gebhart/patrepeval huggingface dataset:
Rate-compatible Low Density Parity Check Codes for Capacity-approaching ARQ Schemes in Packet Data Communications. (2002)

Strong rate-compatible codes is important to achieve high throughput in hybrid automatic repeat request with forward error correction (ARQ/FEC) systems in packet data transmission. This paper focuses on the construction of efficient rate-compatible low density parity check (RC-LDPC) codes over a wide rate range. The conventional approach of puncturing is first studied. Analysis on the code ensemble and the asymptotic performance shows that it works well only at high rates and only when the amount of puncturing is small. To extend the dynamic rate range, a special approach of extending is proposed and is shown to produce good RC-LDPC codes at low rates. Combining both approaches, efficient RC-LDPC codes are constructed and a hybrid ARQ/FEC system using RC-LDPC codes is evaluated. The proposed LDPC-ARQ system can achieve information rate about 1 dB away from the theoretical limit, which is comparable to turbo ARQ systems [1][2], yet with lower decoding complexity.
Robust Video Hashing via Multilinear Subspace Projections (2012)

The goal of video hashing is to design hash functions that summarize videos by short fingerprints or hashes. While traditional applications of video hashing lie in database searches and content authentication, the emergence of websites such as YouTube and DailyMotion poses a challenging problem of anti-piracy video search. That is, hashes or fingerprints of an original video (provided to YouTube by the content owner) must be matched against those uploaded to YouTube by users to identify instances of "illegal" or undesirable uploads. Because the uploaded videos invariably differ from the original in their digital representation (owing to incidental or malicious distortions), robust video hashes are desired. We model videos as order-3 tensors and use multilinear subspace projections, such as a reduced rank parallel factor analysis (PARAFAC) to construct video hashes. We observe that, unlike most standard descriptors of video content, tensor-based subspace projections can offer excellent robustness while effectively capturing the spatio-temporal essence of the video for discriminability. We introduce randomization in the hash function by dividing the video into (secret key based) pseudo-randomly selected overlapping sub-cubes to prevent against intentional guessing and forgery. Detection theoretic analysis of the proposed hash-based video identification is presented, where we derive analytical approximations for error probabilities. Remarkably, these theoretic error estimates closely mimic empirically observed error probability for our hash algorithm. Furthermore, experimental receiver operating characteristic (ROC) curves reveal that the proposed tensor-based video hash exhibits enhanced robustness against both spatial and temporal video distortions over state-of-the-art video hashing techniques.
EPN: Edge-Aware PointNet for Object Recognition from Multi-View 2.5D Point Clouds (2019)

Performance of current 3D point based detectors is limited by the number of points they can process, consequently limiting their accuracy. In this paper we propose a novel architecture coined as Edge-Aware PointNet, that incorporates geometric shape priors as binary maps, integrated in parallel with the PointNet++ framework, through convolutional neural networks (CNNs). The proposed architecture takes individual object instances as input and learns the task of object recognition for 3D shapes. To train the network, we present a dataset of 31k 2.5D synthetic point clouds rendered from ModelNet40. Through 2.5D representation, the network learns object recognition despite occlusion that enables improved performance on objects from real world, while 2D binary maps enable feature learning that is independent of number of points in the point cloud. Comprehensive experimentation shows that the proposed network is able to improve performance by 2.5% on ModelNet40 and 2.6% on ModelNet10 datasets, as compared to the baseline PointNet++. We also show improved performance as compared to state-of-the-art methods, on a real world RGBD dataset where our network improves results by 8%. Our code and dataset is publicly available at github.com/Merium88/Edge-Aware-PointNet.
Frequent item set mining (2012)

Abstract Frequent item set mining is one of the best known and most popular data mining methods. Originally developed for market basket analysis, it is used nowadays for almost any task that requires discovering regularities between (nominal) variables. This paper provides an overview of the foundations of frequent item set mining, starting from a definition of the basic notions and the core task. It continues by discussing how the search space is structured to avoid redundant search, how it is pruned with the a priori property, and how the output is reduced by confining it to closed or maximal item sets or generators. In addition, it reviews some of the most important algorithmic techniques and data structures that were developed to make the search for frequent item sets as efficient as possible. © 2012 Wiley Periodicals, Inc. This article is categorized under: Algorithmic Development > Association Rules Application Areas > Data Mining Software Tools Technologies > Association Rules
X Window System programming (1991)

This tutorial-reference demonstrates how to develop Window-based applications. The first part offers detailed tutorials designed to ease users into the X Window system and to show how to build interactive applications using X. The second part includes X library routines.
An enhanced closed-loop MIMO design for OFDM/OFDMA-PHY (2004)

This document proposes a simple and novel closed-loop transmit precoding scheme to improve the bit-error rate performance of OFDM/OFDMA-PHY in IEEE 802.16e. The proposed scheme requires a feedback of only two bits per OFDM tone for the entire duration of a frame. The feedback rate can even be reduced to one bit per OFDM tone by sacrificing the performance gain. Simulation results are provided to illustrate the performance gain of the proposed closed-loop technique over the existing open-loop operation framework. Purpose Adoption Notice This document has been prepared to assist IEEE 802.16. It is offered as a basis for discussion and is not binding on the contributing individual(s) or organization(s). The material in this document is subject to change in form and content after further study. The contributor(s) reserve(s) the right to add, amend or withdraw material contained herein. Release The contributor grants a free, irrevocable license to the IEEE to incorporate text contained in this contribution, and any modifications thereof, in the creation of an IEEE Standards publication; to copyright in the IEEE’s name any IEEE Standards publication even though it may include portions of this contribution; and at the IEEE’s sole discretion to permit others to reproduce in whole or in part the resulting IEEE Standards publication. The contributor also acknowledges and accepts that this contribution may be made public by IEEE 802.16. Patent Policy and Procedures The contributor is familiar with the IEEE 802.16 Patent Policy and Procedures (Version 1.0) , including the statement “IEEE standards may include the known use of patent(s), including patent applications, if there is technical justification in the opinion of the standards-developing committee and provided the IEEE receives assurance from the patent holder that it will license applicants under reasonable terms and conditions for the purpose of implementing the standard.” Early disclosure to the Working Group of patent information that might be relevant to the standard is essential to reduce the possibility for delays in the development process and increase the likelihood that the draft publication will be approved for publication. Please notify the Chair as early as possible, in written or electronic form, of any patents (granted or under application) that may cover technology that is under consideration by or has been approved by IEEE 802.16. The Chair will disclose this notification via the IEEE 802.16 web site . 2004-08-17 IEEE C802.16e-04/267 2 An enhanced closed-loop MIMO design for OFDM/OFDMAPHY Muhammad Ikram, Eko Onggosanusi, Vasanthan Raghavan, Anand Dabak, and Srinath Hosur Texas Instruments, Inc.
Mutations in the Scaffoldin Gene, <i>cipA</i> , of <i>Clostridium thermocellum</i> with Impaired Cellulosome Formation and Cellulose Hydrolysis: Insertions of a New Transposable Element, IS <i>1447</i> , and Implications for Cellulase Synergism on Crystalline Cellulose (2008)

Mutants of Clostridium thermocellum that had lost the ability to adhere to microcrystalline cellulose were isolated. Six of them that showed diminished ability to depolymerize crystalline cellulose were selected. Size exclusion chromatography of the proteins from the culture supernatant revealed the loss of the supramolecular enzyme complex, the cellulosome. However, denaturing sodium dodecyl sulfate-polyacrylamide gel electrophoresis resulted in extracellular protein patterns comparable to those of isolated cellulosomes, except for a missing CipA band. Sequencing of the six mutant cipA genes revealed a new insertion (IS) element, IS1447, belonging to the IS3 family. It was inserted into the cipA reading frame in four different locations: cohesin module 1, two different positions in the carbohydrate binding module, and cohesin module 3. The IS sequences were identical and consisted of a transposase gene and the inverted repeats IRR and IRS. The insertion resulted in an obviously nonspecific duplication of 3 base pairs within the target sequence. This lack of specificity allows transposition without the need of a defined target DNA sequence. Eighteen copies of IS1447 were identified in the genomic sequence of C. thermocellum ATCC 27405. At least one of them can be activated for transposition. Compared to the wild type, the mutant culture supernatant, with a completely defective CipA protein, showed equal specific hydrolytic activity against soluble beta-glucan but a 15-fold reduction in specific activity with crystalline cellulose. These results identify a genetic basis for the synergistic effect of complex formation on crystalline-cellulose degradation.
Genetic Influences on Physiological and Subjective Responses to an Aerobic Exercise Session among Sedentary Adults (2012)

Objective. To determine whether genetic variants suggested by the literature to be associated with physiology and fitness phenotypes predicted differential physiological and subjective responses to a bout of aerobic exercise among inactive but otherwise healthy adults. Method. Participants completed a 30-minute submaximal aerobic exercise session. Measures of physiological and subjective responding were taken before, during, and after exercise. 14 single nucleotide polymorphisms (SNPs) that have been previously associated with various exercise phenotypes were tested for associations with physiological and subjective response to exercise phenotypes. Results. We found that two SNPs in the FTO gene (rs8044769 and rs3751812) were related to positive affect change during exercise. Two SNPs in the CREB1 gene (rs2253206 and 2360969) were related to change in temperature during exercise and with maximal oxygen capacity (VO(2) max). The SLIT2 SNP rs1379659 and the FAM5C SNP rs1935881 were associated with norepinephrine change during exercise. Finally, the OPRM1 SNP rs1799971 was related to changes in norepinephrine, lactate, and rate of perceived exertion (RPE) during exercise. Conclusion. Genetic factors influence both physiological and subjective responses to exercise. A better understanding of genetic factors underlying physiological and subjective responses to aerobic exercise has implications for development and potential tailoring of exercise interventions.
A novel strategy to monitor microfluidic in-vitro blood-brain barrier models using impedance spectroscopy (2015)

In this work, we present the use of interdigitated electrodes (IDEs) for performing electrical impedance spectroscopy (EIS) measurements to monitor a microfluidic blood brain barrier model. In particular, an electrode configuration which would not impair the optical visualization of the cell culture is proposed. Numerical studies have been performed to evaluate the electrical impedance sensitivity of the proposed tetrapolar configuration along the cell barrier in a given microfluidic chamber geometry. The system has been validated using a home-made cyclo olefin polymer (COP) bioreactor and perforated poly (methyl methacrylate) (PMMA) sheets with different pore densities in order to simulate different cell barrier impedances.
Solubilizing and Stabilizing Proteins in Anhydrous Ionic Liquids through Formation of Protein–Polymer Surfactant Nanoconstructs (2016)

Nonaqueous biocatalysis is rapidly becoming a desirable tool for chemical and fuel synthesis in both the laboratory and industry. Similarly, ionic liquids are increasingly popular anhydrous reaction media for a number of industrial processes. Consequently, the use of enzymes in ionic liquids as efficient, environment-friendly, commercial biocatalysts is highly attractive. However, issues surrounding the poor solubility and low stability of enzymes in truly anhydrous media remain a significant challenge. Here, we demonstrate for the first time that engineering the surface of a protein to yield protein-polymer surfactant nanoconstructs allows for dissolution of dry protein into dry ionic liquids. Using myoglobin as a model protein, we show that this method can deliver protein molecules with near native structure into both hydrophilic and hydrophobic anhydrous ionic liquids. Remarkably, using temperature-dependent synchrotron radiation circular dichroism spectroscopy to measure half-denaturation temperatures, our results show that protein stability increases by 55 °C in the ionic liquid as compared to aqueous solution, pushing the solution thermal denaturation beyond the boiling point of water. Therefore, the work presented herein could provide a platform for the realization of biocatalysis at high temperatures or in anhydrous solvent systems.
Humoral and cellular immunogenicity and safety following a booster dose of a tetravalent dengue vaccine 5+ years after completion of the primary series in Singapore: 2-year follow-up of a randomized phase II, placebo-controlled trial (2021)

The tetravalent dengue vaccine (CYD-TDV) is approved for use as a 3-dose series for the prevention of dengue in seropositive individuals ≥9 years. A randomized, placebo-controlled, phase II study of a booster dose of CYD-TDV in individuals who completed the 3-dose schedule >5 years previously (NCT02824198), demonstrated that a booster restored neutralizing antibody titers to post-dose 3 levels. We present additional immunogenicity assessments up to 24 months post-booster, and B- and T-cell responses in a participant subset. Participants aged 9-45 years that had received all three doses of CYD-TDV were randomized 3:1 to receive a booster dose of CYD-TDV (n = 89) or placebo (n = 29). Neutralizing antibody levels at Months 1, 6, 12, and 24 post-booster were assessed by plaque reduction neutralization test. In a subset, B-cell responses were assessed by a fluorescent immunospot assay, and T-cells analyzed by flow cytometry at Days 0, 7, 12, Months 1 and 12. We observed an increase of antibody titers Month 1 post-booster, then a gradual decline to Month 24. In the CYD-TDV booster group, an increase in plasmablasts was seen at Day 7 declining by Day 14, an increase in memory B-cells was observed at Day 28 with no persistence at Month 12. CYD-TDV booster recalled a CD8+ T-cell response, dominated by IFN-γ secretion, which decreased 12 months post-booster. This study showed a short-term increase in antibody titers and then gradual decrease following CYD-TDV booster injection >5 years after primary immunization, and the presence of memory B-cells activated following the booster, but with low persistence.
Getting it right (2003)

When designing or undertaking any research project, a great deal of time and effort is put into ‘getting it right’. In this context, ‘getting it right’ usually relates to matters of rigour and scientific justification. Consequently, considerable importance is attached to methodological and operational issues such as: the articulation of a precise and unambiguous research question or hypothesis; the clarity of the sampling strategy; the appropriateness of data collection methods and techniques; and the comprehensiveness of any analytical procedures adopted. Common questions are asked of each of these aspects of a study (and more), whether it be as part of the review process for a research proposal submitted to a funding body or when one is asked critically to appraise a piece of published research. Whatever the context, fundamental value judgements are made about the scientific rigour and merit of the research. However, one facet of ‘rigour’ that is often overlooked in published research relates to the degree of influence that a researcher exerts, either intentionally or unintentionally, on all aspects of the research process. In the qualitative research literature this aspect of rigour is addressed through the concept of ‘reflexivity’, while in the quantitative paradigm the constructs of reliability and validity are assumed to account for any such effects.
Out of the iron age: new insights into the critical role of manganese homeostasis in bacteria (2001)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Inducible cardiac arrhythmias caused by enhanced β<sub>1</sub>-adrenergic autoantibody expression in the rabbit (2013)

Previous studies demonstrated burst pacing and intravenous infusion of ACh induced sustained atrial tachycardia when rabbits were immunized to produce β2-adrenergic receptor (β2AR)-activating autoantibodies. The objective of this study was to examine the arrhythmogenic effect of β1-adrenergic receptor (β1AR)-activating autoantibodies in the rabbit. Eight New Zealand white rabbits were immunized with a β1AR second extracellular loop peptide to raise β1AR antibody titers. A catheter-based electrophysiological study was performed on anesthetized rabbits before and after immunization. Arrhythmia occurrence was determined in response to burst pacing before and after ACh infusion in incremental concentrations of 10 μM, 100 μM, and 1 mM. The baseline sinus heart rate before and after immunization averaged 149 ± 17 per min and 169 ± 16 per min, respectively (P < 0.05). In the preimmune studies, there were five sustained (≥10 s) arrhythmias in 32 induction attempts, which occurred in only four of eight rabbits. In the postimmune studies, there were 22 sustained arrhythmias in 32 induction attempts, which occurred in all eight rabbits (P < 0.0001 for the independent effect of immunization). Of the 22 sustained arrhythmias postimmunization, 15 were sinus tachycardia compared with only two before immunization (P < 0.01 for the independent effect of immunization). Postimmune (but not preimmune) rabbit sera demonstrated specific binding to β1AR and induced significant β1AR activation in transfected cells in vitro. No cross-reactivity with β2AR was observed. In conclusion, in contrast with rabbits with β2AR-activating autoantibodies that demonstrate predominantly atrial tachycardias, enhanced autoantibody activation of β1AR in the rabbit leads to tachyarrhythmias mainly in the form of sustained sinus tachycardia.
Mobility Agents: Avoiding the Signaling of Route Optimization on Large Servers (2007)

A foreseeable scenario is where, on the Internet, mobile IPv6 is deployed and a large percentage of the clients are mobile nodes. These mobile clients will communicate with large servers, which under the point of view of mobile IPv6 will be correspondent nodes. In mobile IPv6 if a mobile node wants to communicate with a correspondent node directly (route optimization) it must perform the return routability procedure which includes sending and receiving signaling messages, cryptographic calculations and storing a state. This procedure must be performed for each mobile client connection and for each handover. The return routability procedure would introduce a very significant load on these servers. Moreover the servers must be modified in order to support the route optimization of mobile IPv6. These issues may be a drawback for the deployment of mobile IPv6. In this paper we propose mobility agents, a centralized solution that performs route optimization on behalf the correspondent nodes. Mobility Agents reduce the deployment cost, do not require modifying the servers, they are compatible with NEMO and other mobility protocols. Moreover they allow deploying different extensions of mobile IPv6 such as optimized MIPv6 without modifying the correspondent nodes.
Ultrasound-accelerated Tissue Fixation/Processing Achieves Superior Morphology and Macromolecule Integrity with Storage Stability (2005)

We demonstrate that high-frequency and high-intensity ultrasound (US) can be applied to both tissue fixation and tissue processing to complete the conventional overnight formalin-fixation and paraffin-embedding (FFPE) procedures within 1 hr. US-facilitated FFPE retains superior tissue morphology and long-term room temperature storage stability than conventional FFPE. There is less alteration of protein antigenicity after US-FFPE preservation so that rapid immunohistochemical reactions occur with higher sensitivity and intensity, reducing the need for antigen retrieval pretreatment. US-FFPE tissues present storage stability so that room temperature storage up to 7 years does not significantly affect tissue morphology, protein antigenic properties, RNA distribution, localization, and quantitation. In addition, during fixation, tissue displays physical changes that can be monitored and reflected as changes in transmission US signals. As far as we know, this is the first effort to monitor tissue physical changes during fixation. Further study of this phenomenon may provide a method to control and to monitor the level of fixation for quality controls. The mechanism of less alteration of protein antigenicity by US-FFPE was discussed.
Structure of 1-deoxy-<scp>D</scp>-xylulose 5-phosphate reductoisomerase in a quaternary complex with a magnesium ion, NADPH and the antimalarial drug fosmidomycin (2007)

The crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) from Escherichia coli complexed with Mg(2+), NADPH and fosmidomycin was solved at 2.2 A resolution. DXR is the key enzyme in the 2-C-methyl-D-erythritol 4-phosphate pathway and is an effective target of antimalarial drugs such as fosmidomycin. In the crystal structure, electron density for the flexible loop covering the active site was clearly observed, indicating the well ordered conformation of DXR upon substrate binding. On the other hand, no electron density was observed for the nicotinamide-ribose portion of NADPH and the position of Asp149 anchoring Mg(2+) was shifted by NADPH in the active site.