gebhart/patrepeval huggingface dataset:
Defining Early Human NK Cell Developmental Stages in Primary and Secondary Lymphoid Tissues (2012)

A better understanding of human NK cell development in vivo is crucial to exploit NK cells for immunotherapy. Here, we identified seven distinctive NK cell developmental stages in bone marrow of single donors using 10-color flow cytometry and found that NK cell development is accompanied by early expression of stimulatory co-receptor CD244 in vivo. Further analysis of cord blood (CB), peripheral blood (PB), inguinal lymph node (inLN), liver lymph node (liLN) and spleen (SPL) samples showed diverse distributions of the NK cell developmental stages. In addition, distinctive expression profiles of early development marker CD33 and C-type lectin receptor NKG2A between the tissues, suggest that differential NK cell differentiation may take place at different anatomical locations. Differential expression of NKG2A and stimulatory receptors (e.g. NCR, NKG2D) within the different subsets of committed NK cells demonstrated the heterogeneity of the CD56(bright)CD16⁺/⁻ and CD56(dim)CD16⁺ subsets within the different compartments and suggests that microenvironment may play a role in differential in situ development of the NK cell receptor repertoire of committed NK cells. Overall, differential in situ NK cell development and trafficking towards multiple tissues may give rise to a broad spectrum of mature NK cell subsets found within the human body.
CD4+T Cell Surface CCR5 Density as a Determining Factor of Virus Load in Persons Infected with Human Immunodeficiency Virus Type 1 (2000)

The intensity of expression of the chemokine receptor CCR5 is involved in in vitro cell infectability by human immunodeficiency virus (HIV)-1 R5 isolates. Because CCR5 expression varies among individuals, the hypothesis that this expression could determine virus load in HIV-1-infected persons was tested. The mean number of CCR5 molecules per cell was measured on peripheral blood CD4+ T lymphocytes (CCR5 density) from HIV-1-infected, asymptomatic, nontreated adults. There was a strong correlation between HIV RNA plasma level and CCR5 density (P=.009) that was independent of cell activation and was not due to an HIV-induced CCR5 up-regulation. These data are compatible with the hypothesis that CCR5 density is a key factor governing cell infectability and in vivo virus production and explain the protective effect of the Delta32CCR5 deletion, which results in low CCR5 expression. CCR5 density might be of critical predictive value in HIV infection.
HIF-1: A Target For Cancer, Ischemia and Inflammation—Too Good to be True? (2004)

The histone H2A variant, H2AX, is a core component of chromatin that is phosphorylated in chromatin flanking DNA double strand breaks (DSBs). Here, we summarize H2AX functions and outline a specific "anchoring" model, that can explain the translocation prone phenotype of H2AX-deficient and H2AX/p53-deficient mice. We also discuss how this model of H2AX function could account for some aspects of the genomic instability and cancer prone human phenotypes associated with Ataxia Telangiectasia (AT), Nijmegen Breakage Syndrome (NBS), Ataxia Telangiectasia Like Disorder (ATLD), and Bloom's Syndrome (BS).
Extending the color gamut and dynamic range of an sRGB image using a residual image (2003)

Abstract Image sources, such as digital camera captures and photographic negatives, typically have more information than can be reproduced on a photographic print or a video display. The information that is lost during the tone/color rendering process relates to both the extended dynamic range and color gamut of the original scene. In conventional photographic systems, most of this additional information is archived on the photographic negative and can be accessed by adjusting the way the negative is printed. However, most digital imaging systems have traditionally archived only a rendered video RGB image. As a result, it is not possible to make the same sorts of image manipulations that historically have been possible with conventional photographic systems. This suggests that there would be an advantage to storing images using an extended dynamic range/color gamut color encoding. However, because of file compatibility issues, digital imaging systems that store images using color encoding other than a standard video RGB representation (e.g., sRGB ) would be significantly disadvantaged in the marketplace. In this article, we describe a solution that has been developed to maintain compatibility with existing file formats and software applications, while simultaneously retaining the extended dynamic range and color gamut information associated with the original scenes. With this approach, the input raw digital camera image or film scan is first transformed to the scene‐referred ERIMM RGB color encoding. Next, a rendered sRGB image is formed in the usual way and stored in a conventional image file (e.g., a standard JPEG file). A residual image representing the difference between the original extended dynamic range image and the final rendered image is formed and stored in the image file using proprietary metadata tags. This provides a mechanism for archiving the extended dynamic range/color gamut information, which is normally discarded during the rendering process, without sacrificing interoperability. Appropriately enabled applications can decode the residual image metadata and use it to reconstruct the ERIMM RGB image, whereas applications that are not aware of the metadata will ignore it and only have access to the sRGB image. The residual image is formed such that it will have negligible pixel values for those portions of the image that lie within the sRGB gamut, and will therefore be highly compressible. Tests on a population of 950 real customer images have demonstrated that the extended dynamic range scene information can be stored with an average file size overhead of about 8% compared to the sRGB images alone. © 2003 Wiley Periodicals, Inc. Col Res Appl, 28, 251–266, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/col.10160
Short echo time projection reconstruction MR imaging of cartilage: comparison with fat-suppressed spoiled GRASS and magnetization transfer contrast MR imaging. (1997)

In vitro, short TE projection reconstruction MR imaging provides superior delineation of cartilage lesions when compared with two other sequences. On Spoiled GRASS and MTC images, signal intensity of the superficial layer of cartilage is not a reliable sign for surface integrity.
Nitrogen-bridged conformationally constrained etorphine analogs. Synthesis and biological evaluation (1987)

Three N-C8-bridged analogues 4-6 of the opiate etorphine (3) were synthesized and evaluated for opiate agonism and antagonism. In each case ring closure was effected by intramolecular N-alkylation with a suitably developed C8 side chain. Another key synthetic step was the selective monoprotection of diol 11, which allowed independent elaborations of the C7 and C8 side chains. All three analogues showed distinctly diminished agonist activities when compared to the corresponding N-methyl compound, 19(R)-n-butylorvinol (3). Furthermore, no antagonist activity was detectable. The results demonstrate that the conformation at the amino nitrogen in rigid morphinans is critical for potent opiate activity.
Modulation of antigen‐presenting cells by HDAC inhibitors: implications in autoimmunity and cancer (2011)

There is a growing body of evidence to support the use of histone deacetylase inhibitors (HDACi) in the treatment of diverse conditions from autoimmunity to cancer. In this context, HDACi have been ascribed many immunomodulatory effects, assigning novel and promising roles to these compounds. This review summarizes the current observations arising from both pre-clinical and clinical studies in these pathological conditions. However, it is left to be explained how a single agent can have both pro- and anti-inflammatory effects in either physiological or pathological conditions. This question is explored in greater detail by focusing on the effects of HDACi on antigen-presenting cells (APCs), key regulators of immune activation. In particular, HDACi modulation of molecules involved in antigen processing and presentation, as well as co-stimulatory and adhesion molecules, and cytokines will be discussed in the context of both professional and non-professional APCs. Professional APCs encompass classic immune cells; however, it is increasingly evident that other somatic cells, including cancer cells, are not immunologically inert and can display functions similar to professional APCs, a challenging feature that needs to be explored as a potential therapeutic target. In this way, professional and non-professional APCs can regulate their particular micro-environmental niche, affecting either a pro- or anti-inflammatory milieu.
Focus errors and their correction in microscopic deformation analysis using correlation (2002)

Subpixel digital image correlation has been applied to microscope images to analyze surface deformation. Nonintegral pixel shifting and successive approximation are used to calculate the subpixel element of the sample displacement without introducing systematic interpolation errors. Although in-plane displacement precision of better than 2% of a pixel, or < 15 nm at x10 magnification, is shown to be achievable, the use of even moderate numerical aperture microscope objectives render the technique sensitive to errors or variations in sample focusing. The magnitude of this effect is determined experimentally and a focus compensation method is described and demonstrated.
Real-world interaction using the FieldMouse (1999)

We introduce an inexpensive position input device called the FieldMouse, with which a computer can tell the position of the device on paper or any flat surface without using special input tablets or position detection devices. A FieldMouse is a combination of an ID recognizer like a barcode reader and a mouse which detects relative movement of the device. Using a FieldMouse, a user first detects an ID on paper by using the barcode reader, and then drags it from the ID using the mouse. If the location of the ID is known, the location of the dragged FieldMouse can also be calculated by adding the amount of movement from the ID to the position of the FieldMouse. Using a FieldMouse in this way, any flat surface can work as a pointing device that supports absolute position input, just by putting an ID tag somewhere on the surface. A FieldMouse can also be used for enabling a graphical user interface (GUI) on paper or on any flat surface by analyzing the direction and the amount of mouse movement after detecting an ID. In this paper, we introduce how a FieldMouse can be used in various situations to enable computing in real-world environments.
Quantitative Analysis and Efficient Surface Modification of Silica Nanoparticles (2012)

Aminofunctional trialkoxysilanes such as aminopropyltrimethoxysilane (APTMS) and (3‐trimethoxysilylpropyl)diethylenetriamine (DETAS) were employed as a surface modification molecule for generating monolayer modification on the surface of silica (SiO 2 ) nanoparticles. We were able to quantitatively analyze the number of amine functional groups on the modified SiO 2 nanoparticles by acid‐base back titration method and determine the effective number of amine functional groups for the successive chemical reaction by absorption measurements after treating with fluorescent rhodamine B isothiocyanate (RITC) molecules. The numbers of amine sites measured by back titration were 2.7 and 7.7 ea/nm 2 for SiO 2 ‐APTMS and SiO 2 ‐DETAS, respectively, while the numbers of effective amine sites measured by absorption calibration were about one fifth of the total amine sites, namely, 0.44 and 1.3 ea/nm 2 for SiO 2 ‐APTMS(RITC) and SiO 2 ‐DETAS(RITC), respectively. Furthermore, it was confirmed that the reactivity of amino groups on the surface‐modified silica nanoparticles could be maintained in ethanol for more than 1.5 months without showing any significant differences in the reactivity.
Pneumotoxicity of lipopolysaccharide in nitric oxide-deficient rats is limited by a thromboxane synthase inhibitor. (1997)

Both nitric oxide and arachidonic acid metabolites have been implicated in pathogenesis of septic shock. We have recently described a model of endotoxin-induced acute lung injury in rats in which nitric oxide synthase is inhibited. The possible interplay between nitric oxide and eicosanoids (thromboxane A2, prostacyclin) in this model have been presently studied. Animals were randomly assigned to four experimental groups which received the following treatment. 1. Lipopolysaccharide (LPS) infusion only, 2 mg.kg-1min-1 during 10 min (LPS group). 2. N omega-Nitro-L-Arginine 10 mg.kg-1 (L-NNA, nitric oxide synthase inhibitor) pretreatment followed by LPS infusion (L-NNA + LPS group). 3. L-NNA and camonagrel 25 mg.kg-1 (CAM, thromboxane synthase inhibitor) pretreatment followed by LPS infusion (L-NNA + CAM + LPS group). 4. L-NNA and iloprost 0.3 microgram.kg-1.min-1(ILO, stable analog of prostacyclin) pretreatment followed by LPS infusion (L-NNA + ILO + LPS group). LPS infusion resulted in a biphasic response in mean arterial blood pressure. A transient but deep fall in arterial blood pressure was followed by a long-lasting hypotension that led to death after 278 +/- 49 min. L-NNA + LPS rats died within 22 +/- 5 min among the symptoms of systemic hypotension and acute lung injury. In L-NNA + CAM + LPS group a significant attenuation of early phase of hypotension occurred and survival time was comparable with that of the LPS group (298 +/- 68 min). In rats of the L-NNA + ILO + LPS group survival time increased insignificantly to 48 +/- 41 min. It is concluded that immediate deleterious effects of lipopolysaccharide in NO-deficient rats are at least partially mediated by thromboxane A2 while prostacyclin cannot replace NO in its pneumoprotective action.
Diffusion in strained Si(Ge) (1994)

Experiments on Si-rich SiGe layers show an exponential increase in Ge diffusion and an exponential decrease in B diffusion as a function of compressive strain, indicating a linear dependence of activation energy on strain. The effect arises from the structural relaxation of the lattice around the defect mediating diffusion (inward for a vacancy, outward for an interstitial). We infer the mechanisms of Ge and B diffusion in strain-free and compressively strained Si(Ge) at T1030 \ifmmode^\circ\else\textdegree\fi{}C, and draw some general conclusions on strain-modified diffusion in crystalline solids.
Hybrid III-V semiconductor/silicon nanolaser (2011)

Heterogeneous integration of III-V compound semiconductors on Silicon on Insulator is one the key technology for next-generation on-chip optical interconnects. In this context, the use of photonic crystals lasers represents a disruptive solution in terms of footprint, activation energy and ultrafast response. In this work, we propose and fabricate very compact laser sources integrated with a passive silicon waveguide circuitry. Using a subjacent Silicon-On-Insulator waveguide, the emitted light from a photonic crystal based cavity laser is efficiently captured. We study experimentally the evanescent wave coupling responsible for the funneling of the emitted light into the silicon waveguide mode as a function of the hybrid structure parameters, showing that 90% of coupling efficiency is possible.
Posttraumatic Stress Disorder and Acute Stress Disorder II: Considerations for Treatment and Prevention. (2005)

Posttraumatic stress disorder is a common and often chronic and disabling anxiety disorder that can develop after exposure to highly stressful events characterized by actual or threatened harm to the self or others. This is the second of two invited articles summarizing the nature and treatment of PTSD and the associated condition of acute stress disorder (ASD). The present article reviews evidence for the efficacy of psychological and pharmacological treatments for PTSD and ASD. In summary, cognitive behavior therapy (CBT) has been found efficacious in the treatment of chronic PTSD as well as the treatment of ASD/prevention of PTSD. The selective serotonin reuptake inhibitors, sertraline, paroxetine, and fluoxetine, have been found efficacious in the treatment of chronic PTSD, with sertraline and paroxetine receiving the FDA indication for this condition. There is less evidence for efficacious medications in the treatment of ASD/prevention of PTSD. At present, hydrocortisone and propranolol show the greatest promise. Limitations of these treatments, including dropout and a significant number of patients showing no or only partial response, are discussed as well as issues related to selecting among efficacious treatments.
Transplantation and perfusion of microvascular fragments in a rodent model of volumetric muscle loss injury (2014)

Few clinical options are available for the treatment of volumetric muscle loss (VML). An important consideration that needs to be addressed for the development of treatments for these injuries is the establishment of a vascular supply sufficient to support skeletal muscle regeneration. The objective of the current study was to evaluate the potential for microvascular fragments (MVFs) harvested from adipose tissue to support tissue perfusion for VML. Tibialis anterior muscle defects in rats were replaced with constructs that were created on the day of surgery containing either (1) collagen only (COL), (2) freshly isolated microvascular fragments in collagen (MVF), or (3) adipose tissue derived stem cells (ASCs) in collagen. Muscles were harvested 7 and 14 days after surgery. Defects treated with MVFs had a vessel density higher than the other groups at both 7 and 14 days, and those treated with ASCs had a higher vessel density than COL by day 14 (p < 0.05). Perfused vessels were observed in both the ASC and MVF treated defects at day 14, as well as at day 7 in the MVF. This study supports the use of MVFs as a platform to improve tissue perfusion to treat large VML defects. The use of freshly isolated MVFs on the day of surgery supports their clinical use and application.
Revision osteoarticular allograft transplantation in weight-bearing joints. A clinical review (1991)

The early results of revision osteoarticular allografts in weight-bearing joints are reported. Sixteen consecutive patients underwent surgery over a six-year period between 1982 and 1988. At the time of review eight patients (50%) had surviving second allografts with an average follow-up time of 48 months (range 12 to 87). Five patients were graded excellent according to the Mankin scale, one good and two fair. Eight patients (50%) required further surgery, but only two patients came to amputation.
Potentiation of photodynamic therapy-elicited antitumor response by localized treatment with granulocyte-macrophage colony-stimulating factor. (1996)

Murine squamous cell carcinoma (SCCVII) cells were genetically engineered to produce marine granulocyte-macrophage colony-stimulating factor (GM-CSF). GM-CSF immunotherapy, based on the peritumoral injection of lethally irradiated GM-CSF-producing SCCVII cells, was examined as adjuvant to photodynamic therapy (PDT) treatment of this tumor. The GM-CSF immunotherapy administered three times in 48-h intervals, starting 2 days before the light treatment, substantially improved the curative effect of Photofrin-mediated PDT. A comparable effect of GM-CSF immunotherapy was observed in the combination with benzoporphyrin derivative-mediated PDT. The tumor-localized GM-CSF immunotherapy alone had no obvious effect on the growth of parental SCCVII tumors. This treatment did not significantly alter the differential peripheral WBC count and appeared not to affect tumor leukocyte infiltration. However, GM-CSF treatment did increase the cytotoxic activity of tumor-associated macrophages against SCCVII tumor cells. It appears, therefore, that tumor-localized immune stimulation by GM-CSF amplifies a PDT-induced antitumor immune reaction, which has a potentiating effect on tumor control.
Determination of Granulocyte‐Specific Antigens on Neutrophil Fcγ Receptor IIIb by PCR‐Preferential Homoduplex Formation Assay, and Gene Frequencies in the Japanese Population (1999)

Abstract Background and Objectives: Granulocyte‐specific antigens play an important role in provoking immune neutropenia and transfusion reactions. We developed a new DNA‐typing method, PCR‐preferential homoduplex formation assay (PHFA), to determine granulocyte‐specific antigens on the neutrophil Fcγ receptor IIIb (FcγRIIIb, CD 16b), namely, the NA1, NA2, and SH antigens and their gene frequencies in the Japanese population. Materials and Methods: Four hundred unrelated healthy Japanese blood donors were typed using PCR‐PHFA. To confirm the accuracy of the results of FcγRIIIB genotyping using PCR‐PHFA, PCR‐sequence‐specific primer (SSP) typing and PCR‐restriction fragment length polymorphism (RFLP) typing were carried out in another 20 samples for comparison. Results: The results of PCR‐PHFA typing agreed well with other methods. The frequencies of the FcγRIIIB alleles were 62.2, 37.8, 0 and 0% for NA1, NA2, SH, and ‘NA‐null’, respectively. Conclusion: The PCR‐PHFA method can be semi‐automated easily with computer‐based assignment and is suitable for typing both small and large numbers of samples. In the Japanese population, the frequency of NA1 is about double that in Caucasians (32.5%), and the SH allele is rare.
A character elimination algorithm for lossless data compression (2003)

Summary form only given. We present a detailed description of a lossless compression algorithm intended for use on files with non-uniform character distributions. This algorithm takes advantage of the relatively small distances between character occurrences once we remove the less frequent characters. This allows it to create a compressed version of the file that, when decompressed, is an exact copy of the file that was compressed. We begin by performing a Burrows-Wheeler (1994) Transform (BWT) on the file. The algorithm scans this BWT file to create a character frequency model for the compression phase. To deal with the issue of bit encoding, we write every number as a byte or sequence of bytes to the compressed file and run an arithmetic encoder after the file has been compiled.
<title>Membranotropic photobiomodulation on red blood cell deformability</title> (2007)

To assess modulation of laser on erythrocyte permeability and deformability via cell morphology changes, healthy human echinocytes with shrinking size and high plasmic viscosity due to cellular dehydration were treated with 1 mW, 2 mW, 3 mW, and 5 mW laser power exposure respectively. Image analyzing system on single intact erythrocyte was applied for measuring comprehensive cell morphological parameters (surface area, external membrane perimeter, circle index and elongation index) that were determined by the modulation of erythrocyte water permeability and deformability to detect relationship between erythrocyte water permeability alteration and deformability. Our preliminary experiment showed that exposure under light dose of 5 mW for 5 min could induce more active erythrocyte swelling and deformation. water channel aquaporin-1(AQP-1) was inhibited by the incubation of HgCl<sub>2</sub> in the presence and absence of 5 mW laser irradiation. The result suggested that osmotic water permeability is a primary factor in the procedure of erythrocyte deformability. In addition, no modulation of laser(5mW) on erythrocyte deformability had been found when the echinocytes were cultured with GDP-&#946;-S (G protein inhibitor).