gebhart/patrepeval huggingface dataset:
Image feature analysis for computer-aided diagnosis: Detection of right and left hemidiaphragm edges and delineation of lung field in chest radiographs (1996)

Diaphragm edges, together with ribcage edges, in chest radiographs provide useful information on the location, shape, and size of the lung fields that are required by computer-aided diagnosis (CAD) schemes for automated detection of various abnormalities. In this continued study, we developed a computerized method for detection of the right and left hemidiaphragm edges. First, the right hemidiaphragm edges in a PA (postero-anterior) chest image were determined by edge gradient analysis. An initial vertical ROI was then placed at the middle of the left hemidiaphragm, based on a "standard rule" for determination of the starting points to search for the left hemidiaphragm edges. Seven categories were used to assess the accuracy of the placement of the initial ROI and the selection of the primary left starting point within the initial ROI. For some categories, it was necessary to select a second left starting point besides the primary one. Therefore, for these categories, two sets of "detected left hemidiaphragm edges" resulted from the two left starting points. Two parameters were used as measures to eliminate the false left hemidiaphragm edges which were due to an incorrect left starting point. Two polynomial functions were applied separately which produced smooth curves for the right and left hemidiaphragm edges. Finally, the delineation of the lung field in a chest image was obtained by connecting the right and left hemidiaphragm edge curves with the corresponding ribcage edge curves. The subjective evaluation results indicated that the accuracy for the determination of the right and left hemidiaphragm edges was approximately 97% and 90%, respectively.
Rice Transformation by Agrobacterium Infection (1998)

Efficient production of transgenic plants is a prerequisite for the production of recombinant proteins in plants. In many dicotyledonous plants, Agrobacterium tumefaciens-mediated transformation has been well established. High efficacy and low cost make this the method of choice in many research laboratories for studying gene expression in plants (1).
Expansion of human cardiac stem cells in physiological oxygen improves cell production efficiency and potency for myocardial repair (2010)

the expansion of human adult cardiac stem cells in low oxygen increased cell yield, and the resulting cells were superior by various key in vitro and in vivo metrics of cell quality. Physiological oxygen tensions in culture facilitate the ex vivo expansion of healthy, biologically potent stem cells.
On the Nature of Critical Heat Flux in Microchannels (2005)

The critical heat flux (CHF) limit is an important consideration in the design of most flow boiling systems. Before the use of microchannels under saturated flow boiling conditions becomes widely accepted in cooling of high-heat-flux devices, such as electronics and laser diodes, it is essential to have a clear understanding of the CHF mechanism. This must be coupled with an extensive database covering a wide range of fluids, channel configurations, and operating conditions. The experiments required to obtain this information pose unique challenges. Among other issues, flow distribution among parallel channels, conjugate effects, and instrumentation need to be considered. An examination of the limited CHF data indicates that CHF in parallel microchannels seems to be the result of either an upstream compressible volume instability or an excursive instability rather than the conventional dryout mechanism. It is expected that the CHF in parallel microchannels would be higher if the flow is stabilized by an orifice at the entrance of each channel. The nature of CHF in microchannels is thus different than anticipated, but recent advances in microelectronic fabrication may make it possible to realize the higher power levels.
The carrier blocking effect on 850 nm InAlGaAs/AlGaAs vertical-cavity surface-emitting lasers (2006)

In this study, the carrier blocking effect on 850 nm InAlGaAs/AlGaAs vertical-cavity surface-emitting layers (VCSELs) was theoretically and experimentally investigated. By means of inserting a high-bandgap electron blocking layer, which was either 10 nm thick Al0.75Ga0.25As or 13 nm thick Al0.9Ga0.1As, on the p-side of a quantum-well active region, the laser output performance was theoretically found to be improved. VCSELs with and without an electron blocking layer were also experimentally demonstrated. It was found that the threshold current was reduced from 1.47 to 1.33 mA and the slope efficiency was increased from 0.37 to 0.53 mW mA−1 by inserting a 10 nm thick Al0.75Ga0.25As electron blocking layer. Also, the device became less sensitive to the device temperature, where the amount of increase in the threshold current at an elevated temperature of 95 °C was only 0.27 mA and the slope efficiency dropped by only 24.5%. A peak frequency response of nearly 9 GHz at 5 mA, measured from relative intensity noise (RIN), was obtained in these VCSEL devices.
Fluorescence analysis of carrier rat and human erythrocytes loaded with FITC‐dextran (1996)

Rat and human erythrocytes are inherently different with respect to slow dialysis encapsulation used in preparing carrier erythrocytes. The incorporation process, commonly measured with radioactive tracers, is always larger in human erythrocytes, mainly because the rat carrier cells are more fragile. When FITC-Dextran (Dx) is used in the encapsulation process, and loaded rat and human RBCs are studied by fluorescence intensity, some additional events are evident. Not all cells of each population appear with a fluorescence signal, and not all show similar fluorescence intensity. Human RBCs show a higher percentage of marked cells and a higher fluorescence intensity than rat RBCs. Two populations, of high and low fluorescence, appear in FITC-Dx loaded rat erythrocytes. The human loaded RBCs show a similar peak distribution together with another peak in the middle scale of fluorescence. Therefore, a heterogeneity in the cell population as a result of the encapsulation process is manifested for both species. The fractionation of RBCs, loaded with either FITC-Dx or 125I-CA, by centrifugation on Ficoll-Paque reveals that the low density cells have much more substance incorporation than the counterpart cell subpopulation in the pellet. Therefore, the cell modifications produced by the encapsulation process are independent of the substance being incorporated. On the other hand, FITC-Dx, but not 125I-CA, shows a certain degree of association to RBCs membranes, especially in humans. © 1996 Wiley-Liss, Inc.
Identification of cDNA clones encoding a precursor of rat liver cathepsin B. (1985)

Recent studies have suggested that many lysosomal enzymes, including cathepsin B (EC 3.4.22.1), may be synthesized as larger precursors and proteolytically processed to their mature forms. To determine the structure of the primary translation product of cathepsin B, we have screened a phage cDNA library for clones encoding rat liver cathepsin B. We synthesized two extended DNA oligonucleotides to use as hybridization probes: a 50-mer corresponding to the coding segment for residues 215-231 of mature cathepsin B and a 54-mer corresponding to residues 117-134. After screening 600,000 plaques, five clones were obtained that hybridized to the 32P-labeled 50-mer; of these, two (lambda rCB3 and lambda rCB5) also reacted with the 54-mer. DNA sequence analysis confirmed that lambda rCB3 and lambda rCB5 both encoded rat liver cathepsin B, and the translated sequence is in agreement with the sequence determined [Takio, K., Towatari, T., Katunuma, N., Teller, D. C. & Titani, K. (1983) Proc. Natl. Acad. Sci. USA 80, 3666-3670], except for a tryptophan for glycine substitution at residue 78 and the presence of two amino acids at the junction site of the light and heavy chains. Moreover, the DNA sequence reveals an open reading frame extending beyond the 5' (NH2 terminus), and the predicted COOH terminus of the coding sequence for the mature protein is extended by six amino acids. These results confirm that the biosynthesis of cathepsin B involves a larger precursor form and demonstrate the effectiveness of long oligonucleotide probes for screening to detect rare cloned mRNAs.
Recognizing Student Emotions using Brainwaves and Mouse Behavior Data (2013)

Brainwaves (EEG signals) and mouse behavior information are shown to be useful in predicting academic emotions, such as confidence, excitement, frustration and interest. Twenty five college students were asked to use the Aplusix math learning software while their brainwaves signals and mouse behavior (number of clicks, duration of each click, distance traveled by the mouse) were automatically being captured. It is shown that by combining the extracted features from EEG signals with data representing mouse click behavior, the accuracy in predicting academic emotions substantially increases compared to using only features extracted from EEG signals or just mouse behavior alone. Furthermore, experiments were conducted to assess the prediction accuracy of the system at points during the learning session where several of the extracted features significantly deviate in value from their mean. The experiments confirm that the prediction performance increases as the number of feature values that deviate significantly from the mean increases.
RadNotes: a novel software development tool for radiology education. (1997)

RadNotes is a novel software development tool that enables physicians to develop teaching materials incorporating text and images in an intelligent, highly usable format. Projects undertaken in the RadNotes environment require neither programming expertise nor the assistance of a software engineer. The first of these projects, Thoracic Imaging, integrates image teaching files, concise disease and topic summaries, references, and flash card quizzes into a single program designed to provide an overview of chest radiology. RadNotes is intended to support the academic goals of teaching radiologists by enabling authors to create, edit, and electronically distribute image-oriented presentations. RadNotes also supports the educational goals of physicians who wish to quickly review selected imaging topics, as well as to develop a visual vocabulary of corresponding radiologic anatomy and pathologic conditions. Although Thoracic Imaging was developed with the aim of introducing chest radiology to residents, RadNotes can be used to develop tutorials and image-based tests for all levels; create corresponding World Wide Web sites; and organize notes, images, and references for individual use.
Signal transduction of human interleukin 3 and granulocyte-macrophage colony-stimulating factor through serine and tyrosine phosphorylation (1990)

To elucidate the rapid events in signal transduction of human granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin 3 (IL 3), we examined phosphorylation of proteins on both serine and tyrosine residues in a cytokine-stimulated human myeloid cell line. We found increases in tyrosine phosphorylation within 30 s of stimulation with GM-CSF or IL 3, with peak responses occurring within 2 min. IL 3 and GM-CSF also induced serine phosphorylation, though 10 min of stimulation was required for maximum phosphate incorporation. Interestingly, both IL 3 and GM-CSF stimulated phosphate incorporation in identical substrates, a 68 kDa seryl-phosphoprotein (p68) and a 140 kDa tyrosyl-phosphoprotein (p140). Treatment of AML 193 cells with phorbol myristate acetate resulted in serine phosphorylation of p68; however, p140 was not phosphorylated on tyrosine. Depletion of protein kinase C isoenzymes with high concentrations of phorbol myristate acetate resulted in p68 phosphorylation, which was not further increased by IL 3 or GM-CSF. In contrast, cytokine-induced phosphorylation on tyrosine of p140 was observed after protein kinase C depletion. These data demonstrate the co-ordinate yet independent serine and tyrosine phosphorylation in IL 3- and GM-CSF-treated human myeloid cells, and thus suggest a common set of protein kinases stimulated by each separate ligand.
Can Interstitial Glucose Assessment Replace Blood Glucose Measurements? (2000)

Current treatment regiments for individuals depending on exogenous insulin are based on measurements of blood glucose obtained through painful finger sticks. The shift to minimal or noninvasive continuous glucose monitoring primarily involves a shift from blood glucose measurements to devices measuring subcutaneous interstitial fluid (ISF) glucose. As the development of these devices progresses, details of the dynamic relationship between blood glucose and interstitial glucose dynamics need to be firmly established. This is a challenging task insofar as direct measures of ISF glucose are not readily available. The current article investigated the dynamic relationship between plasma and ISF glucose using a model-based approach. A two-compartment model system previously validated on data obtained with the MiniMed Continuous Glucose Monitoring System (CGMS) is reviewed and predictions from the original two-compartment model were confirmed using new data analysis of glucose dynamics in plasma and hindlimb lymph (lymph is derived from ISF) in the anesthetized dog. From these data sets, the time delay between plasma and ISF glucose in dogs was established (5-12 minutes) and a simulation study was performed to estimate the errors introduced if ISF is taken as a surrogate for blood. From the simulation study, the error component resulting from the differences in plasma and ISF glucose was estimated to be < 6% during normal day-to-day use in an individual with diabetes (error component calculated as the standard deviation of the ISF/plasma glucose differences under conditions where the maximal time delay was used). This difference is most likely within the variance between arterial and venous blood glucose. We conclude that the differences between plasma and ISF glucose will not be a significant obstacle in advancing the use of ISF as an alternative to blood glucose measurements.
Quantitative Analysis of Energy Metabolic Pathways in MCF-7 Breast Cancer Cells by Selected Reaction Monitoring Assay (2012)

To investigate the quantitative response of energy metabolic pathways in human MCF-7 breast cancer cells to hypoxia, glucose deprivation, and estradiol stimulation, we developed a targeted proteomics assay for accurate quantification of protein expression in glycolysis/gluconeogenesis, TCA cycle, and pentose phosphate pathways. Cell growth conditions were selected to roughly mimic the exposure of cells in the cancer tissue to the intermittent hypoxia, glucose deprivation, and hormonal stimulation. Targeted proteomics assay allowed for reproducible quantification of 76 proteins in four different growth conditions after 24 and 48 h of perturbation. Differential expression of a number of control and metabolic pathway proteins in response to the change of growth conditions was found. Elevated expression of the majority of glycolytic enzymes was observed in hypoxia. Cancer cells, as opposed to near-normal MCF-10A cells, exhibited significantly increased expression of key energy metabolic pathway enzymes (FBP1, IDH2, and G6PD) that are known to redirect cellular metabolism and increase carbon flux through the pentose phosphate pathway. Our quantitative proteomic protocol is based on a mass spectrometry-compatible acid-labile detergent and is described in detail. Optimized parameters of a multiplex selected reaction monitoring (SRM) assay for 76 proteins, 134 proteotypic peptides, and 401 transitions are included and can be downloaded and used with any SRM-compatible mass spectrometer. The presented workflow is an integrated tool for hypothesis-driven studies of mammalian cells as well as functional studies of proteins, and can greatly complement experimental methods in systems biology, metabolic engineering, and metabolic transformation of cancer cells.
X-ray and NMR Studies of the DNA Oligomer d(ATATAT):  Hoogsteen Base Pairing in Duplex DNA (2004)

We present and analyze the structure of the oligonucleotide d(ATATAT) found in two different forms by X-ray crystallography and in solution by NMR. We find that in both crystal lattices the oligonucleotide forms an antiparallel double helical duplex in which base pairing is of the Hoogsteen type. The double helix is apparently very similar to the standard B-form of DNA, with about 10 base pairs per turn. However, the adenines in the duplex are flipped over; as a result, the physicochemical features of both grooves of the helix are changed. In particular, the minor groove is narrow and hydrophobic. On the other hand, d(ATATAT) displays a propensity to adopt the B conformation in solution. These results confirm the polymorphism of AT-rich sequences in DNA. Furthermore, we show that extrahelical adenines and thymines can be minor groove binders in Hoogsteen DNA.
The microRNA-342-5p Fosters Inflammatory Macrophage Activation Through an Akt1- and microRNA-155 –Dependent Pathway During Atherosclerosis (2013)

Macrophage-derived miR-342-5p promotes atherosclerosis and enhances the inflammatory stimulation of macrophages by suppressing the Akt1-mediated inhibition of miR-155 expression. Therefore, targeting miR-342-5p may offer a promising strategy to treat atherosclerotic vascular disease.
Impact of a blood management protocol on transfusion rates and outcomes following total hip and knee arthroplasty (2016)

Introduction Preoperative anaemia remains undertreated in the UK despite advice from national agencies to implement blood conservation measures. A local retrospective audit of 717 primary hip/knee replacements in 2008-2009 revealed 25% of patients were anaemic preoperatively. These patients experienced significantly increased transfusion requirements and length of stay. We report the results of a simple and pragmatic blood management protocol in a district general hospital. Methods Since 2010 patients at our institution who are found to be anaemic when listed for hip/knee replacement have been offered iron supplementation and/or erythropoietin depending on haemoglobin and ferritin levels. In this study, postoperative blood transfusions, length of stay and readmissions were assessed retrospectively for all patients undergoing elective primary hip/knee replacement in 2014 and compared with the baseline findings. Results During the 12-month study period, 406 patients were eligible for inclusion and none were excluded. Eighty-nine patients (22%) were anaemic preoperatively and sixty-five received treatment. The transfusion rate fell from the baseline levels of 23.0% and 6.7% to 4.3% and 0.5% for hip and knee replacements respectively (p<0.001). The median length of stay reduced from 6 to 3 days (p<0.001) for both hip and knee replacements. The rate for readmissions within 90 days fell from 13.5% to 8.9% (p<0.05). Conclusions Preoperative anaemia is common in patients listed for hip/knee replacement and it is associated strongly with increased blood transfusion. The introduction of a blood management protocol has led to significant reductions in transfusion and length of stay, sustained over a four-year period. This suggests that improved patient outcomes, conservation of blood stocks and cost savings can be achieved.
Active stereo sound localization (2003)

Estimating the direction of arrival of sound in three-dimensional space is typically performed by generalized time-delay processing on a set of signals from a fixed array of omnidirectional microphones. This requires specialized multichannel A/D hardware, and careful arrangement of the microphones into an array. This work is motivated by the desire to instead only use standard two-channel audio A/D hardware and portable equipment. To estimate direction of arrival of persistent sound, the position of the microphones is made variable by mounting them on one or more computer-controlled pan-and-tilt units. In this paper, we describe the signal processing and control algorithm of a device with two omnidirectional microphones on a fixed baseline and two rotational degrees of freedom. Experimental results with real data are reported with both impulsive and speech sounds in an untreated, normally reverberant indoor environment.
Activation of γδ T Cells by Borrelia burgdorferi Is Indirect via a TLR- and Caspase-Dependent Pathway (2008)

Activation of the innate immune system typically precedes engagement of adaptive immunity. Cells at the interface between these two arms of the immune response are thus critical to provide full engagement of host defense. Among the innate T cells at this interface are gammadelta T cells. gammadelta T cells contribute to the defense from a variety of infectious organisms, yet little is understood regarding how they are activated. We have previously observed that human gammadelta T cells of the Vdelta1 subset accumulate in inflamed joints in Lyme arthritis and proliferate in response to stimulation with the causative spirochete, Borrelia burgdorferi. We now observe that murine gammadelta T cells are also activated by B. burgdorferi and that in both cases the activation is indirect via TLR stimulation on dendritic cells or monocytes. Furthermore, B. burgdorferi stimulation of monocytes via TLR, and secondary activation of gammadelta T cells, are both caspase-dependent.
Eukaryotic start and stop translation sites (1991)

Sequences flanking translational initiation and termination sites have been compiled and statistically analyzed for various eukaryotic taxonomic groups. A few key similarities between taxonomic groups support conserved mechanisms of initiation and termination. However, a high degree of sequence variation at these sites within and between various eukaryotic groups suggest that translation may be modulated for many mRNAs. Multipositional analysis of di-, tri-, and quadrinucleotide sequences flanking start/stop sites indicate significant biases. In particular, strong tri-nucleotide biases are observed at the -3, -2, and -1 positions upstream of the start codon. These biases and the interspecific variation in nucleotide preferences at these three positions have lead us to propose a revised model of the interaction of the 18S ribosomal RNA with the mRNA at the site of translation initiation. Unusually strong biases against the CG dinucleotide immediately downstream of termination codons suggest that they may lead to faulty termination and/or failure of the ribosome to disassociate from the mRNA.