gebhart/patrepeval huggingface dataset:
The Brain as a Target for Inflammatory Processes and Neuroprotective Strategies (2007)

The importance of glial cell-propagated inflammation (i.e., neuroinflammation) disorders such as Alzheimer's disease (AD) was viewed previously as a bystander effect, or epiphenomenon, with inflammation occurring when damaged neurons elicit an activation response by glia. However, an accumulating body of evidence has challenged this earlier perspective and indicates a more active role of neuroinflammation in the pathophysiology of progressive neurodegenerative disorders such as AD, Parkinson's disease, amyotrophic lateral sclerosis, and multiple sclerosis. This insight into pathophysiology evolved in concert with the appreciation that the brain is not as immunologically privileged as once thought. The central nervous system (CNS) has its own resident immune system, in which glial cells (microglia, astrocytes, and oligodendrocytes) not only serve supportive and nutritive roles for neurons but also engage from time to time in several "inflammatory" processes that defend the CNS from pathogens and help it to recover from stress and injury. These otherwise "normal" glial functions can sometimes result in a more severe and chronic neuroinflammatory cycle that actually promotes or propagates neurodegenerative disease. Excessive glial cell activation may thus constitute a viable target for the discovery of and development of neurodegenerative disease therapeutics. Suggestive clinical evidence in support of neuroinflammation as a drug discovery target for chronic neurodegenerative diseases, such as AD, comes from epidemiological and genetic linkage data. For example, long-term use of nonsteroidal anti-inflammatory drugs is correlated with a protective effect against AD, and certain polymorphisms in the genes for interleukin 1 and other proinflammatory mediator genes are associated with increased risk. In AD and Parkinson's disease, activated microglia and complement proteins have been identified in the brain regions most affected in these disorders. This report will briefly review selected clinical and preclinical data that reflect the prevailing approaches targeting neuroinflammation as a pathophysiological process contributing to the onset or progression of neurodegenerative diseases, as well as their neuroprotective potential.
Modular Analysis of Peripheral Blood Gene Expression in Rheumatoid Arthritis Captures Reproducible Gene Expression Changes in Tumor Necrosis Factor Responders (2014)

These data provide evidence that using gene expression modules related to inflammatory disease may provide a valuable method for objective monitoring of the response of RA patients who are treated with TNF inhibitors.
Human cytomegalovirus-specific T-cell receptor engineered for high affinity and soluble expression using mammalian cell display (2019)

T-cell receptors (TCR) have considerable potential as therapeutics and antibody-like reagents to monitor disease progression and vaccine efficacy. Whereas antibodies recognize only secreted and surface-bound proteins, TCRs recognize otherwise inaccessible disease-associated intracellular proteins when they are presented as processed peptides bound to major histocompatibility complexes (pMHC). TCRs have been primarily explored for cancer therapy applications but could also target infectious diseases such as cytomegalovirus (CMV). However, TCRs are more difficult to express and engineer than antibodies, and advanced methods are needed to enable their widespread use. Here, we engineered the human CMV-specific TCR RA14 for high-affinity and robust soluble expression. To achieve this, we adapted our previously reported mammalian display system to present TCR extracellular domains and used this to screen CDR3 libraries for clones with increased pMHC affinity. After three rounds of selection, characterized clones retained peptide specificity and activation when expressed on the surface of human Jurkat T cells. We obtained high yields of soluble, monomeric protein by fusing the TCR extracellular domains to antibody hinge and Fc constant regions, adding a stabilizing disulfide bond between the constant domains and disrupting predicted glycosylation sites. One variant exhibited 50 nm affinity for its cognate pMHC, as measured by surface plasmon resonance, and specifically stained cells presenting this pMHC. Our work has identified a human TCR with high affinity for the immunodominant CMV peptide and offers a new strategy to rapidly engineer soluble TCRs for biomedical applications.
Hierarchical reconstruction using geometry and sinogram restoration (1993)

The authors describe and demonstrate a hierarchical reconstruction algorithm for use in noisy and limited-angle or sparse-angle tomography. The algorithm estimates an object's mass, center of mass, and convex hull from the available projections, and uses this information, along with fundamental mathematical constraints, to estimate a full set of smoothed projections. The mass and center of mass estimates are made using a least squares estimator derived from the principles of consistency of the Radon transform. The convex hull estimate is produced by first estimating the positions of support lines of the object from each available projection and then estimating the overall convex hull using prior shape information. Estimating the position of two support lines from a single projection is accomplished using a generalized likelihood ratio technique for estimating jumps in linear systems. Results for simulated objects in a variety of measurement situations are shown, and several possible extensions to this work are discussed.
Expression of p53 in normal and gamma-irradiated rat testis suggests a role for p53 in meiotic recombination and repair. (1996)

In testis, the expression of tumor suppressor protein p53 is stronger than in other tissues suggesting a role for it in spermatogenesis. We have studied the expression of p53 in both unirradiated and gamma-irradiated rat testis using the stage-specific model of rat seminiferous epithelium. Our results show that p53 is expressed during meiosis in normal rat spermatogenesis and its expression is localized to the preleptotene-early pachytene spermatocytes. The most prominent expression is in zygotene - early pachytene spermatocytes (stages XIII-I of seminiferous epithelium). After irradiation p53 levels increased in a time and a dose-dependent manner being highest with the doses of 6.0 and 12.0 Gy and 4 h after irradiation. This increase occurs in the same cells that normally express elevated levels of p53. These results support the view that p53 is involved in meiosis of the male rat and we suggest that p53 has a role in recombinational processes and/or formation of the synaptonemal complex. We also demonstrate that p53 takes part in the response of primary spermatocytes to irradiation gamma-induced DNA damage.
On the Effects of Small Errors in the Angles of Corner-Cube Reflectors (1960)

When a ray is reflected successively on three mirrors that are approximately mutually perpendicular, the ray is returned nearly parallel to the original direction. If the original and final directions are denoted by unit vectors q and −t, and if a, b, c are the normals to the three mirrors taken in order in a right-handed sense, then it is shown theoretically that t=q+2q×(+αa-βb+γc),to the first order in α, β, γ, where these are the small angles by which the angles between the three mirrors exceed right angles. A geometrical construction to realize this formula is described.If the three reflecting faces are parts of the surface of a symmetrical solid tetrahedron, refraction at the fourth surface increases the angular deviation of the final ray from the incident ray by a factor of μ cosr/cosi for the component of the deviation in the plane defined by the incident ray and the normal, and by a factor of μ for the perpendicular component. (i is the angle of incidence, and μ sinr=sini.)Finally, it is shown theoretically that this type of reflecting unit (with a curved refracting surface), when used at the rear of road vehicles, could have greater efficiency if one of the angles between the reflecting surfaces were 90.14 deg instead of 90 deg.
Model-Driven Development of GPU Applications (2016)

Programming GPUs with low-level libraries like CUDA and OpenCL is a tedious and error-prone task. Fortunately, algorithmic skeletons can shield developers from the complexity of parallel programming by encapsulating common parallel computing patterns. However, this simplification typically constrains programmers to write their applications using the GPU library employed by the skeleton implementation. In this work, we combine skeletal programming with model-driven software development (MDSD) to increase the freedom of choice regarding the employed GPU library instead of leaving all technical decisions to the skeleton implementation. We present a code-generator that transforms models comprising skeletons, their input data and input functions to parallel C++ code while taking care of data-offset calculations. The generator has been tested using different GPU and multi-GPU communication libraries such as Thrust and CUDA-MPI. We demonstrate our novel approach to GPU programming with two example applications: affinity propagation and n-body simulation.
A fully automatic digital camera image refocusing algorithm (2011)

One of the greatest dissatisfiers of consumer digital cameras is autofocus failure. One possible solution currently being investigated by many digital camera manufacturers involves capturing a sequence of through-focus images and postprocessing to produce a desired focused image. Most approaches require significant manual input to define a region of interest (ROI) to be optimized for focus. A new through-focus algorithm is proposed that automatically partitions scene content into regions based on range and then automatically determines the ROI for a given range. When this ROI is combined with standard image fusion operations, this algorithm generates an image with an aesthetically pleasing narrow depth-of-field effect, all with little or no user input, and all within the limited compute environment of a digital camera.
Problems with the post-traumatic stress disorder diagnosis and its future in DSM-V (2008)

Significant issues challenge the diagnosis of post-traumatic stress disorder (PTSD). Yet, applications of the PTSD 'model' have been extended to an increasing array of events and human reactions across diverse cultures. These issues have implications for clinical practice and for those who revise criteria in the DSM-V.
Analysis of p53 mutations in a large series of lymphoid hematologic malignancies of childhood (1993)

p53 mutations are found in a wide variety of cancers, including hematologic malignancies. These alterations apparently contribute to development of the malignant phenotype. We analyzed a large series of lymphoid (330 cases) and a smaller series of myeloid (29 cases) malignancies of childhood for p53 mutations by single-strand conformational polymorphism (SSCP) following polymerase chain reaction. Samples with abnormal SSCP were reamplified and analyzed by direct sequencing method. p53 mutations were detected within the known mutational hotspots (exons 5 to 8) in 8 of 330 lymphoid malignancies, and in none of 29 myeloid malignancies, showing that the frequency of p53 mutations in childhood lymphoid malignancies was very low (8 of 330 cases [2%]). Four of these patients had very aggressive, fatal acute lymphocytic leukemia (ALL). None of 13 infants and none of 48 patients with T-lineage leukemia had detectable p53 mutations in their ALL cells. Exceptionally, p53 mutations were comparatively frequent in a small sample of B-cell non-Hodgkin's lymphomas (2 of 8 cases). Mutations were detected in samples from two patients with ALL at relapse; these were not detected in samples at initial diagnosis from the same patients, suggesting that p53 mutations may be associated with progression to a more malignant phenotype. Seven of eight alterations of p53 were missense mutations, and seven of eight samples may be heterozygous for the mutant p53, indicating that p53 protein may act in a dominant negative fashion.
Respiration tracking in radiosurgery (2004)

Respiratory motion is difficult to compensate for with conventional radiotherapy systems. An accurate tracking method for following the motion of the tumor is of considerable clinical relevance. We investigate methods to compensate for respiratory motion using robotic radiosurgery. In this system the therapeutic beam is moved by a robotic arm, and follows the moving target through a combination of infrared tracking and synchronized x-ray imaging. Infrared emitters are used to record the motion of the patient's skin surface. The position of internal gold fiducials is computed repeatedly during treatment, via x-ray image processing. We correlate the motion between external and internal markers. From this correlation model we infer the placement of the internal target during time intervals where no x-ray images are taken. Fifteen patients with lung tumors have recently been treated with a fully integrated system implementing this new method. The clinical trials confirm our hypothesis that internal motion and external motion are indeed correlated. In a preliminar study we have extended our work to tracking without implanted fiducials, based on algorithms for computing deformation motions and digitally reconstructed radiographs.
Treatment of denervation/disuse osteoporosis in the rat with a capacitively coupled electrical signal: Effects on bone formation and bone resorption (1988)

Utilizing a sciatic neurectomy model of disuse osteoporosis, the effects on rates of bone formation and bone resorption were examined when a capacitively coupled electrical signal was applied to the denervated tibia in the rat. It was found that a low-voltage, symmetrical sine wave, 60-kHz, capacitively coupled signal had no significant effect on the amount of bone resorption occurring in denervated right tibiae in rats previously labeled with [3H]tetracycline. This was true whether the signal was applied while osteoporosis was developing (prevention of osteoporosis) or after it had been established (treatment of osteoporosis). If a similar capacitively coupled signal was applied to rats in which osteoporosis was well established, and the rats were labeled with [3H]tetracycline daily during a 12-day treatment period, it was found that there was statistically significant enhancement of the amount of new bone formation (increased [3H]tetracycline incorporation) in the tibiae that received the signal as compared with that of the controls. These results indicate that prevention or amelioration of disuse osteoporosis that occurs with a capacitively coupled electrical signal is due not to a change in the rate of bone resorption, but to an increase in the rate of bone formation.
Resolution of a Spectrum of Nucleoprotein Species in Sonicated Chromatin (1972)

Sonicated rabbit-liver chromatin is fractionated by ion-exchange chromatography on ECTHAM-cellulose, a weakly cationic adsorbent. The chromatographic procedure provides a series of fractions having a spectrum of thermal denaturation profiles. The earliest-eluting fractions melt cooperatively at a significantly higher temperature than bulk chromatin, and totally lack any of the components of chromatin that melt at low temperatures. In contrast, the latest-eluting fractions are significantly enriched in their content of DNA sequences that melt at low temperatures. Although the protein to DNA mass ratio of all fractions is equal to that of unfractionated chromatin, polyacrylamide gel electrophoresis demonstrates that the relative amounts of individual proteins vary across the chromatographic peak. The most pronounced changes observed are the enrichment of a particular high molecular weight nonhistone protein in the later fractions, and a significant diminution of lysine-rich histone in the last fractions. The results, in conjunction with the demonstration by McConaughy, B. L. & McCarthy, B. J. (Biochemistry 11, 998-1003, 1972) that RNA transcribed in vivo in immature chick erythrocytes hybridizes to the DNA of only the portions of chromatin from these cells that melt at low temperatures, suggest that this fractionation may separate transcribable DNA sequences in chromatin from the repressed segments of a eukaryotic genome.
Effects of electromagnetic radiation exposure on learning and memory function of rat pups (2008)

Objective To determine whether exposure to electromagnetic radiation results in behavioral effects of rat pups.Methods Wistar rats,either male or female,were divided randomly into four groups respectively:control(CTR),100 seconds(S1),1000 seconds(S10)and 3000 seconds(S30),then each of them were exposed to electromagnetic radiation of 100 kV/m field amplitude of corresponding time.For the day of exposure till 2 months later.they were mated with the rats in the same group and their offspring were divided into four groups(F-GTB,F-S1,F-S10,F-S30)correspondingly.Behavioral changes occur in 2-month old and 6-month old rat pups were found between radiation groups and control,and in Y-maze test,beth male and female pups in F-S10 significantly learned fewer times than their control(total study times:male 14.6±3.9 vs 21.1±7.8,female13.4±3.0 vs 25.8±8.8;false times:male 3.5±2.4 vs 7.8±5.4,female 3.4±2.6 vs 11.0±7.2).In open field test,both maze,male pups in F-S1 and F-S30 learned more times than control in total study time(24.2±8.9 vs 14.1±5.2.30.7±12.4 vs 14.1±5.2).In step throush test and open field test,no significant differences were found between radiation groups and control.Conclusion There was significant genetic effect exposed to electromagnetic radiation of 100 kV/m,mainly manifested in rat pups in growth period but without long-term effect.

Key words: 
Electromagnetic radiation; Rat pups; Learning memory; Behavior
Manipulating Acoustic Wavefront by Inhomogeneous Impedance and Steerable Extraordinary Reflection (2013)

We unveil the connection between the acoustic impedance along a flat surface and the reflected acoustic wavefront, in order to empower a wide wariety of novel applications in acoustic community. Our designed flat surface can generate double reflections: the ordinary reflection and the extraordinary one whose wavefront is manipulated by the proposed impedance-governed generalized Snell's law of reflection (IGSL). IGSL is based on Green's function and integral equation, instead of Fermat's principle for optical wavefront manipulation. Remarkably, via the adjustment of the designed specific acoustic impedance, extraordinary reflection can be steered for unprecedented acoustic wavefront while that ordinary reflection can be surprisingly switched on or off. The realization of the complex discontinuity of the impedance surface has been proposed using Helmholtz resonators.
Biocompatibility of echinoderm skeleton with mammalian cells <i>in vitro</i>: Preliminary evidence (1981)

The physical and chemical properties of echinoderm skeleton are reviewed. A method is described for preparing cell-free, sterile echinoderm skeletal plates (ossicles) which were used as porous substrates for cell cultures. Ossicles of the starfish Pisaster ochraceus were evaluated as substrates for the culture of three mammalian cell lines. Each line grew vigorously on ossicles, and fibroblasts quickly infiltrated their porous microstructure. Echinoderm skeletal plates provide a simple, convenient alternative to coverslips and porous membranes for SEM or correlated SEM/TEM studies of cell behavior. More importantly, the preliminary evidence for biocompatibility presented suggests that native echinoderm skeleton has potential use as a biomaterial and, because of its microstructure and relative solubility; deserves evaluation as a kind of biodegradable ceramic.
Identifying the recognition unit for G protein methylation (1991)

Signal transducing G proteins, such as transducin, are prenylated and methylated at carboxyl-terminal cysteine residues. The methylation of transducin occurs by means of a membrane bound S-adenosyl methionine-dependent methyltransferase. This methyltransferase accepts the simple modified amino acid N-acetyl-S-farnesyl-L-cysteine (AFC) as a substrate. This means that the enzyme does not require peptide sequences of transducin in a putative substrate. Moreover, small structural changes in the AFC structural unit all lead to molecules incapable of being substrates. For example, neither N-acetyl-S-farnesylhomocysteine (AFHC) nor the saturated form of AFC are substrates. Interestingly, substitution of the N-acetyl moiety of AFC with a hydrogen atom leads to S-farnesylthiopropionic acid (FTP), which is an excellent substrate for the methyltransferase. The methyltransferase shows great specificity for the the FTP pharmacophore. So far, alterations in this structure have not led to active substrates. For example, removal of a methylene group of FTP, producing S-farnesylthioacetic acid (FTA), abolished substrate activity. FTA is a potent competitive inhibitor of the enzyme. FTP is thus the ultimately simplified substrate for the methyltransferase and does not contain any remnants of the peptide structure of transducin.
Use of Copper Intrauterine Devices and the Risk of Tubal Infertility among Nulligravid Women (2001)

The previous use of a copper IUD is not associated with an increased risk of tubal occlusion among nulligravid women whereas infection with C. trachomatis is.
<title>New approach for old movie restoration</title> (2001)

The role in which old movies play to the society is a priceless part of culture and history. These movies, due mainly to the storage conditions, may present a type of local defect with two characteristics: it does not affect the whole frame; and it is thin along the time axis. In this work, we attack the local defect detection problem and defects in consecutive images with any intersection using an opening by temporal surface, followed by a spatial geodesic reconstruction by dilation using structuring element B<SUB>s</SUB>. The opening by surface, for binary images, extracts the connect components which area is greater than a specific threshold, and for gray level images, it evaluates each connected component produced by successive thresholds of the images, through binary operations. The restoration process using opening by surface can be subdivided in two steps: 1) opening by temporal surface applied to the image sequences that extracts connected components or domes with area greater than or equal to a specific threshold S; 2) spatial reconstruction by geodesic dilation using structuring element applied to a single image. This technique is being applied to a move collection (1920 decade) of the Brazilian ex-president Arthur Bernardes provided by the Arquivo Publico Mineiro in Belo Horizonte, MG, Brazil.