gebhart/patrepeval huggingface dataset:
Methylomic Analysis Identifies Frequent DNA Methylation of Zinc Finger Protein 582 (ZNF582) in Cervical Neoplasms (2012)

Our study shows ZNF582 is frequently methylated in CIN3 and worse lesions, and it is demonstrated as a potential biomarker for the molecular screening of cervical cancer.
Natural Exopolysaccharides Enhance Survival of Lactic Acid Bacteria in Frozen Dairy Desserts (2001)

Viable lactic acid-producing bacteria in frozen dairy desserts can be a source of beta-galactosidase for persons who absorb lactose insufficiently. However, freezing kills many of the cells, causing loss of enzymatic activity. Cultures selected for high beta-galactosidase activities and high survival rates in the presence of bile were examined for survivability during freezing in reduced-fat ice cream. Encapsulated S. thermophilus strains survived better than their nonencapsulated mutants in reduced-fat ice cream after freezing and frozen storage at -29 degrees C for 16 d (28 vs. 19%). However, a small nonencapsulated strain of Lactobacillus delbrueckii sp. bulgaricus survived better than the large encapsulated strain in reduced-fat ice cream. Factors that improved survival of encapsulated S. thermophilus 1068 in ice cream were 1) harvest of cells in the late-log phase of growth at 37 degrees C rather than at 40, 42.5, or 45 degrees C; 2) overrun at 50% rather than 100%; and 3) storage at -17 degrees C rather than -23 or -29 degrees C. Survival of strain ST1068 was unaffected by 1) neutralization of acid during growth or 2) substitution of nitrogen for air in building overrun.
A dual-loop automatic gain control for infrared communication system (2003)

This paper presents a dual-loop automatic gain control (AGC) employed in a 10 Mbps infrared communication system. The AGC is composed of an exponential-type variable-gain amplifier, a shaping filter, a gain/buffer stage, a noncoherent envelope detector, and a pair of integrators that provide dual loop bandwidths. The switch and two integrators are realized by a proposed switched integrator technique. The fast acquisition is accomplished by a 500 kHz loop bandwidth at the initial acquisition state and followed by a 50 kHz loop bandwidth at the steady state. The AGC is implemented in 0.6 /spl mu/m SPTM CMOS technology. According to the post-layout simulation, it achieves an acquisition time of 5 /spl mu/s and provides a constant output of 1V/sub pp/ at a 50 /spl Omega/ load for 20 dB input signal amplitude range. The dual-loop AGC consumes 88 mW power from a single 3.3 V supply and occupies 1.8/spl times/1.8 mm/sup 2/ area.
Sharing Orbitals:  Ultrafast Excited State Deactivations with Different Outcomes in Bucky Ferrocenes and Ruthenocenes (2006)

We report on the singlet ground and singlet/triplet excited-state features of a series of bucky ferrocenes, bucky ruthenocenes, and respective reference compounds. In the bucky ferrocene conjugates, intimate contacts between the fullerenes and ferrocenes result in appreciable ground-state interactions-suggesting a substantial shift of charge density from the electron donor (i.e., ferrocene) to the electron acceptor (i.e., fullerene). In contrast, no prominent charge-transfer features were observed for the bucky ruthenocene conjugates. An arsenal of experimental techniques, ranging from fluorescence (i.e., steady state and time-resolved) and pump probe experiments (i.e., femtosecond and nanoseconds) to pulse radiolysis, were employed to examine excited-state interactions. In the excited states, bucky ferrocene conjugates are dominated by rapid charge separation reactions (0.8 +/- 0.1 ps) to yield metastable radical ion pairs. The radical ion pair lifetimes vary between 27 and 39 ps. No charge separation was, however, found in the corresponding bucky ruthenocence. Instead, an intrinsically faster excited-state deactivation (approximately 200 ps) evolves from the heavier ruthenium center-relative to iron. This effect is further augmented by the unfavorably shifted oxidation potential in ruthenocene of about 0.61 V, which in ruthenocene (-deltaG(ET) = -0.26 eV), in contrast to ferrocene (-deltaG(ET) = 0.35 eV), renders charge separation thermodynamically unfeasible.
Digital Design with Verilog HDL (1990)

Verilog HDL is the standard hardware description language for the design of digital systems and VLSI devices. This volume shows designers how to describe pieces of hardware functionally in Verilog using a top-down design approach, which is illustrated with a number of large design examples. The work is organized to present material in a progressive manner, beginning with an introduction to Verilog HDL and ending with a complete example of the modelling and testing of a large subsystem.
Preliminary study on immunomodulating actions of Actarit in mice (2000)

Objective:To study the immunomodulating actions of Actarit. Methods: Reactions were measured by increasing in weight of the ears challenged with dinitrofluorobenzene(DNFB);Enhanced delayed type hypersensitivity(DTH) reaction was induced by cyclophosphamide (d3 before immunization,250 mg·kg -1 , ip), while suppressed DTH reaction was induced by cyclosphamide (d0, 80 mg·kg -1 ,ip);T lymphocyte subpopulations were measured by indirect immunofluorescened assays. Results: DTH, which was enhanced by cyclophosphamide (Cy,d3 before immunization, 250 mg·kg -1 ,ip), was suppressed by Actarit 50,100 mg·kg -1 ·d -1 ig for 5 d and decreased L3T4 +/Lyt 2 + cell ratio in BALB/c mice. DTH, which was suppressed by Cy(od, 80 mg·kg -1 , ip), was enhanced by Actarit 50, 100 mg·kg -1 ·d -1 , ig for 5 d and Actarit increased the L3T4 +/Lyt 2 + cell ratio in BALB/c mice. Conclusion:The immunomodulating actions of Actarit might be brought about by altering Th/Ts cell ratio.
‘La Chanson c'est pour tout le monde’: an introduction to the music of Georges Brassens (2000)

The singer-songwriter Georges Brassens (1921–81) is one of the most critically lauded and commercially successful French musicians of all time. The author and composer of text and music for around 150 songs, with LP sales of over 20 million, Brassens is perhaps the most widely disseminated French ‘popular’ musician of the post-war era, particularly in French-speaking countries. Regarded by many as a cultural and musical icon, he is seen as a standard bearer for liberal French values, and – transcending standard distinctions between ‘popular’ and ‘serious’ styles – as a pivotal figure in the history of French music, credited with ‘revitaliz[ing] the French post-war song’ by ‘accomplishing the synthesis of popular song and true poetry’.
A State-Based Approach to Testing Aspect-Oriented Programs. (2005)

This paper presents a state-based approach to testing aspect-oriented programs. Aspectual state models, as an extension to the testable FREE state model of classes, are exploited to capture the impact of aspects on the state models of classes. To generate test suites for adequately testing object behavior and interaction between classes and aspects in terms of message sequences, we transform an aspectual state model to a transition tree, where each path from the root to some leaf node indicates a template of test cases, i.e. message sequences. Since the statebased approach is directly built upon the test design patterns for object-oriented programs, it is not only applicable to the simultaneous development of classes and aspects, but also to the incremental development of aspects based on the existing classes. Keywords: Aspect-oriented programming, software testing, state model, transition tree
Implementation of BASEL-II in the Banking Industry (A Case study of Pakistani Banks) (2019)

Banking industry is exposed to different type of risks like credit, operational, interest rate risk, liquidity risk, foreign currency risk, compliance risk, reputational risk, and country risk. Banking industry can only become stable and stronger if they have proper tools to mitigate these risks. Due to product innovation and complexity of operations banks are giving more importance to mitigate these types of risks. Regulators (SBP) are emphasizing banks to develop their tools in order to control these risks. BASEL-II is a basic tool which is used internationally in banking sector to mitigate these risks. Our study is focused on the implementation of BASEL-II in Pakistani Banking Industry. Researcher has analyzed that its implementation will bring positive effect in the Pakistani banking industry. Moreover what are the basic challenges banks are facing during its implementation. Data have been collected from fifteen banks a combination of Large, Medium, Small, Islamic and foreign banks operating in Pakistan selected on random basis. Results are analyzed through Pie Charts. This research will be helpful for the banking professional especially associated with risk management division and working towards the implementation of BASEL-II. Basel-II is still in the phase of implementation in the Banking industry in Pakistan. This research will provide the base to those want to study the after implementation effects of Basel-II in the Banking industry.
Quantification of contrast agent materials using a new image- domain multi material decomposition algorithm based on dual energy CT (2019)

Objective: Dual-Energy CT (DECT) is an imaging modality in which the objects are scanned by two different energy spectra. Using these two measurements, two type of materials can be separated and density image pairs can be generated as well. Decomposing more than two materials is necessary in both clinical and industrial CT applications. Methods: In our MMD, barycentric coordinates were chosen using an innovative local clustering method. Local clustering increases precision in the barycentric coordinates assignment by decreasing search domain. Therefore the algorithm can be run in parallel. For optimizing coordinates selection, a fast bi-directional Hausdorff distance measurement is used. To deal with the significant obstacle of noise, we used Doubly Local Wiener Filter Directional Window (DLWFDW) algorithm. Results: Briefly, the proposed algorithm separates blood and fat ROIs with errors of less than 2 and 9 % respectively on the clinical images. Also, the ability to decompose different materials with different concentrations is evaluated employing the phantom data. The highest accuracy obtained in separating different materials with different concentrations was 93 % (for calcium plaque) and 97.1 % (for iodine contrast agent) respectively. The obtained results discussed in detail in the following results section. Conclusion: In this study, we propose a new material decomposition algorithm. It improves the MMD work flow by employing tools which are easy to implement. Furthermore, in this study, an effort has been made to turn the MMD algorithm into a semi-automatic algorithm by employing clustering concept in material coordinate’s assignment. The performance of the proposed method is comparable to existing methods from qualitative and quantitative aspects. Advances in knowledge: All decomposition methods have their own specific problems. Image- domain decomposition also has barriers and problems, including the need for a predetermined table for the separation of different materials with specified coordinates. In the present study, it attempts to solve this problem by using clustering methods and relying on the intervals between different materials in the attenuation domain.
Cardiac Resynchronization Therapy for Patients With Left Ventricular Systolic Dysfunction (2007)

CRT reduces morbidity and mortality in patients with LV systolic dysfunction, prolonged QRS duration, and NYHA class 3 or 4 symptoms when combined with optimal pharmacotherapy. The incremental benefits of combined CRT plus implantable cardioverter-defibrillator devices vs CRT-alone devices in patients with LV systolic dysfunction remain uncertain.
Resonant Rydberg Dressing of Alkaline-Earth Atoms via Electromagnetically Induced Transparency (2016)

We develop an approach to generate finite-range atomic interactions via optical Rydberg-state excitation and study the underlying excitation dynamics in theory and experiment. In contrast to previous work, the proposed scheme is based on resonant optical driving and the establishment of a dark state under conditions of electromagnetically induced transparency (EIT). Analyzing the driven dissipative dynamics of the atomic gas, we show that the interplay between coherent light coupling, radiative decay, and strong Rydberg-Rydberg atom interactions leads to the emergence of sizable effective interactions while providing remarkably long coherence times. The latter are studied experimentally in a cold gas of strontium atoms for which the proposed scheme is most efficient. Our measured atom loss is in agreement with the theoretical prediction based on binary effective interactions between the driven atoms.
Lymphocyte-Fibroblast Interactions (1997)

Chronic inflammatory reactions are usually characterized by inflammatory cell accumulation in the extravascular connective tissue. In such sites, inappropriate activation of circulating or resident lymphocytes becomes self-perpetuating and can lead to chronic tissue destruction. In addition to that, the locally infiltrated lymphocytes should have an opportunity to interact directly with fibroblasts composing the connective tissue. The direct interactions of those different cell types seem to play important roles in lymphocyte lodging and retention in such sites. Thus, for clarification of the immunopathogenesis of the chronic inflammatory diseases, including periodontitis, it is important that the molecular mechanisms involved in the heterotypic cell-cell interactions be revealed. In fact, it has been demonstrated that lymphocytes interact with various non-hematopoietic cells, such as epithelial cells and endothelial cells. Regarding interactions with fibroblasts, it has been shown that IFN gamma-stimulated fibroblasts can regulate the proliferative responses of T-lymphocytes both positively and negatively. Furthermore, activated lymphocytes have demonstrated strong binding ability to various fibroblast cell lines. Blocking experiments utilizing monoclonal antibodies specific to various cell adhesion molecules revealed that very late antigen (VLA) integrins, lymphocyte-function-associated antigen (LFA-1)/intercellular adhesion molecule-1 (ICAM-I), CD44/hyarulonate are, at least in part, involved in lymphocyte-fibroblast interactions. In addition, recent findings raised the possibility that the adhesive interactions between lymphocytes and fibroblasts influenced the various cellular functions of each cell type. In fact, it was recently demonstrated that the adhesive interactions stimulated fibroblasts to increase expression of inflammatory cytokine mRNA. These results strongly suggest that fibroblasts are not merely innocent bystanders but actively participate in local inflammatory reactions by directly interacting with locally infiltrated lymphocytes.
Urokinase plasminogen activator protects cardiac myocytes from oxidative damage and apoptosis via hOGG1 induction (2017)

The role of uPA in tissue remodeling and cell migration is already well established. In addition, uPA was reported to stabilize p53, a key cell cycle control, DNA repair and apoptosis initiation protein. We aimed to determine the role of uPA-uPAR signaling towards cell survival or apoptosis in human adult cardiac myocytes (HACM). HACM were stimulated with uPA and DNA damage was inflicted by incubating cells with 200 µM H<sub>2</sub>O<sub>2</sub>. To analyze for apoptotic cells we applied TUNEL staining. Oxidative damage foci were analyzed by staining for 8-oxoguanine base pairs. In vivo qPCR analysis from RNA extracted from failing human hearts demonstrated a close relation of uPA with apoptosis and the p53 pathway. Furthermore, we observed a close correlation of uPA and p53 protein in homogenized tissue lysates. In vitro studies revealed that uPA preincubation protected HACM from oxidative damage induced cell death and reduced oxidative damage foci. uPA protection is independent of its catalytic activity, as the amino terminal fragment of uPA showed similar protection. A key enzyme for repairing oxidative DNA damage is the p53 target hOGG1. We found a significant increase of hOGG1 after pretreatment of HACM with uPA. Knockdown of hOGG1 completely abrogated the protective effect of uPA. We conclude that uPA might have a tissue protective role in human hearts besides its role in tissue remodeling. Tissue protection is mediated by the DNA repair protein hOGG1. This might be beneficial during tissue remodeling and thus could be a target for therapeutic approaches in the diseased heart.
Gene Cloning and Characterization of an Acidic Xylanase from<i>Acidobacterium capsulatum</i> (1998)

The gene xynA encoding an acid endo-beta-1,4-xylanase from an acidophilic bacterium, Acidobacterium capsulatum 161, was cloned and expressed in Eschrichia coli. The nucleotide sequence of the 1.6-kb DNA fragment containing xynA was analyzed, revealing an open reading frame of 1,215 bp encoding a peptide of 405 amino acid residues. The deduced amino acid sequence of XynA was very similar to other xylanases that are from the glycosyl hydrolase family 10. XynA was purified to homogeneity by SDS-polyacrylamide gel electrophoresis from E. coli transformants. The molecular mass and isoelectric point of XynA were 41 kDa and 7.3, respectively. The xylanase activity of the cloned XynA is an endo-acting enzyme that shows optimal activity at pH 5.0 and 65 degrees C, and is stable pH between 3.0 and 8.0. The K(m) and Vmax with oat spelt xylan as a substrate at pH 5.0 and 30 degrees C are 3.5 mg/ml and 403 mumol/min/mg.
Causality for Machine Learning (2022)

Graphical causal inference as pioneered by Judea Pearl arose from research on artificial intelligence (AI), and for a long time had little connection to the field of machine learning. This article discusses where links have been and should be established, introducing key concepts along the way. It argues that the hard open problems of machine learning and AI are intrinsically related to causality, and explains how the field is beginning to understand them.
Recent progress in luteinizing hormone/human chorionic gonadotrophin hormone research (2009)

The role of luteinizing hormone (LH) and human chorionic gonadotrophin hormone (hCG) in the regulation of normal reproductive functions in males and females is quite well established. Besides the use of hCG in the development of diagnostic immunoassays, it has been successfully used in the induction of final follicular maturation and ovulation in the assisted reproductive technologies. The basic and clinical research on the nongonadal actions of LH/hCG in the recent years has extended the potential of using these hormones in several clinical indications. Hereby we will analyze the advances in the LH/hCG research (briefly emphasizing the nongonadal research), which has the potential for multiple novel therapies in reproductive and the other areas of medicine.
Nucleation and growth of chemical beam epitaxy gallium nitride thin films (1997)

Gallium nitride films have been grown on (0001) sapphire substrates by chemical beam epitaxy (CBE) using triethyl gallium (TEG) and ammonia (NH3) precursors. Prior to the CBE epi-GaN layer growth, electron cyclotron resonance plasma-assisted metal-organic molecular beam epitaxy was utilized to deposit a nucleation layer at lower temperatures. The crystallinity of CBE-grown GaN films was found to be strongly growth–temperature dependent. The degree of crystallinity was correlated with the surface carbon composition as measured in situ by mass spectroscopy of recoiled ions. The optimum growth–temperature range for CBE GaN growth was found to be between 800 and 825 °C. Within this narrow window, thin films with streaky two-dimensional reflection high-energy electron diffraction patterns and good photoluminescence properties were obtained. The surface rms roughness, as measured by atomic force microscopy, was as low as 40 Å/1 μm2 for the highest quality thin films; lattice-resolved images supported the deposition of crystalline GaN revealing hexagonal structures with the spacing anticipated for GaN.
Fluorine substitutent effects on poly(2,6‐diphenylphenylene ether) (1993)

Abstract A series of fluoro‐substituted poly(2,6‐diphenylphenylene ether)s (P 3 O) with systematically varied structures were prepared. The properties of the polymers change significantly with the variations in the polymer structures. By increasing the number of fluorine substituents on P 3 O polymer, the melting points and the tendency to crystallize for these polymers decrease significantly. Random copolymers from fluoro‐substituted 2,6‐diphenylphenols and 2,6‐diphenylphenol were also prepared. The influence of copolymer structure on the transition temperatures and crystallinity of the resulting copolymers is described. © 1993 John Wiley & Sons, Inc.
Transesterification of <i>Camelina Sativa</i> Oil using Supercritical and Subcritical Methanol with Cosolvents (2009)

Transesterification of camelina oil using supercritical methanol with hexane as a cosolvent and subcritical methanol along with potassium hydroxide as a cosolvent/catalyst was investigated to study the methyl ester conversion process. It was found that cosolvents play a vital role in reducing the severity of critical operational parameters and maximize the biodiesel yield. The experimental results from the process parametric evaluation studies show that supercritical methanol with hexane as a cosolvent could produce maximum methyl esters using the following conditions: reaction temperature of 290 °C, methanol to oil ratio of 45, and reaction time of 40 min. For subcritical methanol condition with 0.3 wt % potassium hydroxide as a cosolvent, methyl ester yields of +90% are obtained using the following conditions: reaction temperature of 180 °C, methanol to oil molar ratio of 30, and a reaction time of 20 min. Process variables critical to the methyl ester conversion are determined to be cosolvent ratio, molar ratio of alcohol to oil, and reaction time. Fuel properties of the biodiesel produced are comparable to those of regular diesel and conform to the ASTM standards.
A three-dimensional DFT algorithm using the fast Hartley transform (1987)

A three-dimensional (3-D) Discrete Fourier Transform (DFT) algorithm for real data using the one-dimensional Fast Hartley Transform (FHT) is introduced. It requires the same number of one-dimensional transforms as a direct FFT approach but is simpler and retains the speed advantage that is characteristic of the Hartley approach. The method utilizes a decomposition of the cas function kernel of the Hartley transform to obtain a temporary transform, which is then corrected by some additions to yield the 3-D DFT. A Fortran subroutine is available on request.