gebhart/patrepeval huggingface dataset:
Dynamic Time Warping Averaging of Time Series Allows Faster and More Accurate Classification (2014)

Recent years have seen significant progress in improving both the efficiency and effectiveness of time series classification. However, because the best solution is typically the Nearest Neighbor algorithm with the relatively expensive Dynamic Time Warping as the distance measure, successful deployments on resource constrained devices remain elusive. Moreover, the recent explosion of interest in wearable devices, which typically have limited computational resources, has created a growing need for very efficient classification algorithms. A commonly used technique to glean the benefits of the Nearest Neighbor algorithm, without inheriting its undesirable time complexity, is to use the Nearest Centroid algorithm. However, because of the unique properties of (most) time series data, the centroid typically does not resemble any of the instances, an unintuitive and underappreciated fact. In this work we show that we can exploit a recent result to allow meaningful averaging of 'warped' times series, and that this result allows us to create ultra-efficient Nearest 'Centroid' classifiers that are at least as accurate as their more lethargic Nearest Neighbor cousins.
Anticoccidial derivatives of 6-azauracil. 5. Potentiation by benzophenone side chains (1983)

Attachment of p-benzophenone side chains at N1 was found to be one of the most effective modifications for enhancing the potency of 6-azauracil against a broad spectrum of coccidia in chickens. Compound 20 was about 1000-fold more potent than 6-azauracil. Structure-activity relationships paralleled those found in a previously reported series of related analogues containing diphenyl sulfide and sulfone side chains. Drug metabolism studies showed the ketones to be reduced rapidly to carbinols, which are the prevalent species in vivo.
Decreased Adherence of Enterohemorrhagic <i>Escherichia coli</i> to HEp-2 Cells in the Presence of Antibodies That Recognize the C-Terminal Region of Intimin (1999)

Antiserum raised against intimin from enterohemorrhagic Escherichia coli (EHEC) O157:H7 strain 86-24 has been shown previously by our laboratory to inhibit adherence of this strain to HEp-2 cells. In the present study, we sought to identify the region(s) of intimin important for the effect of anti-intimin antisera on EHEC adherence and to determine whether antisera raised against intimin from an O157:H7 strain could reduce adherence of other strains. Compared to preimmune serum controls, polyclonal sera raised against the histidine-tagged intimin protein RIHisEae (intimin(O157)) or against His-tagged C-terminal fragments of intimin from strain 86-24 reduced adherence of this strain. Furthermore, an antibody fraction purified from the anti-RIHisEae serum that contained antibodies to the C-terminal third of intimin, the putative receptor-binding domain, also reduced adherence of strain 86-24, but a purified fraction containing antibodies to the N-terminal two-thirds of intimin did not inhibit adherence. The polyclonal anti-intimin(O157) serum raised against RIHisEae inhibited, to different degrees, the adherence of another O157:H7 strain, an EHEC O55:H7 strain, one of two independent EHEC O111:NM isolates tested, and one of two EHEC O26:H11 strains tested. Adherence of the other O26:H11 and O111:NM strains and an EPEC O127:H6 strain was not reduced. Finally, immunoblot analysis indicated a correlation between the antigenic divergence in the C-terminal third of intimins from different strains and the capacity of anti-intimin(O157) antiserum to reduce adherence of heterologous strains. Taken together, these data suggest that intimin(O157) could be used as an immunogen to elicit adherence-blocking antibodies against O157:H7 strains and closely-related EHEC.
Induction of antigen-specific cytotoxic T lymphocytes by fusion cells generated from allogeneic plasmacytoid dendritic and tumor cells (2014)

Previous work has demonstrated that fusion cells generated from autologous monocyte-derived dendritic cells (MoDCs) and whole tumor cells induce efficient antigen-specific cytotoxic T lymphocytes. A major limitation to the use of this strategy is the availability of adequate amounts of autologous tumor cells. Moreover, MoDCs from cancer patients are often defective in their antigen-processing and presentation machinery. In this study, two types of allogeneic cells, a leukemia plasmacytoid dendritic cell (pDC) line (PMDC05) and pancreatic cancer cell lines (PANC-1 or MIA PaCa-2), were fused instead of autologous MoDCs and tumor cells. We created four types of pDC/tumor fusion cells by alternating fusion partners and treating with lipopolysaccharide (LPS): i) PMDC05 fused with PANC-1 (pDC/PANC-1), ii) PMDC05 fused with MIA PaCa-2 (pDC/MIA PaCa-2), iii) LPS-stimulated pDC/PANC-1 (LPS-pDC/PANC-1) and iv) LPS-stimulated pDC/MIA PaCa-2 (LPS-pDC/MIA PaCa-2) and examined their antitumor immune responses. The LPS-pDC/tumor cell fusions were the most active, as demonstrated by their: i) upregulated expression of HLA-DR and CD86 on a per-fusion-cell basis, ii) increased production of IL-12p70, iii) generation of a higher percentage of IFN-γ-producing CD4⁺ and CD8⁺ T cells and iv) augmented induction of MUC1-specific CD8⁺ T cells that lyse target tumor cells. This study provides the first evidence for an in vitro induction of antigen-specific cytotoxic T lymphocytes by LPS-stimulated fusion cells generated from leukemia plasmacytoid DCs and tumor cells and suggests that this strategy has potential applicability to the field of adoptive immunotherapy.
Hammer Toe Correction Using an Absorbable Intramedullary Pin (2007)

This procedure can be used for hammer toe deformities requiring surgery when the metatarsophalangeal joint is stable, the skin is not compromised, and the intramedullary canal of the proximal phalanx is 2.0 mm or less. It also has been useful in stabilizing hammertoe correction when there are severe pre-existing metal allergies.
Effect of nonstationarities on detrended fluctuation analysis (2002)

Detrended fluctuation analysis (DFA) is a scaling analysis method used to quantify long-range power-law correlations in signals. Many physical and biological signals are "noisy," heterogeneous, and exhibit different types of nonstationarities, which can affect the correlation properties of these signals. We systematically study the effects of three types of nonstationarities often encountered in real data. Specifically, we consider nonstationary sequences formed in three ways: (i) stitching together segments of data obtained from discontinuous experimental recordings, or removing some noisy and unreliable parts from continuous recordings and stitching together the remaining parts-a "cutting" procedure commonly used in preparing data prior to signal analysis; (ii) adding to a signal with known correlations a tunable concentration of random outliers or spikes with different amplitudes; and (iii) generating a signal comprised of segments with different properties-e.g., different standard deviations or different correlation exponents. We compare the difference between the scaling results obtained for stationary correlated signals and correlated signals with these three types of nonstationarities. We find that introducing nonstationarities to stationary correlated signals leads to the appearance of crossovers in the scaling behavior and we study how the characteristics of these crossovers depend on (a) the fraction and size of the parts cut out from the signal, (b) the concentration of spikes and their amplitudes (c) the proportion between segments with different standard deviations or different correlations and (d) the correlation properties of the stationary signal. We show how to develop strategies for preprocessing "raw" data prior to analysis, which will minimize the effects of nonstationarities on the scaling properties of the data, and how to interpret the results of DFA for complex signals with different local characteristics.
Visualizing web search results using glyphs (2011)

While the Web provides a lot of useful information to managers and decision makers in organizations for decision support, it requires a lot of time and cognitive effort for users to sift through a search result list returned by search engines to find useful information. Previous research in information visualization has shown that visualization techniques can help users comprehend information and accomplish information tasks more efficiently and effectively. However, only a limited number of such techniques have been applied to Web search result visualization with mixed evaluation results. Using a design science approach, this research designed and implemented a glyph (a graphical object that represents the values of multiple dimensions using multiple visual parameters) and a system for visualizing Web search results. A flower metaphor was adopted in the glyph design to represent the characteristics and metadata of Web documents. Following the cognitive fit theory, an experimental study was conducted to evaluate three displays: a numeric display, a glyph display, and a combined display which showed numbers only, glyphs only, and both, respectively. Experimental results showed that the glyph display and the combined display performed better when task complexity was high, and the numeric display and the combined display performed better when task complexity was low. The combined display also received the best perceived usability from the subjects. Based on the findings, the implications of the study to research and practice are discussed and some future research directions are suggested.
A mathematical model of glutathione metabolism (2008)

We show that the glutathione pools in hepatic cells and in the blood are quite insensitive to fluctuations in amino acid input and offer an explanation based on model predictions. In contrast, we show that hepatic glutathione pools are highly sensitive to the level of oxidative stress. The model shows that overexpression of genes on chromosome 21 and an increase in oxidative stress can explain the metabolic profile of Down syndrome. The model also correctly simulates the metabolic profile of autism when oxidative stress is substantially increased and the adenosine concentration is raised. Finally, we discuss how individual variation arises and its consequences for one-carbon and glutathione metabolism.
Magnetooptic bubble-domain devices (1971)

The practical feasibility of display and sensing systems using the magnetooptic properties of the three most widely discussed bubble-domain materials is discussed; the orthoferrites (100 μm bubbles), the garnets (10 μm bubbles), and the hexaferrites (1 μm bubbles). It is found that on a per bubble basis, the incident light intensity at the surface of the magnetic platelet necessary for both applications is remarkably close for all three materials, varying only between several microwatts and several tens of microwatts. Because of the large range of bubble diameters, however, the power per unit area varies from a quite tolerable 0.025 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> in orthoferrites to a prohibitive 114 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for hexaferrite. Thus orthoferrite magnetooptic devices should be relatively straightforward, garnet devices will require careful heat sinking, and hexaferrite devices seem very doubtful.
Soil Management for Sustainable Agriculture 2013 (2014)

Agricultural sustainability can be defined as the ability of a system to maintain stable levels of production and quality in the long term without compromising economic profitability or the environment. The conservation of soil quality is fundamental to agricultural sustainability. The soil provides, amongst other things, a substrate for plant anchorage, a buffered supply of essential mineral elements and water, a repository for carbon, a reservoir of functional biodiversity, and a filter for reducing the pollution of air and water by agrochemicals. This is the second special issue on soil management for sustainable agriculture. It comprises ten papers describing (1) the preservation of soil organic matter and the phytoavailability of essential mineral elements in soils through the recycling of organic residues to agricultural land, (2) the effects of agricultural management on the accumulation of potentially toxic mineral elements in soils and plants, (3) agricultural practices that reduce losses of organic carbon and nitrogen from soils, restrict soil erosion, and maintain agricultural productivity, and (4) agronomic strategies to manipulate soil chemistry to reduce the abundance of problematical weeds.
Resource-driven MPEG-4 FGS for universal multimedia access (2003)

The universal multimedia access (UMA) paradigm is aimed at enabling multimedia data to be accessed by a large number of users/clients at any time, and from anywhere, based on their preferences, communication channel characteristics and device capabilities. For the implementation of the UMA framework, "universal" scalable video coding techniques that enable adaptive video transmission based on these three parameters are essential. Fine-granular-scalability (FGS) has recently been adopted as the MPEG-4 standard for the efficient and flexible distribution of multimedia over heterogeneous wired and wireless networks. While it has already been proven that FGS fulfils the first two UMA requirements (adaptive and robust transmission based on the channel characteristics and user preferences) due to its bit-rate scalability, the ability of FGS to provide device-based complexity-scalability was hitherto unproven. This paper proposes using an information theoretic framework, based on rate-distortion-complexity theory, for evaluating bit-rate and complexity scalable coding techniques for UMA. In this context, the ability of FGS to provide bit-rate and complexity scalability that allows easy and smooth navigation across the operational rate-distortion-complexity surface is demonstrated. Moreover, a comparison with non-scalable MPEG schemes is also given. Furthermore, we illustrate how this framework can be used in an FGS-based resource-driven video streaming system.
Enantioselective Total Synthesis of Eunicenone A (2001)

An enantioselective, stereocontrolled total synthesis of eunicenone A (1) is described starting from geranylgeranylacetylene (9) in 14 steps via intermediates 10-20. The most critical construction in the synthesis is the highly effective Diels-Alder combination of the achiral components 2-bromoacrolein and diene 13 in the presence of the chiral Lewis acid catalyst 14 to form 15 (85% yield, 97% ee, >98:2 endo-exo ratio). The synthesis utilizes a novel reagent (12) for introduction of silicon, which serves to activate and direct the diene 13 for Diels-Alder reaction and to provide for eventual oxygen functionality of homoallylic alcohol 17 under mild conditions. Other noteworthy steps include the position selective and diastereoselective epoxidation 17 --> 18, the methoxycarbonylation with allylic transposition 19 --> 20, and the alpha,beta-enone unmasking 20 --> 1.
Chemistry Around Pinene and Pinane: A Facile Synthesis of Cyclobutanes and Oxatricyclo‐Derivative of Pinane from <i>cis</i>‐ and <i>trans</i>‐Pinanols (2008)

Alpha-pinene and beta-pinene are abundantly represented in nature; they are obtained from renewable sources and are irreplaceable synthons for commercial-scale production of other terpenes. In a well-known process practiced by Millennium Specialty Chemicals (MSC), hydrogenation of pinenes gives cis- and trans-pinanes, which are oxidized to hydroperoxides, whose reduction gives cis- and trans-pinanols, respectively. Pyrolysis of the pinanols gives linalool. Industrial availability of the pinanols makes them attractive objects for further synthetic research. We found that, in a very simple process of 'chlorooxidation', cis- and trans-pinanols react with hypochloric acid producing a novel chloroketone 1-[3-(2-chloroethyl)-2,2-dimethylcyclobutyl]ethanone and a tricyclic ether 6,9-dimethyl-7-oxatricyclo[4.3.0.0(3,9)]nonane, respectively. Both compounds offer new broad synthetic opportunities, providing access to numerous dimethylcyclobutane derivatives and to C(9)-functionalized pinenes and pinanes. The chlorooxidation reaction was also extended to other terpene alcohols such as dihydroplinol, tetrahydromyrcenol, and tetrahydrolinalool. This review, based on a presentation at the RSC/SCI conference Flavours & Fragrances 2007 in London, September 24-26, 2007, will touch on environmental issues related to pinenes, give a brief overview of the existing pinene-based technologies, and discuss the new experimental results.
Perfusion Improves Tissue Architecture of Engineered Cardiac Muscle (2002)

Cardiac muscle with a certain threshold thickness, uniformity of tissue architecture, and functionality would expand the therapeutic options currently available to patients with congenital or acquired cardiac defects. Cardiac constructs cultured in well-mixed medium had an approximately 100-microm-thick peripheral tissue-like region around a relatively cell-free interior, a structure consistent with the presence of concentration gradients within the tissue. We hypothesized that direct perfusion of cultured constructs can reduce diffusional distances for mass transport, improve control of oxygen, pH, nutrients and metabolites in the cell microenvironment, and thereby increase the thickness and spatial uniformity of engineered cardiac muscle. To test this hypothesis, constructs (9.5-mm-diameter, 2-mm-thick discs) based on neonatal rat cardiac myocytes and fibrous polyglycolic acid scaffolds were cultured either directly perfused with medium or in control spinner flasks. Perfusion improved the spatial uniformity of cell distribution and enhanced the expression of cardiac-specific markers, presumably due to the improved control of local microenvironmental conditions within the forming tissue. Medium perfusion could thus be utilized to better mimic the transport conditions within native cardiac muscle and enable in vitro engineering of cardiac constructs with clinically useful thicknesses.
Assessment of the suitability of filters for use in clinical studies with an HFA fluticasone propionate pressurized metered dose inhaler (pMDI) and a valved holding chamber (VHC) (2011)

The assessment of delivered dose is an integral part of the development process for new aerosol delivery devices, especially in pediatric patients in which pharmacokinetic studies are difficult to perform. The aim of this study was to evaluate the dose collection efficiency of a 3M Filtrete G-200 (G-200) filter in a low dead space filter holder for use in ex vivo tests using a preproduction OptiChamber Diamond VHC (Diamond; Philips Respironics). Two preproduction Diamond VHCs were tested over 10 runs. Five fluticasone propionate (Flovent HFA 220 μg) pMDIs were primed before use. The mouthpiece of the VHC was sealed to a filter holder containing two 67mm G-200 filters. The pMDI was actuated into the VHC, followed by 20 s extraction (at 90 L/min), repeated 25 times. Filters and VHC deposits were analyzed using HPLC (Agilent 1100/1200). The percentage of total emitted dose deposited on the 2nd filters over 10 runs was calculated; where the amount of drug detected on the 2nd filter was below the Limit of Quantification (LOQ; 25μg) the LOQ was used to calculate the total, and where the amount detected was zero the Limit of Detection (LOD; 2.5μg) was used to calculate the total (overestimates the total amount on the 2nd filters significantly), the total was then divided by total recovered drug. The amount of drug deposited on the 2nd filters was below the LOQ for all the filters and <0.645% of the total was calculated to have deposited on the 2nd filters. Recovered doses were within the expected range. Less than 1% of the emitted dose was deposited on the 2nd filter and thus passed the 1st filter.
Prevention of experimental diffuse lamellar keratitis using a novel platelet-activating factor receptor antagonist (2004)

Induction of DLK was blocked by a PAF receptor antagonist in rabbit eyes. The histopathological evaluation and immunohistochemical studies showed that treatment with LAU 0901 blocked keratocyte apoptosis, transformation of fibroblasts to myofibroblasts and migration to the wound site, and chemotaxis of inflammatory cells, inhibiting the inflammatory response and promoting adequate healing of the flap interface and adjacent stroma.
Gene copy-number polymorphism in nature (2010)

Differences between individuals in the copy-number of whole genes have been found in every multicellular species examined thus far. Such differences result in unique complements of protein-coding genes in all individuals, and have been shown to underlie adaptive phenotypic differences. Here, we review the evidence for copy-number variants (CNVs), focusing on the methods used to detect them and the molecular mechanisms responsible for generating this type of variation. Although there are multiple technical and computational challenges inherent to these experimental methods, next-generation sequencing technologies are making such experiments accessible in any system with a sequenced genome. We further discuss the connection between copy-number variation within species and copy-number divergence between species, showing that these values are exactly what one would expect from similar comparisons of nucleotide polymorphism and divergence. We conclude by reviewing the growing body of evidence for natural selection on copy-number variants. While it appears that most genic CNVs--especially deletions-are quickly eliminated by selection, there are now multiple studies demonstrating a strong link between copy-number differences at specific genes and phenotypic differences in adaptive traits. We argue that a complete understanding of the molecular basis for adaptive natural selection necessarily includes the study of copy-number variation.
Notes on <i>Poterioceras pyriforme</i> from the Carboniferous Limestone of Lanarkshire (1872)

On 17th December 1868 I presented to the Society a large Cephalopod which, judging from its external characteristics, which were very imperfect, and not having the advantage of comparing it with other specimens, I named Orthoceras fusiforme. The specimen is very much defaced and crushed. Dr Page, on seeing it, said he thought it was an Ascoceras, and very like those he had seen in certain museums in the West of Scotland. It was accordingly named by the Society Ascoceras, and was supposed to have come from one of the carboniferous limestones of the west, probably Lanarkshire. An abstract of my paper appeared in the ‶Geological Magazine,″ which attracted the attention of M. Barrande of Prague, the distinguished author of the ‶Systeme Silurien de Boheme,″ and on the 17th of March I received a communication from that gentleman requesting me to send him a sketch of this interesting fossil with any observations I might make upon it. He remarked, that the re-appearance of a class, after so long an intermittance in time, interested him very much, because, he continued to say, ‶I have recently drawn the attention of the scientific world to this subject in a small brochure which I now send you on the re-appearance of the class Arethusina (Trilobite). In the case of your Ascoceras the long interval of this class is still greater than that of the Arethusina, of which an account is given in my memoir.″ Accordingly, after receiving this letter, I put myself in communication