gebhart/patrepeval huggingface dataset:
<title>Pattern classification approach to segmentation of chest radiographs</title> (1993)

In digital chest radiography, the goal of segmentation is to automatically and reliably identify anatomic regions such as the heart and lungs. Aids to diagnosis such as automated anatomic measurements, methods that enhance display of specific regions, and methods that search for disease processes, all depend on a reliable segmentation method. The goal of this research is to develop a segmentation method based on a pattern classification approach. A set of 17 chest images was used to train each of the classifiers. The trained classifiers were then tested of a different set of 16 chest images. The linear discriminant correctly classified greater than 70%, the k-nearest neighbor correctly classified greater than 70% and the neural network classified greater than 76% of the pixels from the test images. Preliminary results are favorable for this approach. Local features do provide much information, but further improvement is expected when addition information, such as location, can be incorporated.
Efficient Substrate Cleavage Catalyzed by Hammerhead Ribozymes Derivatized with Selenium for X-Ray Crystallography (2006)

Because oxygen and selenium are in the same group (Family VI) in the periodic table, the site-specific mutagenesis at the atomic level by replacing RNA oxygen with selenium can provide insights on the structure and function of catalytic RNAs. We report here the first Se-derivatized ribozymes transcribed with all nucleoside 5'-(alpha-P-seleno)triphosphates (NTPalphaSe, including A, C, G, and U). We found that T7 RNA polymerase recognizes NTPalphaSe Sp diastereomers as well as the natural NTPs, whereas NTPalphaSe Rp diastereomers are neither substrates nor inhibitors. We also demonstrated the catalytic activity of these Se-derivatized hammerhead ribozymes by cleaving the RNA substrate, and we found that these phosphoroselenoate ribozymes can be as active as the native one. These hammerhead ribozymes site-specifically mutagenized by selenium reveal the close relationship between the catalytic activities and the replaced oxygen atoms, which provides insight on the participation of oxygen in catalysis or intramolecular interaction. This demonstrates a convenient strategy for the mechanistic study of functional RNAs. In addition, the active ribozymes site-specifically derivatized by selenium will allow for convenient MAD phasing in X-ray crystal structure studies.
Migration of Resident Cardiac Stem Cells in Myocardial Infarction (2012)

Ischemic heart disease is a major cause of morbidity and mortality worldwide. Stem cell-based therapy, which aims to restore cardiac structure and function by regeneration of functional myocardium, has recently been proposed as a novel alternative treatment modality. Resident cardiac stem cells (CSCs) in adult hearts are a key cell type under investigation. CSCs have been shown to be able to repair damaged myocardium and improve myocardial function in both human and animal studies. This approach relies not only on the proliferation of the CSCs, but also upon their migration to the site of injury within the heart. Here, we briefly review reported CSC populations and discuss signaling factors and pathways required for the migration of CSCs.
Protective Role of Polyphenols against Vascular Inflammation, Aging and Cardiovascular Disease (2018)

Aging is a major risk factor in the development of chronic diseases affecting various tissues including the cardiovascular system, muscle and bones. Age-related diseases are a consequence of the accumulation of cellular damage and reduced activity of protective stress response pathways leading to low-grade systemic inflammation and oxidative stress. Both inflammation and oxidative stress are major contributors to cellular senescence, a process in which cells stop proliferating and become dysfunctional by secreting inflammatory molecules, reactive oxygen species (ROS) and extracellular matrix components that cause inflammation and senescence in the surrounding tissue. This process is known as the senescence associated secretory phenotype (SASP). Thus, accumulation of senescent cells over time promotes the development of age-related diseases, in part through the SASP. Polyphenols, rich in fruits and vegetables, possess antioxidant and anti-inflammatory activities associated with protective effects against major chronic diseases, such as cardiovascular disease (CVD). In this review, we discuss molecular mechanisms by which polyphenols improve anti-oxidant capacity, mitochondrial function and autophagy, while reducing oxidative stress, inflammation and cellular senescence in vascular smooth muscle cells (VSMCs) and endothelial cells (ECs). We also discuss the therapeutic potential of polyphenols in reducing the effects of the SASP and the incidence of CVD.
Analysis of lymphocyte subgroups in Crimean-Congo hemorrhagic fever (2008)

Higher levels of CD3+CD8+ T lymphocytes were detected in fatal compared to non-fatal CCHF cases. Despite this cytotoxic immune activation, a fatal outcome could not be prevented. We hypothesize that high viral load and other factors may influence this outcome, although more studies are required to explain the pathogenesis of CCHF.
Somatic deletions in hereditary breast cancers implicate 13q21 as a putative novel breast cancer susceptibility locus (2000)

A significant proportion of familial breast cancers cannot be explained by mutations in the BRCA1 or BRCA2 genes. We applied a strategy to identify predisposition loci for breast cancer by using mathematical models to identify early somatic genetic deletions in tumor tissues followed by targeted linkage analysis. Comparative genomic hybridization was used to study 61 breast tumors from 37 breast cancer families with no identified BRCA1 or BRCA2 mutations. Branching and phylogenetic tree models predicted that loss of 13q was one of the earliest genetic events in hereditary cancers. In a Swedish family with five breast cancer cases, all analyzed tumors showed distinct 13q deletions, with the minimal region of loss at 13q21-q22. Genotyping revealed segregation of a shared 13q21 germ-line haplotype in the family. Targeted linkage analysis was carried out in a set of 77 Finnish, Icelandic, and Swedish breast cancer families with no detected BRCA1 and BRCA2 mutations. A maximum parametric two-point logarithm of odds score of 2.76 was obtained for a marker at 13q21 (D13S1308, theta = 0.10). The multipoint logarithm of odds score under heterogeneity was 3.46. The results were further evaluated by simulation to assess the probability of obtaining significant evidence in favor of linkage by chance as well as to take into account the possible influence of the BRCA2 locus, located at a recombination fraction of 0.25 from the new locus. The simulation substantiated the evidence of linkage at D13S1308 (P < 0.0017). The results warrant studies of this putative breast cancer predisposition locus in other populations.
Copper-Catalyzed Synthesis of Medium- and Large-Sized Nitrogen Heterocycles via N-Arylation of Phosphoramidates and Carbamates (2005)

[reaction: see text] We have developed an efficient method for the preparation of medium- and large-sized nitrogen heterocycles via copper-catalyzed intramolecular N-arylation of phosphoramidates and carbamates. Introduction of the phosphoryl group or tert-butoxycarbonyl at N-termini can improve intramolecular cyclization under copper catalysis, and the phosphoryl and tert-butoxycarbonyl can easily be removed under the mild conditions; thus, the convenient and efficient method is suitable for the preparation of medium- and large-sized nitrogen heterocycles.
Crystallization of human neutrophil elastase. (1987)

Human neutrophil elastase was inactivated by methoxysuccinyl-L-Ala-L-Ala-L-Pro-L-Ala-chloromethane. The modified enzyme was crystallized from 40 mM ammonium phosphate, pH 7.0 in the hexagonal space group P6(3) with unit cell parameters a = 74.53 A, b = 74.53 A, c = 70.88 A, alpha = beta = 90 degrees, gamma = 120 degrees. These crystals were resistant to radiation damage and diffracted beyond 1.84-A resolution. The asymmetric unit contained one 25,000-dalton monomer of human neutrophil elastase. Crystals were also grown from the enzyme modified with the analogous iodinated inactivator, p-iodoanilinosuccinyl-L-Ala-L-Ala-L-Pro-L-Ala-chloromethane. These crystals proved to be isomorphous with those of methoxysuccinyl-L-Ala-L-Ala-L-Pro-L-Ala-chloromethane-modified human neutrophil elastase, and served as a single-site, heavy atom derivative for solving the tertiary structure of the enzyme.
CD30 expression on circulating memory CD4<sup>+</sup> T cells as a Th2‐dominated situation in patients with atopic dermatitis (2000)

Th2 clones have been reported to express CD30 preferentially, but whether T cells producing Th2-type cytokines may favor CD30 expression in the in vivo state remains unknown. We investigated the expression of CD30 on circulating T cells in atopic dermatitis (AD) as a Th2-dominated disorder. Peripheral blood mononuclear cells were prepared from 51 AD patients and 14 nonatopic controls, and their phenotypes were analyzed with flow cytometry. Cytokine production by stimulated CD4+ T cells was also assessed by the single-cell-staining method. Flow cytometric analysis clearly revealed that CD30+ T cells were identifiable in the blood of AD patients with greater frequency compared to controls. The important finding was that CD30 expression was restricted to a small but substantial population of memory (CD45RO+) CD4+ T cells, but not CD8+ ones. In AD patients, it was demonstrated that the percentages of CD30+ cells within CD45RO+ CD4+ T cells correlated well with the disease severity, serum IgE levels, peripheral eosinophil counts, and tendency toward Th2-dominant cytokine pattern as determined by the ratio of interleukin-4 to interferon-gamma production. This study suggests that CD30 expression in circulating T cells might serve as an in vivo marker for the Th2-dominated condition.
Activin A Induction of Cell-Cycle Arrest Involves Modulation of<i>Cyclin D2</i>and<i>p21</i><sup>CIP1/WAF1</sup>in Plasmacytic Cells (1997)

Activins, members of the transforming growth factor-beta family, have been implicated in the regulation of growth and differentiation of various types of cells. We have recently found that activin A induces apoptotic cell death of plasmacytic cells including B cell hybridoma cells and myeloma cells. In the present study, we demonstrated that activin A caused cell-cycle arrest in the G1 phase before appearance of apoptotic cells in mouse B cell hybridoma cells. Phosphorylation of retinoblastoma protein (Rb) and in vitro Rb kinase activity of cyclin-dependent kinase (CDK)4 was inhibited in activin A-treated cells. Analysis of expression of genes regulating Rb phosphorylation revealed that activin A suppressed cyclin D2, the sole D-type cyclin gene expressed in the hybridoma cells, and activated p21CIP1/WAF1 but had no effect on expression of cyclin-dependent kinases (CDK2, CDK4, CDK6) and other CDK inhibitors (p27KIP1, p16INK4a, p15INK4b). Modulation of cyclin D2 and p21CIP1/WAF1 expression resulted in a decrease in level of cyclin D2-CDK4 complex and an increase in level of CDK4 complexed with p21CIP1/WAF1. Moreover, overexpression of cyclin D2 partially abrogated inhibition of Rb phosphorylation and G1 arrest in the hybridoma cells.
Ultracapacitors using P- and N- dopable poly(3-arylthiophene)s (1995)

The unique p- and n- dopability of polythiophenes was utilized to prepare ultracapacitors that promise high energy density and power density. To understand the charge transport mechanisms that occur during the electrochemical switching between the neutral and doped states, we prepared series of Poly(3-(p-X-phenyl)thiophene)s (X=-CMe{sub 3,} -Me, -OMe, -H,-F,-Cl,-Br-CF{sub 3,}-SO{sub 2}Me). Their electrochemical polymerization, electronic and ionic conductivity, solvent and electrolyte transport were studied using various techniques. Ultracapacitors prepared with these polymers as the active materials were examined for their cell ;impedance and effective capacitance during continuous charge/discharge cycles.
An Electrolytic Capacitor-Less High Power Factor LED Driver Based on a “One-and-a-Half Stage” Forward-Flyback Topology (2017)

A “one-and-a-half stage” forward-flyback converter for electrolytic capacitor-less light-emitting diode (LED) driver with high power factor (PF), high efficiency, low output ripple current, and long lifetime has been proposed and studied in this paper. The basic topology of the proposed topology is a single-switch forward-flyback converter for achieving high PF. In addition, a buck converter is inserted between the forward subconverter and the load for creating two paralleled power transfer paths. The most of input energy directly reaches the load through flyback subconverter, and only about 1/4 of total energy is transferred to the load through forward subconverter and buck converter. Therefore, the proposed topology is a “one-and-a-half stage” converter and can achieve higher efficiency than the traditional two-stage topologies. At the same time, power decoupling can be realized and the electrolytic capacitor can be eliminated. Optimal control scheme, detailed analysis, and design considerations for this improved converter are presented. Finally, an experimental prototype for 28 V/700 mA LED driver was built up to verify the theoretical analysis.
Materials and structures for hypersonic vehicles (1989)

Hypersonic vehicles are envisioned to require, in addition to carbon-carbon and ceramic-matrix composities for leading edges heated to above 2000 F, such 600 to 1800 F operating temperature materials as advanced Ti alloys, nickel aluminides, and metal-matrix composited; These possess the necessary low density and high strength and stiffness. The primary design drivers are maximum vehicle heating rate, total heat load, flight envelope, propulsion system type, mission life requirements and liquid hydrogen containment systems. Attention is presently given to aspects of these materials and structures requiring more intensive development.
Algebraic Decomposition of Fat and Water in MRI (2009)

The decomposition of magnetic resonance imaging (MRI) data to generate water and fat images has several applications in medical imaging, including fat suppression and quantification of visceral fat. We introduce a novel algorithm to overcome some of the problems associated with current analytical and iterative decomposition schemes. In contrast to traditional analytical schemes, our approach is general enough to accommodate any uniform echo-shift pattern, any number of metabolites and signal samples. In contrast to region-growing method that use a smooth field-map initialization to resolve the ambiguities with the IDEAL algorithm, we propose to use an explicit smoothness constraint on the final field-map estimate. Towards this end, we estimate the number of feasible solutions at all the voxels, prior to the evaluation of the roots. This approach enables the algorithm to evaluate all the feasible roots, thus avoiding the convergence to the wrong solution. The estimation procedure is based on a modification of the harmonic retrieval (HR) framework to account for the chemical shift dependence in the frequencies. In contrast to the standard linear HR framework, we obtain the frequency shift as the common root of a set of quadratic equations. On most of the pixels with multiple feasible solutions, the correct solution can be identified by a simple sorting of the solutions. We use a region-merging algorithm to resolve the remaining ambiguity and phase-wrapping. Experimental results indicate that the proposed algebraic scheme eliminates most of the difficulties with the current schemes, without compromising the noise performance. Moreover, the proposed algorithm is also computationally more efficient.
CEA, NSE and SCC Ag in bronchial lavage in patients with lung cancer. (1997)

CEA, NSE and SCC Ag levels were measured in bronchial lavage (BL) and serum in patients with endobronchial lung cancer (LC) and in patients with nonmalignant lung diseases (NMLD). In both groups of patients 100 ml of normal saline solution was used during the lavage procedure. Tumor markers were detected using radioimmunoassay. CEA levels in BL and in serum were measured in 84 patients with LC and in 94 patients with NMLD. BL CEA levels were significantly increased in patients with LC (97.4 +/- 56.4 ng/ml) in comparison to patients with NMLD (4.2 +/- 6.3 ng/ml). Patients with LC had CEA levels in lavage fluid about 30 times higher than in serum. Significantly increased BL CEA levels in patients with LC were found in the cases with more advanced bronchoscopic tumor and in those with positive bronchial secretion cytology than in other groups of patients with LC. NSE levels were measured in BL and in serum in 21 patients with small cell lung cancer, SCC Ag levels were measured in BL and in serum in 21 patients with squamous cell carcinoma. The control group consisted of 28 patients with NMLD and 8 patients with adenocarcinoma. Determination of CEA levels in BL can be useful additional diagnostic method in patients with LC. The measurement of NSE and SCC Ag levels in BL in LC patients was considered to be not useful because of the low diagnostic sensitivity and specificity.
Trigger Factor Associates with GroEL in Vivo and Promotes Its Binding to Certain Polypeptides (1997)

Trigger factor (TF) is a putative molecular chaperone recently found to function together with GroEL in the degradation of the fusion protein, CRAG. TF overproduction enhanced the ability of GroEL to form complexes with CRAG, as well as fetuin or histone. To define further this effect on GroEL binding, affinity columns containing a variety of denatured proteins were used. When cell extracts were applied onto a fetuin column, both TF and GroEL bound but not GroES. Upon ATP addition, TF and GroEL were eluted together and remained tightly associated (even in presence of GroES) in complexes containing one TF per GroEL 14-mer. Overproduction of TF enhanced the capacity of GroEL to bind to many denatured proteins. Moreover, GroEL-TF complexes isolated from such cells showed much greater binding capacity than GroEL from TF-deficient cells. Furthermore, the addition of pure TF to pure GroEL also enhanced markedly its binding capacity. The affinity of GroEL for CRAG also rises during heat shock due to GroEL phosphorylation. TF expression, however, did not promote GroEL phosphorylation. Moreover, heat shock and TF overproduction affected GroEL binding to other denatured polypeptides in distinct ways; only TF promoted binding to certain polypeptides, whereas only phosphorylation increased binding to others. Thus, association with TF and phosphorylation are independent regulators of GroEL function. This enhanced affinity of TF-GroEL complexes for unfolded proteins may also be important in protein folding, because TF has prolyl isomerase activity and associates with nascent polypeptides.
Metabolomics Biomarkers for Detection of Colorectal Neoplasms: A Systematic Review (2018)

Panels of metabolites consisting of amino acids in blood and nucleosides in urinary samples might be useful biomarkers for early detection of advanced colorectal neoplasms. However, to make metabolomic biomarkers clinically applicable, future research in larger studies and external validation of the results is required.
Detection of genital human papillomavirus by single-tube nested PCR and type-specific oligonucleotide hybridization (1995)

Cervical cancer is, on a global scale, the second most common form of cancer in women. Development of cervical carcinoma is strongly associated with infection by certain types of human papillomavirus (HPV). To facilitate the detection and molecular typing of HPV in clinical samples, nested-PCR amplification systems were developed for regions of the E1 and L1 genes. The nested amplifications were performed in a single reaction tube, and shifting between inner and outer primer pairs was achieved by a two-phase amplification with different annealing temperatures. This method eliminates cross-contamination between samples during transfer from the first to the second amplification step. A set of type-specific oligonucleotide probes were designed for the E1 system and used to distinguish 19 genital HPV types. The sensitivities of our amplification systems compare favorably with that for the L1 system on the basis of the MY09-MY11 primer pair (M.M. Manos, Y. Ting, D. K. Wright, A. J. Lewis, T. R. Broker, and S. M. Wolinsky, Cancer Cells 7:209-214, 1989) and our systems can be used on materials such as HPV-infected cell lines, cytobrush samples, cancer biopsies, and recent as well as archival Papanicolaou (Pap) smears. The high sensitivity coupled with the effective elimination of contamination in the transfer between the two amplification steps of the nested PCR makes these systems suitable for research as well as clinical analyses.
Galvanic skin response (GSR) as an index of cognitive load (2007)

Multimodal user interfaces (MMUI) allow users to control computers using speech and gesture, and have the potential to minimise users. experienced cognitive load, especially when performing complex tasks. In this paper, we describe our attempt to use a physiological measure, namely Galvanic Skin Response (GSR), to objectively evaluate users. stress and arousal levels while using unimodal and multimodal versions of the same interface. Preliminary results show that users. GSR readings significantly increase when task cognitive load level increases. Moreover, users. GSR readings are found to be lower when using a multimodal interface, instead of a unimodal interface. Cross-examination of GSR data with multimodal data annotation showed promising results in explaining the peaks in the GSR data, which are found to correlate with sub-task user events. This interesting result verifies that GSR can be used to serve as an objective indicator of user cognitive load level in real time, with a very fine granularity.
Toxicity of polymerized hemoglobin solutions. (1988)

Four solutions of bovine polymerized hemoglobin (BPHS) and rabbit plasma were used to replace one-third of the blood volume in five groups of rabbits. The first three solutions were "impure" because of the presence of stromal phosphatidyl-ethanolamine and phosphatidyl-serine in BPHS-1, environmental endotoxins in BPHS-2, and a large amount of higher molecular weight hemoglobin-glutaraldehyde polymers in BPHS-3. These solutions caused a 33 per cent mortality rate and significant morbidity which was characterized by hemodynamic instability, respiratory and renal insufficiency, elevation of hepatic enzyme levels, thrombocytopenia, leukopenia, disseminated intravascular coagulation (DIC) and activation of the alternate pathway of complement. Histopathologic changes found in the heart, lungs, liver, spleen and kidney were characterized by a combination of ischemic and inflammatory lesions. Fibrin thrombi were visible by immunofluorescence in the microcirculation. In contrast, the fourth solution (BPHS-4) was free of the aforementioned impurities; caused no deaths and minimal morbidity, which was limited to elevated levels of serum glutamic pyruvic transaminase and reduction of creatinine clearance; no DIC or complement activation, and mild histopathologic changes which were exclusively ischemic in nature. The results of this study indicated that the toxicity of polymerized hemoglobin solutions is due principally to the presence of impurities. Pure hemoglobin does exhibit mild toxicity when compared with a control solution which is most likely due to a vasoconstrictor effect of oxyhemoglobin.