GM-CSF mAb treatment. These results suggest that the major effect of GM-CSF in CIA is on mediating the effector phase of the inflammatory reaction to type II collagen. The results also highlight the essential role of GM-CSF in the ongoing development of inflammation and arthritis in CIA, with possible therapeutic implications for rheumatoid arthritis.
Determination of the attenuation map in emission tomography. (2003)

Reliable attenuation correction methods for quantitative emission CT (ECT) require accurate delineation of the body contour and often necessitate knowledge of internal anatomic structure. Two broad classes of methods have been used to calculate the attenuation map: transmission-less and transmission-based attenuation correction techniques. Whereas calculated attenuation correction belonging to the first class of methods is appropriate for brain studies, more adequate methods must be performed in clinical applications, where the attenuation coefficient distribution is not known a priori, and for areas of inhomogeneous attenuation such as the chest. Measured attenuation correction overcomes this problem and uses different approaches to determine this map, including transmission scanning, segmented magnetic resonance images, or appropriately scaled CT scans acquired either independently on separate or simultaneously on multimodality imaging systems. Combination of data acquired from different imagers suffers from the usual problems of working with multimodality images--namely, accurate co-registration from the different modalities and assignment of attenuation coefficients. A current trend in ECT is to use transmission scanning to reconstruct the attenuation map. Combined ECT/CT imaging is an interesting approach; however, it considerably complicates both the scanner design and the data acquisition and processing protocols. Moreover, the cost of such systems may be prohibitive for small nuclear medicine departments. A dramatic simplification could be made if the attenuation map could be obtained directly from the emission projections, without the use of a transmission scan. This is being investigated either using a statistical model of emission data or applying the consistency conditions that allow one to identify the operator of the problem and, thus, to reconstruct the attenuation map. This article presents the physical and methodologic basis of attenuation correction and summarizes recent developments in algorithms used to compute the attenuation map in ECT. Other potential applications are also discussed.
Ex-vivo analysis of human Natural Killer T cells demonstrates heterogeneity between tissues and within established CD4+ and CD4− subsets (2012)

Our understanding of human type 1 natural killer T (NKT) cells has been heavily dependent on studies of cells from peripheral blood. These have identified two functionally distinct subsets defined by expression of CD4, although it is widely believed that this underestimates the true number of subsets. Two recent studies supporting this view have provided more detail about diversity of the human NKT cells, but relied on analysis of NKT cells from human blood that had been expanded in vitro prior to analysis. In this study we extend those findings by assessing the heterogeneity of CD4(+) and CD4(-) human NKT cell subsets from peripheral blood, cord blood, thymus and spleen without prior expansion ex vivo, and identifying for the first time cytokines expressed by human NKT cells from spleen and thymus. Our comparative analysis reveals highly heterogeneous expression of surface antigens by CD4(+) and CD4(-) NKT cell subsets and identifies several antigens whose differential expression correlates with the cytokine response. Collectively, our findings reveal that the common classification of NKT cells into CD4(+) and CD4(-) subsets fails to reflect the diversity of this lineage, and that more studies are needed to establish the functional significance of the antigen expression patterns and tissue residency of human NKT cells.
Survivability of Optical Fiber for Harsh Environments (2008)

Abstract Today, optical-fiber systems are used in the oilfield for sensing and telemetry applications. The most commonly used downhole is the distributed temperature sensing (DTS) system which collects permanent real-time temperature well logs. These logs are extremely useful for real-time production allocation, heavy oil thermal recovery (e.g., steam-assisted gravity drainage, SAGD), steam-well management, and well-integrity monitoring. Unfortunately, optical fibers are not immune to degradation under downhole conditions. Hydrogen, present in the wells because of corrosion or other factors, can attack the optical-fiber components causing attenuation increase. This attenuation can have a negative effect on the performance of the system, such as decreasing accuracy or resolution. Understanding the process and the impact of this degradation is of great importance to the reliable operation of these optical-fiber systems. This article shows how a combination of controlled testing and modeling calculations can be used to provide an estimation of the attenuation increase expected from the fiber with time and downhole conditions. Test results for attenuation of optical fiber in hydrogen atmospheres and under downhole temperatures will be shown. The article also provides results from the testing of a new optical fiber that was designed to give a considerable improvement in resistance to hydrogen attack. These results give an order of magnitude improvement in comparison with commercially available optical fibers. Early field tests are consistent with the results of the study.
A Course in Game Theory (1994)

A Course in Game Theory presents the main ideas of game theory at a level suitable for graduate students and advanced undergraduates, emphasizing the theory's foundations and interpretations of its basic concepts. The authors provide precise definitions and full proofs of results, sacrificing generalities and limiting the scope of the material in order to do so. The text is organized in four parts: strategic games, extensive games with perfect information, extensive games with imperfect information, and coalitional games. It includes over 100 exercises.
Combination Chemotherapy in Advanced Adrenocortical Carcinoma (2012)

Rates of response and progression-free survival were significantly better with EDP plus mitotane than with streptozocin plus mitotane as first-line therapy, with similar rates of toxic events, although there was no significant difference in overall survival. (Funded by the Swedish Research Council and others; FIRM-ACT ClinicalTrials.gov number, NCT00094497.).
Regulation of Ferritin-Mediated Cytoplasmic Iron Storage by the Ferric Uptake Regulator Homolog (Fur) of Helicobacter pylori (2000)

Homologs of the ferric uptake regulator Fur and the iron storage protein ferritin play a central role in maintaining iron homeostasis in bacteria. The gastric pathogen Helicobacter pylori contains an iron-induced prokaryotic ferritin (Pfr) which has been shown to be involved in protection against metal toxicity and a Fur homolog which has not been functionally characterized in H. pylori. Analysis of an isogenic fur-negative mutant revealed that H. pylori Fur is required for metal-dependent regulation of ferritin. Iron starvation, as well as medium supplementation with nickel, zinc, copper, and manganese at nontoxic concentrations, repressed synthesis of ferritin in the wild-type strain but not in the H. pylori fur mutant. Fur-mediated regulation of ferritin synthesis occurs at the mRNA level. With respect to the regulation of ferritin expression, Fur behaves like a global metal-dependent repressor which is activated under iron-restricted conditions but also responds to different metals. Downregulation of ferritin expression by Fur might secure the availability of free iron in the cytoplasm, especially if iron is scarce or titrated out by other metals.
Glycosaminoglycan Mimetic Biomaterials. 4. Synthesis of Sulfated Lactose-Based Glycopolymers That Exhibit Anticoagulant Activity (2002)

Cyanoxyl persistent radicals can be used as chain-growth moderators of the statistical copolymerization of a variety of monomers. We report herein the preparation of fully sulfated lactose-based glycopolymers by cyanoxyl (.OC[triple bond]N)-mediated free-radical polymerization of acrylamide derivatized glycomonomers in good yield (60-80%) and low polydispersity (1.1 < M(w)/M(n) < 1.6). Prolongation of the activated partial thromboplastin time (aPTT) was observed, and structure-activity relationships were defined. Specifically, the anticoagulant effect varied in response to both polymer molecular weight and the density of pendant sulfated lactose units. Nonetheless, measured thrombin times were only modestly prolonged suggesting that the observed anticoagulant effect is not primarily related to direct thrombin inhibition.
The Thermal Properties of Bovine Joint Capsule (1997)

Orthopaedic surgeons have recently adapted the holmium: yttrium-aluminum-garnet (YAG) laser for the shrinkage of capsular tissues for treatment of glenohumeral instability. The molecular mechanism of capsular shrinkage has not been documented to date. This study examined the effects of heating on bovine calf knee capsule and subsequent shrinkage of the capsule. Capsule specimens were placed in a saline bath at temperatures ranging from 55 degrees to 75 degrees C for 1, 3, 5, and 10 minutes. Shrinkage was quantified by digital imaging, and the tissue was examined by light and polarized light microscopy. Tissue contraction was not measurable at or below 57.5 degrees C. At 60 degrees C, tissue shrinkage occurred with corresponding basophilic staining and loss of birefringence in collagen fibers. For specimens heated at 60 degrees C and 62 degrees C, shrinkage directly correlated with duration of thermal exposure. Maximal shrinkage of approximately 50% in length occurred at and above 65 degrees C with thermal exposures of 1 minute or greater. This study demonstrates that thermal shrinkage of bovine knee capsule correlates with denaturation of collagen fibers and depends on both time and temperature. Capsular shrinkage treatments may be performed with any energy source that is capable of well-controlled heating of capsular tissue and does not depend on the special properties of laser light.
Detection of chromosome aneuploidy in interphase nuclei from human primary breast tumors using chromosome-specific repetitive DNA probes. (1988)

We have used in situ hybridization with chromosome specific repetitive DNA sequences as a probe to reveal particular chromosomes as distinct spots or clusters of signal within interphase nuclei. Using karyotypically defined cells and cell lines, we show that the number of signals obtained per nucleus correlates with the number of particular chromosomes present in that nucleus. Further, admixtures of karyotypically different cell lines could be detected. In situ hybridization of nuclei and metaphase spreads derived from the breast cancer cell line MCF-7 shows that a deviant number of spots/nucleus indicates a numerical and/or structural chromosomal aberration. In seven primary breast tumors studied, we detected numerical aberrations of the target sites of chromosomes 1 and/or 18. Although all had a single peak in DNA flow measurements, six of the cases appeared to be heterogeneous with respect to their spots/nucleus content.
Label-Free Biomarker Sensing in Undiluted Serum with Suspended Microchannel Resonators (2010)

Improved methods are needed for routine, inexpensive monitoring of biomarkers that could facilitate earlier detection and characterization of cancer. Suspended microchannel resonators (SMRs) are highly sensitive, batch-fabricated microcantilevers with embedded microchannels that can directly quantify adsorbed mass via changes in resonant frequency. As in other label-free detection methods, biomolecular measurements in complex media such as serum are challenging due to high background signals from nonspecific binding. In this report, we demonstrate that carboxybetaine-derived polymers developed to adsorb directly onto SMR SiO(2) surfaces act as ultralow fouling and functionalizable surface coatings. Coupled with a reference microcantilever, this approach enables detection of activated leukocyte cell adhesion molecule (ALCAM), a model cancer biomarker, in undiluted serum with a limit of detection of 10 ng/mL.
Quantification of arterial flow using digital subtraction angiography (2012)

The in vitro and clinical results indicate that it is feasible to estimate blood flow in routine interventional procedures. The availability of an x-ray based method for quantitative flow estimation is particularly clinically useful for intra-cranial applications, where other methods, such as ultrasound Doppler, are not available.
Advances in adenoviral vectors: from genetic engineering to their biology (1997)

Ad2 and Ad5 belong to a group of human cytolytic viruses that target the respiratory airways for reproduction, whereas latent infections establish within other tissues. Signals therefore exist that control this dichotomic process in different cell types, perhaps including cis and/or trans elements of viral origin. Since 1993, Ad2- and Ad5-based adenoviruses lacking all or part of the E1 regulatory region have been undergoing evaluation in phase I trials that target cancer and cystic fibrosis. These viruses are extremely attenuated and actually do not reproduce in most human cells. However, they retain most of the virus genetic program and often promote a significant cytotoxicity after infection, emphasizing the need to further cripple the virus biology to extend the duration of transgene expression, if required. We will review the strategies currently followed to engineer a professional lytic virus for epithelial cells into an innocuous gene delivery vehicle. Potential effects on the transducing properties of the vector that may result from the inactivation of viral activities that normally allow/regulate extrachromosomal gene expression during wild-type infection are discussed.
Historical development of whiteners: clinical safety and efficacy. (1997)

Since the introduction in 1989 of a home tooth-bleaching technique, the practice has become widespread in the USA. Safety concerns led the Food and Drug Administration (FDA) to temporarily ban sales in 1991 but the ban was later lifted, and the American Dental Association (ADA) now issues guidelines for safety and efficacy. Early information on safety of home bleaching products was often skewed because they were being compared out of context with those designed to be used only in the dental office. The early studies also failed to put the risks into perspective with the risks from other routine dental procedures. The risks are minimized with the systems supplied by dentists because he or she is able to diagnose any problems or special needs, to plan appropriate treatment and to fabricate, fit and adjust the prosthesis used to apply the material. A wide variety of disfigurements may now be treated successfully at home using preparations supplied by the dental practitioner.
Stable MLV-VL30 Dicistronic Retroviral Vectors with a VL30 or MoMLV Sequence Promoting Both Packaging of Genomic RNA and Expression of the 3′ Cistron (1996)

The Friend murine leukemia virus (MLV) and VL30 5' leader sequences were recently found to possess an internal ribosomal entry signal (IRES) and promote cap-independent translation of a downstream cistron. The use of an IRES to generate a dicistronic message provides a way to express two exogenous proteins efficiently and stably within cells. In the present study, we used the VL30 and Moloney (Mo)MLV 5' leader sequences with both RNA translation (IRES) and packaging (E/DLS) functions to construct dicistronic retroviral vectors designed to express human placental alkaline phosphatase (plap) and neomycin phosphotransferase (neo). Vectors containing the VL30 (positions 205-794) and MoMLV (positions 210-1,035) 5' sequences between two cistrons were able to direct synthesis of exogenous proteins and were produced at a high titer, indicating that the IRES and packaging elements were functional in such dicistronic retroviral vectors. In addition, long-term selection for neo expression did not impair plap gene activity. In general, no major genetic rearrangement of the integrated recombinant provirus was observed with the dicistronic constructs upon prolonged culture of the infected cells.
ALBERTO URBINA DEL RASO, PROFESOR EN EL SENTIDO M S RICO Y PLENO DE LA PALABRA (1998)

LA COMUNIDAD DE LA FACULTAD DE QUIMICA (FQ), FUNCIONARIOS UNIVERSITARIOS, FAMILIARES, AMIGOS Y EXALUMNOS DEL MAESTRO EMERITO ALBERTO URBINA DEL RASO, PILAR DE LA INGENIERIA QUIMICA EN MEXICO Y FORJADOR DE PROFESIONALES EN ESA RAMA POR M S DE CUATRO D‚CADAS, LE RINDIERON UN HOMENAJE LUCTUOSO AL CUMPLIRSE EL PRIMER ANIVERSARIO DE SU MUERTE. EN LA CEREMONIA SE PROPUSO QUE EL LABORATORIO DE LA ESPECIALIDAD LLEVE EL NOMBRE DE ESTE ILUSTRE UNIVERSITARIO, Y EL RECTOR FRANCISCO BARNES DE CASTRO ENTREGO UN RECONOCIMIENTO A LA SENORA CECILIA ALARCON, VIUDA DEL INGENIERO URBINA DEL RASO.
Purification and characterization of recombinant murine immune interferon (1986)

The recombinant murine immune interferon (rMu-IFN-gamma) was purified to homogeneity from Escherichia coli harboring the expression vector of murine IFN-gamma. The purified rMu-IFN-gamma showed an Mr of 15 000 in SDS-polyacrylamide gel electrophoresis. Results of amino acid analysis, amino- and carboxyl-terminal analyses and peptide mapping of rMu-IFN-gamma suggest that it has the complete protein sequence predicted on the basis of cDNA except for lack of four amino acid residues from the mature carboxyl-terminus.
CD4+ T cell clones obtained from Plasmodium falciparum sporozoite-immunized volunteers recognize polymorphic sequences of the circumsporozoite protein. (1993)

CD4+ T cell clones were derived from three volunteers who were protected against malaria after immunization with Plasmodium falciparum sporozoites. T cells specific for an epitope, Pf Th/Tc, contained in amino acids 326 to 345 of the circumsporozoite (CS) protein of P. falciparum (NF54) were derived from all three volunteers. DR1-, -4-, -7-, and -9-restricted T cell clones were found to recognize overlapping, but distinct, epitopes within a 20-mer peptide representing the amino acid 326 to 345 sequence. The Pf Th/Tc epitope contains part of the highly conserved region II as well as part of a polymorphic domain of the P. falciparum CS protein. All of the overlapping epitopes within peptide 326-345 contained at least three amino acids of the amino terminus of the conserved region II, in addition to a variable number of amino acids in the polymorphic region. The DR4-, -7-, and -9-restricted but not the DR1-restricted T cell clones recognized variant peptides representing this polymorphic region of the CS protein of P. falciparum isolates from Africa, Asia, and South America.
A persistent rescheduled-page cache for low overhead object code compatibility in VLIW architectures (1996)

Object-code compatibility between processor generations is an open issue for VLIW architectures. A potential solution is a technique termed dynamic rescheduling, which performs run-time software rescheduling at the first-time page faults. The time required for rescheduling the pages constitutes a large portion of the overhead of this method. A disk caching scheme that uses a persistent rescheduled-page cache (PRC) is presented. The scheme reduces the overhead associated with dynamic rescheduling by saving rescheduled pages on disk, across program executions. Operating system support is required for dynamic rescheduling and management of the PRC. The implementation details for the PRC are discussed. Results of simulations used to gauge the effectiveness of PRC indicate that: the PRC is effective in reducing the overhead of dynamic rescheduling; and due to different overhead requirements of programs, a split PRC organization performs better than a unified PRC. The unified PRC was studied for two different page replacement policies: LRU and overhead-based replacement. It was found that with LRU replacement, all the programs consistently perform better with increasing PRC sizes, but the high-overhead programs take a consistent performance hit compared to the low-overhead programs. With overhead-based replacement, the performance of high-overhead programs improves substantially, while the low-overhead programs perform only slightly worse than in the case of the LRU replacement.