gebhart/patrepeval huggingface dataset:
To Petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics (2020)

As computational biologists continue to be inundated by ever increasing amounts of metagenomic data, the need for data analysis approaches that keep up with the pace of sequence archives has remained a challenge. In recent years, the accelerated pace of genomic data availability has been accompanied by the application of a wide array of highly efficient approaches from other fields to the field of metagenomics. For instance, sketching algorithms such as MinHash have seen a rapid and widespread adoption. These techniques handle increasingly large datasets with minimal sacrifices in quality for tasks such as sequence similarity calculations. Here, we briefly review the fundamentals of the most impactful probabilistic and signal processing algorithms. We also highlight more recent advances to augment previous reviews in these areas that have taken a broader approach. We then explore the application of these techniques to metagenomics, discuss their pros and cons, and speculate on their future directions.
Online Topic-based Social Influence Analysis for the Wimbledon Championships (2015)

Various industries are turning to social media to identify key influencers on topics of interest. Following this trend, the All England Lawn Tennis and Croquet Club (AELTC) is keen to analyze the `social pulse' around the famous Wimbledon Championships. IBM developed and deployed social influence analysis capability for AELTC during the 2014 edition of the Championship. The design and implementation of influence analysis technology in the real world involves several challenges. In this paper, we define various functional and usability criteria that social influence scores should satisfy, and propose a multi-dimensional definition of influence that satisfies these criteria. We highlight the need to identify both all-time influencers and recent influencers, and track user influences over multiple time-scales for this purpose. We also stress the importance of aspect-specific influence analysis, and investigate an approach that uses an aspect hierarchy that annotates tweets with topics or aspects before analyzing them for influence. We also describe interesting insights discovered by our tool and the lessons that we learnt from this engagement.
Artificial Bubble Cloud Targets for Underwater Acoustic Remote Sensing (1995)

This article describes a technique that uses polymer additives to suspend air bubbles to form stable artificial bubble clouds. The results presented include the range of polymer concentrations for an effective bubble suspension; the void fraction, bubble size distribution, and stability of the generated artificial bubble clouds; and the effects of polymer on the acoustic properties of the bubble clouds, especially the acoustic velocity. It is concluded that, for low-frequency applications (less than 1 kHz), polymer concentrations of less than 1% do not modify significantly the acoustic velocity of bubble clouds. The stability of the produced bubble clouds can be made to last from a few hours to days or even months depending on the polymer concentration and the bubble size. Because only a low polymer concentration and small void fraction (both less than 1%) are needed to generate effective scattering, the density of the produced bubble cloud target and its response to hydrostatic pressure are similar to those of the ambient sea water; thus, adjustment to quasi-neutral buoyancy is not difficult. These results suggest that underwater acoustic targets and quasi-neutrally buoyant tracers that are small but have large acoustic cross sections can be produced with artificial bubble clouds suspended and stabilized by polymers.
Wideband Two-Section Impedance Transformer With Flat Real-to-Real Impedance Matching (2016)

This letter presents the design of an impedance transformer with wideband, maximally flat real-to-real impedance matching. The design formulas for two-section quarter-wave transformer are presented and exact solutions for transmission lines' parameters are derived in explicit form for any impedance transformation ratio. The results of this study are useful for a number of practical design problems, especially power amplification circuits. To validate the design formulas, three impedance transformers terminated in a fixed impedance of 50 Ω and three target impedances of 100, 150, and 200 Ω are fabricated and measured. Measurements show a good agreement with theory and simulations.
Salivary microR‐153 and microR‐223 Levels as Potential Diagnostic Biomarkers of Idiopathic Parkinson's Disease (2019)

Salivary miR-153 and miR-223 levels may serve as useful, noninvasive, and relatively inexpensive diagnostic biomarkers of idiopathic PD. © 2019 International Parkinson and Movement Disorder Society.
GRISM-based probe for spectrally encoded confocal microscopy (2003)

Spectrally encoded confocal microscopy (SECM) is a novel approach for high resolution, depth-sectioned imaging of tissue microstructure. By encoding one spatial dimension in wavelength, imaging probes can be simplified enabling endoscopic implementation. The novel use of a single-optical-axis element based on high index-of-refraction prisms and a transmission grating enables the design of narrow diameter SECM devices. Images were obtained from a 10.0 mm probe with 1.1 &mu;m transverse resolution and a 650 &mu;m FOV.
Response and Remission After 16 Weeks of Ustekinumab: An All Patients Analysis From the UNITI Crohnʼs Studies (2017)

Introduction: UST has been shown to induce&maintain clinical response & remission in moderate-severe Crohn's disease(CD) in 2 induction[(UNITI-1(anti-TNF failures)&UNITI-2(anti-TNF non-failures) &1 maintenance(IM-UNITI)] randomized, PBO-controlled Ph3 trials. We evaluated efficacy (response & remission) for all pts who received an IV induction dose of approximately 6mg/kg, including responders(CDAI decrease ≥100)&non-responders, 8wks after first UST maintenance dose of 90mg SC, ie, 6wks from the IV induction dose. Methods: Pts achieving clinical response 8wks after a single IV induction dose were randomized to SC PBO, UST 90mg q12wks or q8wks. UST pts not in clinical response 8wks after IV induction dose were given UST90mg SC & if in clinical response 8wks later were continued on 90mg SC q8w. A total of 458pts were exposed to an IV induction dose of 6mg/kg(UNITI-1,N=249 & in UNITI-2 N=209) with a response rate at wk8 of 37.8%&57.9% vs PBO response rate of 20.2%&32.1% respectively. The remission rate at wk8 in UNITI-1 & UNITI-2 was 20.9%&40.7 vs PBO of 7.3%&19.6% respectively. For this evaluation, response & remission status of the entire population exposed to an IV induction dose of 6mg/kg of UST was evaluated 8wks after the first SC maintenance dose of UST. All pts who received 6mg/kg IV UST induction were included, including responders randomized to SC PBO(who did not receive SC UST at wk8). Results: Of the 219 pts not in clinical response in UNITI 1&2, 37.6%&60.5% respectively were in clinical response 8wks after first maintenance UST dose (90 mg SC). Evaluating all pts exposed to 6mg/kg IV UST induction, response rates 8wks after first SC injection(16wks after IV induction dose) for UNITI1&2 are 47.4%&73.7% respectively (Table). Similar assessments were calculated in the sub-population who were anti-TNF naïve upon enrolment into UNITI-2.Table: Table. Response rates and remission rates for all pts 16wks after induction of 6mg/kg IV USTConclusion: These numbers at wk16 are expected to reflect real world experience in pts who receive the induction dose & one additional maintenance dose 8wks later. The resulting rates of response & remission are higher than previously reported in induction studies across all populations(anti-TNF non-failures & anti-TNF failures). About 73% of anti-TNF non-failures attain clinical response & over half are in remission.The data support clinical rationale for providing at least one SC maintenance dose of UST irrespective of clinical response 8wks after IV induction.
Radical Polymers for Organic Electronic Devices: A Radical Departure from Conjugated Polymers? (2009)

Abstract Radical polymers are aliphatic or nonconjugated polymers bearing organic robust radicals as pendant groups per repeating unit. A large population of the radical redox sites allows the efficient redox gradient‐driven electron transport through the polymer layer by outer‐sphere self‐exchange reactions in electrolyte solutions. The radical polymers are emerging as a new class of electroactive materials useful for various kinds of wet‐type energy storage, transport, and conversion devices. Electric‐field‐driven charge transport by hopping between the densely populated radical sites is also a remarkable aspect of the radical polymers in the solid state, which leads to many dry‐type devices such as organic memories, diodes, and switches.
rimertown (2019)

A poetic charting of Laura Walker's rural, southern hometown, Rimertown/an atlas delves into the startling landscapes created by the passage of time through people and through place; it is an atlas born of image and voice. Composed of four interwoven strands—a collection of "maps," a collection of "stories," a series of vernacular prose poems, and a fractured narrative—the volume explores various geographies: of the physical world, of the intersection of natural and peopled landscapes, of the passage of time, of leaving and returning, of human relationships, of soldiers and war. Walker asks: how is "home" carried in memory, in landscape, in story, in time? Her poems break and merge, stitching and fragmenting narrative, syntax, and image as they push toward their own geography, "a fever doll, tapered song/ engineered into dusk/ hold the watery stream, its buck and clanging. "
Tellurium Nanowire-Induced Room Temperature Conversion of Graphite Oxide to Leaf-like Graphenic Structures (2009)

A simple nanomaterial-based reduction strategy that can form leaf-like graphenic structures from graphite oxide (GO) at room temperature is described. Mixing of Te nanowires (Te NWs) with GO at room temperature was found to reduce GO while Te NWs are oxidized to TeO32−. The reaction was followed time-dependently with use of UV/vis spectroscopy, fluorescence spectroscopy, and transmission electron microscopy (TEM). Raman spectroscopy was used to characterize the graphenic material. The G band, which was blue-shifted (with respect to graphite) in the case of GO, came back to the original position confirming the reduction. From IR spectroscopy, it was confirmed that the carboxylic acid groups in the GO are not getting reduced and the product gets stabilized electrostatically because of the repulsion between the negatively charged carboxylic acid groups. Reduction was confirmed by X-ray photoelectron spectroscopy (XPS) also. The reaction showed strong pH dependence and was found to be happening only in basic pH. In acidic medium, GO aggregates, making reduction difficult, while at higher temperature, the reaction was faster and at lower temperature it was retarded considerably.
Permeation of Styryl Dyes through Nanometer-Scale Pores in Membranes (2011)

Styryl dyes are widely used to study synaptic vesicle (SV) recycling in neurons; vesicles are loaded with dye during endocytosis, and dye is subsequently released via exocytosis. During putative kiss-and-run exocytosis, efflux of dye from individual SVs has been proposed to occur via two sequential steps: dissociation from the membrane followed by permeation through a small fusion pore. To improve our understanding of the kinetics of efflux of dye from vesicles during kiss-and-run events, we examined the rates of efflux of different dyes through nanometer-scale pores formed in membranes by the toxins melittin and α-hemolysin; these pores approximate the size of fusion pores measured in neuroendocrine cells. We found that the axial diameter of each dye was a crucial determinant for permeation. Moreover, the two dyes with the largest cross-sectional areas were completely unable to pass through pores formed by a mutant α-hemolysin that has a slightly smaller pore than the wild-type toxin. The overall time constant for efflux (seconds) of each dye was orders of magnitude slower than the time constant for dissociation from membranes (milliseconds). Thus, the permeation step is rate-limiting, and this observation was further supported by atomistic molecular dynamics simulations. Together, the data reported here help provide a framework for interpreting dye destaining rates from secretory vesicles.
Assessment of Inflation in a Human Cadaveric Lung with Dark-Field Chest Radiography (2022)

Dark-field chest radiography signal intensity appeared to correlate with inflation status in a cadaveric lung.
99mTc Hynic-rh-Annexin V scintigraphy for in vivo imaging of apoptosis in patients with head and neck cancer treated with chemoradiotherapy (2007)

The purpose of this study was to determine the value of 99mTc Hynic-rh-Annexin-V-Scintigraphy (TAVS), a non-invasive in vivo technique to demonstrate apoptosis in patients with head and neck squamous cell carcinoma. TAVS were performed before and within 48 h after the first course of cisplatin-based chemoradiation. Radiation dose given to the tumour at the time of post-treatment TAVS was 6–8 Gy. Single-photon emission tomography data were co-registered to planning CT scan. Complete sets of these data were available for 13 patients. The radiation dose at post-treatment TAVS was calculated for several regions of interest (ROI): primary tumour, involved lymph nodes and salivary glands. Annexin uptake was determined in each ROI, and the difference between post-treatment and baseline TAVS represented the absolute Annexin uptake: Delta uptake (ΔU). In 24 of 26 parotid glands, treatment-induced Annexin uptake was observed. Mean ΔU was significantly correlated with the mean radiation dose given to the parotid glands (r = 0.59, p = 0.002): Glands that received higher doses showed more Annexin uptake. ΔU in primary tumour and pathological lymph nodes showed large inter-patient differences. A high correlation was observed on an inter-patient level (r = 0.71, p = 0.006) between the maximum ΔU in primary tumour and in the lymph nodes. Within the dose range of 0–8 Gy, Annexin-V-scintigraphy showed a radiation-dose-dependent uptake in parotid glands, indicative of early apoptosis during treatment. The inter-individual spread in Annexin uptake in primary tumours could not be related to differences in dose or tumour volume, but the Annexin uptake in tumour and lymph nodes were closely correlated. This effect might represent a tumour-specific apoptotic response.
Partially Observable Minimum-Age Scheduling: The Greedy Policy (2020)

This paper studies the minimum-age scheduling problem in a wireless sensor network where an access point (AP) monitors the state of an object via a set of sensors. The freshness of the sensed state, measured by the age-of-information (AoI), varies at different sensors and is not directly observable to the AP. The AP has to decide which sensor to query/sample in order to get the most updated state information of the object (i.e., the state information with the minimum AoI). In this paper, we formulate the minimum-age scheduling problem as a multi-armed bandit problem with partially observable arms and explore the greedy policy to minimize the expected AoI sampled over an infinite horizon. To analyze the performance of the greedy policy, we 1) put forth a relaxed greedy policy that decouples the sampling processes of the arms, 2) formulate the sampling process of each arm as a partially observable Markov decision process (POMDP), and 3) derive the average sampled AoI under the relaxed greedy policy as a sum of the average AoI sampled from individual arms. Numerical and simulation results validate that the relaxed greedy policy is an excellent approximation to the greedy policy in terms of the expected AoI sampled over an infinite horizon.
Rapid isothermal amplification and portable detection system for SARS-CoV-2 (2020)

The COVID-19 pandemic provides an urgent example where a gap exists between availability of state-of-the-art diagnostics and current needs. As assay protocols and primer sequences become widely known, many laboratories perform diagnostic tests using methods such as RT-PCR or reverse transcription loop mediated isothermal amplification (RT-LAMP). Here, we report an RT-LAMP isothermal assay for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and demonstrate the assay on clinical samples using a simple and accessible point-of-care (POC) instrument. We characterized the assay by dipping swabs into synthetic nasal fluid spiked with the virus, moving the swab to viral transport medium (VTM), and sampling a volume of the VTM to perform the RT-LAMP assay without an RNA extraction kit. The assay has a limit of detection (LOD) of 50 RNA copies per μL in the VTM solution within 30 min. We further demonstrate our assay by detecting SARS-CoV-2 viruses from 20 clinical samples. Finally, we demonstrate a portable and real-time POC device to detect SARS-CoV-2 from VTM samples using an additively manufactured three-dimensional cartridge and a smartphone-based reader. The POC system was tested using 10 clinical samples, and was able to detect SARS-CoV-2 from these clinical samples by distinguishing positive samples from negative samples after 30 min. The POC tests are in complete agreement with RT-PCR controls. This work demonstrates an alternative pathway for SARS-CoV-2 diagnostics that does not require conventional laboratory infrastructure, in settings where diagnosis is required at the point of sample collection.
New trends in extraction and separation processes (2008)

The market of botanical derivatives in industrialized countries is in constant increase with different market positioning, of the various compounds used today, country by country. In the past the most significant efforts, at the discovery level, have been focused on pharmaceutical molecules, isolating pure compounds from the botanical source and then following the approaches of medicinal chemistry and international regulations for drugs.
Adobe's Secure Real-Time Media Flow Protocol (2013)

This memo describes Adobe's Secure Real-Time Media Flow Protocol
(RTMFP), an endpoint-to-endpoint communication protocol designed to
securely transport parallel flows of real-time video, audio, and data
messages, as well as bulk data, over IP networks. RTMFP has features
that make it effective for peer-to-peer (P2P) as well as client-server
communications, even when Network Address Translators (NATs) are used.
Comparative Study of Monolithic Microstrip and Coplanar Strips Lines for Electrooptic Light Modulators (1992)

In this communication, double heterostructure GaAs/GaAlAs MMIC microstrip and coplanar strips structures are studied over the 2-18 GHz band, for their use as travelling wave electrooptic modulators. The obtained theoretical and experimental results show that the coplanar strips configuration, under odd mode excitation, presents less insertion losses and quite less dispersion in comparison to the microstrip structure.
Blowing in the wind! [In My View] (2008)

Examines the search for silver bullet solutions to the energy crisis.
Association of testosterone therapy with disease progression in older males with COVID‐19 (2022)

This study showed that testosterone therapy was not associated with decreased risks of COVID-19 adverse outcomes. These findings may provide clinically relevant information regarding testosterone treatment in older men with COVID-19 and other respiratory viral infections with similar pathogenesis.
The structure of small GaAs clusters (1997)

Semiconductor clusters, particularly gallium arsenide , have potential applications in nonlinear optical devices. Special interest is generated by the fact that their optical and electronic behavior depends on the size of the cluster. Direct evidence is presented for the occurrence of hexagonal, i.e., wurtzite‐type structure, GaAs in clusters, whereas bulk GaAs has zinc‐blende structure. High‐resolution transmission electron microscopy, atomic force microscopy and electron diffraction results are reported and interpreted. Suggestions are made for further work.
Coxeter Pairs, Ammann Patterns and Penrose-like Tilings (2016)

We identify a precise geometric relationship between: (i) certain natural pairs of irreducible reflection groups (``Coxeter pairs"); (ii) self-similar quasicrystalline patterns formed by superposing sets of 1D quasi-periodically-spaced lines, planes or hyper-planes (``Ammann patterns"); and (iii) the tilings dual to these patterns (``Penrose-like tilings"). We use this relationship to obtain all irreducible Ammann patterns and their dual Penrose-like tilings, along with their key properties in a simple, systematic and unified way, expanding the number of known examples from four to infinity. For each symmetry, we identify the minimal Ammann patterns (those composed of the fewest 1d quasiperiodic sets) and construct the associated Penrose-like tilings: 11 in 2D, 9 in 3D and one in 4D. These include the original Penrose tiling, the four other previously known Penrose-like tilings, and sixteen that are new. We also complete the enumeration of the quasicrystallographic space groups corresponding to the irreducible non-crystallographic reflection groups, by showing that there is a unique such space group in 4D (with nothing beyond 4D).
ChemInform Abstract: Two Novel and Potent 3‐[(o‐Methoxyphenyl)piperazinylethyl]‐5‐phenylthieno [2,3‐d]pyrimidine‐2,4‐diones Selective for the α1D Receptor. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Model reduction of positive real systems (2005)

This paper considers the general model reduction problem for a positive real system under the constraint that the reduced model is also positive real. The authors present solutions based on the balanced stochastic truncation, balancing linear matrix inequalities and approximating the spectral factors with associated H/sub /spl infin// norm error bounds. An example is given to illustrate the performance of these methods.