gebhart/patrepeval huggingface dataset:
Correcting index databases improves metagenomic studies (2019)

Abstract Assessing the taxonomic composition of metagenomic samples is an important first step in understanding the biology and ecology of microbial communities in complex environments. Despite a wealth of algorithms and tools for metagenomic classification, relatively little effort has been put into the critical task of improving the quality of reference indices to which metagenomic reads are assigned. Here, we inferred the taxonomic composition of 404 publicly available metagenomes from human, marine and soil environments, using custom index databases modified according to two factors: the number of reference genomes used to build the databases, and the monophyletic strictness of species definitions. Index databases built following the NCBI taxonomic system were also compared to others using Genome Taxonomy Database (GTDB) taxonomic redefinitions. We observed a considerable increase in the rate of read classification using modified reference index databases as compared to a default NCBI RefSeq database, with up to a 4.4-, 6.4- and 2.2-fold increase in classified reads per sample for human, marine and soil metagenomes, respectively. Importantly, targeted correction for 70 common human pathogens and bacterial genera in the index database increased their specific detection levels in human metagenomes. We also show the choice of index database can influence downstream diversity and distance estimates for microbiome data. Overall, the study shows a large amount of accessible information in metagenomes remains unexploited using current methods, and that the same data analysed using different index databases could potentially lead to different conclusions. These results have implications for the power and design of individual microbiome studies, and for comparison and meta-analysis of microbiome datasets.
Atom transfer radical polymerization of alkyl methacrylates using T-triazine as ligand (2000)

A new multidentate amine ligand, 1,3,5-tris[(3-dimethylamino)propyl]-hexahydro-1,3,5-triazine (T-triazine) was developed for the atom transfer radical polymerization of methacrylates (dimethylaminoethyl methacrylate (DMAEMA) and methyl methacrylate (MMA)). It was found that with T-triazine as ligand, CuBr mediated a living polymerization of DMAEMA and MMA, producing polymers with controlled molecular weight and narrow polydispersity. The DMAEMA bulk polymerization and MMA solution polymerization in THF and γ-butyrolactone (γBL) followed first order kinetics with respect to the monomer. At lower temperature, both polymerizations had an induction period and the induction time decreased with increasing temperature. The measured apparent active energy was 67.8 kJ/mol for DMAEMA polymerization. The NMR spectra confirmed that the polymerizations proceeded via an atom transfer radical process.
Blow: a single-scale hyperconditioned flow for non-parallel raw-audio voice conversion (2019)

End-to-end models for raw audio generation are a challenge, specially if they have to work with non-parallel data, which is a desirable setup in many situations. Voice conversion, in which a model has to impersonate a speaker in a recording, is one of those situations. In this paper, we propose Blow, a single-scale normalizing flow using hypernetwork conditioning to perform many-to-many voice conversion between raw audio. Blow is trained end-to-end, with non-parallel data, on a frame-by-frame basis using a single speaker identifier. We show that Blow compares favorably to existing flow-based architectures and other competitive baselines, obtaining equal or better performance in both objective and subjective evaluations. We further assess the impact of its main components with an ablation study, and quantify a number of properties such as the necessary amount of training data or the preference for source or target speakers.
Telemetry Frame Processor (1995)

Report describes program for creating and editing telemetry frames on personal computer. Menu-driven and creates or edits digital telemetry manually or automatically by occurrence of event. Stream of telemetric data used to test operation of hardware and software parts of telemetry-receiving station. Program useful in satellite-data-processing facilities like remote-sensing stations.
A Flexible Transparent Touch Panel Based on Ionic Liquid Channel (2013)

A flexible transparent touch panel based on conductive liquid channels is developed. The channel structures are monolithically produced in the transparent silicone resin by sacrificial etching. The height, width, and length of the flow channel are 0.017, 1.0, and 55 mm, respectively. The pitch of the channels is 10 mm. Ionic liquid as a conductive solution is introduced into the channels. The channel structures become almost invisible by filling the channel with the ionic liquid. Fabricated flexible transparent touch panels are mounted on both the flat and round surfaces, and the touch force detection is evaluated. The electrical resistances in both cases increases with increasing applied load until 6 N when a metal rod with a diameter of 5.0 mm is pushed against the surface of the touch panel.
Liquid intrusion and alternative methods for the characterization of macroporous materials (IUPAC Technical Report) (2011)

This document deals with the characterization of porous materials having pore widths in the macropore range of 50 nm to 500 μm. In recent years, the development of advanced adsorbents and catalysts (e.g., monoliths having hierarchical pore networks) has brought about a renewed interest in macropore structures. Mercury intrusion–extrusion porosimetry is a well-established method, which is at present the most widely used for determining the macropore size distribution. However, because of the reservations raised by the use of mercury, it is now evident that the principles involved in the application of mercury porosimetry require reappraisal and that alternative methods are worth being listed and evaluated. The reliability of mercury porosimetry is discussed in the first part of the report along with the conditions required for its safe use. Other procedures for macropore size analysis, which are critically examined, include the intrusion of other non-wetting liquids and certain wetting liquids, capillary condensation, liquid permeation, imaging, and image analysis. The statistical reconstruction of porous materials and the use of macroporous reference materials (RMs) are also examined. Finally, the future of macropore analysis is discussed.
Induction of fuzzy production rules (2002)

The problem of inducing new production rules from a rule bank of an expert system is treated. Criteria and methods for such an induction are proposed for rules with Boolean premises and conclusion and with certainty factors. The results are extended to rules with fuzzy expressions as premises and conclusions and with certainty factors for them. Examples are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Developing a Structured Forecasting and Policy Analysis System to Support Inflation-Forecast Targeting (IFT) (2009)

This paper presents a basic plan for developing a Forecast and Policy Analysis System designed to support an inflation-forecast targeting regime at a central bank. It includes discussion of the development of data management and reporting processes; the creation of a forecast team and the development of human capital; the implementation of a simple model, plus possible extensions; and the management of regular economic projections. We emphasize that it is better to implement simple models earlier and use them well, rather than wait in an attempt to develop an all-encompassing model.
Ranging Mechanism, Preamble Generation, and Performance with IEEE 802.15.4a Low-Rate Low-Power UWB Systems (2006)

IEEE 802.15.4a task group is defining an ultra low power consumption and low cost radio for wireless personal area networks (WPANs) applications using ultra-wideband (UWB) technology with high precision ranging capability. Ternary preamble sequences of two different lengths have been proposed and adopted in the IEEE 802.15.4a specification for ranging. In order for a IEEE 802.15.4a low cost UWB device to support multiple frequency bands across the available spectrum and ranging features, as many as twenty-four ternary sequences is required. A sizeable amount of memory is needed to store the codes. In this paper, we propose a method to generate the ternary codes using linear feedback shift registers (LFSRs) as and when it is required, resulting in significant memory savings. The ranging performance using the proposed ternary preamble sequence is evaluated through simulation
Network Anomaly Detection: A Survey and Comparative Analysis of Stochastic and Deterministic Methods (2013)

We present five methods to the problem of network anomaly detection. These methods cover most of the common techniques in the anomaly detection field, including Statistical Hypothesis Tests (SHT), Support Vector Machines (SVM) and clustering analysis. We evaluate all methods in a simulated network that consists of nominal data, three flow-level anomalies and one packet-level attack. Through analyzing the results, we point out the advantages and disadvantages of each method and conclude that combining the results of the individual methods can yield improved anomaly detection results.
Multiplexed arrays of chemosensors by parallel dip-pen nanolithography (2011)

Miniaturized combined arrays of three different pH indicators allowing for sensitive, robust and broad-range acidity detection are prepared by parallel dip-pen nanolithography, which proves the potential of this technique to fabricate multiplexed platforms at the micro- and nanoscale that can act as sensors.
Characterization of simple and complex hepatitis C virus quasispecies by heteroduplex gel shift analysis: correlation with nucleotide sequencing (1995)

In infected humans, hepatitis C virus (HCV) exists as a quasispecies typically characterized by multiple nucleotide substitutions within the second envelope gene hypervariable region 1 (HVR1). In the current study, we used heteroduplex gel shift analysis (GSA) of HVR1 sequences amplified directly from patients' sera to define two patterns of HCV quasispecies: (i) simple quasispecies, which gave a mostly homogeneous gel shift profile with a single predominant band and (ii) complex quasispecies, which gave a gel shift profile with multiple bands. Recombinant HVR1 libraries were generated from two patients with complex HCV quasispecies (cases 1 and 2) and two patients with simple HCV quasispecies (cases 3 and 4), and 129 individual clones were analysed by either GSA, nucleotide sequencing or both techniques. In case 1 we identified a highly complex HCV quasispecies with 11 distinct HVR1 variants differing by 1-51 nucleotide changes. We found a general but not absolute correlation between GSA pattern and the number or position of nucleotide changes within HVR1. In case 2, the complex HCV quasispecies consisted of three distinct major variants; GSA of individual HVR1 clones allowed us to reconstruct the complex quasispecies pattern in vitro. In case 3, the simple quasispecies comprised 66% homogeneous clones and 33% unique minor variants differing by 1-3 nucleotides from the consensus sequence. In case 4, the simple quasispecies was 84% homogeneous, but six unique major shift variants were identified among 31 clones by GSA. In summary, HCV quasispecies can be characterized based on GSA profiles following direct PCR amplification of HVR1 sequences from patients' serum; the GSA profiles approximate the clonal population of HCV as determined by clonal analysis. GSA of HVR1 clones showed a strong correlation with nucleotide sequencing.
Neurons derived from transplanted neural stem cells restore disrupted neuronal circuitry in a mouse model of spinal cord injury (2010)

The body's capacity to restore damaged neural networks in the injured CNS is severely limited. Although various treatment regimens can partially alleviate spinal cord injury (SCI), the mechanisms responsible for symptomatic improvement remain elusive. Here, using a mouse model of SCI, we have shown that transplantation of neural stem cells (NSCs) together with administration of valproic acid (VPA), a known antiepileptic and histone deacetylase inhibitor, dramatically enhanced the restoration of hind limb function. VPA treatment promoted the differentiation of transplanted NSCs into neurons rather than glial cells. Transsynaptic anterograde corticospinal tract tracing revealed that transplant-derived neurons reconstructed broken neuronal circuits, and electron microscopic analysis revealed that the transplant-derived neurons both received and sent synaptic connections to endogenous neurons. Ablation of the transplanted cells abolished the recovery of hind limb motor function, confirming that NSC transplantation directly contributed to restored motor function. These findings raise the possibility that epigenetic status in transplanted NSCs can be manipulated to provide effective treatment for SCI.
Collective oscillations of the superconducting gap of multilayered Josephson junctions (2005)

Collective modes involving the gap amplitude $\ensuremath{\Delta}$ and phase $\ensuremath{\Phi}$ in a multilayered superconducting junction are considered. The junction is formed by a sequence of ``clean'' superconducting layers $S$ separated by insulating barriers $I$. Using the quasiclassical Green function method, we derive the self-consistent linear equations describing the collective amplitude $\ensuremath{\delta}$ and phase $\ensuremath{\varphi}$ oscillations. We find that the $\ensuremath{\delta}$ and $\ensuremath{\varphi}$ modes in ``clean'' multilayered Josephson junctions may be long lived for a range of magnitudes of the barrier transparency and Cooper coupling strength. We find that the frequency of the resonances in a multilayered junction can be tuned by applying a bias supercurrent across the adjacent subjunction.
<i>Aspergillus</i> Sinusitis: Clinical Aspects and Treatment Outcomes (1996)

Seventy-two cases of Aspergillus sinusitis were analyzed during a period of 14 years from January 1980 through October 1993. There were 60 cases of primary type and 12 cases of secondary type. The maxillary and ethmoid sinuses were most commonly affected in both primary and secondary types. The sphenoid sinus was commonly involved in secondary type. Fourteen (23%) cases of primary type and 4 (33%) cases of secondary type demonstrated sinus wall destruction on computed tomography or magnetic resonance images. Seventy percent of primary type and all cases of secondary type showed focal or diffuse areas of increased attenuation in the soft tissue mass on computed tomography scans. Sixteen cases assessed by magnetic resonance imaging showed decreased signal intensities on T1-weighted images and markedly reduced signal intensities on T2-weighted images. Fifty-nine (98%) of 60 cases of primary type were noninvasive, and 1 was invasive. In secondary type, 10 (83%) of 12 patients had noninvasive disease. The most common coexisting disease in secondary aspergillosis was diabetes mellitus. Thickened mucosa with necrotic brownish green material, which was the most common finding in both types, was found in 33 patients with primary type and in 5 with secondary type. Surgery was performed in most cases, among which 4 patients received chemotherapy after surgery with amphotericin B with or without flucytosine. All patients were cured without recurrence during a mean follow-up period of 13 months.
Transmission of corneal collagen during arf excimer laser ablation (1993)

The time-resolved transmission of collagen films and 10-microns sections of bovine cornea during ArF laser ablation has been investigated. The film studies were performed on thin layers of extracted bovine corneal collagen, the principal chromophore in 193 nm photoablation. Transmission measurements were made on both dry and water-saturated films to assess the sensitivity of the ablation process to hydration. Distinct transient optical changes were observed in both fully desiccated and rehydrated films. Dehydrated films exhibit rapid reduction in film absorption over the time-course of the ablating laser pulse, presumably due to chromophore bleaching or annihilation. In contrast, rehydrated films demonstrate a short-lived enhancement of the attenuation. In either case, a single ablative laser pulse increased the long-term transmission of the film, although this increase was a factor of five greater for dehydrated films than for rehydrated samples. Results obtained from corneal tissue sections were essentially identical to those derived from hydrated collagen films.
Diethoxytriphenylphosphorane: a mild, regioselective cyclodehydrating reagent for conversion of diols to cyclic ethers: stereochemistry, synthetic utility, and scope (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiethoxytriphenylphosphorane: a mild, regioselective cyclodehydrating reagent for conversion of diols to cyclic ethers: stereochemistry, synthetic utility, and scopePhilip L. Robinson, Carey N. Barry, Jeffery W. Kelly, and Slayton A. Evans Jr.Cite this: J. Am. Chem. Soc. 1985, 107, 18, 5210–5219Publication Date (Print):September 1, 1985Publication History Published online1 May 2002Published inissue 1 September 1985https://pubs.acs.org/doi/10.1021/ja00304a030https://doi.org/10.1021/ja00304a030research-articleACS PublicationsRequest reuse permissionsArticle Views4327Altmetric-Citations55LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Customized services over virtual wireless networks: The path towards networks without borders (2013)

We propose a\nnew architecture to enable wireless networks to meet th\ne\nchallenges of ever\n-\nincreasing demand for high data rate services and ubiquitous\nconnectivity, heterogeneity of access technologies, and spectrum scarcity.\nThis\narchitecture, which we call\nNetworks without Borders, envisions a pool of resources\n(spectrum,\ninfrastructure,\nnetwork management, authentication, subscriber tracking\nservices, etc.) from which a virtual wireless network can be\norchestrated\nand\ninstantiated. Flexibility and technology neutrality are key goals of this architecture,\nmirroring the Int\nernet, where user services are independent of the underlying\nnetwork control mechanisms or infrastructure.\nWe outline some of the major trends\nin networking research and commercial deployments that provide a\nn evolutionary\npath towards Networks without Bord\ners.\nThese trends include\nvirtualization, reliance\non small cells, dynamic spectrum sharing, crowdsourcing of wireless access, and\ninter\n-\nmobile operator resource sharing
Vehicle Lateral Stability Control Based on Sliding Mode Control (2007)

In view of the vehicle cornering or path changing under ultimate handling maneuver, a 4-DOF nonlinear vehicle dynamics model which takes the longitudinal velocity, lateral velocity, yaw rate and body roll angle as the state variables is presented. Based on the dynamic analysis, the method which using additional yaw moment produced by different longitudinal braking force among each wheels to improving vehicle handling stability in emergency situations is discussed. Considering the slip angle of the centroid as the one of the vehicle state variables is difficult to measuring, the slip angle estimation method based on vehicle dynamic model and kinematics is designed. And then, based on the theory of sliding model control, the combining sliding mode control system is founded, which taking the vehicle yaw rate and body centroid slip angle errors between the estimated and the real as the input variables, and taking the braking torque and the steering angle as control aims. The simulation results indicate that the control method can effectively improve the vehicle lateral handling stability.
RADIOIMMUNOASSAYS EMPLOYING IMMUNOSORBENTS (1969)

ABSTRACT The use of a reaction between compounds in a two phase system – a solid phase and a liquid phase – has simplified the technical procedure of the radioimmunoassays. Antigens or antibodies can be coupled covalently to insoluble polymers to form stable conjugates with retention of immunological binding capacity. Such immunosorbents can be used in radioimmunoassays in many different ways and with the solid phase in different forms. Some of these techniques seem to be universally applicable for the assay of antigens or antibodies. In one of these, antigens or antibodies are chemically coupled to cyanogen bromide activated insoluble polysaccharides in a particle form. This method which has several advantages when compared with most other radioimmunological methods is discussed in particular. Finally, a detailed description of the preparation of an immunosorbent and its use in such a radioimmunoassay system is given.
Virtual environment display system. (1986)

A head-mounted, wide-angle, stereoscopic display system controlled by operator position, voice and gesture has been developed for use as a multipurpose interface environment. The system provides a multisensory, interactive display environment in which a user can virtually explore a 360-degree synthesized or remotely sensed environment and can viscerally interact with its components. Primary applications of the system are in telerobotics, management of large-scale integrated information systems, and human factors research. System configuration, application scenarios, and research directions are described.
An automated system for impedance measurements in milk (2007)

Measurement of milk quality is important for commercial food safety and in the dairy processing industry. Several techniques have been investigated before, and measurements range from impedance detection time (for shelf-life prediction just after pasteurization) and conductivity (mostly for mastitis detection) to pH and capacitance. Most techniques use invasive probes, for which a good reference in milk is not yet available. This article discusses the design and results of an automated measurement system used to characterize impedance probes for bacterial content measurement in milk. With a reliable, repeatable measurement system, probe characterization and calibration is improved, which leads to faster and more accurate measurements of bacterial content and remaining shelf-life.