gebhart/patrepeval huggingface dataset:
3D comparison of low, intermediate, and advanced hippocampal atrophy in MCI (2010)

We applied the hippocampal radial atrophy mapping technique to the baseline and follow-up magnetic resonance image data of 169 amnestic mild cognitive impairment (MCI) participants in the imaging arm of the Alzheimer's Disease Cooperative Study MCI Donepezil/Vitamin E trial. Sixty percent of the subjects with none to mild hippocampal atrophy rated with the visual medial temporal atrophy rating scale (MTA score < 2) and 33.8% of the subjects with moderate to severe (MTA > or = 2) hippocampal atrophy converted to Alzheimer's disease (AD) during 3-year follow-up. MTA > or = 2 showed a trend for greater left sided hippocampal atrophy versus MTA < 2 groups at baseline (P(corrected) = 0.08). Higher MTA scores were associated with progressive atrophy of the subiculum and the CA1-3 subregions. The MTA < 2 group demonstrated significant bilateral atrophy progression at follow-up (left P(corrected) = 0.008; right P(corrected) = 0.05). Relative to MTA < 2 nonconverters, MTA < 2 converters showed further involvement of the subiculum and CA1 and additional involvement of CA2-3 at follow-up. Right CA1 atrophy was significantly associated with conversion to dementia (for 1 mm greater right CA1 radial distance subjects had 50% reduced hazard for conversion). Greater CA1 and subicular atrophy can be demonstrated early and is predictive of future conversion to AD, whereas CA2-3 involvement becomes more evident as the disease progresses.
Heat and moisture exchangers as a treatment option in the post-operative rehabilitation of laryngectomized patients (1995)

A multi-institutional, prospective clinical study was undertaken to investigate whether the use of a heat and moisture exchanger (HME) in the period following total laryngectomy could prevent the development or reduce the severity of respiratory symptoms. Fifty-nine patients from three hospitals were provided with HMEs, either immediately post-surgery or, in the case of post-surgical radiotherapy, upon completion of the radiotherapy. For the total sample (n= 59) statistically significant improvements over time (between 3 and 6 months) could be found in forced expectoration (P < 0.05), in the perceived voice quality (P < 0.001), social anxiety (P < 0.001), social interactions (P < 0.001) and in feelings of anxiety and depression (P < 0.05). Repeated measures analysis of variance indicated statistically significant group differences over time in forced expectoration and stoma cleaning (P < 0.05). No statistically significant differences over time were noted between the regular and non(regular) HME user groups in voice quality or in various aspects of daily living.
Infection efficiency of type 5 adenoviral vectors in synovial tissue can be enhanced with a type 16 fiber (2001)

Synoviocytes hardly express CAR, which hampers Ad5-mediated gene transfer. Ad5.fib16 is superior to Ad5 vectors for transducing synoviocytes, without compromising the specificity of infection. Our data suggest that Ad5.fib16-mediated gene transfer to synovial tissue improves the therapeutic window.
Kinetics of internalization and recycling of transferrin and the transferrin receptor in a human hepatoma cell line. Effect of lysosomotropic agents. (1983)

Growing HepG2 cells contain 50,000 functional surface transferrin-binding sites (Ciechanover, A., Schwartz, A.L., and Lodish, H.F. (1983) Cell 32,267-275) and 100,000 intracellular sites. At saturating concentrations of [59Fe]transferrin, and under conditions in which protein synthesis is blocked, iron uptake is linear for several hours at a rate of 9,500 transferrin molecules/cell/min. Thus, each receptor must recycle a ligand, on the average, each 15.8 min. Surface-bound transferrin is rapidly endocytosed (t1/2 = 3.5 min). All of the iron remains within the cell, while the apotransferrin is rapidly (t1/2 = 5.0 min) secreted into the medium. Previously, we showed (Dautry-Varsat, A., Ciechanover, A., and Lodish, H.F. (1983) Proc. Natl. Acad. Sci. U.S.A. 80, 2258-2262) that exposure of a ferrotransferrin-receptor complex to medium of pH less than 5.0 results in dissociation of iron, but that apotransferrin remains bound to its receptor. If the pH is raised to 7.0, such as would occur when an acidic intracellular vesicle fuses with the plasma membrane, apotransferrin is very rapidly dissociated (t1/2 = 17 s at 37 degrees C) from its receptor. Taken together, these results indicate that transferrin remains bound to its receptor throughout the endocytic cycle. In the present study, we have directly measured all the kinetic parameters involved in the transferrin receptor cycle. They are similar to those of the asialoglycoprotein receptor in the same cell line, and can be described by a simple kinetic model. In the presence of lysosomotropic agents, ferrotransferrin binds to its surface receptor and is internalized normally. However, iron is not dissociated from transferrin, and ferrotransferrin recycles back to the cell surface and is secreted into the medium. We conclude that the low pH in endocytic vesicles is essential for the dissociation of iron from transferrin and its delivery to the cell, but is not required for recycling of transferrin, and presumably of its receptor.
Promoter trapping reveals significant differences in integration site selection between MLV and HIV vectors in primary hematopoietic cells (2004)

Recent reports have indicated that human immunodeficiency virus (HIV) and murine leukemia virus (MLV) vectors preferentially integrate into active genes. Here, we used a novel approach based on genetic trapping to rapidly score several thousand integration sites and found that MLV vectors trapped cellular promoters more efficiently than HIV vectors. Remarkably, 1 in 5 MLV integrations trapped an active promoter in different cell lines and primary hematopoietic cells. Such frequency was even higher in growth-stimulated lymphocytes. We show that the different behavior of MLV and HIV vectors was dependent on a different integration pattern within transcribed genes. Whereas MLV-based traps showed a strong bias for promoter-proximal integration leading to efficient reporter expression, HIV-based traps integrated throughout transcriptional units and were limited for expression by the distance from the promoter and the reading frame of the targeted gene. Our results indicate a strong propensity of MLV to establish transcriptional interactions with cellular promoters, a behavior that may have evolved to enhance proviral expression and may increase the insertional mutagenesis risk. Promoter trapping efficiency provides a convenient readout to assess transcriptional interactions between the vector and its flanking genes at the integration site and to compare integration site selection among different cell types and in different growth conditions.
Tumor Cells Secrete a Vascular Permeability Factor That Promotes Accumulation of Ascites Fluid (1983)

Tumor ascites fluids from guinea pigs, hamsters, and mice contain activity that rapidly increases microvascular permeability. Similar activity is also secreted by these tumor cells and a variety of other tumor cell lines in vitro. The permeability-increasing activity purified from either the culture medium or ascites fluid of one tumor, the guinea pig line 10 hepatocarcinoma, is a 34,000- to 42,000-dalton protein distinct from other known permeability factors.
Activated Protein C for Severe Sepsis (2002)

To the Editor: In this issue of the Journal, Warren et al.1 and Siegel2 offer their views on the approval of drotrecogin alfa (activated), or recombinant human activated protein C, for the treatment of severe sepsis. We concur with Dr. Siegel's comments regarding the extensive testing to ensure the potency and consistency of drotrecogin alfa (activated) used in the Recombinant Human Activated Protein C Worldwide Evaluation in Severe Sepsis (PROWESS) trial.3 It is fortunate that the master cell bank used to produce the drug administered in the latter portion of the trial will be sufficient to meet clinical needs for . . .
Glucocorticoids inhibit transcriptional and post-transcriptional expression of interleukin 1 in U937 cells. (1987)

We investigated effects of corticosteroids on interleukin 1 (IL-1) production in monocyte-like tumor cell line, U937. Release of IL-1 activity by bacterial toxin-stimulated cells was completely blocked by 10 nM dexamethasone (Dex). We examined the question whether corticosteroids suppress IL-1 production by blocking transcription of IL-1 mRNA, or by blocking IL-1 synthesis at a post-transcriptional step. Northern blot hybridization analysis indicated that Dex, 10 nM, completely blocked accumulation of IL-1 beta-encoding mRNA in U937 cells. Dex-mediated inhibition of IL-1 release appeared to be glucocorticoid receptor-mediated and was abrogated by progesterone. In addition, Dex at high concentrations could inhibit post-transcriptional synthesis of IL-1 by prestimulated U937 cells. Although Dex, 500 nM, did not change IL-1 mRNA levels in prestimulated cells, it completely blocked IL-1 release and induced a transient increase in cellular cyclic adenosine 3',5'-monophosphate (cAMP) levels. Dex-mediated inhibition of IL-1 release in prestimulated cells is likely to occur via increased levels of cAMP, which have been shown to block post-transcriptional IL-1 synthesis. Our results indicate that glucocorticoids suppress IL-1 synthesis by two distinct mechanisms, blocking transcription of IL-1 mRNA during monocyte activation, and blocking post-transcriptional IL-1 synthesis via cAMP.
Reevaluation of color constancy algorithm performance (2006)

The relative performance of color constancy algorithms is evaluated. We highlight some problems with previous algorithm evaluation and define more appropriate testing procedures. We discuss how best to measure algorithm accuracy on a single image as well as suitable methods for summarizing errors over a set of images. We also discuss how the relative performance of two or more algorithms should best be compared, and we define an experimental framework for testing algorithms. We reevaluate the performance of six color constancy algorithms using the procedures that we set out and show that this leads to a significant change in the conclusions that we draw about relative algorithm performance as compared with those from previous work.
Methods for the Determination of the Purity of Exosomes (2019)

Combinations of various techniques have to be applied to reach the required purity and quality control of exosome preparations.
Methods for Genomic Partitioning (2009)

The emergence of massively parallel DNA sequencing platforms has made resequencing an affordable approach to study genetic variation. However, the cost of whole genome resequencing remains too high to apply to large numbers of human samples. Genomic partitioning methods allow enrichment for regions of interest at a scale that is matched to the throughput of the new sequencing platforms. We review general categories of methods for genomic partitioning including multiplex PCR, capture-by-circularization, and capture-by-hybridization. Parameters that are relevant to the performance of any given method include multiplexity, specificity, uniformity, input requirements, scalability, and cost. The successful development of genomic partitioning strategies will be key to taking full advantage of massively parallel sequencing, at least until resequencing of complete mammalian genomes becomes widely affordable.
SYNTHESIS OF 5-ALKYLRESORCINOLS (1962)

A number of synthetic routes to 2-(3,5-dihydroxyphenyl)-3- methyloctane were investigated. The most practical route starts from 1,3,5- trichlorobenzene, which is converted in two steps to 3,5- dimethoxyphenylmagnesium chloride. This Grignard reagent is reacted with 2- methylheptanonitrile, and the resulting ketone is reacted with methylmagnesium halide to give 2-(3,5-dimethoxyphenyl)-3-methyloctanol-2. This carbinol is dehydrated, reduced, and cleaved to produce the de ired resorcinol. Other routes and variations in individual steps were also investigated and detailed comparisons of their merits are included. The synthesis of six related alkylresorcinols was also investigated. Two of these were prepared: 2-(3,5- dihydroxyphenyl)-3,4-dimethyloctane and 2-(3,5-dihydroxyphenyl)-3, 3dimethyloctane. A key precursor for three of the others was prepared.
Ilodecakin. Schering-Plough Corp. (1999)

Schering-Plough's interleukin (IL)-10 (ilodecakin) is under investigation for the potential treatment of autoimmune diseases, solid tumors, ulcerative colitis, Crohn's disease and organ transplantation. In June 1996, ilodecakin entered phase II trials for Crohn's disease, ulcerative colitis and rheumatoid arthritis and, as of June 1999 was reported to be in phase III trials for Crohn's disease and rheumatoid arthritis. It has also demonstrated promising effects in the treatment of inflammatory bowel disease. In January 1997, phase I trials began in HIV-infected patients. Initial results from a pilot study, carried out by the National Institute of Allergy and Infectious Disease Control, indicated that a single dose of IL-10 decreases the blood viral load. The results, however, were transient. Early clinical studies are ongoing in acute lung injury, ischemia-reperfusion injury, multiple sclerosis and psoriasis. In February 1999, Morgan Stanley Dean Witter predicted sales of US $50 million in 2000 rising to US $325 million in 2005.
Improvement of Nitrogen Assimilation and Fermentation Kinetics under Enological Conditions by Derepression of Alternative Nitrogen-Assimilatory Pathways in an IndustrialSaccharomyces cerevisiaeStrain (1998)

Metabolism of nitrogen compounds by yeasts affects the efficiency of wine fermentation. Ammonium ions, normally present in grape musts, reduce catabolic enzyme levels and transport activities for nonpreferred nitrogen sources. This nitrogen catabolite repression severely impairs the utilization of proline and arginine, both common nitrogen sources in grape juice that require the proline utilization pathway for their assimilation. We attempted to improve fermentation performance by genetic alteration of the regulation of nitrogen-assimilatory pathways in Saccharomyces cerevisiae. One mutant carrying a recessive allele of ure2 was isolated from an industrial S. cerevisiae strain. This mutation strongly deregulated the proline utilization pathway. Fermentation kinetics of this mutant were studied under enological conditions on simulated standard grape juices with various nitrogen levels. Mutant strains produced more biomass and exhibited a higher maximum CO2 production rate than the wild type. These differences were primarily due to the derepression of amino acid utilization pathways. When low amounts of dissolved oxygen were added, the mutants could assimilate proline. Biomass yield and fermentation rate were consequently increased, and the duration of the fermentation was substantially shortened. S. cerevisiae strains lacking URE2 function could improve alcoholic fermentation of natural media where proline and other poorly assimilated amino acids are the major potential nitrogen source, as is the case for most fruit juices and grape musts.
Infection of Primary Human Bronchial Epithelial Cells by Haemophilus influenzae : Macropinocytosis as a Mechanism of Airway Epithelial Cell Entry (1999)

Nontypeable Haemophilus influenzae is an exclusive human pathogen which infects the respiratory epithelium. We have initiated studies to explore the interaction of the nontypeable H. influenzae strain 2019 with primary human airway epithelial cells by electron and confocal microscopy. Primary human airway cell cultures were established as monolayers on glass collagen-coated coverslips or on semipermeable membranes at an air-fluid interface. Scanning electron microscopy indicated that bacteria adhered to nonciliated cells in the population. The surface of infected cells showed evidence of cytoskeletal rearrangements manifested by microvilli and lamellipodia extending toward and engaging bacteria. Confocal microscopic analysis demonstrated that infection induced actin polymerization with an increase in cortical actin as well as evidence of actin strands around the bacteria. Transmission electron microscopic analysis showed lamellipodia and microvilli surrounding organisms, as well as organisms adherent to the cell surface. These studies also demonstrated the presence of bacteria within vacuoles inside of airway cells. Confocal microscopic studies with Texas red-labeled dextran (molecular weight, 70,000) indicated that H. influenzae cells were entering cells by the process of macropinocytosis. These studies indicate that nontypeable H. influenzae can initiate cytoskeletal rearrangement within human airway epithelium, resulting in internalization of the bacteria within nonciliated human airway epithelial cells by the process of macropinocytosis.
Long-Wave Infrared Hyperspectral Remote Sensing of Chemical Clouds: A focus on signal processing approaches (2014)

This paper focusses on the signal processing approaches necessary to achieve the three main tasks of gas-phase remote sensing: detection of a plume, identification of its constituent gases, and quantification of the amounts present. A tutorial introduction to the radiance phenomenology is given that drives the models on which exploitation algorithms are based which is followed by the fundamental aspects of the data-exploitation problem, develop algorithms that can successfully exploit data from many different sensors, and discuss the many challenges that remain open to the signal processing community. Results using real hyperspectral data sets are also presented.
Metabolic Connection of Inflammatory Pain: Pivotal Role of a Pyruvate Dehydrogenase Kinase-Pyruvate Dehydrogenase-Lactic Acid Axis (2015)

The mitochondrial pyruvate dehydrogenase (PDH) kinases (PDKs) and their substrate PDH orchestrate the conversion of pyruvate either aerobically to acetyl-CoA or anaerobically to lactate. Lactate, the predominant end product of glycolysis, has recently been identified as a signaling molecule for neuron-glia interactions and neuronal plasticity. Pathological metabolic shift and subsequent lactic acid production are thought to play an important role in diverse painful states; however, their contribution to inflammation-driven pain is still to be comprehended. Here, we report that the PDK-PDH-lactic acid axis constitutes a key component of inflammatory pain pathogenesis. Our findings establish an unanticipated link between metabolism and inflammatory pain. This study unlocks a previously ill-explored research avenue for the metabolic control of inflammatory pain pathogenesis.
Specific synthetic lethal killing of RAD54B-deficient human colorectal cancer cells by FEN1 silencing (2009)

Mutations that cause chromosome instability (CIN) in cancer cells produce "sublethal" deficiencies in an essential process (chromosome segregation) and, therefore, may represent a major untapped resource that could be exploited for therapeutic benefit in the treatment of cancer. If second-site unlinked genes can be identified, that when knocked down, cause a synthetic lethal (SL) phenotype in combination with a somatic mutation in a CIN gene, novel candidate therapeutic targets will be identified. To test this idea, we took a cross species SL candidate gene approach by recapitulating a SL interaction observed between rad54 and rad27 mutations in yeast, via knockdown of the highly sequence- and functionally-related proteins RAD54B and FEN1 in a cancer cell line. We show that knockdown of RAD54B, a gene known to be somatically mutated in cancer, causes CIN in mammalian cells. Using high-content microscopy techniques, we demonstrate that RAD54B-deficient human colorectal cancer cells are sensitive to SL killing by reduced FEN1 expression, while isogenic RAD54B proficient cells are not. This conserved SL interaction suggests that extrapolating SL interactions observed in model organisms for homologous genes mutated in human cancers will aid in the identification of novel therapeutic targets for specific killing of cancerous cells exhibiting CIN.
Correlation of CT and MR with Impedance Monitoring and Histopathology in Stereotactic Biopsies (1990)

Magnetic Resonance Imaging (MR) and Computer Assisted Tomography (CT) guided stereotaxis combined with intraoperative impedance monitoring and multiple sequential biopsies provides the opportunity to correlate the results of radiologic imaging with impedance and histopathology. The authors present the methods used and preliminary results obtained from 30 stereotactic biopsies with complete correlation in 12 cases. Impedance changes correlate accurately with lesion margins as defined by histology. CT images of enhancing lesions correlate quite closely to the histopathologic lesion margins whereas the appearance of the lesion on MR images is often larger than subsequently identified by either impedance or at pathologic examination. Impedance monitoring is a useful adjunct to stereotactic biopsy as it helps to accurately define lesion margins and can help direct the choice of biopsy sites.
Anisotropic shaping of macroporous silicon (2015)

Various high-aspect structures fabricated from macroporous silicon with an ordered lattice by additional treatment in anisotropic etchants are considered. The conditions and specific features of the fabrication of structures with walls formed by a single type of slow-etched (110) or (100) planes and the dependence of their porosity and specific internal surface area on the wall thickness are determined. Zigzag, grid-like, and pillar-shaped structures fabricated on the basis of macroporous silicon by anisotropic treatment in aqueous KOH solutions are experimentally demonstrated.
Identifying and Estimating Significant Geologic Parameters With Experimental Design (2001)

Summary Variability in production predictions caused by geologic heterogeneity and uncertainty was examined with a new method. The experimental design maximized the information derived from the flow simulation of various geologic models. Empirical response surface models were fit to simulation results to assess the consequences of varying several geologic factors. Posterior distributions of geologic parameters were estimated from flow responses. Improvements in the accuracy of the reservoir model were quantified by computing changes in factor uncertainties resulting from response measurements. Monte Carlo simulations with prior and posterior factor distributions illustrate uncertainty reduction. This approach can be used for model comparison, sensitivity analysis, and estimation of probability distributions of geologic model parameters.
Optimal resource allocation in the OFDMA downlink with imperfect channel knowledge (2009)

Previous research efforts on OFDMA resource allocation have typically assumed the availability of perfect channel state information (CSI). Unfortunately, this is unrealistic, primarily due to channel estimation errors, and more importantly, channel feedback delay. In this paper, we develop optimal resource allocation algorithms for the OFDMA downlink assuming the availability of only partial (imperfect) CSI. We consider both continuous and discrete ergodic weighted sum rate maximization subject to total power constraints, and average bit error rate constraints for the discrete rate case. We approach these problems using a dual optimization framework, allowing us to solve these problems with O(MK) complexity per symbol for an OFDMA system with K used subcarriers and M active users, while achieving relative optimality gaps of less than 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-5</sup> for continuous rates and less than 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> for discrete rates in simulations based on realistic parameters.