gebhart/patrepeval huggingface dataset:
How to assess sympathetic activity in humans (1999)

Sympathetic factors play a central role not only in cardiovascular homeostatic control but also in the pathogenesis and/or in the progression of several cardiovascular diseases, such as essential hypertension, myocardial infarction, cardiac arrhythmias and congestive heart failure. This explains why assessment of adrenergic neural function in humans has been, and certainly still remains, one of the major fields in cardiovascular research. The present paper will review in detail the haemodynamic, pharmacological, biochemical, neurophysiological, neurochemical and neural imaging techniques by which sympathetic activity is assessed in humans, highlighting the main advantages and limitations of each of them. Although plasma noradrenaline measurement represents a useful guide to assess sympathetic neural function, direct recording of sympathetic nerve traffic via microneurography and noradrenaline radiotracer methods have in recent years largely supplanted the plasma noradrenaline approach. This is because they allow (1) discrimination between the central or peripheral nature of increased plasma noradrenaline levels, and (2) precise estimation of the behaviour of regional sympathetic neural function both under physiological and pathological conditions. In contrast, the approach based on spectral analysis of heart rate and blood pressure signals has been shown to have important limitations which prevent the method from faithfully reflecting sympathetic cardiovascular drive. Neural imaging techniques, which require expensive technical support, allow direct visualization of sympathetic enervation of human organs, thus providing information on the 'in vivo' metabolism of noradrenaline in different cardiovascular districts. Although technical improvements have allowed a more precise assessment of human adrenergic function, no technique so far available can be viewed as a 'gold standard' with which the others might be compared. Limitations and disadvantages of the various techniques may be reduced if these methods are seen as being complementary and employed in combination, allowing more reliable information to be achieved on the sympathetic abnormalities characterizing cardiovascular diseases, and thus hopefully providing a stronger rationale for newer therapeutic approaches involving pharmacological modification of the sympathetic nervous system and adrenoreceptors.
Epidemiology, Genetics, and Ecology of Toxigenic <i>Vibrio cholerae</i> (1998)

Cholera caused by toxigenic Vibrio cholerae is a major public health problem confronting developing countries, where outbreaks occur in a regular seasonal pattern and are particularly associated with poverty and poor sanitation. The disease is characterized by a devastating watery diarrhea which leads to rapid dehydration, and death occurs in 50 to 70% of untreated patients. Cholera is a waterborne disease, and the importance of water ecology is suggested by the close association of V. cholerae with surface water and the population interacting with the water. Cholera toxin (CT), which is responsible for the profuse diarrhea, is encoded by a lysogenic bacteriophage designated CTXPhi. Although the mechanism by which CT causes diarrhea is known, it is not clear why V. cholerae should infect and elaborate the lethal toxin in the host. Molecular epidemiological surveillance has revealed clonal diversity among toxigenic V. cholerae strains and a continual emergence of new epidemic clones. In view of lysogenic conversion by CTXPhi as a possible mechanism of origination of new toxigenic clones of V. cholerae, it appears that the continual emergence of new toxigenic strains and their selective enrichment during cholera outbreaks constitute an essential component of the natural ecosystem for the evolution of epidemic V. cholerae strains and genetic elements that mediate the transfer of virulence genes. The ecosystem comprising V. cholerae, CTXPhi, the aquatic environment, and the mammalian host offers an understanding of the complex relationship between pathogenesis and the natural selection of a pathogen.
Cover Image (2018)

The cover image, by Zhuo Chen et al., is based on the Correspondence The clinical characteristics and histopathological features of chronic rhinosinusitis with unilateral nasal polyps in 136 patients in Southern China, DOI: 10.1111/coa.13147.
Some Case Histories of Remedial Work Resulting from Water Tracer Surveys (1966)

Abstract Use of water tracer surveys to improve the over-all performance of waterfloods has long been recognized. Remedial work to water injection wells is becoming more important as the ratio of secondary reserves to primary reserves increases. While the proper use of tracer surveys does not necessarily mean a workover after every survey, too little significance is often given surveys where they could be of real productive use. This paper lists several case histories where tracer surveys were run and properly analyzed, resulting in thoughtful remedial work. What actual effect this remedial work had on production in the immediate area it also shown, when available. Introduction During the past 10 years, waterflood operators have tended to rely more on the use of quantitative water injection profiles. Though there are several different types and methods being used today to obtain this quantitative information, this paper will not discuss their principles or merits; rather, the assumption is made that quantitative water injection profiles can be run by a variety of service companies. Concern over what can and has happened from this point is the basis of this paper. This work was undertaken to present evidence from actual case histories where water tracer surveys were used, relied upon and found capable of being highly informative and of utmost practical value. During the search for such histories, an effort was made to stay away from examples where evaluation of remedial work could only be done at the injection well. Instead, examples are sought where direct production results confirmed proper water tracer survey evaluation of injection well remedial work, regardless of its success. This had a tendency to lead the author away from any but the most positive cases-where any cause for production changes, other than the success or failure of the remedial work, was extremely remote. Case History 5 is somewhat of an exception to this aim. Case History 1 This case history was taken from a dolomite flood in which a northwest-southeast breakthrough system had been indicated (Fig. 1). Well 63 was converted to water injection in March, 1964. By June, 1964, Well 124 started to increase in water production with no increase in oil production (Fig. 2). This trend continued until Well 124 was producing over 100 BWPD and very little oil (2 to 3 B/D). JPT P. 791ˆ
Multiple-scattering suppression by cross correlation (1997)

We describe a new method for characterizing particles in turbid media by cross correlating the scattered intensity fluctuations at two nearby points in the far field. The cross-correlation function selectively emphasizes single scattering over multiple scattering. The usual dynamic light-scattering capability of inferring particle size from decay rate is thus extended to samples that are so turbid as to be visually opaque. The method relies on single-scattering speckle being physically larger than multiple-scattering speckle. With a suitable optical geometry to select nearby points in the far field or equivalently slightly different scattering wave vectors (of the same magnitude), the multiple-scattering contribution to the cross-correlation function may be reduced and in some cases rendered insignificant. Experimental results demonstrating the feasibility of this approach are presented.
Potential Methods for Detecting Pits in Tart Cherries (1991)

Approximately 98% of the U.S. tart cherry crop is pitted and processed into canned, frozen, and dried fruit or made into juice. U.S. Grade A pitted tart cherries are currently allowed to contain up to 1 pit per 1.1 kg (2.5 lb) of finished cherries. To minimize product liability, and maximize end-user and consumer acceptance of pitted cherries, a finished pack having not over 1 pit per 28.3 kg (62.4 lb) of cherries is desired. Potential methods for the automatic detection and rejection of unpitted cherries and loose pits were investigated. Light transmission coupled with machine vision and image analysis provided evidence for the highest possibility of success at this time.
Augmented example-based synthesis using relational perturbation properties (2019)

Example-based specifications for program synthesis are inherently ambiguous and may cause synthesizers to generate programs that do not exhibit intended behavior on unseen inputs. Existing synthesis techniques attempt to address this problem by either placing a domain-specific syntactic bias on the hypothesis space or heavily relying on user feedback to help resolve ambiguity. We present a new framework to address the ambiguity/generalizability problem in example-based synthesis. The key feature of our framework is that it places a semantic bias on the hypothesis space using "relational perturbation properties" that relate the perturbation/change in a program output to the perturbation/change in a program input. An example of such a property is permutation invariance: the program output does not change when the elements of the program input (array) are permuted. The framework is portable across multiple domains and synthesizers and is based on two core steps: (1) automatically augment the set of user-provided examples by "applying" relational perturbation properties and (2) use a generic example-based synthesizer to generate a program consistent with the augmented set of examples. Our framework can be instantiated with three different user interfaces, with varying degrees of user engagement to help infer relevant relational perturbation properties. This includes an interface in which the user only provides examples and our framework automatically infers relevant properties. We implement our framework in a tool SKETCHAX specialized to the SKETCH synthesizer and demonstrate that SKETCHAX is effective in significantly boosting the performance of SKETCH for all three user interfaces.
Model Reduction for Large-Scale Systems with High-Dimensional Parametric Input Space (2008)

A model-constrained adaptive sampling methodology is proposed for the reduction of large-scale systems with high-dimensional parametric input spaces. Our model reduction method uses a reduced basis approach, which requires the computation of high-fidelity solutions at a number of sample points throughout the parametric input space. A key challenge that must be addressed in the optimization, control, and probabilistic settings is the need for the reduced models to capture variation over this parametric input space, which, for many applications, will be of high dimension. We pose the task of determining appropriate sample points as a PDE-constrained optimization problem, which is implemented using an efficient adaptive algorithm that scales well to systems with a large number of parameters. The methodology is demonstrated using examples with parametric input spaces of dimension 11 and 21, which describe thermal analysis and design of a heat conduction fin, and compared with statistically based sampling methods. For these examples, the model-constrained adaptive sampling leads to reduced models that, for a given basis size, have error several orders of magnitude smaller than that obtained using the other methods.
Geologically consistent velocities obtained by high definition tomography (2011)

Velocity model building remains a crucial step in seismic depth imaging. Advances in residual move‐out picking, which can now be performed very densely in 5D, and in applied mathematics (solvers can now apply to huge linear systems) make it possible to fine‐tune the tomography with the view of improving the definition of the estimated velocity models. By carefully choosing velocity model parameters and by tailoring inversion criterion to locally coherent events picked with maximum density, data term in cost function can be maximized with respect to smoothing term, and high definition velocity models can be obtained. We illustrate the method on both synthetic and real examples involving structural complexities.
Inhibition of the specific 3H-DL-Glu binding in the hippocampus of rat brain by lead. (1998)

The effect of Pb2+ on 3H-DL-Glutamate (3H-DL-Glu) binding in the membrane preparations from the hippocampus of rat brain was investigated with a view to explaining the cognitive and learning deficits produced by the heavy metal. The results indicated that Pb2+ (3.1-25.0 mumol.L-1) inhibited 3H-DL-Glu binding in a concentration-dependent manner. Scatchard analysis further revealed that at a concentration of 6.3 mumol.L-1 Pb2+ interfered with binding mainly through significantly decreasing the density of binding sites. This finding provided an important insight into Pb2(+)-induced impairments in learning and memory previously documented in children and in experimental animals chronically exposed to Pb2+.
[Autopsy case of malignant carcinoid tumor of the ascending colon]. (1983)

A 72-year-old female operated for ascending colon cancer was histologically diagnosed as having co-existing goblet cell-like carcinoid and rosette-forming carcinoid. The tumor cells were positive for the argyrophil reaction, but negative for the argentaffin reaction. A few tumor cells had both argyrophil granules and sulfated acid mucin in their cytoplasm. Despite combination chemotherapy she expired 10 months after the operation. Autopsy revealed local recurrence and metastases to the liver, lung, pancreas, left adrenal and many lymph nodes.
Retaining the Nano in Nanocrystalline Alloys (2012)

Judicious alloying can prevent grain growth in nanocrystalline metals, preserving their useful properties at high temperatures.
Genome-wide identification of peroxisome proliferator response elements using integrated computational genomics (2006)

Peroxisome proliferator-activated receptor (PPAR) agonists are currently used therapeutically in humans, even though many of their direct gene targets are unknown. Because PPARs can directly regulate gene expression through peroxisome proliferator response elements (PPREs), we pursued the computational prediction of PPREs on a genome-wide scale. Contrary to current hypotheses, PPREs are not isotype-specific, nor do flanking nucleotides confer additional information. However, a position weight matrix-based search for PPREs within upstream conserved elements yielded sufficient selectivity for a genome-wide search. Additionally, a novel motif occurring with greater prevalence than PPREs was revealed. Microarray and gene ontology analyses further validated our search technique and provided new functional clusters of genes that were not previously known to be directly regulated by PPARs (e.g., chromatin remodeling, DNA damage response, Wnt, and mitogen-activated protein kinase signaling). This first genome-wide library of high-confidence predicted PPAR target genes will be a valuable resource to PPAR biologists.
Chk1 inhibition and Wee1 inhibition combine synergistically to impede cellular proliferation (2011)

Inhibition of the checkpoint kinase Chk1, both as a monotherapy and in combination with DNA damaging cytotoxics, is a promising therapeutic approach for the treatment of a wide array of human cancers. However, much remains to be elucidated in regard to the patient populations that will respond best to a Chk1 inhibitor and the optimal therapeutics to combine with a Chk1 inhibitor. In an effort to discover sensitizing mutations and novel combination strategies for Chk1 inhibition, an siRNA screen was performed in combination with the selective Chk1 inhibitor AR458323. This screen employed a custom made library of siRNAs targeting 195 genes, most of which are involved in cell-cycle control or DNA damage repair. One of the most prominent and consistent hits across runs of the screen performed in three different cancer cell lines was Wee1 kinase. MK-1775 is a small molecule inhibitor of Wee1 that is currently in early stage clinical trials. In confirmation of the results obtained from the siRNA screen, AR458323 and MK-1775 synergistically inhibited proliferation in multiple cancer cell types. This antiproliferative effect correlated with a synergistic induction of apoptosis. In cellular mechanistic studies, the combination of the two molecules resulted in dramatic decreases in inhibitory phosphorylation of cyclin-dependent kinases, an increase in DNA damage, alterations in cell-cycle profile, and collapse of DNA synthesis. In conclusion, the clinical combination of a Chk1 inhibitor and a Wee1 inhibitor holds promise as an effective treatment strategy for cancer.
Validation using CASE tools (2003)

Describes how computer assisted software engineering (CASE) tools were used in the process of validation of several reactor physics codes. ARCHY is a tool that automates most of the drudgery involved in making a programmer's reference manual. When FORTRAN source code is read by ARCHY, it outputs a data dictionary that includes a categorization of variables and common block information. It also prints structure charts and Yourdon diagrams in PostScript format. The author also describes how several off-the-shelf products were used in validating critical reactor analysis software. FORTRAN-Lint is a useful tool for correcting deviations from the FORTRAN-77 standard. DEC Test Manager and the IBM-MVS SuperCE utility are useful for regression testing. DEC's Performance and Coverage Analyzer is a powerful tool for assessing the completeness of a test suite.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Anti-idiotypic antibody response to monoclonal anti-CD4 preparations in nonhuman primate species (1991)

A series of mouse monoclonal anti-CD4 preparations was characterized for the ability to recognize overlapping epitopes on CD4 and to inhibit HIV/simian immunodeficiency virus (SIV) syncytium formation. Based on this characterization, mAb able to recognize CD4 epitopes overlapping the HIV binding site were selected and used to immunize nonhuman primates to elicit the production of specific anti-Id antibodies. Five baboons and five rhesus monkeys were immunized with either individual or a cocktail consisting of several monoclonal anti-CD4 preparations. All the nonhuman primates produced specific anti-Id that recognized either private or cross-reactive Id depending on the monoclonal anti-CD4 used to generate the anti-Id response. Inhibition assays were performed to ascertain the ability of: 1) soluble CD4 to inhibit the Id-anti-Id reaction and 2) the various anti-Id to inhibit the CD4-monoclonal anti-CD4 reaction. These studies demonstrated that some of the anti-Id recognized a cross-reactive Id that was associated with the Ag-combining site. In addition, some of the anti-Id weakly recognized SIV gp120 by Western blot analysis. These studies may be useful in designing experiments that may lead to a better understanding of the CD4-HIV gp120 interaction and to the production of Id and/or anti-Id reagents that might be used to manipulate this virus-receptor interaction.
MICROFABRICATED NANOCHANNELS: NEW TOOLS FOR MOLECULAR MOTION CONTROL (2009)

This paper presents a review of work on the fabrication and use of nanochannels in silicon and polymers for the control\nof molecular transport. The method of Sacrifi cial Layer Lithography is reviewed and demonstrated for silicon and polymers. A novel\ntechnique for the productions of conical nanopores through a polymer membrane is also reviewed. Nanochannels and nanopores\nhave many potential applications for drug delivery, immunoprotection of cell implants, blocking of globular proteins from biosensor\nsurfaces, and diagnostic devices. All of these applications benefi t from the more direct interactions of devices with biomolecules.
Comparative genomics tools applied to bioterrorism defence (2003)

Rapid advances in the genomic sequencing of bacteria and viruses over the past few years have made it possible to consider sequencing the genomes of all pathogens that affect humans and the crops and livestock upon which our lives depend. Recent events make it imperative that full genome sequencing be accomplished as soon as possible for pathogens that could be used as weapons of mass destruction or disruption. This sequence information must be exploited to provide rapid and accurate diagnostics to identify pathogens and distinguish them from harmless near-neighbours and hoaxes. The Chem-Bio Non-Proliferation (CBNP) programme of the US Department of Energy (DOE) began a large-scale effort of pathogen detection in early 2000 when it was announced that the DOE would be providing bio-security at the 2002 Winter Olympic Games in Salt Lake City, Utah. Our team at the Lawrence Livermore National Lab (LLNL) was given the task of developing reliable and validated assays for a number of the most likely bioterrorist agents. The short timeline led us to devise a novel system that utilised whole-genome comparison methods to rapidly focus on parts of the pathogen genomes that had a high probability of being unique. Assays developed with this approach have been validated by the Centers for Disease Control (CDC). They were used at the 2002 Winter Olympics, have entered the public health system, and have been in continual use for non-publicised aspects of homeland defence since autumn 2001. Assays have been developed for all major threat list agents for which adequate genomic sequence is available, as well as for other pathogens requested by various government agencies. Collaborations with comparative genomics algorithm developers have enabled our LLNL team to make major advances in pathogen detection, since many of the existing tools simply did not scale well enough to be of practical use for this application. It is hoped that a discussion of a real-life practical application of comparative genomics algorithms may help spur algorithm developers to tackle some of the many remaining problems that need to be addressed. Solutions to these problems will advance a wide range of biological disciplines, only one of which is pathogen detection. For example, exploration in evolution and phylogenetics, annotating gene coding regions, predicting and understanding gene function and regulation, and untangling gene networks all rely on tools for aligning multiple sequences, detecting gene rearrangements and duplications, and visualising genomic data. Two key problems currently needing improved solutions are: (1) aligning incomplete, fragmentary sequence (eg draft genome contigs or arbitrary genome regions) with both complete genomes and other fragmentary sequences; and (2) ordering, aligning and visualising non-colinear gene rearrangements and inversions in addition to the colinear alignments handled by current tools.