gebhart/patrepeval huggingface dataset:
Less is more: strategies to remove marker genes from transgenic plants (2013)

Selectable marker genes (SMGs) and selection agents are useful tools in the production of transgenic plants by selecting transformed cells from a matrix consisting of mostly untransformed cells. Most SMGs express protein products that confer antibiotic- or herbicide resistance traits, and typically reside in the end product of genetically-modified (GM) plants. The presence of these genes in GM plants, and subsequently in food, feed and the environment, are of concern and subject to special government regulation in many countries. The presence of SMGs in GM plants might also, in some cases, result in a metabolic burden for the host plants. Their use also prevents the re-use of the same SMG when a second transformation scheme is needed to be performed on the transgenic host. In recent years, several strategies have been developed to remove SMGs from GM products while retaining the transgenes of interest. This review describes the existing strategies for SMG removal, including the implementation of site specific recombination systems, TALENs and ZFNs. This review discusses the advantages and disadvantages of existing SMG-removal strategies and explores possible future research directions for SMG removal including emerging technologies for increased precision for genome modification.
Erythrocytes in sickle cell anemia are heterogeneous in their rheological and hemodynamic characteristics. (1983)

To understand the contribution to the pathophysiology of sickle cell anemia of the different erythrocyte density types present in the blood of these patients, we have studied the viscosimetric and hemodynamic characteristics of four major classes of hemoglobin SS erythrocytes. We have isolated reticulocytes, discocytes, dense discocytes, and irreversibly sickled cells (fractions I-IV) on Percoll-Renografin density gradients. Bulk viscosity was studied in a coneplate viscosimeter and the hemodynamic studies were performed on the isolated, artificially perfused mesoappendix vasculature of the rat (Baez preparation). Bulk viscosity measurements at shear rates of 230 S-1 demonstrate that when the cells are oxygenated, fraction I (reticulocyte rich) has a higher viscosity than expected from its low intracellular hemoglobin concentration. The rest of the fractions exhibit moderate increases in bulk viscosity pari-passu with the corresponding increases in density (mean corpuscular hemoglobin concentration). When deoxygenated, all cell fractions nearly doubled their bulk viscosity and the deoxy-oxy differences remained constant. The Baez preparation renders a different picture: oxygenated fractions behave as predicted by the viscosimetric data, but, when deoxygenated, cell fractions exhibit dramatically increased peripheral resistance and the deoxy-oxy difference are directly proportional to cell density, thus, the largest increases were observed for fractions III and IV. The differences between the rheological and the hemodynamic measurements are most probably due to the different sensitivity of the two methods to the extent of intracellular polymerization. These results also demonstrate that the hitherto unrecognized fraction III cells (very dense discocytes that change shape very little on deoxygenation) are as detrimental to the microcirculation as the irreversibly sickled cell-rich fraction IV. They may, however, induce obstruction by a different mechanism. As the extent to which these fractions are populated by erythrocytes varies considerably from patient to patient, the distribution function of cell densities in each sickle cell anemia patient might have consequences for the type of pathophysiological events occurring in their microcirculation.
Response of LNCaP spheroids after treatment with an alpha-particle emitter (213Bi)-labeled anti-prostate-specific membrane antigen antibody (J591). (2001)

A theoretical drawback to alpha-particle therapy with 213Bi is the short range of the particle track coupled with the short half-life of the radionuclide, thereby potentially limiting effective cytotoxicity to rapidly accessible, disseminated individual tumor cells (e.g., as in leukemia). In this work, a prostate carcinoma spheroid model was used to evaluate the feasibility of targeting micrometastatic clusters of tumor cells using 213Bi-labeled anti-prostate-specific membrane antigen (PSMA) antibody, J591. In prostate cancer, vascular dissemination of tumor cells or tumor cell clusters to the marrow constitutes an important step in the progression of this disease to widespread skeletal involvement, an incurable state. Such prevascularized clusters are ideal targets for radiolabeled antibodies because the barriers to antibody penetration that are associated with the capillary basal lamina have not yet formed. Beta- and gamma-emitting radionuclides such as 131I, which are widely used in radioimmunotherapy, are not expected to be effective when targeting single cells or small cell clusters. This is because the range of the emissions is one to two orders of magnitude greater than the target size, and the energy deposited per traversal is insufficient to produce any significant radiobiological effect. Spheroids of the prostate cancer cell line, LNCaP-LN3, were used as a model of prevascularized micrometastases; their response to an anti-PSMA antibody, J591, radiolabeled with the alpha-particle emitter 213Bi (T(1/2), 45.6 min.) has been measured. The time course of spheroid volume reductions was found to be sensitive to the initial spheroid volume. J591 labeled with 0.9 MBq/ml 213Bi resulted in a 3-log reduction in spheroid volume on day 33, relative to control, for spheroids with an initial diameter of 130 microm; 1.8 MBq/ml were required to achieve a similar response for spheroids with an initial diameter of 180 microm. Equivalent spheroid responses were observed after 12 Gy of acute external beam photon irradiation. Monte Carlo-based microdosimetric analyses of the 213Bi decay distribution in individual spheroids of 130-microm diameter yielded an average alpha-particle dose of 3.7 Gy to the spheroids, resulting in a relative biological effectiveness factor of 3.2 over photon irradiation. The activity concentrations used in the experiments were clinically relevant, and this work supports the possibility of using 213Bi-labeled antibodies not only for disseminated single tumor cells, as found in patients with leukemia, but also for micrometastatic tumor deposits up to 180 microm in diameter (1200 cells).
Gas imaging by infrared gas-correlation spectrometry (1996)

We describe a new method for visualization of gas flows based on infrared absorption and gas-correlation techniques. This result is a gray-scale or false color-coded image showing the distribution of a specific gas in the area studied. A sequence of images showing the workplace test setup with a turbulent flowing gas is presented.
T Regulatory Cells 1 Inhibit a Th2-Specific Response In Vivo (2000)

We recently described a new population of CD4(+) regulatory T cells (Tr1) that inhibits proliferative responses of bystander T cells and prevents colitis induction in vivo through the secretion of IL-10. IL-10, which had been primarily described as a Th2-specific cytokine inhibiting Th1 responses, has displayed in several models a more general immune suppression on both types of effector T cell responses. Using an immediate hypersensitivity model in which BALB/c mice immunized with OVA (alum) normally generate Th2-dominated responses, we examined the ability of OVA-specific Tr1 T cell clones to inhibit OVA-specific cytokines and Ab responses. In contrast to Th2 or Th1 T cell clones, transfer of Tr1 T cell clones coincident with OVA immunization inhibited Ag-specific serum IgE responses, whereas IgG1 and IgG2a synthesis were not affected. This specific inhibition was mediated in part through IL-10 secretion as anti-IL-10 receptor Abs treatment reverted the inhibitory effect of Tr1 T cell clones. Although specifically targeted to IgE responses, Tr1 clones' inhibitory effects were more profound as they affected Ag-specific Th2 cell priming both in term of proliferative responses and cytokine secretion. These results suggest that regulatory T cells may play a fundamental role in maintaining the balance of the immune system to prevent allergic disorders.
Pure Carbon Nanoscale Devices: Nanotube Heterojunctions (1996)

Introduction of pentagon-heptagon pair defects into the hexagonal network of a single carbon nanotube can change the helicity of the tube and alter its electronic structure. Using a tight-binding method to calculate the electronic structure of such systems we show that they behave as nanoscale metal/semiconductor or semiconductor/semiconductor junctions. These junctions could be the building blocks of nanoscale electronic devices made entirely of carbon.
Ferroelectric microdomain reversal on Y-cut LiNbO 3 surfaces (1991)

A periodic, electric field induced reversal of ferroelectric microdomains on (+Y)- and (—Y)- LiNbO3 surfaces was achieved for the first time at temperatures (&lt; 400 °C) well below the Curie point. Contrary to the recently developed domain inversion processes on Z-cut substrates, no modification of the material (e.g. by a Ti-doping) nor an electron bombardment was necessary. The pyroelectric effect was used to generate an electrical field between photolithographically structured, periodic Al-electrodes on the surface of the crystal concentrating the electric field in the small volume of the microdomains to be inverted. As (+Y)- and (—Y)-LiNbO3 faces have strongly different etching rates in HF/HNO3, a successful domain reversal could be identified by selective etching. Microdomains of different dimensions (of typical 6x 15xO.25tm3), number of periodicities (100 and 1500) and periodicities (3Opm, 6.5,um and 7.6im) have been fabricated not only in undoped LiNbO3 surface layers, but also in Ti:LiNbO3 optical strip waveguides. The chosen periodicities will allow quasi-phase matched optical second harmonic generation.
InGaAs/InP double heterostructures on InP/Si templates fabricated by wafer bonding and hydrogen-induced exfoliation (2003)

Hydrogen-induced exfoliation combined with wafer bonding has been used to transfer ∼600-nm-thick films of (100) InP to Si substrates. Cross-section transmission electron microscopy (TEM) shows a transferred crystalline InP layer with no observable defects in the region near the bonded interface and an intimately bonded interface. InP and Si are covalently bonded as inferred by the fact that InP/Si pairs survived both TEM preparation and thermal cycles up to 620 °C necessary for metalorganic chemical vapor deposition growth. The InP transferred layers were used as epitaxial templates for the growth of InP/In0.53Ga0.47As/InP double heterostructures. Photoluminescence measurements of the In0.53Ga0.47As layer show that it is optically active and under tensile strain, due to differences in the thermal expansion between InP and Si. These are promising results in terms of a future integration of Si electronics with optical devices based on InP-lattice-matched materials.
REVERSIBLE PHOTODIMERIZATION OF WATER-SOLUBLE ANTHRACENES INCLUDED IN γ-CYCLODEXTRIN (1984)

Abstract Anthracene-1- or 2-sulfonic and 2-carboxylic acids were found to form one host-two guest inclusion complexes with γ-cyclodextrin in aqueous solutions. The complex formation greatly enhanced the photodimerization of these anthracenes.
A 45.6μ 2 13.4μw 7.1v/v resolution sub-threshold based digital process-sensing circuit in 45nm CMOS (2011)

Process optimization and yield enhancement techniques rely on physical sensors to provide them with feedback to perform accurate process-characterization across the die. The increased susceptibility of circuit performance characteristics to parameter variations in deep sub-micron technologies motivates the need for low-overhead (area/power) and high-sensitivity process monitoring circuits which can be used by compensation schemes to tune the process and meet frequency targets or power-budgets. To this end, we have proposed and implemented in 45nm CMOS-SOI, a novel, digital, on-chip process sensing circuit with a high sensitivity of 7.1V per volt variation in NMOS Vth, low power dissipation of 13.4¼W and a compact layout occupying 45.6¼2. The design is robust towards temperature variations and supply induced noise incurring an accuracy loss of 5mV (worst-case) and 4mV (1-A) respectively of the NMOS threshold-voltage.
Assessment of Cardiac Dysfunction in a Randomized Trial Comparing Doxorubicin and Cyclophosphamide Followed by Paclitaxel, With or Without Trastuzumab As Adjuvant Therapy in Node-Positive, Human Epidermal Growth Factor Receptor 2–Overexpressing Breast Cancer: NSABP B-31 (2005)

Administering trastuzumab with paclitaxel after AC increases incidence of CHF and lesser CD. Potential cardiotoxicity should be carefully considered when discussing benefits and risks of this therapy.
Surface‐Plasmon‐Fluorescence Spectroscopy for DNA Hybridization Reactions (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Pericapillary hemorrhage as criterion of severe human digestive graft-versus-host disease (2004)

In an experimental model we demonstrated that endothelial cells of all organs are targets of the alloimmune reaction. Here, in 68 digestive biopsies, we found endothelial lesions by immunohistochemistry and ultrastructure in patients with severe acute graft-versus-host disease (GVHD). In contrast, no such endothelial cell alterations were found either in patients without GVHD or in nongrafted controls. In the biopsies with severe GVHD lesions, ultrastructure showed rupture of the capillary basal membrane and extravased red blood cells. These pericapillary hemorrhages were highly correlated with GVHD severity. In a separate cohort of 39 patients who underwent an allogeneic transplantation after a nonmyeloablative conditioning, 8 patients had intestinal biopsies. Three of these latter patients had both severe pathologic lesions of GVHD and similar endothelial lesions, thus, strengthening the concept that endothelial lesions are linked to GVHD severity and not to the intensity of the conditioning regimen. (Blood. 2004;103:4681-4684)
Lysyl oxidase: A lung adenocarcinoma biomarker of invasion and survival (2010)

Higher expression of LOX is associated with invasion and is an independent predictor of poor prognosis in patients with early stage lung adenocarcinoma.
Whither design space? (2006)

Design space exploration is a long-standing focus in computational design research. Its three main threads are accounts of designer action, development of strategies for amplification of designer action in exploration, and discovery of computational structures to support exploration. Chief among such structures is the design space, which is the network structure of related designs that are visited in an exploration process. There is relatively little research on design spaces to date. This paper sketches a partial account of the structure of both design spaces and research to develop them. It focuses largely on the implications of designers acting as explorers.
Particle filter-based heading estimation using magnetic compasses for mobile robot navigation (2006)

Heading information is critical for the control and/or navigation of mobile devices and robots. To get accurate heading information robustly, we propose a method which combines particle filtering with magnetic compasses. Although magnetic compasses can provide absolute heading angle, they have not been used for indoor applications since serious magnetic interferences are commonly founded in home/office environments. We overcome this difficulty by 1) suggesting statistical calibration of a magnetic compass, 2) deriving necessary conditions of the Earth's magnetic field area, and 3) designing an event-based particle filter based on likelihood calculated from conditional probability. Particle filter is an emerging key technology which can be applied to nonlinear/non-Gaussian model, beyond the limitations of Kalman filter. We take advantage of particle filter to optimally fuse the information from both magnetic compasses and odometry data. Experimental results on mobile robot navigation in indoor environments show reliability and robustness of the proposed method
PLC based ignition system (2003)

A PLC based ignition system which controls the ignition of oil and gas fired appliances and provides levels of safety, reliability and stability, is developed. The brain of the system is a programmable logic controller (PLC). The control module provides multilevel component fault detection and tolerance in critical areas such as in flame sensing and valve control circuits. The control module is designed for reliable operation far beyond normal appliances life. The program minimizes shutdowns by providing recycling under certain conditions to establish normal operation before checking out. A timer provides precise timing for ignition and flame failure. An online timer and remote flame sensor are the main advantages of the system. The facility of input/output force on, force off, monitoring the inputs and outputs are also advantages. The facilities of input/output are also provided. Finally this system is factory programmable to provide different warm up times for ignitor systems.
Nanocapsules for Drug Delivery: An Updated Review of the Last Decade (2019)

The present study discusses and summarizes patents related to preparation methods of and recent studies from the last 10 years on nanocapsules as drug delivery systems.
Gaussian KD-trees for fast high-dimensional filtering (2009)

We propose a method for accelerating a broad class of non-linear filters that includes the bilateral, non-local means, and other related filters. These filters can all be expressed in a similar way: First, assign each value to be filtered a position in some vector space. Then, replace every value with a weighted linear combination of all values, with weights determined by a Gaussian function of distance between the positions. If the values are pixel colors and the positions are ( x, y ) coordinates, this describes a Gaussian blur. If the positions are instead ( x, y, r, g, b ) coordinates in a five-dimensional space-color volume, this describes a bilateral filter. If we instead set the positions to local patches of color around the associated pixel, this describes non-local means. We describe a Monte-Carlo kd-tree sampling algorithm that efficiently computes any filter that can be expressed in this way, along with a GPU implementation of this technique. We use this algorithm to implement an accelerated bilateral filter that respects full 3D color distance; accelerated non-local means on single images, volumes, and unaligned bursts of images for denoising; and a fast adaptation of non-local means to geometry. If we have n values to filter, and each is assigned a position in a d -dimensional space, then our space complexity is O(dn ) and our time complexity is O(dn log n ), whereas existing methods are typically either exponential in d or quadratic in n .
What Causes Cost Overrun in Transport Infrastructure Projects? (2004)

Results from the first statistically significant study of the causes of cost escalation in transport infrastructure projects are presented. The study is based on a sample of 258 rail, bridge, tunnel and road projects worth US$90 billion. The focus is on the dependence of cost escalation on: (1) the length of the project‐implementation phase, (2) the size of the project and (3) the type of project ownership. First, it was found, with very high statistical significance, that cost escalation was strongly dependent on the length of the implementation phase. The policy implications are clear: decision‐makers and planners should be highly concerned about delays and long implementation phases because they translate into risks of substantial cost escalations. Second, projects have grown larger over time, and for bridges and tunnels larger projects have larger percentage cost escalations. Finally, by comparing the cost escalation for three types of project ownership—private, state‐owned enterprise and other public ownership—it was shown that the oft‐seen claim that public ownership is problematic and private ownership effective in curbing cost escalation is an oversimplification. The type of accountability appears to matter more to cost escalation than type of ownership.
The history and future of T-cell depletion as graft-versus-host disease prophylaxis for allogeneic hematopoietic stem cell transplantation (2001)

Despite significant progress in the past 20 years, graft-versus-host disease (GVHD) remains a significant cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation (HSCT). T-cell depletion (TCD) of the donor graft offers the potential for prevention of GVHD without
Management of Retinal Vein Occlusion – Consensus Document (2011)

Retinal vein occlusion (RVO) can have severe consequences for the people affected by the disease, including visual loss with costly social repercussions. Currently, there is no European consensus with regard to the management of RVO. Following a careful review of the medical literature as well as the data from several clinical trials, a collaborative group of retina specialists put forth practical recommendations based on the best available scientific evidence for the clinical approach to RVO. Taking into consideration the recent advances in diagnostic tools and management options, the present document aims to provide the European ophthalmologists with guidelines for clinical practice to the benefit of their patients.
Predictive Value of Tumor Ki-67 Expression in Two Randomized Trials of Adjuvant Chemoendocrine Therapy for Node-Negative Breast Cancer (2008)

Several small studies have reported that having a high percentage of breast tumor cells that express the proliferation antigen Ki-67 (ie, a high Ki-67 labeling index) predicts better response to neoadjuvant chemotherapy. However, the predictive value of a high Ki-67 labeling index for response to adjuvant chemotherapy is unclear. To investigate whether Ki-67 labeling index predicts response to adjuvant chemoendocrine therapy, we assessed Ki-67 expression in tumor tissue from 1924 (70%) of 2732 patients who were enrolled in two randomized International Breast Cancer Study Group trials of adjuvant chemoendocrine therapy vs endocrine therapy alone for node-negative breast cancer. A high Ki-67 labeling index was associated with other factors that predict poor prognosis. Among the 1521 patients with endocrine-responsive tumors, a high Ki-67 labeling index was associated with worse disease-free survival but the Ki-67 labeling index did not predict the relative efficacy of chemoendocrine therapy compared with endocrine therapy alone. Thus, Ki-67 labeling index was an independent prognostic factor but was not predictive of better response to adjuvant chemotherapy in these studies.