gebhart/patrepeval huggingface dataset:
Immunohistochemical Identification of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Antigen in the Heart and Lymphoid System of Three-week-old Colostrum-deprived Pigs (1995)

Porcine reproductive and respiratory syndrome virus (PRRSV) antigens were detected by a streptavidin-biotin complex technique in tissues of 3-week-old colostrum-deprived pigs that had been inoculated intranasally with PRRSV and had developed moderate respiratory disease. Moderate, multifocal, tan-colored consolidation of the lungs and severe enlargement of the lymph nodes were noted at necropsy. Severe interstitial pneumonia characterized by type 2 pneumocyte proliferation, septal infiltration with mononuclear cells, and accumulation of macrophages and necrotic cells in alveolar spaces was observed at 4 and 9 days postinoculation. Moderate multifocal perivascular lymphohistiocytic myocarditis was observed at 9 days postinoculation. Marked lymphoid follicular hyperplasia and follicular necrosis in the tonsil, spleen, and lymph nodes was observed. A monoclonal antibody that recognizes a conserved epitope of PRRSV nucleocapsid protein was used as primary antibody for immunohistochemistry. Antigen was readily detected in alveolar macrophages in the lung and in endothelial cells and macrophages in the heart. Macrophages and cells resembling dendritic cells in tonsil, lymph nodes, thymus, and spleen also stained intensely positive for viral antigen. PRRSV appears to replicate primarily within macrophages in the respiratory and lymphoid systems of the pig.
Viral vectors for gene therapy : methods and protocols (2011)

The huge potential for gene therapy to cure a wide range of diseases has led to high expectations and a great increase in research efforts in this area, particularly in the study of delivery via viral vectors, widely considered to be more efficient than DNA transfection. In Viral Vectors for Gene Therapy: Methods and Protocols, experts in the field present a collection of their knowledge and experience featuring methodologies that involve virus production, transferring protocols, and evaluating the efficacy of gene products. While thoroughly covering the most popular viral vector systems of adenovirus, retrovirus, and adeno-associated virus, this detailed volume also explores less common viral vector systems such as baculovirus, herpes virus, and measles virus, the growing interest in which is creating a considerable demand for large scale manufacturing and purification procedures. Written in the highly successful Methods in Molecular Biology™ series format, many chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and vital tips on troubleshooting and avoiding known pitfalls. Comprehensive and practical, Viral Vectors for Gene Therapy: Methods and Protocols provides basic principles accessible to scientists from a wide variety of backgrounds for the development of gene therapy viral products that are safe and effective
Polymer crystallization/melting induced thermal switching in a series of holographically patterned Bragg reflectors (2005)

Holographic photopolymerization (H-P) is a simple, fast and attractive means to fabricate one-, two- and three-dimensional complex structures. Liquid crystals, nanoparticles and silicate nano-plates have been patterned into submicron periodical structures. In this article, we report fabrication of a one-dimensional reflection grating structure by patterning a semicrystalline polymer, polyethylene glycol (PEG), in Norland resin (thiol-ene based UV curable resin) matrix using the H-P technique. Sharp notches observed in the reflection grating of this Norland/PEG system indicate a finite Δ present in the system due to spatial segregation of the PEG and Norland resin. The notch position red shifts upon heating and the diffraction efficiency (ratio between diffraction and incident light intensity, DE) increases from ∼20% to 60% for the Norland 65/PEG 4600 grating. This dynamic behavior of the reflection grating is also fully reversible. The unique thermal switching behavior is attributed to the melting/formation of PEG crystals during heating/cooling. By employing different molecular weight PEGs which have different melting temperatures, a series of switching temperatures have been achieved. Since PEG can be easily coupled with a variety of functional groups, this research might shed light on fabricating multifunctional Bragg gratings using the H-P technique.
Two-dimensional nanosecond electric field mapping based on cell electropermeabilization (2009)

Nanosecond, megavolt-per-meter electric pulses cause permeabilization of cells to small molecules, programmed cell death (apoptosis) in tumor cells, and are under evaluation as a treatment for skin cancer. We use nanoelectroporation and fluorescence imaging to construct two-dimensional maps of the electric field associated with delivery of 15 ns, 10 kV pulses to monolayers of the human prostate cancer cell line PC3 from three different electrode configurations: single-needle, five-needle, and flat-cut coaxial cable. Influx of the normally impermeant fluorescent dye YO-PRO-1 serves as a sensitive indicator of membrane permeabilization. The level of fluorescence emission after pulse exposure is proportional to the applied electric field strength. Spatial electric field distributions were compared in a plane normal to the center axis and 15-20 μm from the tip of the center electrode. Measurement results agree well with models for the three electrode arrangements evaluated in this study. This live-cell method for measuring a nanosecond pulsed electric field distribution provides an operationally meaningful calibration of electrode designs for biological applications and permits visualization of the relative sensitivities of different cell types to nanoelectropulse stimulation. PACS Codes: 87.85.M-
Development of complex atherosclerotic lesions in pigs with inherited hyper-LDL cholesterolemia bearing mutant alleles for apolipoprotein B. (1991)

The development of atherosclerotic lesions was studied in pigs aged 4 to 54 months with inherited hyperlow-density lipoprotein (LDL) and hypercholesterolemia (IHLC pigs). These pigs bear the Lpb5 and Lpu1 mutant alleles for apolipoproteins B and U and demonstrate spontaneously elevated cholesterol levels, due primarily to elevated LDL. By 1 year of age, IHLC pigs exhibited focal lesions in the major coronary, iliac, and femoral arteries that were composed of macrophage-derived from cells and smooth muscle cells. Peripheral arterial lesions were more fibrous than those found in the coronaries. By 2 years of age, complicated stenotic lesions containing fibrous caps, necrotic cores, cholesterol clefts, granular calcium deposits, and neovascularization deep within the lesion were common in the major coronary vessels. Peripheral vascular lesions were more smooth muscle cell-rich and fibrotic. By 3 years of age, neovascularization was observed throughout the intimal lesion, and hemorrhage and rupture were common. The extent of complicated lesion formation correlated with both the degree and duration of hypercholesterolemia, with the most stenotic lesions observed in the coronary arteries of the oldest animals having the highest cholesterol levels. Thus IHLC pigs with mutant apolipoproteins B and U develop complicated atherosclerotic plaques that closely resemble advanced atherosclerotic lesions found in humans.
Substrate Specificity of MMPs (2001)

Matrix metalloproteinases (MMPs) are secreted or cell surface-bound zinc metalloendopeptidases that act on extracellular matrix (ECM) macromolecules. Thus, isolated MMPs have been tested against various components of ECM. Based on similarities in primary structure and the abilities to cleave ECM components, MMPs are grouped into collagenases, gelatinases, stromelysins, membrane-type MMP(MT-MMPs), and others which do not belong to those subgroups. Most MMPs consist of four typical domain structures: propeptide, catalytic, linker region, and a C-terminal hemopexin-like domains. The catalytic domain share structural similarity with interstitial collagenase (MMP-1). The propeptide domain has least similarities among MMPs, all but except MMP-23 (1) have the so-called cysteine switch sequence motif, PRCG[V/N]PD, whose cysteinyl residue ligates the catalytic zinc atom of the active site as the fourth ligand and maintain inactive proenzyme. Another conserved sequence is the zinc binding motif HEXGHXXGXXH, in which three histidines bind to Zn2+. Three dimensional structures of the catalytic domains of MMPs [MMP-1 (2–6), MMP-3 (7–9), MMP-7 (10), MMP-8 (11,12), MMP-14 (13)] indicate that the polypeptide fold of the catalytic domains are essentially identical, although their substrate specificities are sufficiently different when peptide substrates were tested (14). In addition, the action of MMPs on natural protein substrates is not only dectated by the subsite requirement of the catalytic domains, but it is often influenced by the domains other than the catalytic domain. This chapter describes activities of MMPs on natural substrates and substrate specificity based on synthetic substrates.
Lack of behavioral effects in the rhesus monkey: High peak microwave pulses at 1.3 GHz (1989)

The current safety standards for radiofrequency and microwave exposure do not limit the peak power of microwave pulses for general or occupational exposures. While some biological effects, primarily the auditory effect, depend on pulsed microwaves, hazards associated with very high peak-power microwave pulses in the absence of whole-body heating are unknown. Five rhesus monkeys, Macaca mulatta, were exposed to peak-power densities of 131.8 W/cm2 (RMS) while performing a time-related behavioral task. The task was composed of a multiple schedule of reinforcement consisting of three distinct behavioral components: inter-response time, time discrimination, and fixed interval. Trained monkeys performed the multiple schedule during exposure to 1.3-GHz pulses at low pulse-repetition rates (2-32 Hz). No significant change was observed in any behavior during irradiation as compared to sham-irradiation sessions. Generalization of these findings to experimental results with higher peak-power densities, other pulse rates, different carrier frequencies, or other behaviors is limited.
Active Learning and Crowd-Sourcing for Machine Translation (2018)

In recent years, corpus based approaches to machine translation have become predominant, with Statistical Machine Translation (SMT) being the most actively progressing area. Success of these approaches depends on the availability of parallel corpora. In this paper we propose Active Crowd Translation (ACT), a new paradigm where active learning and crowd-sourcing come together to enable automatic translation for low-resource language pairs. Active learning aims at reducing cost of label acquisition by prioritizing the most informative data for annotation, while crowd-sourcing reduces cost by using the power of the crowds to make do for the lack of expensive language experts. We experiment and compare our active learning strategies with strong baselines and see significant improvements in translation quality. Similarly, our experiments with crowd-sourcing on Mechanical Turk have shown that it is possible to create parallel corpora using non-experts and with sufficient quality assurance, a translation system that is trained using this corpus approaches expert quality.
Peptide-Mediated Immunoregulation (1995)

Quantitative and qualitative characteristics of the signals received by a T cell determine whether receptor ligation results in cell activation, cell death, or the induction of antigen-specific non-responsiveness. Environmental factors such as the nature of costimulation, antigen-presenting cell type, peptide structure and cytokine levels also influence the differentiation of CD4+ helper T cells into functionally distinct subsets, which now appear pivotal in many immune-mediated disorders, including autoimmunity and allergy. Selective manipulation of the immune response, such as the functional inactivation or deviation of the cytokine secretion patterns of specific T cells, may be an effective strategy for immunotherapy.
Multimodal deep learning for robust RGB-D object recognition (2015)

Robust object recognition is a crucial ingredient of many, if not all, real-world robotics applications. This paper leverages recent progress on Convolutional Neural Networks (CNNs) and proposes a novel RGB-D architecture for object recognition. Our architecture is composed of two separate CNN processing streams - one for each modality - which are consecutively combined with a late fusion network. We focus on learning with imperfect sensor data, a typical problem in real-world robotics tasks. For accurate learning, we introduce a multi-stage training methodology and two crucial ingredients for handling depth data with CNNs. The first, an effective encoding of depth information for CNNs that enables learning without the need for large depth datasets. The second, a data augmentation scheme for robust learning with depth images by corrupting them with realistic noise patterns. We present state-of-the-art results on the RGB-D object dataset [15] and show recognition in challenging RGB-D real-world noisy settings.
Cooperative antiproliferative effects of 8-chloro-cyclic AMP and 528 anti-epidermal growth factor receptor monoclonal antibody on human cancer cells. (1995)

8-Chloro-cyclic AMP (8-Cl-cAMP), a site-selective cAMP analogue, is a specific inhibitor of type I cAMP-dependent protein kinase (PKAI) and induces growth inhibition in several human and rodent tumor cell lines. The anti-epidermal growth factor receptor (EGFR) mAb 528 is a blocking antibody able to inhibit the in vitro and in vivo growth of several human cancer cell lines that express functional EGFRs. Since enhanced levels of PKAI are generally found in tumor cells and an increase in PKAI expression is induced by transformation through a transforming growth factor alpha/EGFR autocrine pathway, we have evaluated whether treatment with mAb 528 in combination with 8-Cl-cAMP may have an additive or synergistic growth inhibitory effect on human cancer cells. A dose-dependent inhibition of monolayer cell growth was observed in two human colon cancer cell lines (GEO and CBS) and in a human breast cancer cell line (MDA-468) by treatment with either mAb 528 or 8-Cl-cAMP with 50% inhibitory concentration of 2-10 microgram/ml or 20-25 micrometer, respectively. The combined treatment with low noninhibitory doses of mAb 528 (0.25 microgram/ml) and with 8-Cl-cAMP had a more than additive growth inhibitory effect with a 3- to 5-fold reduction in the 8-Cl-cAMP 50% inhibitory concentration in all cell lines tested. This combined treatment was similarly effective in inhibiting the soft agar cloning efficiency of GEO cells. 8-Cl-cAMP treatment of GEO cells induced a dose-dependent increase in cell membrane-associated EGFRs with a maximum 3- to 4-fold increase within 48-72 h of treatment. These results suggest that a double blockade of the PKAI serine-threonine kinase-dependent and of the EGFR tyrosine kinase-dependent pathways is potentially useful in cancer therapy.
Accelerated synthesis of titanium oxide nanostructures using microfluidic chips (2006)

The synthesis of one-dimensional titanium oxide nanostructures has been accelerated by performing the reaction in a microfluidic environment as opposed to a classical batch process.
On the mechanism of the anticlotting action of vitamin E quinone. (1995)

Vitamin E in the reduced, alpha-tocopherol form shows very modest anticlotting activity. By contrast, vitamin E quinone is a potent anticoagulant. This observation may have significance for field trials in which vitamin E is observed to exhibit beneficial effects on ischemic heart disease and stroke. Vitamin E quinone is a potent inhibitor of the vitamin K-dependent carboxylase that controls blood clotting. A newly discovered mechanism for the inhibition requires attachment of the active site thiol groups of the carboxylase to one or more methyl groups on vitamin E quinone. The results from a series of model reactions support this interpretation of the anticlotting activity associated with vitamin E.
Analysis of CRISPR in Streptococcus mutans suggests frequent occurrence of acquired immunity against infection by M102-like bacteriophages (2009)

Clustered regularly interspaced short palindromic repeats (CRISPR) consist of highly conserved direct repeats interspersed with variable spacer sequences. They can protect bacteria against invasion by foreign DNA elements. The genome sequence of Streptococcus mutans strain UA159 contains two CRISPR loci, designated CRISPR1 and CRISPR2. The aims of this study were to analyse the organization of CRISPR in further S. mutans strains and to investigate the importance of CRISPR in acquired immunity to M102-like phages. The sequences of CRISPR1 and CRISPR2 arrays were determined for 29 S. mutans strains from different persons. More than half of the CRISPR1 spacers and about 35 % of the CRISPR2 spacers showed sequence similarity with the genome sequence of M102, a virulent siphophage specific for S. mutans. Although only a few spacers matched the phage sequence completely, most of the mismatches had no effect on the amino acid sequences of the phage-encoded proteins. The results suggest that S. mutans is often attacked by M102-like bacteriophages, and that its acquisition of novel phage-derived CRISPR sequences goes along with the presence of S. mutans phages in the environment. Analysis of CRISPR1 of M102-resistant mutants of S. mutans OMZ 381 showed that some of them had acquired novel spacers, and the sequences of all but one of these matched the phage M102 genome sequence. This suggests that the acquisition of the spacers contributed to the resistance against phage infection. However, since not all resistant mutants had new spacers, and since the removal of the CRISPR1 array in one of the mutants and in wild-type strains did not lead to loss of resistance to infection by M102, the acquisition of resistance must be based on further elements as well.
Use of Plasma RNA for Real-Time Quantitative RT-PCR to Monitor Imatinib Therapy in Patients with Chronic Myeloid Leukemia. (2004)

Abstract Monitoring minimal residual disease (MRD) in chronic myeloid leukemia after imatinib therapy can help in determining therapeutic strategy. Sensitive methods based on the detection of the BCR/ABL fusion gene or its fusion transcript by FISH or RT-PCR, respectively, are used to monitor residual leukemia in peripheral blood or bone marrow cells. While sensitive, these methods require an invasive procedure to obtain bone marrow. The patchy nature of the residual disease may cause some of the reported variation in detecting MRD. We hypothesized that plasma RNA level reflects total body disease and is unaffected by the tendency of some myeloid cells not to circulate. We measured the BCR/ABL fusion transcript by real-time quantitative RT-PCR using RNA isolated from blood plasma. We used a quantitative RT-PCR assay capable of measuring both the b2a2 and b3a2 BCR/ABL fusion transcripts by targeting exon 13 of BCR with the 5′ and exon 2 of ABL by the 3′ primer. RNA isolated from 10–30 μl of frozen plasma was subjected to real-time quantitative RT-PCR using the Taqman technology. Quantification was achieved by extrapolation from a standard curve generated from a ten-fold dilution series of a synthetic oligonucleotide corresponding to the (+) strand of the target sequence. To normalize the fusion mRNA levels we also measured β-actin mRNA from the same samples. Assays were run in duplicate. The results of plasma RT-PCR were correlated with results of conventional cytogenetic analysis, FISH, and quantitative RT-PCR of bone marrow suspension (“bone marrow PCR”). Plasma and bone marrow samples were obtained at 3, 6, 9, 12 and 15 months after imatinib therapy. Ninety-five plasma samples were analyzed. There was a strong positive correlation between the results of plasma RT-PCR vs. positive cytogenetics (n=95, p&amp;lt;0.00001), FISH (n=88, p&amp;lt;0.00001), and bone marrow RT-PCR (n=74, p&amp;lt;0.00001). At 12 months after imatinib therapy all but 2 of the 29 patients were in complete hematologic and cytogenetic remission (CR); one patient was in partial remission (PR) and one in hematologic, but not cytogenetic, remission. These two non-CR patients were positive by both bone marrow and plasma-based RT-PCR assay for the fusion transcript. Three of the four CR patients positive by both plasma and bone marrow PCR at 12 months progressed and converted to PR/minimal response at 15 months post-therapy. The level of plasma BCR/ABL fusion mRNA at 12 months was significantly higher (p=0.04) in these patients than in those who did not progress. Our results show that, by using 10–30 μl of plasma per assay, RT-PCR is at least as sensitive as cytogenetic or FISH analysis of bone marrow cells in monitoring MRD.
Techniques and Applications of Path Integration (1981)

Partial table of contents: Probabilities and Probability Amplitudes for Paths. Correspondence Limit for the Path Integral (Heuristic). Vector Potentials and Another Proof of the Path Integral Formula. Doing the Integral: Free Particle and Quadratic Lagrangians. Brownian Motion and the Wiener Integral Kac's Proof. Perturbation Theory and Feynman Diagrams. SELECTED APPLICATIONS OF THE PATH INTEGRAL. Asymptotic Analysis. The Calculus of Variations. WKB Near Caustics. The Phase of the Semiclassical Amplitude. Scattering Theory. Geometrical Optics. The Polaron. Spin and Related Matters. Quantum Mechanics on Curved Spaces. Relativistic Propagators and Black Holes. Applications to Statistical Mechanics. Critical Droplets. Alias Instantons, and Metastability. Phase Space Path Integral. Omissions, Miscellany, and Prejudices. Indexes.
On a nonvolatile memory cell based on micro-electro-mechanics (2002)

An integrated micro-electro-mechanical nonvolatile memory cell is investigated. It essentially consists of a surface-micromachined bridge that is longitudinally stressed so that it buckled and becomes mechanically bistable. This bistable bridge performs the memory function. The read and write operation is performed by sensing the capacitance of the bridge and by electrostatically switching the bridge from one stable state into the other, respectively. The performance of such a device has been roughly estimated by a simple analytical model and experimental samples have been fabricated using a slightly adapted MOS process. The results appear promising.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>