gebhart/patrepeval huggingface dataset:
Mesenchymal-Epithelial Interactome Analysis Reveals Essential Factors Required for Fibroblast-Free Alveolosphere Formation (2018)

Lung epithelial cells and fibroblasts are key cell populations in lung development. Fibroblasts support type 2 alveolar epithelial cells (AEC2) in the developing and mature lung. However, fibroblast-AEC2 interactions have not been clearly described. We addressed this in the present study by time course serial analysis of gene expression sequencing (SAGE-seq) of epithelial cells and fibroblasts of developing and mature murine lungs. We identified lung fibroblast-epithelial interactions that potentially regulate alveologenesis and are mediated by fibroblast-expressed ligands and epithelial cell surface receptors. In the epithelial-fibroblast co-culture alveolosphere formation assay, single intervention against fibroblast-expressed ligand or associated signaling cascades promoted or inhibited alveolosphere growth. Adding the ligand-associated molecules fibroblast growth factor 7 and Notch ligand and inhibitors of bone morphogenetic protein 4, transforming growth factor β, and glycogen synthase kinase-3β to the culture medium enabled fibroblast-free alveolosphere formation. The results revealed the essential factors regulating fibroblast-AEC2 interactions.
Human teeth with and without caries studied by laser scattering, fluorescence, and absorption spectroscopy (1984)

The visible elastic light scattering and fluorescence emission from carious and noncarious regions of teeth were measured and compared. Carious teeth regions scattered light less effectively than noncarious regions for the spectral region 480-600 nm. The spectral shape of the fluorescence excited by a coherent source was similar to emission produced by incoherent (lamp) excitation. For both modes of excitation the emission peaks at approximately 550 nm. Differences in the fluorescence and light scattering spectra from carious and noncarious regions at a given wavelength was found not to be constant across the spectrum. Laser-induced fluorescence spectra for gamma irradiated teeth (total dose of 2000 rad) showed differences from control samples; the emission was blue shifted relative to the unirradiated samples. In addition, the relative visible absorption spectra for a tooth was measured in the visible region.
Puncturing effects on turbo codes (2002)

The authors address various important issues related to punctured turbo codes. A modified technique for finding the transfer function of punctured turbo codes is developed. This modified technique provides a means of deterministic evaluation of the weight distribution of the code, as well as a possibility of studying various puncturing patterns. These advantages are shown with some illustrative examples. Moreover, the paper explains some characteristics of the puncturing pattern, and arrives at useful guidelines for the design of a good puncturing matrix.
Diagnostic efficiency of an ultrarapid endoscopy room test for Helicobacter pylori. (1991)

There are several reliable methods for detecting Helicobacter pylori but all have as a major disadvantage the time required to yield a definitive result. We have modified the standard urease test so that a positive result is available in one minute. We describe the use of this test in biopsy specimens from the gastric antrum from 220 consecutive patients referred for upper gastrointestinal endoscopy. The performance of the 'one minute test' was compared with a standard urease test, Gram stain, and microbiological culture. Using culture as the 'gold standard' 80 (36%) of the patients were H pylori positive. The one minute test produced no false positives and showed a sensitivity of 89% and specificity of 100%, while the predictive values of a positive and negative test were 100% and 94% respectively. The diagnostic efficiency of the test was 96% compared to 85% for both the Gram stain and direct urease test. All positive results using the one minute test were available within one minute. The test is easy to prepare and costs approximately pounds 0.04. This new modification of the urease test should be superior to the currently available urease tests because a reliable result will be available in almost 90% of infected individuals even before endoscopy is completed.
Could Helicobacter pylori infection increase the risk of coronary heart disease by modifying serum lipid concentrations? (1996)

The impact of H pylori infection as an independent risk factor for CHD seems to be minor. On the other hand the results are consistent with the hypothesis that H pylori infection might modify the serum lipid concentrations in a way that could increase the risk of CHD.
Bias reformulation for one-shot function induction (2014)

Abstract. In recent years predicate invention has been under-explored as a bias reformulation mechanism within Inductive Logic Programming due to difficulties in formulating efficient search mech-anisms. However, recent papers on a new approach called Meta-Interpretive Learning have demonstrated that both predicate inven-tion and learning recursive predicates can be efficiently implemented for various fragments of definite clause logic using a form of abduc-tion within a meta-interpreter. This paper explores the effect of bias reformulation produced by Meta-Interpretive Learning on a series of Program Induction tasks involving string transformations. These tasks have real-world applications in the use of spreadsheet tech-nology. The existing implementation of program induction in Mi-crosoft’s FlashFill (part of Excel 2013) already has strong perfor-mance on this problem, and performs one-shot learning, in which a simple transformation program is generated from a single example instance and applied to the remainder of the column in a spreadsheet. However, no existing technique has been demonstrated to improve learning performance over a series of tasks in the way humans do. In this paper we show how a functional variant of the recently devel-oped MetagolD system can be applied to this task. In experiments we study a regime of layered bias reformulation in which size-bounds of hypotheses are successively relaxed in each layer and learned pro-grams re-use invented predicates from previous layers. Results indi-cate that this approach leads to consistent speed increases in learning, more compact definitions and consistently higher predictive accu-racy over successive layers. Comparison to both FlashFill and human performance indicates that the new system, MetagolDF, has perfor-mance approaching the skill level of both an existing commercial system and that of humans on one-shot learning over the same tasks. The induced programs are relatively easily read and understood by a human programmer. 1
Roadmap to Monetization of Unconventional Resources (2009)

Abstract What has been regarded as unconventional by many has been conventional for the few that have developed viable, and in many cases, very profitable projects that succeeded in extending the envelope of recoverable hydrocarbons. The range of recoverable hydrocarbons is bounded by physical constraints like reservoir properties, unfavorable hydrocarbon characteristics, or in many cases, hydrocarbons still captured in the formations. The methods of extraction that have been devised to address such challenges frequently combine applications of enhanced recovery, intensive stimulation, or advanced drilling. The distinction between conventional and unconventional can be reasoned not in the context of new versus old, more or less prolific accumulation attributes, or the method of extraction, but in the approach that is followed. A conventional development approach would cover the entire field with increasing intensity; an unconventional approach would pursue intensive development sequentially from the more prolific to the less prolific parts of the field. Although it is easy to see the technical benefits of unconventional methods, their integration with economic and market parameters is necessary in order to provide a successful implementation. The purpose of this paper is to present a set of features that are found as common denominators in successful developments of such resources. These common features could be viewed as unconventional resource development principals that outline the areas where particular attention is required for their ultimate success. In that context, the influence of market pricing, cost structure and resource evaluation are examined and offer a platform for project implementation that can be viewed as a "road map". The basic premise in this reasoning is that while it is not possible to develop a universal technological solution, careful adaptation of technology to the subsurface and operational realities allow synergies to develop that improve the chance of economic success. The recognition of key risks in unconventional resource development is instrumental in addressing the reasoning in resource classification. In that sense, while geological risks are often viewed as key in conventional resources, unconventional resources carry more risks as more complex extraction methods are implemented. Once development commences, it could maintain a positive outlook with changing market conditions as the associated costs relate to some extent to fuel costs that are in turn dependent on the product prices. The long development cycle of such projects lasting more than 20 years reduces the exposure to fluctuating prices as long as a reasonable average trend is considered at the onset. With evolving methods of extraction, the oil industry is shifting focus from exploration into intensive exploitation. Inevitably, the terms unconventional resources and a non conventional approach present a new direction for realizing the fuel sources of the future.
Two-Dimensional Optical Proximity Effects (1986)

In projection printing the proximity effects between adjacent two-dimensional features such as concentric elbows can be the limiting factor in designing layout rules. An aerial image simulation code based on the imaging algorithms in SAMPLE has been developed and used to investigate these proximity effects. The program accepts arbitrary polygonal shapes constructed of rectangular and triangular patches. The image is calculated using Hopkins transmission cross coefficient formulation and uses rapid integral evaluation techniques. The cpu time for this FORTRAN F77 program depends on the size of the mask and the partial coherence factor as 0.25[(1 + σ) 2A(NA/λ)2]2 seconds on a DEC VAX 11/780 using double precision, where A is the mask area, σ the coherence factor, NA the numerical aperture and λ the wavelength. The output intensity can be displayed with graphics tools such as UNIGRAFIX or cross-sectioned for input to SAMPLE development simulation along critical paths. Proximity effects in critical regions between features such as nested elbows, contacts near contacts and lines, and lines near large pads are studied. For small contacts studies show that a contact hole can be placed as close as 0.5λ/NA microns to another contact hole. For nested elbows the critical effect is the variation in intensity in the straight regions just adjacent to the corner. This undesirable variation is primarily due to the intrafeature intensity interactions and is not greatly influenced by the proximity of another nested elbow. For general feature shapes the proximity effects are reduced by increasing the partial coherence factor to 0.5 or higher but at the cost of reducing contrast and peak intensity. For contact masks a partial coherence of 0.3 is recommended for higher edge slope and peak intensities. Proximity effects of small defects are also illustrated.
MALAT1 in human adipose stem cells modulates survival and alternative splicing of PKCδII in HT22 cells (2016)

Brain injury may be caused by trauma or may occur in stroke and neurodegenerative diseases. Because the central nervous system is unable to regenerate efficiently, there is utmost interest in the use of stem cells to promote neuronal survival. Of interest here are human adipose-derived stem cells (hASCs), which secrete factors that enhance regeneration and survival of neurons in sites of injury. We evaluated the effect of hASC secretome on immortalized mouse hippocampal cell line (HT22) after injury. Protein kinase C δ (PKCδ) activates survival and proliferation in neurons and is implicated in memory. We previously showed that alternatively spliced PKCδII enhances neuronal survival via B-cell lymphoma 2 Bcl2 in HT22 neuronal cells. Our results demonstrate that following injury, treatment with exosomes from the hASC secretome increases expression of PKCδII in HT22 cells and increases neuronal survival and proliferation. Specifically, we demonstrate that metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a long noncoding RNA contained in the hASC exosomes mediates PKCδII splicing, thereby increasing neuronal survival. Using antisense oligonucleotides for MALAT1 and RNA immunoprecipitation assays, we demonstrate that MALAT1 recruits splice factor serine-arginine-rich splice factor 2 (SRSF2) to promote alternative splicing of PKCδII. Finally, we evaluated the role of insulin in enhancing hASC-mediated neuronal survival and demonstrated that insulin treatment dramatically increases the association of MALAT1 and SRSF2 and substantially increases survival and proliferation after injury in HT22 cells. In conclusion, we demonstrate the mechanism of action of hASC exosomes in increasing neuronal survival. This effect of hASC exosomes to promote wound healing can be further enhanced by insulin treatment in HT22 cells.
Cycloaddition von N‐Phenylmaleinimid an (1,2,3,6‐Tetrahydropyridyl)‐indole (1968)

Abstract 1‐Methyl‐2‐and 1‐methyl‐3‐(1‐methyl‐1,2,3,6‐tetrahydro‐4‐pyridyl)‐indole undergo 1,4‐cycloaddition (formally of the D IELS ‐A LDER ‐type) with N‐phenyl‐maleimide, leading to the pentacyclic compounds III and IV.
Effects of dexamethasone on mediator release from human lung fragments and purified human lung mast cells. (1983)

Purified human lung mast cells released histamine, leukotrienes, prostaglandin (PG) D2, thromboxane B2 (TxB2), and PGF2 alpha in response to anti-IgE stimulation. Incubation of the cells for 24 h with 10(-6) M dexamethasone, a treatment that inhibits mediator release from human basophils, had no effect on the release of these mediators from mast cells. Dexamethasone treatment of human lung fragments led to little or no inhibition of anti-IgE-induced release of the mast cell-derived mediator, histamine, but produced a significant inhibition of the release of PGE2, PGF2 alpha, and 6-keto-PGF1 alpha. As was the case with purified mast cells, the steroid did not inhibit the release of PGD2 or TxB2 from human lung fragments. Comparison of the quantities of PGD2 and TxB2 produced by purified cells and human lung fragments reveals that the mast cells produce quantities of these metabolites sufficient to account for the entire amount produced by challenged lung fragments. Dexamethasone inhibited spontaneous release from lung fragments of all cyclooxygenase products measured. These results suggest that the human lung parenchymal mast cell phospholipase is not inhibited by dexamethasone, whereas other phospholipase(s) in the lung are inhibited by the steroid. These results may be useful in explaining the resistance of acute allergic reactions, including anaphylaxis, to steroids, despite the potent antiinflammatory activity of steroids on subacute and chronic inflammation, such as in bronchial asthma, which may be initiated by IgE-dependent mechanisms.
Retrospective analysis of 22 patients with chronic pain treated by peripheral nerve stimulation (1980)

Twenty-two patients with chronic pain, chiefly from posttraumatic neuropathy, were treated by implanted peripheral nerve stimulators located proximal to the pain. Thirteen of these (62%) have experienced pain control for an average of 25 months. The experience of the surgeon is thought to be a major factor contributing to the successful results. There are theoretical and practical advantages to electrical stimulation and proximal portions of the peripheral nervous system. The surgical technique for implantation is described and the necessity for reoperation in some patients is explained.
Context-Aware Query Refinement for Mobile Web Search (2007)

Mobile Web search engines as well as fixed ones become much more important for our Web access in the near future. However, mobile computing environments have troublesome limitations, as compared with traditional desktop computing environments. In order to solve the so-called "mismatched query problem" due to more shortness and ambiguity of mobile users' original queries, this paper proposes a novel method for context-aware query refinement based on their current geographic location and real-world contexts which are inferred from the place-names representing the location and the Web as a knowledge database
Efficiency of energy conversion using shock waves (1985)

The flux-corrected transport algorithm has been used to simulate shock-wave flows in linear and spherically converging and diverging tubes in order to determine the energy distributions in the flows and the conversion efficiencies of energy to mechanical work. This was done to evaluate the possibility of using the positive phase of a shock wave, rather than combustion products, as the driving mechanism in an internal-combustion engine, and to suggest the optimum configuration of a supercharging device that uses shock waves to extract energy from the exhaust gases of internal-combustion engines. It is concluded that the positive phase of a shock wave would not be especially useful as the primary driving mechanism of an internal-combustion engine. In the case of the supercharging energy exchangers, the simulations indicate that for charging pressure ratios lower than about 5:1, a linear tube with a compression-chamber length of about 40% would be most efficient, while at higher pressure ratios a converging conical tube with a compression-chamber length of about 10% would be preferred.
Rough-Neural Image Classification using Wavelet Transform (2007)

Image classification plays an important role in many tasks, which is still a challenging problem. This paper proposes a hybrid image classification method, which integrates wavelet transform, rough set approach, and artificial neural networks (ANNs). Wavelet transform is employed to decompose the original images into different frequency sub-bands, then a set of statistical features are extracted from the wavelet coefficients, the feature set can be viewed as an information system. Although wavelet transform well decorrelates images, there still exist dependencies between coefficients. Hence the features extracted from the coefficients may be correlated. If the features from one sub-band are dependent on the features from another sub-band, the later one can be removed. Rough set approach is utilized to remove the correlated or redundant features. The reduced information system finally fed into neural network for classification. The performance of the method is evaluated in terms of training accuracy and testing accuracy, the experimental results confirm the effectiveness of the proposed approach.
Parallel‐coupled phase‐matched multiring optical filters (2005)

Abstract A periodic bandpass filter that is based on the phase‐matching principle and consists of several parallel‐coupled microrings is presented. The rings are identical in size; the coupling coefficients are chosen to provide maximally flat or equal ripple passband. Simulated filter characteristics exhibit steep roll‐off and large stopband rejection. Expressions are given to estimate the passband insertion loss and the stopband rejection level. The effects of loss and fabrication tolerances is examined. © 2005 Wiley Periodicals, Inc. Microwave Opt Technol Lett 44: 536–540, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20689
Juxtaposition of two viral DNA ends in a bimolecular disintegration reaction mediated by multimers of human immunodeficiency virus type 1 or murine leukemia virus integrase (1994)

Integration of retroviral DNA involves a coordinated joining of the two ends of a viral DNA molecule into precisely spaced sites on target DNA. In this study, we designed an assay that requires two separate oligonucleotides to be brought together via interactions between integrase promoters to form a "crossbones" substrate that mimics the integration intermediate. The crossbones substrate contains two viral DNA ends, each joined to one strand of target DNA and separated by a defined length of target DNA. We showed that purified integrases of human immunodeficiency virus type 1 (HIV-1) and murine leukemia virus (MLV) could mediate a concerted strand cleavage-ligation between the two half-substrates at one or both viral DNA joining sites (trans disintegration). Another major product, termed fold-back, resulted from an intramolecular attack on the phosphodiester bond at the viral-target DNA junction by the 3'-OH group of the same DNA molecule (cis disintegration). The activity of integrase on the crossbones substrate depended on the presence of viral DNA sequences. For trans disintegration, the optimal length of target DNA between the viral DNA joining sites of the crossbones substrate corresponded to the spacing between the staggered joints formed on two opposite strands of target DNA during retroviral DNA integration in vivo. The activity of integrases on crossbones did not require complementary base pairing between the two half-substrates, indicating that the half-substrates were juxtaposed solely through protein-DNA interactions. The crossbones assay, therefore, measures the ability of integrase to juxtapose two viral DNA ends, an activity which heretofore has been difficult to detect by using purified integrase in conventional assays. Certain mutant integrases that were otherwise inactive with the crossbones substrate could complement one another, indicating that no single protomer in the integrase multimer requires a complete set of functional domains either for catalytic activity or for juxtaposition of the two viral DNA ends by the active multimer.
Requirements and options for communications services in support of the Systems Autonomy Demonstration Project (1987)

A study of the requirements and options for interconnecting the development systems and demonstration test beds at NASA centers supporting the Systems Autonomy Demonstration Project (SADP) is presented. The communications requirements of SADP development and demonstration environments are described, potential communications protocols are examined, and expected communications error rates and system availability are described.
Generating automatically the documentation from PLC code by D4T3 to improve the usability and life cycle management of software in automation (2015)

D4T3 (i.e. Doxygen for TwinCAT3) was developed to generate automatically the documentation from a set of documented and/or undocumented PLC source files. D4T3 documentation was designed to support traditional PLC-world features (e.g. inputs, programs, tasks, etc.) and more recent Object Oriented features of IEC61131-3 (e.g. interfaces, inheritance, etc.). Moreover, this documentation was designed to be generated as an on-line manual (i.e. HTML) and/or as an off-line reference manual (e.g. L <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">A</sup> TEX, CHM, etc.). The usability, maintainability and understanding of documented PLC software was found significantly improved when the software was provided with its D4T3 documentation. Additionally, D4T3 reduced the time spent on documentation and managed the differences among versions. Thus, the automated documentation generator can be used to simplify/overcome the usability and life-cycle-management challenges in automation. It can also lead PLC vendors to design a common tool to generate the PLC software documentation supporting system engineers and software engineers in automation.