gebhart/patrepeval huggingface dataset:
Antigens from <i>trichinella spiralis</i> that induce a protective response in the mouse. (1984)

A series of monoclonal antibodies was generated for the purpose of studying antigens of the infective L1 larva of Trichinella spiralis. Primary immunization of donor BALB/c mice was by oral infection with L1 larvae. Secondary immunization and screening procedures for hybridoma clones employed a pool of affinity-purified antigens recognized by pooled serum from infected rabbits. Three monoclonal antibodies, chosen for their high reactivity in screening assays and their unique specificities, were raised in quantity, purified, and attached to Sepharose 4B for affinity chromatography. The antigens selected by each affinity column were of different m.w. (37K, 48K, and 50/55K) and possessed different abilities to induce protection. The 48K antigen induced a high level of protection at biologically relevant doses (1.0 and 0.1 micrograms protein/mouse). The 50/55K antigen induced a lower level of protection than the 48K antigen, but was still effective at similar doses. The 37K antigen elicited protection only at a dose of 50 micrograms protein/mouse, and was not as effective as the unpurified antigen at any dose. Earlier studies indicated that many antigens involved in the immune response are secreted. Therefore, worm secretions and two subcellular fractions of homogenized worms (S2 = cytosol, S3 = soluble portion of the large particle fraction) were analyzed for content of the three purified antigens by a double antibody sandwich enzyme-linked assay. The 48K and 50/55K antigens represent significant components of the secretions (12% and 5%, respectively) but relatively minor components of the S2 and S3 fractions. The 37K antigen represents a major component of the S2 fraction, but is essentially absent from S3 and secretions. Immunocytolocalization studies employing immunoperoxidase methods on infected muscle tissue show that the 48K antigen is located in the beta-stichocytes, the lining of the gut, and the surface of the cuticle. The 50/55K antigen was detected in the alpha-stichocytes and was occasionally observed in the gut or on the cuticle. The 37K antigen was detected only in the pseudocoelom. The results from the quantitative ELISA and immunocytolocalization show that the two antigens that induce a protective response are secreted proteins. These data constitute the first account of antigens purified from a nematode that induce a strong protective response. One of these (48K) confers a level of protection comparable to that elicited by exposure of an entire infection.
Dynamic mechanical properties of curaua composites (2012)

Abstract In this study, we aimed to evaluate the characteristics of curaua composites using dynamic mechanical analysis. Curaua composites with distinct fiber volume fractions (11–38%) were studied, and their storage and loss moduli were found to increase with reinforcement content. On the other hand, the activation energy of the relaxation process in the glass‐transition region decreased with the curaua content; this conclusion was corroborated by the elastic chain concentration results. The Cole–Cole plots became flattened as the curaua content increased; this was indicative of a more homogeneous system, and the tan δ peak height and peak width at half‐height decreased. © 2012 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
Polycystic Kidneys Associated with Marfan Syndrome in An Adult (1994)

A 41-year-old man with Marfan syndrome was found to have polycystic renal disease and underwent emergency surgery for dissecting aneurysm of the ascending aorta. To our knowledge only two cases of this rare combination of hereditary disorders have been described in the literature.
188Re(V)-DMSA revisited (1998)

Methods of preparation and biodistribution in mice of tin-free 99Tcm(V)-DMSA and 188Re(V)-DMSA, a potential matching pair of radiopharmaceuticals for diagnosis and therapy of certain cancers, are described. Preparation of tin-free 188Re(V)-DMSA (I) is based on reduction with either SO2-releasing compounds like Na2S2O4 (30 mg Na2S2O4, 10 mg DMSA, 1 mg L-ascorbic acid, 37°C, 60 min incubation), Na2S2O5 (as before, 70°C, 15 min incubation), or HBr (0.2 ml 48% HBr, 0.2 ml 7 M HCl, 10 mg DMSA, 1 mg L-ascorbic acid, 70°C, 60 min incubation). I exhibits significantly lower kidney uptake than tin-containing 188Re(V)-DMSA (II) (2–3% and 49% injected dose per gram organ, 1 h post-injection, respectively). HPLC profiles of I and II are similar. DMSA excess in tin-free 188Re(V)-DMSA is not responsible for the low kidney uptake of I. High kidney uptake of II is explained by formation of a mixed 188Re(V)-Sn-DMSA complex in vivo. Age-linked bone uptake in mice dependent on the maturation of the bone is demonstrated for both I and II.
A controlled multicenter clinical study of citalopram and placebo in elderly depressed patients with and without concomitant dementia (1992)

A total of 149 patients in 7 centers in Denmark, Norway and Sweden entered a 6-week double-blind trial intended to assess the antidepressant effect and safety of citalopram vs placebo in depressed elderly patients (65 years of age or older) who might also suffer from somatic disorders and/or senile dementia. Results of ratings on the Hamilton Rating Scale for Depression, the Montgomery-Asberg Depression Rating Scale and the Clinical Global Impression Scale provided consistent evidence that the citalopram-treated patients improved more than the placebo-treated patients. Results of ratings on the Gottfries-Bråne-Steen dementia rating scale indicated that both cognitive and emotional functioning improved significantly more in the citalopram-treated subgroup of patients with dementia than in the placebo-treated subgroup.
Detection and segmentation of the Left Ventricle in Cardiac MRI using Deep Learning (2018)

Manual segmentation of the Left Ventricle (LV) is a tedious and meticulous task that can vary depending on the patient, the Magnetic Resonance Images (MRI) cuts and the experts. Still today, we consider manual delineation done by experts as being the ground truth for cardiac diagnosticians. Thus, we are reviewing the paper - written by Avendi and al. - who presents a combined approach with Convolutional Neural Networks, Stacked Auto-Encoders and Deformable Models, to try and automate the segmentation while performing more accurately. Furthermore, we have implemented parts of the paper (around three quarts) and experimented both the original method and slightly modified versions when changing the architecture and the parameters.
The fine structure of the surface epithelium of the human ovary (1971)

ABSTRACT The surface epithelium has been studied on human adult ovarian biopsies, one foetal ovary and an ovarian biopsy from a woman 12 weeks pregnant. In the adult, the surface of the ovary is covered by a single, patchy layer of epithelium which varies from squamous, through cuboidal to columnar in shape. Cytoplasmic projections extend into the peritoneal cavity from the free surface of the cells and their lateral borders are connected by desmosomes. The nucleus is irregular and the dense cytoplasm contains many polysomes, free ribosomes and tono-filaments. Intracellular vacuoles and extracellular channels contain materials of low to moderate density. Lipid droplets and compound aggregates are present and both coated and smooth vesicles occur in the peripheral cytoplasm. Focal degenerative changes may be seen which range from loss of density in the basal cytoplasm to complete desquamation. In pregnancy the basal surface of the epithelium is deeply infolded with an increase in cytoplasmic lipid. In the foetal ovary the entire surface is covered with an epithelium. From these studies and the work of others, it seems clear that, although the prime function of the ovarian surface epithelium is its contribution of pregranulosa cells during foetal development, many features remain which suggest that it has an important role in transport. It may also influence follicular development in the foetus and appears to have some potential for steroid metabolism. The patchiness and degenerative changes found in the adult human ovary may be related to fluctuations in hormonal balance.
Comparison of resampling schemes for particle filtering (2005)

This contribution is devoted to the comparison of various resampling approaches that have been proposed in the literature on particle filtering. It is first shown using simple arguments that the so-called residual and stratified methods do yield an improvement over the basic multinomial resampling approach. A simple counter-example showing that this property does not hold true for systematic resampling is given. Finally, some results on the large-sample behavior of the simple bootstrap filter algorithm are given. In particular, a central limit theorem is established for the case where resampling is performed using the residual approach.
Simulation of compressible cake filtration (1994)

The equations derived from modern filtration theory for compressible cake filtration at apparently constant pressure have been programmed into a conventional computer spreadsheet package. Simulations were then performed, including investigations of the effect of increasing the slurry concentration before filtering, and the distribution of pressure between the filter medium and the cake with increasing filtration time. When the medium resistance is finite the pressure drop across the cake is not constant and, consequently, the cake concentration and specific resistance are functions of time, and must be iteratively deduced. The cell formulas for the computer spreadsheet are provided, together with example outputs from demonstration simulations.
Progress in characterizing and imaging prostate tissues for guiding biopsies and planning and targeting treatment of prostate cancer (2004)

Our objective is to develop imaging methods that can distinguish viable cancerous tissue from other prostate tissues in order to improve biopsy guidance and treatment targeting. To do this, we acquired ultrasonic RF echo-signal data and clinical variables, e.g., PSA, for over 3,000 biopsies, and computed spectral-parameter values for each biopsied region. Using a neural network trained with these data, we generated a lookup table that translated parameter values at each pixel location into a local score for cancer likelihood. Images displaying the map of local scores are called tissue-type images (TTIs). ROC-curve areas were greater for neural-network classification than for classification using conventional B-mode-based methods, and predicted a sensitivity improvement of more than 20% over conventional, ultrasound-guided biopsies. We are initiating studies of prostate tissue characterization using magnetic resonance spectroscopy (MRS), and are investigating the feasibility of combining information from ultrasound and MRS for improved imaging of prostate cancer. TTIs applied in real time may markedly improve cancer-detection by directing biopsies to cancerous regions. TTI data combined with MRS parameters potentially can provide a powerful new hybrid 3-D imaging method for detecting, evaluating, and treating prostate cancer.
The cartilaginous fracture callus in rats (1987)

The right tibia was broken manually in 56 rats weighing 100 g; the fracture was stabilized with an intramedullary steel wire. Groups of rats were killed after 3-30 days. The fracture with its surrounding musculature was dissected out and immediately frozen to -70 degrees C. Cryostat sections of the fracture region were stained with hematoxylin/eosin, toluidine blue, and immunoenzymatically with collagen II antibodies. Another series of 30 fractured rats were killed after 1-15 days, and the fractures were examined histologically after decalcification with EDTA. Two types of callus were observed. The periosteal-endosteal callus started as proliferation of pre-osteoblasts without inflammatory cells on Day 1 and developed bone trabeculae from Day 3 until Days 8-10, but not thereafter. The cartilaginous callus was formed by condensation of fibroblast-like mesenchymal cells mixed with inflammatory cells outside the periosteal callus and started on Day 5 at the fracture fragments denuded of periosteum. The cells differentiating to cartilage seemed to migrate from the surrounding musculature and its newly formed vessels. The enchondral bone formation started close to the periosteal callus from which vessels were piercing into the then hypertrophic and mineralized chondrocytes on Day 11. We conclude that the bridging callus is formed by fundamentals of periosteal callus derived from predetermined cells and the bridge of enchondrally formed bone trabeculae by cells migrating from outside.
Optimal access point placement in simultaneous broadcast system using OFDM for indoor wireless LAN (2002)

This paper investigates the optimal access point placement in a simultaneous broadcast system using orthogonal frequency division multiplexing (OFDM) for high data rate indoor wireless LAN. We aim to determine the best combination of multiple AP placements that minimizes the average bit error rate (BER) of terminals when input information including an indoor configuration, a number of APs, and total transmission power is given a priori. Since this AP placement problem is categorized as a hard combinatorial problem with many variables and constraints, we applied a nonlinear optimization scheme called very fast simulated annealing to search for an approximate optimal solution. The simulation results demonstrate that the algorithm has been successfully applied to the AP placement problem and its effectiveness was also confirmed in comparison with a local search algorithm.
Real-Time Simulation in Grid Environments: Communicating Data from Sensors to Scientific Simulations (2007)

Abstract Across many fields of science and engineering computers now play a significant role in scientific discovery through both large scale simulation and real time data acquisition. As these scientific simulations increasingly require new levels of complexity and fidelity, and leveraging increasing computational capabilities, scientists are migrating their applications back and forth from workstations to supercomputers, high performance clusters, and new distributed grids of computers. For applications which depend on live real world data, the migration to varied and distributed resources provides additional challenges. This migration involves reassigning and testing individual sensor communications and data path integrity for the application before the application is ready for a real time operating environment. This paper presents one general approach for communicating live real world data to simulations deployed on high-end computational resources. The architecture and design are presented for generic applications, before focusing on a particular scenario for drilling dynamics optimizations. In this scenario, simulations of drilling behavior depend on real time data from on-site (remote) sensors. Sensor data is streamed through to a simulation framework. The framework (available on a desktop computer or a supercomputer) displays relevant information, starts simulations with real time inputs then presents results and recommendations. For our application, we will use the Cactus Code (www.cactuscode.org) open-source high performance scientific computing framework as the simulation framework, and LabVIEW (www.ni.com/LabVIEW) as the data acquisition software. The advances in architecture portability allowed by the framework are summarized, and experiences of system uses are presented. Discussion will include opportunities found and learnings from using this platform in various environments highlighting drilling optimization.
A "serum-free" medium for the production of erythropoietic bursts by murine bone marrow cells. (1984)

We describe a culture medium that does not require the addition of serum, in which erythropoietic bursts are produced from murine bone marrow cells with efficiencies at least as great as those of serum-containing media. Four ingredients were shown to be essential: bovine serum albumin (BSA), transferrin, cholesterol, and erythropoietin. The system supported burst formation without the addition of conditioned medium as source of burst-promoting factor(s). To include cholesterol in the medium we found that there was no necessity for sonication, nor for subsequent evaporation of the ethanol in which the cholesterol was dissolved. Filtration of cholesterol and delipidation of BSA both impaired the ability of the medium to support burst production. The "serum-free" medium described here, even though not truly defined, is useful for erythropoietic culture: it is reliable, highly efficient in supporting burst formation, and simple and economical to prepare from ingredients readily available from commercial sources without the need for special testing.
Cold induction of <i>EARLI1</i>, a putative Arabidopsis lipid transfer protein, is light and calcium dependent (2004)

ABSTRACT As sessile organisms, plants must adapt to their environment. One approach toward understanding this adaptation is to investigate environmental regulation of gene expression. Our focus is on the environmental regulation of EARLI1 , which is activated by cold and long‐day photoperiods. Cold activation of EARLI1 in short‐day photoperiods is slow, requiring several hours at 4 °C to detect an increase in mRNA abundance. EARLI1 is not efficiently cold‐activated in etiolated seedlings, suggesting that photomorphogenesis is necessary for its cold activation. Cold activation of EARLI1 is inhibited in the presence of the calcium channel blocker lanthanum chloride or the calcium chelator EGTA. Addition of the calcium ionophore Bay K8644 results in cold‐independent activation of EARLI1 . These data suggest that EARLI1 is not an immediate target of the cold response, and that calcium flux affects its expression. EARLI1 is a putative secreted protein and has motifs found in lipid transfer proteins. Over‐expression of EARLI1 in transgenic plants results in reduced electrolyte leakage during freezing damage, suggesting that EARLI1 may affect membrane or cell wall stability in response to low temperature stress.
14-3-3β Binds to and Negatively Regulates the Tuberous Sclerosis Complex 2 (TSC2) Tumor Suppressor Gene Product, Tuberin (2003)

TSC2, or tuberin, is the product of the tuberous sclerosis tumor suppressor gene TSC2 and acts downstream of the phosphatidylinositol 3-kinase-Akt signaling pathway to negatively regulate cellular growth. One mechanism underlying its function is to assemble into a heterodimer with the TSC1 gene product TSC1, or hamartin, resulting in a reduction in phosphorylation, and hence activation, of the ribosomal subunit S6 kinase (S6K). We identified a novel interaction between TSC2 and 14-3-3beta. We found that 14-3-3beta does not interfere with TSC1-TSC2 binding and can form a ternary complex with these two proteins. Association between 14-3-3beta and TSC2 requires phosphorylation of TSC2 at a unique residue that is not a known Akt phosphorylation site. The overexpression of 14-3-3beta compromises the ability of the TSC1-TSC2 complex to reduce S6K phosphorylation. The antagonistic activity of 14-3-3beta toward TSC is dependent on the 14-3-3beta-TSC2 interaction, since a mutant of TSC2 that is not recognized by 14-3-3beta is refractory to 14-3-3beta. We suggest that 14-3-3 proteins interact with the TSC1-TSC2 complex and negatively regulate the function of the TSC proteins.
Peripheral Biomarkers of Alzheimer's Disease (2015)

Currently available diagnostic tests have moved the field closer to early diagnosis of Alzheimer's disease (AD); however, a definitive diagnosis is made only with the development of clinical dementia and the presence of amyloid plaques and neurofibrillary tangles at autopsy. An ideal antemortem AD biomarker should satisfy the following criteria: the ability to diagnose AD with high sensitivity and specificity as confirmed by the gold standard of autopsy validation; the ability to detect early-stage disease and track the progression of AD; and monitor therapeutic efficacy. AD biomarker technologies currently under development include in vivo brain imaging with PET and MRI (i.e., imaging of amyloid plaques, biochemical assays in cerebrospinal fluid (CSF) and peripheral tissues. CSF biomarkers have received increased attention in the past decade. However, it is unclear whether these biomarkers are capable of early diagnosis of AD, prior to Aβ accumulation, or whether they can differentiate between AD and non-AD dementias. In addition, CSF biomarkers may not lend themselves to diagnostic screening of elderly patients, given the invasiveness of lumbar puncture, inter-laboratory variability in techniques and sample handling, and the circadian fluctuation of CSF components. Although commonly viewed as an abnormality of the brain, AD is a systemic disease with associated dysfunction in metabolic, oxidative, inflammatory, and biochemical pathways in peripheral tissues, such as the skin and blood cells. This has led researchers to investigate and develop assays of peripheral AD biomarkers (a few with high sensitivity and specificity) that require minimally invasive skin or blood samples.
Dead or alive: gene expression profiles of advanced atherosclerotic plaques from autopsy and surgery (2007)

Since inclusion of atherosclerotic tissues from different sources is often indispensable to study the full atherogenic spectrum, we investigated to what extent the expression profiles of advanced, stable atherosclerotic lesions obtained during autopsy and surgery are comparable. The gene expression profiles of human carotids with advanced atherosclerosis obtained at autopsy and at vascular surgery were studied by microarray analysis. Expression analysis was performed both at the single gene (Rosetta, Gene Ontology) and at the pathway level using Ingenuity and Gene Set Enrichment Analysis. In addition, mRNA and protein expression levels were validated using quantitative (q) RT-PCR and immunohistochemistry on unrelated advanced carotid lesions from autopsy and surgery. Microarray analysis indicated that the 97.2% of genes showed similar expression levels in advanced atherosclerotic lesions from autopsy and surgery. While the expression data revealed no differences in common atherosclerotic related pathways such as lipid metabolism and inflammation, the differentially expressed genes were mainly involved in basal cell metabolism and hypoxia driven pathways. qRT-PCR confirmed the differential expression of hypoxia-driven genes VEGF-A (2.3-fold upward arrow), glucose transporter (GLUT)-1 (2.5-fold upward arrow), GLUT3 (8.3-fold upward arrow), and hexokinase 1 (2.4-fold upward arrow) in autopsy vs. surgical specimens. Immunohistochemistry revealed that the transcriptional differences in these hypoxia-related genes were not reflected at the protein level. The gene expression profiles of advanced atherosclerotic lesions from autopsy and surgery are largely similar. However, >500 genes, mostly involved in basal cell metabolism and hypoxia were differentially expressed at mRNA, but not at the protein level.