gebhart/patrepeval huggingface dataset:
Retroviral vectors for gene therapy of AIDS and cancer. (2001)

Both AIDS and cancer are linked to immune dysfunctions of the body which are characterized by the persistence of disease-afflicted cells. To effect a cure with novel gene therapy approaches, these diseased cells must be eliminated either directly or indirectly using cytotoxic or suicide genes, or via activation of specific immune functional cells. Retroviral vectors are useful tools for long-term genome modification owing to their ability to integrate into host chromosomes. However, most oncoretroviruses, including murine leukemia virus (MLV), require cell division to facilitate nuclear entry; this has restricted the application of murine oncoretroviral vectors to cell targets that are actively dividing. Accordingly, gene transfer into hematopoietic stem cells (HSCs) and terminally differentiated cells such as muscles, neurons and dendritic cells (DCs) has been limited with the conventional oncoretroviral vectors. The lentiviral family of retroviruses, including human immunodeficiency virus type 1 (HIV-1), has been developed into useful gene transfer tools. Lentiviral vectors carry several nuclear entry viral proteins, and therefore can target slowly-dividing and non-dividing cells. To activate immune response against cancer or HIV infection, long-term marking of the target cells is not necessary. However, to establish intracellular defense to prevent HIV infection, prolonged genetic modification of target cells such as HSCs will be required. Due to the poor transduction efficiency and the problem of transgene silencing over time with oncoretroviral vectors, most gene therapy studies for AIDS and cancer using oncoretroviral vectors remain proof-of-concept studies. Here we will discuss recent developments in the use of retroviral vectors, including HIV-1-derived lentiviral vectors, for the treatment of AIDS and cancer, and their future therapeutic potential.
Neuropeptide Conversion to Bioactive Fragments - An Important Pathway in Neuromodulation (2003)

Biosynthetic pathways for the formation of neuroactive peptides and the processes for their inactivation include several enzymatic steps. In addition to enzymatic processing and degradation, several neuropeptides have been shown to undergo enzymatic conversion to fragments with retained or modified biological activity. This has most clearly been demonstrated for e.g. opioid peptides, tachykinins, calcitonin gene-related peptide (CGRP) as well as for peptides belonging to the renin-angiotensin system. Sometimes the released fragment shares the activity of the parent compound. However, in many cases the conversion reaction is linked to a change in the receptor activation profile, i.e. the generated fragment acts on and stimulates a receptor not recognized by the parent peptide. This review will describe the characteristics of certain neuropeptide fragments having the ability to modify the biological action of the peptide from which they are derived. Focus will be directed to the tachykinins, the opioid peptides, angiotensins as well as to CGRP, bradykinin and nociceptin. The kappa opioid receptor selective opioid peptide, dynorphin, recognized for its ability to produce dysphoria, is converted to the delta opioid receptor agonist Leu-enkephalin, with euphoric properties. The tachykinins, typified by substance P (SP), is converted to the bioactive fragment SP(1-7), a heptapeptide mimicking some but opposing other effects of the parent peptide. The bioactive angiotensin II, known to bind to and stimulate the AT-1 and AT-2 receptors, is converted to angiotensin IV (i.e. angiotensin 3-8) with preference for the AT-4 sites or to angiotensin (1-7), not recognized by any of these receptors. Both angiotensin IV and angiotensin (1-7) are biologically active. For example angiotensin (1-7) retains some of the actions ascribed for angiotensin II but is shown to counteract others. Thus, it is obvious that the activity of many neuroactive peptides is modulated by bioactive fragments, which are formed by the action of a variety of peptidases. This phenomenon appears to represent an important regulatory mechanism that modulates many neuropeptide systems but is generally not acknowledged.
Detented Quantization to Suppress Flicker Artifacts in Periodically Inserted Intra-Coded Pictures in H.264 Video Coding (2006)

This paper describes a new flicker suppression method for periodically inserted intra-coded pictures (I-pictures) in H.264 video coding. An H.264 encoder periodically inserts I-pictures for channel hopping and random access. The coding noise pattern for I-pictures differs from that of previously appearing Predictive-coded Pictures (P-pictures) because, unlike with P-pictures, inter-frame prediction is not used with I-pictures. This discontinuity in coding noise patterns generates intra-flicker and heavily degrades subjective video quality at low bit rates. We propose detented quantization (DQ) to reduce the discontinuity in coding noise patterns between P-pictures and I-pictures. DQ stabilizes the representation levels of input coefficients in I-pictures on the basis of a derivation of those of the inter-coded images produced from previous P-pictures. Simulation results show that DQ reduces intra-flicker by more than 50% in H.264 video coder JM8.6, and it significantly improves subjective video quality.
Trimeric Tau Is Toxic to Human Neuronal Cells at Low Nanomolar Concentrations (2013)

In Alzheimer's disease (AD), tau aggregates into fibrils and higher order neurofibrillary tangles, a key histopathological feature of AD. However, soluble oligomeric tau species may play a more critical role in AD progression since these tau species correlate better with neuronal loss and cognitive dysfunction. Recent studies show that extracellular oligomeric tau can inhibit memory formation and synaptic function and also transmit pathology to neighboring neurons. However, the specific forms of oligomeric tau involved in toxicity are still unknown. Here, we used two splice variants of recombinant human tau and generated monomeric, dimeric, and trimeric fractions of each isoform. The composition of each fraction was verified chromatographically and also by atomic force microscopy. The toxicity of each fraction toward both human neuroblastoma cells and cholinergic-like neurons was assessed. Trimeric, but not monomeric or dimeric, tau oligomers of both splice variants were neurotoxic at low nanomolar concentrations. Further characterization of tau oligomer species with disease-specific modifications and morphologies is necessary to identify the best targets for the development of biomarker and therapeutic development for AD and related tauopathies.
Triangular systolic array with reduced latency for QR-decomposition of complex matrices (2006)

The novel CORDIC-based architecture of the triangular systolic array for QRD of large size complex matrices is presented. The proposed architecture relies on QRD using a three angle complex rotation approach that provides significant reduction of latency (systolic operation time) and makes the QRD in such a way that the upper triangular matrix R has only real diagonal elements.
Oxidative Cycloaddition of Thiophenophanes – [n](2.5)Parathiophenophane (n = 8,10–12,14), [8](2,4)Metathiophenophane and [2.2](2,5)Parametathiophenophane (1998)

The oxidative cycloaddition of 3,4-dibromo-[n](2,5)thiophenophanes 12b–e and (2,4)[8]thiophenophane 16 with dienophiles gave stereoselectively OS-bridged cycloadducts 18, 19 and 24. The X-ray analysis of cycloadduct 18a shows it to have a rigid conformation. The molecules can be regarded as a new series of paddlanes. Under the same oxidative conditions, 3,4-dibromo-[8](2,5)thiophenophane (12a) gave the two dimers 29 and 30. The results of the X-ray analysis of 29 are discussed.
Successful Treatment of Human Genital Herpes Infections With 2-Deoxy-D-glucose (1979)

Thirty-six women with genital herpes infections (proved by virological or cytological means) were treated in a double-blind placebo-controlled study with the glucose analogue 2-deoxy-D-glucose for a three-week period. In initial mucocutaneous cases, 89% were cured, with two recurrences after 24 months; in the case of recurrent or secondary infections, 90% had a notable improvement manifested by no or less-frequent recurrences, fewer lesions, or shortened duration of symptoms. In initial infections, discomfort cleared within 12 to 72 hours of therapy; 90% of the patients were asymptomatic within four days. In both cases, virus shedding was notably reduced by 2-deoxy-D-glucose. Concomitant controls treated with placebos failed to respond within this time frame. The use of 2-deoxy-D-glucose provides a simple and unique approach to the treatment of genital herpesvirus infections.
Comparative Antifungal Activity of Four Phosphonate Compounds Against Isolates of Nine<i>Phytophthora</i>Species (1989)

The systemic fungicide potassium phosphonate, three alkyl-substituted phosphonate compounds (monoethyl, dimethyl, and diethyl phosphonate), and potassium hypophosphonate were compared for their activity in vitro against 34 isolates of nine species of Phytophthora. Potassium phosphonate proved to be the most inhibitory compound against most isolates. In contrast, potassium hypophosphonate was the least inhibitory, in some cases over 100 times less than potassium phosphonate
Peroxygenase-Catalyzed Fatty Acid Epoxidation in Cereal Seeds (Sequential Oxidation of Linoleic Acid into 9(S),12(S),13(S)-Trihydroxy-10(E)-Octadecenoic Acid) (1996)

Peroxygenase-catalyzed epoxidation of oleic acid in preparations of cereal seeds was investigated. The 105,000g particle fraction of oat (Avena sativa) seed homogenate showed high peroxygenase activity, i.e. 3034 [plus or minus] 288 and 2441 [plus or minus] 168 nmol (10 min)-1 mg-1 protein in two cultivars, whereas the corresponding fraction obtained from barley (Hordeum vulgare and Hordeum distichum), rye (Secale cereale), and wheat (Triticum aestivum) showed only weak activity, i.e. 13 to 138 nmol (10 min)-1 mg-1 protein. In subcellular fractions of oat seed homogenate, peroxygenase specific activity was highest in the 105,000g particle fraction, whereas lipoxygenase activity was more evenly distributed and highest in the 105,000g supernatant fraction. Incubation of [1-14C]linoleic acid with the 105,000g supernatant of oat seed homogenate led to the formation of several metabolites, i.e. in order of decreasing abundance, 9(S)-hydroxy-10(E),12(Z)-octadecadienoic acid, 9(S),12(S),13(S)-trihydroxy-10(E)-octadecenoic acid, cis-9,10-epoxy-12(Z)-octadecenoic acid [mainly the 9(R),10(S) enantiomer], cis-12,13-epoxy-9(Z)-octadecenoic acid [mainly the 12(R),13(S) enantiomer], threo-12,13-dihydroxy-9(Z)-octadecenoic acid, and 12(R),13(S)-epoxy-9(S)-hydroxy-10(E)-octadecenoic acid. Incubation of linoleic acid with the 105,000g particle fraction gave a similar, but not identical, pattern of metabolites. Conversion of linoleic acid into 9(S),12(S),13(S)-trihydroxy-10(E)-octadecenoic acid, a naturally occurring oxylipin with antifungal properties, took place by a pathway involving sequential catalysis by lipoxygenase, peroxygenase, and epoxide hydrolase.
Hyperacute lung rejection in the pig-to-human model. III. platelet receptor inhibitors synergistically modulate complement activation and lung injury (2003)

Platelet protein receptor adhesive interactions play an important role in amplification of complement activation during hyperacute lung rejection. Inhibiting recruitment of platelets at the site of initial immunologic injury to endothelial cells may protect porcine organs against thrombosis and inflammation during the initial exposure to human blood.
Security for Mobile Networks and Platforms (2006)

Introduction. Identification, Authentication, Authorization, and Non-Repudiation. Part I: Platform Security Cryptographic Techniques. Hardware Security. Software Security. Security Verification and Certification. Part II: Security Protocols Higher Layer Security. IP Layer Security. Authentication, Authorization, and Accounting. Extensible Authentication Protocol and IEEE 802.1x. Part III: Security in Wireless Communications Systems WPANs and Ad-Hoc Security. WLAN Security. WiMAX Security. IEEE 802.20 Security. 3GPP/UMTS Security. Future Security Challenges. Appendix.
Statistics of modifier distributions in mixed network glasses (2013)

The constituents of any network glass can be broadly classified as either network formers or network modifiers. Network formers, such as SiO2, Al2O3, B2O3, P2O5, etc., provide the backbone of the glass network and are the primary source of its rigid constraints. Network modifiers play a supporting role, such as charge stabilization of the network formers or alteration of the network topology through rupture of bridging bonds and introduction of floppy modes. The specific role of the modifiers depends on which network formers are present in the glass and the relative free energies of modifier interactions with each type of network former site. This variation of free energy with modifier speciation is responsible for the so-called mixed network former effect, i.e., the nonlinear scaling of property values in glasses having fixed modifier concentration but a varying ratio of network formers. In this paper, a general theoretical framework is presented describing the statistical mechanics of modifier speciation in mixed network glasses. The model provides a natural explanation for the mixed network former effect and also accounts for the impact of thermal history and relaxation on glass network topology.
Microfibrillated Cellulose Sheets Coating Oxygen-Permeable PDMS Membranes Induce Rat Hepatocytes 3D Aggregation into Stably-Attached 3D Hemispheroids (2011)

Here we report the use of natural, chemically-unmodified, microfibrillated cellulose (MFC) as a matrix for hepatocyte culture. We developed an original cell-culture design composed of a thin 3D-microstructured fibrous substrate consisting of a MFC sheet coating a highly O(2)-permeable polydimethylsiloxane (PDMS) membrane. The MFC-coated PDMS membranes were obtained according to a simple process where cellulose fibres were deposited from an aqueous suspension on the PDMS surfaces and the films were dried under mild conditions. To enable oxygen diffusion through the membranes, they were assembled on bottomless frames ('O(2)+' condition). Rat hepatocytes primary-cultured on such MFC-PDMS membranes quickly organized themselves into large hemispherical 3D aggregates which were tightly anchored to the MFC sheets. In contrast, hepatocytes cultured on smooth PDMS membranes in the O(2)+ system (O(2)+, PDMS) organized into unstable 2D monolayers which easily detached from the surfaces. Hepatocyte 3D cultures obtained on MFC-PDMS membranes exhibited higher liver-specific functions over a 2-week culture period, as assessed by both the higher albumin secretion and urea synthesis rate. The MFC-PDMS membranes appear suitable for obtaining stably-attached and functional hepatocyte 3D cultures and appear interesting for drug/chemical screenings in a microplate format, but also for microfluidic applications.
Compact evanescent optical switch and attenuator with electromechanical actuation (1999)

We report the design and the realization of an out-of-plane bending structure supporting a waveguide that is used as an optical attenuator and an optical switch. Both devices are based on evanescent field interaction induced by spatial confinement either between two waveguides or between one waveguide and an absorbing medium. The attenuator exhibits typical attenuation of 65 dB/cm. Even if the bad quality of the waveguide has prevented the correct operation of the switch, we show that the attenuation figure establishes the feasibility of a compact evanescent optical coupler with mechanical drive featuring a total length below 1 mm.
Most of ADP·glucose linked to starch biosynthesis occurs outside the chloroplast in source leaves (2004)

Sucrose and starch are end products of two segregated gluconeogenic pathways, and their production takes place in the cytosol and chloroplast of green leaves, respectively. According to this view, the plastidial ADP.glucose (ADPG) pyrophosphorylase (AGP) is the sole enzyme catalyzing the synthesis of the starch precursor molecule ADPG. However, a growing body of evidences indicates that starch formation involves the import of cytosolic ADPG to the chloroplast. This evidence is consistent with the idea that synthesis of the ADPG linked to starch biosynthesis takes place in the cytosol by means of sucrose synthase, whereas AGP channels the glucose units derived from the starch breakdown. To test this hypothesis, we first investigated the subcellular localization of ADPG. Toward this end, we constructed transgenic potato plants that expressed the ADPG-cleaving adenosine diphosphate sugar pyrophosphatase (ASPP) from Escherichia coli either in the chloroplast or in the cytosol. Source leaves from plants expressing ASPP in the chloroplast exhibited reduced starch and normal ADPG content as compared with control plants. Most importantly however, leaves from plants expressing ASPP in the cytosol showed a large reduction of the levels of both ADPG and starch, whereas hexose phosphates increased as compared with control plants. No pleiotropic changes in photosynthetic parameters and maximum catalytic activities of enzymes closely linked to starch and sucrose metabolism could be detected in the leaves expressing ASPP in the cytosol. The overall results show that, essentially similar to cereal endosperms, most of the ADPG linked to starch biosynthesis in source leaves occurs in the cytosol.
Attention is not Explanation (2019)

Attention mechanisms have seen wide adoption in neural NLP models. In addition to improving predictive performance, these are often touted as affording transparency: models equipped with attention provide a distribution over attended-to input units, and this is often presented (at least implicitly) as communicating the relative importance of inputs. However, it is unclear what relationship exists between attention weights and model outputs. In this work, we perform extensive experiments across a variety of NLP tasks that aim to assess the degree to which attention weights provide meaningful `explanations' for predictions. We find that they largely do not. For example, learned attention weights are frequently uncorrelated with gradient-based measures of feature importance, and one can identify very different attention distributions that nonetheless yield equivalent predictions. Our findings show that standard attention modules do not provide meaningful explanations and should not be treated as though they do. Code for all experiments is available at https://github.com/successar/AttentionExplanation.
Inhibition of type I natural killer T cells by retinoids or following sulfatide‐mediated activation of type II natural killer T cells attenuates alcoholic liver disease in mice (2014)

Type I, but not type II, NKT cells become activated after alcohol feeding. Type I NKT cell-induced inflammation and neutrophil recruitment results in liver tissue damage whereas type II NKT cells protect from injury in ALD. Inhibition of type I NKT cells by retinoids or by sulfatide prevents ALD. Given that the CD1d pathway is highly conserved between mice and humans, NKT cell subsets might be targeted for potential therapeutic intervention in ALD.
Refractive index and birefringence of In <sub> <i>x</i> </sub> Ga <sub> 1– <i>x</i> </sub> N films grown by MOCVD (2005)

The refractive index and birefringence of InxGa1–xN films grown on GaN layers were measured by prism coupling used in conjunction with multilayer optical waveguide analysis. Samples with x = 0.036, 0.049, 0.060, and 0.066 were examined at the separate wavelengths of 442, 457.9, 476.5, 488, 514.5, 532, and 632.8 nm. The In fraction x was determined by Rutherford backscattering spectroscopy. Separate measurements of the film thicknesses were performed by cross-sectional field-emission scanning electron microscopy (FESEM). Film thickness information was required in order to constrain the numerical simulation used to solve for the ordinary (no) and extraordinary (ne) refractive indices. We found that no is a weak function of both x and wavelength for the InGaN layers and could only be well distinguished from GaN (x = 0) for the two shortest wavelengths used. On the other hand, ne for the InGaN layers was resolved from GaN for all the wavelengths and x values. The measurements for ne are limited by optical scattering observed at the shortest wavelengths and the higher values of x. Cross-sectional FESEM reveals that a source of this scattering is most likely triangular pits at the InGaN/GaN upper interface. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Inflammasomes and IL-1 biology in the pathogenesis of allograft dysfunction (2017)

Inflammasomes are high-molecular-weight cytosolic complexes that mediate the activation of caspases. There are many inflammasomes, and each is influenced by a unique pattern-recognition receptor response. Two signals are typically involved in the inflammasome pathways. Signal one involves recognition of pathogen-associated molecular patterns (PAMPs), such as LPS or other colonizing/invading microbes, that interact with TLRs, which induce the downstream production of pro-IL-1β. This is followed by signal two, which involves recognition of PAMPs or damage-associated molecular patterns (DAMPs), such as uric acid or ATP, via NLRP3, which leads to caspase-1-dependent cleavage of pro-IL-1β to active IL-1β and pyroptosis. Ultimately, these two signals cause the release of multiple proinflammatory cytokines. Both PAMPs and DAMPs can be liberated by early insults to the allograft, including ischemia/reperfusion injury, infections, and rejection. The consequence of inflammasome activation and IL-1 expression is the upregulation of adhesion molecules and chemokines, which leads to allograft neutrophil sequestration, mononuclear phagocyte recruitment, and T cell activation, all of which are key steps in the continuum from allograft insult to chronic allograft dysfunction.
Cache Conscious Algorithms for Relational Query Processing (1994)

The current main memory (DRAM) access speeds lag far behind CPU speeds. Cache memory, made of static RAM, is being used in today&amp;apos;s architectures to bridge this gap. It provides access latencies of 2--4 processor cycles, in contrast to main memory which requires 15--25 cycles. Therefore, the performance of the CPU depends upon how well the cache can be utilized. We show that there are significant benefits in redesigning our traditional query processing algorithms so that they can make better use of the cache. The new algorithms run 8%--200% faster than the traditional ones. 1 Introduction The DRAM access speeds have not reduced much compared to the CPU cycle time reduction resulting from the improvements in VLSI technology. Cache memories, made of fast static RAM, help alleviate this disparity by exploiting the spatial and temporal locality in the data accesses of a program. However, programs with poor access locality waste significantly many cycles transferring the data to and from th...