gebhart/patrepeval huggingface dataset:
Direct visualization of antigen-specific T cells: HTLV-1 Tax11–19- specific CD8+T cells are activated in peripheral blood and accumulate in cerebrospinal fluid from HAM/TSP patients (1998)

Human T lymphotropic virus type 1 (HTLV-1) -associated myelopathy/tropic spastic paraparesis is a demyelinating inflammatory neurologic disease associated with HTLV-1 infection. HTLV-1 Tax11-19-specific cytotoxic T cells have been isolated from HLA-A2-positive patients. We have used a peptide-loaded soluble HLA-A2-Ig complex to directly visualize HTLV-1 Tax11-19-specific T cells from peripheral blood and cerebrospinal fluid without in vitro stimulation. Five of six HTLV-1-associated myelopathy/tropic spastic paraparesis patients carried a significant number (up to 13.87%) of CD8(+) lymphocytes specific for the HTLV-1 Tax11-19 peptide in their peripheral blood, which were not found in healthy controls. Simultaneous comparison of peripheral blood and cerebrospinal fluid from one patient revealed 2.5-fold more Tax11-19-specific T cells in the cerebrospinal fluid (23.7% vs. 9.4% in peripheral blood lymphocyte). Tax11-19-specific T cells were seen consistently over a 9-yr time course in one patient as far as 19 yrs after the onset of clinical symptoms. Further analysis of HTLV-1 Tax11-19-specific CD8(+) T lymphocytes in HAM/TSP patients showed different expression patterns of activation markers, intracellular TNF-alpha and gamma-interferon depending on the severity of the disease. Thus, visualization of antigen-specific T cells demonstrates that HTLV-1 Tax11-19-specific CD8(+) T cells are activated, persist during the chronic phase of the disease, and accumulate in cerebrospinal fluid, showing their pivotal role in the pathogenesis of this neurologic disease.
Filter-Protected Carotid Stenting Via a Minimal Cervical Access With Transitory Aspirated Reversed Flow During Initial Passage of the Target Lesion (2006)

Our preliminary observations from this small early experience suggest that this variant CAS technique is feasible and probably diminishes the neuroembolic risk during initial navigation of the ICA target stenosis.
Outer membrane localization of murein hydrolases: MltA, a third lipoprotein lytic transglycosylase in Escherichia coli (1997)

Lytic transglycosylases are a unique lysozyme-like class of murein hydrolases believed to be important for growth of Escherichia coli. A membrane-bound lytic transglycosylase with an apparent molecular mass of 38 kDa, which was designated Mlt38, has previously been purified and characterized (A. Ursinus and J.-V. Höltje, J. Bacteriol. 176:338-343, 1994). On the basis of four tryptic peptides, the gene mltA was mapped at 63 min on the chromosomal map of E. coli K-12 and cloned by reverse genetics. The open reading frame was found to contain a typical lipoprotein consensus sequence, and the lipoprotein nature of the gene product was demonstrated by [3H]palmitate labeling. On the basis of the distribution of MltA in membrane fractions obtained by sucrose gradient centrifugation, a localization in the outer membrane is indicated. Overexpression of MltA at 30 degrees C, the optimal temperature for enzyme activity, but not at 37 degrees C results in the formation of spheroplasts. Not only a deletion mutant in mltA, but also double mutants in mltA and one of the two other well-characterized lytic transglycosylases (either sltY or mltB), as well as a triple mutant in all three enzymes, showed no obvious phenotype. However, dramatic changes in the structure of the murein sacculus indicate that lytic transglycosylases are involved in maturation of the murein sacculus.
Imaging of Affinity Microcontact Printed Proteins by Using Liquid Crystals (2004)

This paper reports the design of surfaces on which thermotropic liquid crystals can be used to image affinity microcontact printed proteins. The surfaces comprise gold films deposited onto silica substrates at an oblique angle of incidence and then functionalized with a monolayer formed from 2-mercaptoethylamine. Ellipsometric measurements confirm the transfer of anti-biotin IgG to these surfaces from affinity stamps functionalized with biotinylated bovine serum albumin (BSA), while control experiments performed using anti-goat IgG confirmed the specificity of the IgG capture on the stamp. On these surfaces, anti-biotin IgG caused nematic phases of 4-cyano-4'-pentylbiphenyl (5CB, Delta epsilon = epsilon(parallel) - epsilon(perpendicular) > 0) to assume orientations that were parallel to the surfaces (planar anchoring) but with azimuthal orientations that were distinct from those assumed by the liquid crystals on the amine-terminated surfaces not supporting IgGs. Following incubation of these samples for >8 h at 36 degrees C, we observed that the amine-terminated regions of the surface not supporting IgG cause 5CB to undergo a transition from planar to perpendicular (homeotropic). Because N-(4-methoxybenzylidene)-4-butylaniline (MBBA) (Delta epsilon < 0) does not undergo a similar transition in orientation, this transition is consistent with the effects of an electrical double layer formed at the amine-terminated surface on the liquid crystal. Following the transition to homeotropic anchoring, the liquid crystals provide high optical contrast between regions of the surface supporting and not supporting IgG. We conclude that amine-terminated surfaces (I) uniformly align liquid crystals when not supporting proteins and (II) have sufficiently high surface free energy to capture proteins delivered to the surface from an affinity stamp, and thus they form the basis of a useful class of surfaces on which affinity microcontact printed proteins can be imaged using liquid crystals.
Approximate matrix inversion for high-throughput data detection in the large-scale MIMO uplink (2013)

The high processing complexity of data detection in the large-scale multiple-input multiple-output (MIMO) uplink necessitates high-throughput VLSI implementations. In this paper, we propose - to the best of our knowledge - first matrix inversion implementation suitable for data detection in systems having hundreds of antennas at the base station (BS). The underlying idea is to carry out an approximate matrix inversion using a small number of Neumann-series terms, which allows one to achieve near-optimal performance at low complexity. We propose a novel VLSI architecture to efficiently compute the approximate inverse using a systolic array and show reference FPGA implementation results for various system configurations. For a system where 128 BS antennas receive data from 8 single-antenna users, a single instance of our design processes 1.9M matrices/s on a Xilinx Virtex-7 FPGA, while using only 3.9% of the available slices and 3.6% of the available DSP48 units.
The role of phenylalanine-119 of the reverse transcriptase of mouse mammary tumour virus in DNA synthesis, ribose selection and drug resistance (2002)

Phe-119 in the reverse transcriptase (RT) of mouse mammary tumour virus (MMTV) is homologous with Tyr-115 in HIV type 1 (HIV-1) RT and to Phe-155 in murine leukaemia virus (MLV) RT. By mutating these residues in HIV-1 and MLV RTs (which are strict DNA polymerases) the enzymes were shown to function also as RNA polymerases. Owing to the uniqueness of MMTV as a type B retrovirus, we have generated a Phe-119-Val mutant of MMTV RT to study the involvement of this residue in affecting the catalytic features of this RT. The data presented here show that the mutant MMTV RT can incorporate both deoxyribonucleosides and ribonucleosides while copying either RNA or DNA. In addition, this mutant RT shows resistance to nucleoside analogues and an enhanced fidelity of DNA synthesis; all relative to the wild-type enzyme. The Phe-119-Val mutant is also different from the wild-type enzyme in its preference for most template primers tested and in its ability to synthesize DNA under non-processive and processive conditions. Overall, it is likely that the aromatic side chain of Phe-119 is located at the dNTP-binding site of MMTV RT and thus might be part of a putative "steric gate" that prevents the incorporation of nucleoside triphosphates. Since the only three-dimensional structures of RTs published so far are those of HIV-1 and MLV, it is likely that MMTV RT folds quite similarly to these RTs.
Effects of defibrotide on prostacyclin release from isolated rabbit kidneys and protection from post-ischemic acute renal failure in vivo. (1991)

We evaluated whether defibrotide, a single-stranded polydeoxyribonucleotide that enhances prostacyclin (PGI2) release from various isolated organs, could also release PGI2 from the rabbit kidney and prove effective against renal ischemic injury. Isolated perfused kidneys responded to defibrotide (100, 250 and 500 micrograms ml-1 min-1) with a dose-dependent release of immunoreactive 6-keto-PGF1 alpha (4-fold increase at highest dose), which was prevented by indomethacin pre-treatment. In vivo, venous blood withdrawn from heparinized rabbits (and representative of renal outflow) was conveyed over a collagen matrix, onto which platelets adhered and aggregated. Recording the weight increase of the matrix was used as a bioassay to follow the time-course of released PGI2. We observed that renal outflowing blood from defibrotide treated animals (50 mgKg-1 i.v.) displayed lower (P less than 0.05 versus controls) platelet activation, consistent with enhanced PGI2 release from the kidneys. Furthermore, the duration of this effect was longer lasting than that predicted from the known plasma half-life of the drug. After transient (30 min) occlusion of the renal arteries, glomerular filtration rate (GFR) dropped by about 50% (P less than 0.01) during the first reperfusion hour in control animals, with only mild recovery having occurred 4 h later. Defibrotide (16 mgKg-1 bolus + 16 mgKg-1h-1, i.v.) could not antagonize the initial impairment (40% GFR reduction), but allowed full recovery at the end of the observation period (P less than 0.05 vs controls). Indomethacin, instead, caused a dramatic reduction of GFR (70%) during early reperfusion, with no subsequent recovery.(ABSTRACT TRUNCATED AT 250 WORDS)
ONCOLYSIS BY CLOSTRIDIA. III. EFFECTS OF CLOSTRIDIA AND CHEMOTHERAPEUTIC AGENTS ON RODENT TUMORS. (1964)

Intravenously injected spores of a number of species of nonpathogenic clostridia localized and germinated in tumor tissue but not in normal tissues of the mouse. In tumors of sufficient size liquefaction of an apparently substantial amount of viable tumor tissue occurred leading to statistically significant reduction of tumor weight in treated animals. Conditions for the quantitative measurement of clostridial oncolysis of Sarcoma 180 are described. Even extensive lysis did not lead to permanent eradication of the tumor in the majority of animals. With synchronously grown cultures of clostridia it has been shown that all growth phases of the microorganism were equally effective in producing oncolysis of solid tumors on intravenous injection.

In hamsters bearing the amelanotic Melanoma #4, clostridial spores localized rapidly in the tumor and produced almost complete liquefaction in a short time, although the animals usually died at the height of the lysis. In hamsters bearing the renal adenocarcinoma, the extent of lysis was variable and limited. There was no evidence of localization of organisms in small primary tumors or in metastases.

Treatment of Sarcoma 180 with clostridial spores in combination with a number of chemotherapeutic agents has been tested. A series of antimetabolites, quinones, and peroxides did not improve the effect of the spores. Improvement of clostridial oncolysis has been observed in combination therapy with 5-fluorodeoxyuridine. Combination with alkylating agents of the ethyleneimino type also significantly improved the effect on tumor weight reduction but also led to increased toxicity. By suitable adjustment of drug therapy improved results could be obtained without prohibitive toxicity.
Microbioreactors for high-throughput cytotoxicity assays. (2008)

Cell culture plays a fundamental role in the biotechnology and pharmaceutical industries, impacting both drug discovery and manufacturing as well as regenerative medicine. In drug discovery, cell-based assays are increasingly being used for drug target validation and drug ADMET (absorption, distribution, metabolism, elimination and toxicity) studies because cells can provide more representative responses to drugs than simple molecular assays and are easier to use in a high-throughput format than animals. There are, however, intrinsic drawbacks associated with conventional in vitro cellular tests using two-dimensional cultures, in that they lack a three-dimensional (3D) scaffold to support cell growth and proper tissue function, and cannot mimic in vivo cellular conditions. Tailoring scaffold properties for 3D cell cultures is therefore essential in developing a representative in vitro tissue model for cytotoxicity assays. Recently, microfluidic bioreactors with miniaturized culturing vessels and high controllability for operation and on-line monitoring/sensing have gained popularity in bioprocess development and cell-based assays. The advancement in this field has been enabled by the development of novel cell lines and reporter gene techniques, as well as new microfabrication, microfluidics and optical and electrochemical sensor technologies. Non-invasive detection methods using reporter genes and label-free techniques allow for real-time dynamic monitoring of viable cell number and cellular activities. Microbioreactors with continuous perfusion allow for long-term culturing to study chronic toxicity effects. Systemic toxicity and interactions between different cell types can also be studied on a biochip. High-density microfluidic arrays provide a platform for future high-throughput and high-content screening that will contribute to drug discovery and bioprocess development.
Learning a Deep Embedding Model for Zero-Shot Learning (2017)

Zero-shot learning (ZSL) models rely on learning a joint embedding space where both textual/semantic description of object classes and visual representation of object images can be projected to for nearest neighbour search. Despite the success of deep neural networks that learn an end-to-end model between text and images in other vision problems such as image captioning, very few deep ZSL model exists and they show little advantage over ZSL models that utilise deep feature representations but do not learn an end-to-end embedding. In this paper we argue that the key to make deep ZSL models succeed is to choose the right embedding space. Instead of embedding into a semantic space or an intermediate space, we propose to use the visual space as the embedding space. This is because that in this space, the subsequent nearest neighbour search would suffer much less from the hubness problem and thus become more effective. This model design also provides a natural mechanism for multiple semantic modalities (e.g.,~attributes and sentence descriptions) to be fused and optimised jointly in an end-to-end manner. Extensive experiments on four benchmarks show that our model significantly outperforms the existing models.
Cutting Edge: Emergence of CD127high Functionally Competent Memory T Cells Is Compromised by High Viral Loads and Inadequate T Cell Help (2005)

In this report we have inspected whether difficulties in controlling viral infections negatively impacts the generation of CD127(high) memory T cells. Using both MHC class I and II tetramers we reveal that CD127(low) T cells are not necessarily rapidly deleted but can persist in a pseudoeffector state in which they display the hallmarks of activated effector cells but are functionally inferior. CD127(high) cells can, however, emerge if the infection is contained. We also show that in the absence of CD4 T cell help significant populations of CD127(high) CD8 T cells fail to emerge. Analyses of cytokine-producing activities by both mouse and human CD8 T cells further document that the extended maintenance of T cells in a CD127(low) state has functional consequences which manifest as an impairment of IL-2 production.
An Introduction to Kernel and Nearest-Neighbor Nonparametric Regression (1992)

Abstract Nonparametric regression is a set of techniques for estimating a regression curve without making strong assumptions about the shape of the true regression function. These techniques are therefore useful for building and checking parametric models, as well as for data description. Kernel and nearest-neighbor regression estimators are local versions of univariate location estimators, and so they can readily be introduced to beginning students and consulting clients who are familiar with such summaries as the sample mean and median.
Characterization of a 0.35T MR system for phantom image quality stability and in vivo assessment of motion quantification (2015)

ViewRay is a novel MR-guided radiotherapy system capable of imaging in near real-time at four frames per second during treatment using 0.35T field strength. It allows for improved gating techniques and adaptive radiotherapy. Three cobalt-60 sources (~ 15,000 Curies) permit multiple-beam, intensity-modulated radiation therapy. The primary aim of this study is to assess the imaging stability, accuracy, and automatic segmentation algorithm capability to track motion in simulated and in vivo targets. Magnetic resonance imaging (MRI) characteristics of the system were assessed using the American College of Radiology (ACR)-recommended phantom and accreditation protocol. Images of the ACR phantom were acquired using a head coil following the ACR scanning instructions. ACR recommended T1- and T2-weighted sequences were evaluated. Nine measurements were performed over a period of seven months, on just over a monthly basis, to establish consistency. A silicon dielectric gel target was attached to the motor via a rod. 40 mm total amplitude was used with cycles of 3 to 9 s in length in a sinusoidal trajectory. Trajectories of six moving clinical targets in four canine patients were quantified and tracked. ACR phantom images were analyzed, and the results were compared with the ACR acceptance levels. Measured slice thickness accuracies were within the acceptance limits. In the 0.35 T system, the image intensity uniformity was also within the ACR acceptance limit. Over the range of cycle lengths, representing a wide range of breathing rates in patients imaged at four frames/s, excellent agreement was observed between the expected and measured target trajectories. In vivo canine targets, including the gross target volume (GTV), as well as other abdominal soft tissue structures, were visualized with inherent MR contrast, allowing for preliminary results of target tracking.
Serum antibodies against prostasomal clusterin in prostate cancer patients (2008)

The correlation between serum anti-clusterin antibody titres and other clinico-pathological variables was generally weak in prostate cancer patients, although clusterin has been assigned an important role in tumourigenesis and progression of prostate cancer. However, the anti-clusterin antibody titre appeared to be related to prostate volume, correlating to both transitional zone volume and total volume of the prostate.
Midkine, a heparin‐binding growth factor, is fundamentally involved in the pathogenesis of rheumatoid arthritis (2004)

MK participates in each of the two distinct phases of RA development, namely, migration of inflammatory leukocytes and osteoclast differentiation, and is a key molecule in the pathogenesis of RA.
Comparison between optical and electrical interconnects based on power and speed considerations (1988)

Conditions are determined for which optical interconnects can transmit information at a higher data rate and consume lc3s power than the equivalent electrical interconnections. The analysis is performed for free-space optical intrachip communication links. Effects of scaling circuit dimensions, presence of signal fan-out, and the use of light modulators as optical signal transmitters are also discussed.
Renal interleukin-6 production in normotensive and hypertensive rats (1994)

These findings demonstrate that renal interleukin-6 was not produced constitutively under normal physiological conditions. Moreover, in spite of the development of hypertension from two causes, genetic and renin-dependent, renal interleukin-6 was not expressed even though there is a deficit in immunological function in the SHR and damage to the renal tissue of the 2-K,1C rats.
Progression to AIDS in the absence of a gene for vpr or vpx (1995)

Rhesus monkeys (Macaca mulatta) were experimentally infected with strains of simian immunodeficiency virus (SIV) derived from SIVmac239 lacking vpr, vpx, or both vpr and vpx genes. These auxiliary genes are not required for virus replication in cultured cells but are consistently conserved within the SIVmac/human immunodeficiency virus type 2/SIVsm group of primate lentiviruses. All four rhesus monkeys infected with the vpr deletion mutant showed an early spike in plasma antigenemia, maintained high virus burdens, exhibited declines in CD4+ lymphocyte concentrations, and had significant changes in lymph node morphology, and two have died to date with AIDS. The behavior of the vpr deletion mutant was indistinguishable from that of the parental, wild-type virus. Rhesus monkeys infected with the vpx deletion mutant showed lower levels of plasma antigenemia, lower virus burdens, and delayed declines in CD4+ lymphocyte concentrations but nonetheless progressed with AIDS to a terminal stage. The vpr+vpx double mutant was severely attenuated, with much lower virus burdens and no evidence of disease progression. These and other results indicate that vpr provides only a slight facilitating advantage for wild-type SIVmac replication in vivo. Thus, progression to AIDS and death can occur in the absence of a gene for vpr or vpx.
Participation of target Fas protein in apoptosis pathway induced by CD4+ Th1 and CD8+ cytotoxic T cells. (1994)

The results presented here provide evidence that the presence of Fas protein in target cells is essential to permit cytotoxicity (resulting in apoptosis) mediated by cloned CD4+ Th1 cells. Using mitogen-activated B cells as targets, antigen-dependent lysis by CD4+ Th1 effectors was observed with MRL/MpJ+ but not with MRL/MpJ-lpr targets. The congenic MRL/MpJ-lpr strain is defective in Fas expression. Target cells from various lymphoid tissues of C3H.MRL-lpr mice were also resistant to the lectin-dependent cytotoxicity of Th1 effectors, whereas C3H/HeJ targets were sensitive. Moreover, a rapid DNA fragmentation prior to 51Cr release was induced only in C3H/HeJ targets. Thus, cytotoxicity induced by Th1 effectors correlates with target Fas expression. In contrast to Th1 effectors, CD8+ cytotoxic T lymphocytes (CTLs) killed C3H.MRL-lpr targets. When cytotoxicity was assayed in the presence of EGTA and MgCl2, which chelates extracellular Ca2+ [(Ca2+)ext], only C3H.MRL-lpr targets became resistant to CD8+ CTLs. This (Ca2+)ext-independent cytotoxicity of both Th1 and CD8+ effectors could be inhibited with unlabeled C3H/HeJ thymocytes or with a transfectoma carrying a murine Fas-human mu gene construct. In comparison, C3H.MRL-lpr thymocytes and the nontransfected parental cell line were poor inhibitors. Our study demonstrates that CD4+ Th1 cells and CD8+ CTLs differ in their (Ca2+)ext-dependent cytotoxicity but share a (Ca2+)ext-independent cytotoxicity that requires participation of Fas molecules for cytotoxic signal transduction leading to target apoptosis.
Counselor reinvests experience (1993)

Role-switching at the Hole in the Wall Gang Camp is a pretty common thing, although it can take years to actually happen. Many of today9s counselors are yesterday9s campers — confronted with a life-threatening illness, but surpassing preconceived limitations. Their insights, empathy and ability to serve as positive role models prove invaluable at the camp. Dan Cote, a 20-year-old counselor diagnosed with acute lymphoblastic leukemia at age 8, made the camper-to-counselor conversion.