gebhart/patrepeval huggingface dataset:
The importance of bone health in end-stage renal disease: out of the frying pan, into the fire? (2004)

In the early stages of renal failure, hyperparathyroidism develops as a compensatory mechanism to control serum levels of calcium, phosphorus and calcitriol. As kidney disease progresses, this ability to maintain mineral homeostasis is lost, leading to the development of renal osteodystrophy (ROD). Over the past decade, the pattern of ROD seen in patients with chronic kidney disease (CKD) has changed. Previously, the majority of patients had mixed uraemic osteodystrophy or aluminium-related osteomalacia. The decreased use of aluminium-based phosphate binders, coupled with improvements in the management of hyperphosphataemia, led to a reduction in the prevalence of these types of ROD. Since the mid-1990s, there has been an increase in the prevalence of adynamic bone disease as a result of increased suppression of parathyroid hormone through the use of calcium-based phosphate binders and calcitriol therapy. Adynamic bone disease is also associated with several clinical factors, such as older age, use of continuous ambulatory peritoneal dialysis and the presence of diabetes mellitus, as well as the use of calcitriol therapy. Studies of calcium metabolism in patients with CKD have shown that adynamic bone disease is a distinct clinical condition that leads to hypercalcaemia via mechanisms different from that seen in high-turnover bone disease. As high calcium x phosphorus product has been associated with soft tissue and vascular calcifications, and increased mortality, optimizing bone health may be an important way of reducing cardiovascular risk in patients with CKD. To do this, novel, effective, non-calcium, non-aluminium phosphate binders will be necessary.
Rb intrinsically promotes erythropoiesis by coupling cell cycle exit with mitochondrial biogenesis (2008)

Regulation of the cell cycle is intimately linked to erythroid differentiation, yet how these processes are coupled is not well understood. To gain insight into this coordinate regulation, we examined the role that the retinoblastoma protein (Rb), a central regulator of the cell cycle, plays in erythropoiesis. We found that Rb serves a cell-intrinsic role and its absence causes ineffective erythropoiesis, with a differentiation block at the transition from early to late erythroblasts. Unexpectedly, in addition to a failure to properly exit the cell cycle, mitochondrial biogenesis fails to be up-regulated concomitantly, contributing to this differentiation block. The link between erythropoiesis and mitochondrial function was validated by inhibition of mitochondrial biogenesis. Erythropoiesis in the absence of Rb resembles the human myelodysplastic syndromes, where defects in cell cycle regulation and mitochondrial function frequently occur. Our work demonstrates how these seemingly disparate pathways play a role in coordinately regulating cellular differentiation.
C-MYC: evidence for multiple regulatory functions. (1990)

The nuclear c-myc proto-oncogene promotes cell proliferation and can inhibit terminal differentiation as well as induce immortalisation in its oncogenic form. There is increasing evidence that c-myc exerts these biological activities by modulating transcription and by directly affecting the initiation of DNA replication. The regulation of these disparate activities may involve the carboxyl end of the c-myc protein, which is essential for transformation and autosuppression of c-myc transcription. Conserved motifs in this region of the c-myc protein may mediate complex formation and sequence-specific nucleic acid binding.
Charged polylactide co-glycolide microparticles as antigen delivery systems (2004)

Polymeric microparticles with encapsulated antigens have become well-established in the last decade as potent antigen delivery systems and adjuvants, with experience being reported from many groups. However, the authors have recently shown that an alternative approach involving charged polylactide co-glycolide (PLG) microparticles with surface adsorbed antigen(s) can also be used to deliver antigen into antigen-presenting cell populations. The authors have described the preparation of cationic and anionic PLG microparticles that have been used to adsorb a variety of agents, to include plasmid DNA, recombinant proteins and adjuvant active oligonucleotides. These novel PLG microparticles were prepared using a w/o/w solvent evaporation process in the presence of the anionic surfactants, such as dioctyl sodium sulfosuccinate, or cationic surfactants, such as hexadecyl trimethyl ammonium bromide. Antigen binding to the charged PLG microparticles was influenced by both electrostatic interaction and other mechanisms, including hydrophobic interactions. Adsorption of antigens to microparticles resulted in the induction of significantly enhanced immune responses in comparison with alternative approaches. The surface adsorbed microparticle formulation offers an alternative way of delivering antigens as a vaccine formulation.
Characterization of the tuberculous granuloma in murine and human lungs: cellular composition and relative tissue oxygen tension (2005)

The granulomatous reaction is the hallmark of the host response to infection with Mycobacterium tuberculosis. Despite its apparent importance to host defence against the tubercle bacillus, the granulomatous response remains to be completely defined. The present study used histological, immunohistochemical and flow-cytometric analyses to characterize pulmonic granulomatous tissues of tuberculous mice and humans. The kinetics of recruitment of neutrophils, macrophages, dendritic cells, and T and B lymphocytes into the lungs of mice infected aerogenically with the virulent Erdman strain of M. tuberculosis was evaluated in detail in both the acute and persistent phase of infection. A hypoxia-sensing compound based on the 2-nitroimidazole structure (EF5), together with immunohistochemical studies targeting endothelial cells were used to examine the relative oxygen tension in tuberculous granulomatous tissues in mice. The results have provided evidence that: (i) the granulomatous tissues are a highly organized structure whose formation is regulated by orderly recruitment of specific immune cells exhibiting distinct spatial relationship with one another; (ii) the granulomatous reaction, at least in the mouse, may represent an exaggerated response to the tubercle bacillus that can play a role in the development of immunopathology; (iii) B lymphoid aggregates are a prominent feature in both murine and human granulomatous tissues, although the immune cells that are most prominently associated with these clusters vary among the two species; (iv) murine tuberculous granulomatous tissues are relatively aerobic, suggesting that mouse models of persistent tuberculosis may not be suitable for the study of any hypoxic response of M. tuberculosis.
Expression Profile of Human Fc Receptors in Mucosal Tissue: Implications for Antibody-Dependent Cellular Effector Functions Targeting HIV-1 Transmission (2016)

The majority of new Human Immunodeficiency Virus (HIV)-1 infections are acquired via sexual transmission at mucosal surfaces. Partial efficacy (31.2%) of the Thai RV144 HIV-1 vaccine trial has been correlated with Antibody-dependent Cellular Cytotoxicity (ADCC) mediated by non-neutralizing antibodies targeting the V1V2 region of the HIV-1 envelope. This has led to speculation that ADCC and other antibody-dependent cellular effector functions might provide an important defense against mucosal acquisition of HIV-1 infection. However, the ability of antibody-dependent cellular effector mechanisms to impact on early mucosal transmission events will depend on a variety of parameters including effector cell type, frequency, the class of Fc-Receptor (FcR) expressed, the number of FcR per cell and the glycoslyation pattern of the induced antibodies. In this study, we characterize and compare the frequency and phenotype of IgG (CD16 [FcγRIII], CD32 [FcγRII] and CD64 [FcγRI]) and IgA (CD89 [FcαR]) receptor expression on effector cells within male and female genital mucosal tissue, colorectal tissue and red blood cell-lysed whole blood. The frequency of FcR expression on CD14+ monocytic cells, myeloid dendritic cells and natural killer cells were similar across the three mucosal tissue compartments, but significantly lower when compared to the FcR expression profile of effector cells isolated from whole blood, with many cells negative for all FcRs. Of the three tissues tested, penile tissue had the highest percentage of FcR positive effector cells. Immunofluorescent staining was used to determine the location of CD14+, CD11c+ and CD56+ cells within the three mucosal tissues. We show that the majority of effector cells across the different mucosal locations reside within the subepithelial lamina propria. The potential implication of the observed FcR expression patterns on the effectiveness of FcR-dependent cellular effector functions to impact on the initial events in mucosal transmission and dissemination warrants further mechanistic studies.
Single-layer HDR video coding with SDR backward compatibility (2016)

The migration from High Definition (HD) TV to Ultra High Definition (UHD) is already underway. In addition to an increase of picture spatial resolution, UHD will bring more color and higher contrast by introducing Wide Color Gamut (WCG) and High Dynamic Range (HDR) video. As both Standard Dynamic Range (SDR) and HDR devices will coexist in the ecosystem, the transition from Standard Dynamic Range (SDR) to HDR will require distribution solutions supporting some level of backward compatibility. This paper presents a new HDR content distribution scheme, named SL-HDR1, using a single layer codec design and providing SDR compatibility. The solution is based on a pre-encoding HDR-to-SDR conversion, generating a backward compatible SDR video, with side dynamic metadata. The resulting SDR video is then compressed, distributed and decoded using standard-compliant decoders (e.g. HEVC Main 10 compliant). The decoded SDR video can be directly rendered on SDR displays without adaptation. Dynamic metadata of limited size are generated by the pre-processing and used to reconstruct the HDR signal from the decoded SDR video, using a post-processing that is the functional inverse of the pre-processing. Both HDR quality and artistic intent are preserved. Pre- and post-processing are applied independently per picture, do not involve any inter-pixel dependency, and are codec agnostic. Compression performance, and SDR quality are shown to be solidly improved compared to the non-backward and backward-compatible approaches, respectively using the Perceptual Quantization (PQ) and Hybrid Log Gamma (HLG) Opto-Electronic Transfer Functions (OETF).
A stereo matching algorithm with an adaptive window: theory and experiment (1994)

A central problem in stereo matching by computing correlation or sum of squared differences (SSD) lies in selecting an appropriate window size. The window size must be large enough to include enough intensity variation for reliable matching, but small enough to avoid the effects of projective distortion. If the window is too small and does not cover enough intensity variation, it gives a poor disparity estimate, because the signal (intensity variation) to noise ratio is low. If, on the other hand, the window is too large and covers a region in which the depth of scene points (i.e., disparity) varies, then the position of maximum correlation or minimum SSD may not represent correct matching due to different projective distortions in the left and right images. For this reason, a window size must be selected adaptively depending on local variations of intensity and disparity. The authors present a method to select an appropriate window by evaluating the local variation of the intensity and the disparity. The authors employ a statistical model of the disparity distribution within the window. This modeling enables the authors to assess how disparity variation, as well as intensity variation, within a window affects the uncertainty of disparity estimate at the center point of the window. As a result, the authors devise a method which searches for a window that produces the estimate of disparity with the least uncertainty for each pixel of an image: the method controls not only the size but also the shape (rectangle) of the window. The authors have embedded this adaptive-window method in an iterative stereo matching algorithm: starting with an initial estimate of the disparity map, the algorithm iteratively updates the disparity estimate for each point by choosing the size and shape of a window till it converges. The stereo matching algorithm has been tested on both synthetic and real images, and the quality of the disparity maps obtained demonstrates the effectiveness of the adaptive window method.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Phase III study of gemcitabine [G] plus cetuximab [C] versus gemcitabine in patients [pts] with locally advanced or metastatic pancreatic adenocarcinoma [PC]: SWOG S0205 study (2007)

LBA4509 Background: Epidermal growth factor receptor [EGFR] pathway is a rational target for therapeutic intervention. This study tested the efficacy of an anti-EGFR monoclonal antibody and gemcitabine [G] combination in the Phase III setting in patients with advanced PC. Methods: Eligibility included locally advanced unresectable or metastatic PC; adequacy of organ function; performance status (PS) 0- 2; no prior EGFR therapy; no prior systemic chemotherapy except for adjuvant chemotherapy; and submission of tumor for EGFR immunostaining. The primary endpoint was overall survival. Secondary endpoints included objective response, time to progression, pain control, and quality of life. Assuming 6 months median survival, the study was designed to detect a median improvement to 8 months (1.33 hazard ratio) with 90% power, based on a one-sided 0.0125 test, and 704 eligible patients. Primary analyses used a Cox regression model, stratified for factors used in the randomization. Patients were stratified by PS, stageand prior pancreatectomy, and randomized to either G alone or G plus C. G was given at a dose of 1,000 mg/m 2 /wk for seven weeks out of 8, then 3 weeks on and one week off. C was given as a loading dose of 400 mg/m 2 on week 1 and then 250 mg/m 2 weekly. Results: 766 pts (735 eligible) with a median age of 64 (30–91) were enrolled by SWOG and CTSU between January 2004 and April 2006. Of those, 51% were males, 21.5% had locally advanced disease, and 13% had PS of 2. The study closed with full accrual. The median survival was 6 months in the G arm and 6.5 months in the G plus C arm for an overall HR of 1.09 (95% CI 0.93–1.27, p= 0.14) . The corresponding PFS was 3 months and 3.5 months, for G and G+C arms, respectively (HR =1.13, 95%CI .97–1.3, p=.058). The confirmed response probabilities were 7 % in each arm, and inclusion of unconfirmed responses yielded 14% in the G arm and 12% in the G + C arm.702 pts were evaluable for toxicity. 90 pts experienced at least one grade 4 toxicity; 14% on the G plus C, 11% on G alone. Conclusions: This study failed to demonstrate a clinically significant advantage of the addition of cetuximab to gemcitabine for overall survival, PFS and response in advanced PC. No significant financial relationships to disclose.
A computerized tomography-computer graphics approach to stereotaxic localization (1979)

This paper describes the use of three-dimensional computer graphics to display structures visible in computerized tomography (CT) scans and to accurately determine optimum stereotaxic probe placement relative to those structures. A prototype Lucite stereotaxic frame designed for use in CT body scanners was fitted with a phantom consisting of small Lucite spheres representing intracranial tumors with diameters of 6 to 19 mm. A series of CT scans was obtained of the frame and phantom together. Edge outlines of the spheres were extracted from each scan in the series. A three-dimensional visual representation of the spheres was obtained by displaying their outlines from all CT scans. A superimposed visual simulation of the stereotaxic frame was adjusted interactively using several analog dials in order to simulate trajectory choice and probe depth before actual surgery. The frame settings and probe depth calculated by the graphical computer were then applied to the actual prototype frame in order to assess the accuracy of this combined CT-computer graphics approach to stereotaxic localization. The results of 22 such experiments and the implications for future clinical use of this new and precise localization technique are discussed.
Differential expression of the capsaicin receptor TRPV1 and related novel receptors TRPV3, TRPV4 and TRPM8 in normal human tissues and changes in traumatic and diabetic neuropathy (2007)

The accumulation of TRPV1 and TRPV3 in peripheral nerves after injury, in spared axons, matches our previously reported changes in avulsed DRG. Reduction of TRPV1 levels in nerve fibres in diabetic neuropathy skin may result from the known decrease of nerve growth factor (NGF) levels. The role of TRPs in keratinocytes is unknown, but a relationship to changes in NGF levels, which is produced by keratinocytes, deserves investigation. TRPV1 represents a more selective therapeutic target than other TRPs for pain and hypersensitivity, particularly in post-traumatic neuropathy.
Development of a Theoretical Model for Chromatographic-Based Competitive Binding Immunoassays with Simultaneous Injection of Sample and Label (1999)

This study examined the theory and behavior of an HPLC-based chromatographic competitive binding immunoassay with the simultaneous injection of sample and a labeled analyte analogue. Equations based on nonlinear chromatographic theory were derived to describe the calibration curve for this assay in a system with adsorption-limited kinetics and homogeneous binding sites. These equations related the assay response (B/Bo) to the column's binding capacity, the moles of injected analyte or labeled analogue, and the flow rate/adsorption kinetics of the system. There was good agreement between the predicted theoretical response and experimental data obtained for the binding of human serum albumin (HSA) to an immobilized anti-HSA antibody column. This theory was also successful in describing the changes that occurred in the calibration curve when the flow rate or amount of labeled analogue applied to the column was varied. A comparison was made between the results of this study and previous theoretical work that examined the behavior of a related, sequential injection competitive binding method. On the basis of the results reported in this work, several general guidelines were developed for the design and optimization of simultaneous injection methods for use in such areas as clinical testing, pharmaceutical analysis, and environmental monitoring.
PCR primer design (2007)

PCR primer design. Contents Part I. Basic Principles and software for PCR primer design Chapter 1. Physical Principles and Visual-OMP Software for Optimal PCR Design Chapter 2. Oligo 7 Primer Analysis Software Chapter 3. Selection for 3' end triplets for polymerase chain reaction primers Chapter 4. The reference point method in primer design Chapter 5. PCR primer design using statistical modeling Chapter 6. Developing a Statistical Model for Primer Design Part II. Genome scale PCR primer design Chapter 7. GST-PRIME: An Algorithm for Genome-Wide Primer Design Chapter 8. Genome-Scale Probe and Primer Design with PRIMEGENS Repeat masking for PCR primer design Chapter 9. SNPbox: web-based high-throughput primer design with an eye for repetitive sequences. Chapter 10. Fast masking of repeated primer binding sites in eukaryotic genomes Multiplex PCR primer design Chapter 11. Degenerate Primer Design: Theoretical Analysis and the HYDEN program Chapter 12. An Iterative Method for Selecting Degenerate Multiplex PCR Primers Chapter 13. Primer-design for multiplexed genotyping Chapter 14. MultiPLX: automatic grouping and evaluation of PCR primers Chapter 15. MultiPrimer: A system for Microarray PCR Primer Design Allele-specific PCR Chapter 16. Modified oligonucleotides as tools for allele-specific amplification Chapter 17. AlleleID: A Pathogen Detection and Identification System Long PCR primer design Chapter 18. GenoFrag, a software package for the design of primers dedicated to whole genome scanning by LR-PCR. DNA methylation mapping Chapter 19. Designing PCR primer for DNA methylation mapping Chapter 20. BiSearch: ePCR tool for native or bisulfite treated genomic template. Chapter 21. Graphical design of primers with PerlPrimer
Mid-infrared intersublevel absorption of vertically electronically coupled InAs quantum dots (2005)

We have studied mid-infrared intersublevel absorption of samples containing two layers of vertically self-aligned, self-assembled InAs quantum dots separated by a thin GaAs barrier. Samples with coupled quantum dots exhibiting different average size between the two layers are investigated. The electronically coupled quantum dot absorption is compared with the absorption of a reference sample containing uncoupled quantum dots. Electronically coupled quantum dots present a spectrally narrow absorption line (∼20meV full width at half maximum) mainly polarized along the growth axis in the range 110–150meV. This absorption is attributed to the bound-to-bound transition between bonding (symmetric-like) and antibonding (antisymmetric-like) s state combinations of the double quantum dot structure. This assignment is supported by the electronic structure of the coupled quantum dots as calculated by the three-dimensional resolution of the Schrödinger equation written in the 8-band k.p envelope function formalism.
The taser intrusion recovery system (2005)

Recovery from intrusions is typically a very time-consuming operation in current systems. At a time when the cost of human resources dominates the cost of computing resources, we argue that next generation systems should be built with automated intrusion recovery as a primary goal. In this paper, we describe the design of Taser, a system that helps in selectively recovering legitimate file-system data after an attack or local damage occurs. Taser reverts tainted, i.e. attack-dependent, file-system operations but preserves legitimate operations. This process is difficult for two reasons. First, the set of tainted operations is not known precisely. Second, the recovery process can cause conflicts when legitimate operations depend on tainted operations. Taser provides several analysis policies that aid in determining the set of tainted operations. To handle conflicts, Taser uses automated resolution policies that isolate the tainted operations. Our evaluation shows that Taser is effective in recovering from a wide range of intrusions as well as damage caused by system management errors.