gebhart/patrepeval huggingface dataset:
Antigenic and immunogenic evaluation of permutations of soluble hepatitis C virus envelope protein E2 and E1 antigens (2021)

Yearly, about 1.5 million people become chronically infected with hepatitis C virus (HCV) and for the 71 million with chronic HCV infection about 400,000 die from related morbidities, including liver cirrhosis and cancer. Effective treatments exist, but challenges including cost-of-treatment and wide-spread undiagnosed infection, necessitates the development of vaccines. Vaccines should induce neutralizing antibodies (NAbs) against the HCV envelope (E) transmembrane glycoprotein 2, E2, which partly depends on its interaction partner, E1, for folding. Here, we generated three soluble HCV envelope protein antigens with the transmembrane regions deleted (i.e., fused peptide backbones), termed sE1E2 (E1 followed by E2), sE2E1 (E2 followed by E1), and sE21E (E2 followed by inverted E1). The E1 inversion for sE21E positions C-terminal residues of E1 near C-terminal residues of E2, which is in analogy to how they likely interact in native E1/E2 complexes. Probing conformational E2 epitope binding using HCV patient-derived human monoclonal antibodies, we show that sE21E was superior to sE2E1, which was consistently superior to sE1E2. This correlated with improved induction of NAbs by sE21E compared with sE2E1 and especially compared with sE1E2 in female BALB/c mouse immunizations. The deletion of the 27 N-terminal amino acids of E2, termed hypervariable region 1 (HVR1), conferred slight increases in antigenicity for sE2E1 and sE21E, but severely impaired induction of antibodies able to neutralize in vitro viruses retaining HVR1. Finally, comparing sE21E with sE2 in mouse immunizations, we show similar induction of heterologous NAbs. In summary, we find that C-terminal E2 fusion of E1 or 1E is superior to N-terminal fusion, both in terms of antigenicity and the induction of heterologous NAbs. This has relevance when designing HCV E1E2 vaccine antigens.
A Multi-Watermarking Method Based on Wavelets Combined with the EZW Coder (2005)

International audience
MERIT: Model-driven Rehoming for VNF Chains (2020)

Network service providers often run service chains of Virtual Network Functions (VNFs) on privately owned clouds with limited capacity. These specialized service chains need to meet strict Service Level Objectives (SLOs), especially along the lines of availability (e.g., First responder services). Hence, VNFs in such thinly provisioned clouds may need to be frequently moved, or rehomed, when reacting to various cloud events like hotspots, failures and upgrades. In this paper, we perform a detailed measurement study to show that naive strategies for rehoming, applied uniformly across all VNFs of the service chain, are often sub-optimal when considering different metrics like the user-perceived service downtime and the provider-incurred time delay to complete the rehoming. We propose a novel ModEl-driven RehomIng Technique (MERIT) for VNF chains and empirically analyze the effect of various system parameters on different rehoming actions. Based on our analysis, we develop generic rehoming cost models and further, design and implement an autonomous rehoming system based on MERIT that identifies and executes the optimal rehoming action for each VNF in a service chain. Our experimental results on OpenStack using real-world chains show that MERIT can reduce the chain rehoming delay by up to 47% and the chain downtime by up to 49%.
The Validity and Reliability of the Microsoft Kinect for Measuring Trunk Compensation during Reaching (2020)

Compensatory movements at the trunk are commonly utilized during reaching by persons with motor impairments due to neurological injury such as stroke. Recent low-cost motion sensors may be able to measure trunk compensation, but their validity and reliability for this application are unknown. The purpose of this study was to compare the first (K1) and second (K2) generations of the Microsoft Kinect to a video motion capture system (VMC) for measuring trunk compensation during reaching. Healthy participants (n = 5) performed reaching movements designed to simulate trunk compensation in three different directions and on two different days while being measured by all three sensors simultaneously. Kinematic variables related to reaching range of motion (ROM), planar reach distance, trunk flexion and lateral flexion, shoulder flexion and lateral flexion, and elbow flexion were calculated. Validity and reliability were analyzed using repeated-measures ANOVA, paired <i>t</i>-tests, Pearson's correlations, and Bland-Altman limits of agreement. Results show that the K2 was closer in magnitude to the VMC, more valid, and more reliable for measuring trunk flexion and lateral flexion during extended reaches than the K1. Both sensors were highly valid and reliable for reaching ROM, planar reach distance, and elbow flexion for all conditions. Results for shoulder flexion and abduction were mixed. The K2 was more valid and reliable for measuring trunk compensation during reaching and therefore might be prioritized for future development applications. Future analyses should include a more heterogeneous clinical population such as persons with chronic hemiparetic stroke.
Interplay between Orientation at Electrodes and Copper Activation of Thermus thermophilus Laccase for O2 Reduction (2019)

Multicopper oxidases (MCOs) catalyze the oxidation of a variety of substrates while reducing oxygen into water through four copper atoms. As an additional feature, some MCOs display an enhanced activity in solution in the presence of Cu<sup>2+</sup>. This is the case of the hyperthermophilic laccase HB27 from <i>Thermus thermophilus</i>, the physiologic role of which is unknown. As a particular feature, this enzyme presents a methionine rich domain proposed to be involved in copper interaction. In this work, laccase from <i>T. thermophilus</i> was produced in <i>E. coli</i>, and the effect of Cu<sup>2+</sup> on its electroactivity at carbon nanotube modified electrodes was investigated. Direct O<sub>2</sub> electroreduction is strongly dictated by carbon nanotube surface chemistry in accordance with the enzyme dipole moment. In the presence of Cu<sup>2+</sup>, an additional low potential cathodic wave occurs, which was never described earlier. Analysis of this wave as a function of Cu<sup>2+</sup> availability allows us to attribute this wave to a cuprous oxidase activity displayed by the laccase and induced by copper binding close to the Cu T1 center. A mutant lacking the methionine-rich hairpin domain characteristic of this laccase conserves its copper activity suggesting a different site of copper binding. This study provides new insight into the copper effect in methionine rich MCOs and highlights the utility of the electrochemical method to investigate cuprous oxidase activity and to understand the physiological role of these MCOs.
A Theoretical Study of the Effect of Zr-, Nb-Doped and Vacancy-like Defects on H Desorption on MgH2 (110) Surface (2014)

DFT calculations were used to study hydrogen desorption energy in a set of pure, Nb- or Zr-doped systems, containing vacancy-like defects and a MgH2 (110) defect-free surface. The preferential location site for dopants was determined by means of occupation energy analysis. Both transition metal atoms (Nb and Zr) preferred interstitial sites. The effect of vacancies in the systems was also considered. MgH2 with a Nb interstitial atom and MgH2 with a Zr interstitial atom containing a Mg vacancy modifies the surface geometry and weakens the Mg–H bonds thus easing the H desorption process.
Modeling the joint dynamics of relational events and individual states (2016)

Networks evolve at multiple levels; edges or relations may change, and the characteristics of the individuals within the network may change as well. Often these processes are intertwined, and in order to study them, statistical models must be developed that account for coevolution of multiple network components. The increased availability of continuous time network data has prompted new models for network inference such as the relational event framework. While network data may be continuously observable, the characteristics or state of an individual can still only be observed periodically. This type of panel data can be readily analyzed using actor-oriented models, but these methods do not accommodate continuous network data. We propose a model that integrates the relational event framework with actor-oriented models for behavioral change, allowing us to model the joint dynamics of relational events and individual states. This composite model preserves the advantages of each method, while leveraging the richer information available in relational event data. We apply our model to datasets collected from virtual team experiments to highlight the utility of our method.
Applications of S‐theory in the study of soil physical degradation and its consequences (2007)

Abstract The S ‐theory for soil physical quality is introduced. It is shown how values of S can be determined from the water retention characteristic curve. It is also explained how, when experimental data are not available, pedotransfer functions can be used to obtain estimates of S . Although S was first introduced as an index of soil physical quality, it is being increasingly found that it is a useful numerical quantity that can be used in equations for prediction of a range of soil physical properties. Its use is illustrated with examples for hydraulic conductivity, friability, tillage, compaction, penetrometer resistance, plant‐available water, root growth and readily dispersible clay. The main merit of S derives from the fact that given values of S have the same meaning and consequences in different soils. It is described how S can be used to identify areas of land where physical degradation or amelioration are taking place, and to evaluate management practices that will give sustainable land use. Copyright © 2007 John Wiley &amp; Sons, Ltd.
Analysis of DNN approaches to speaker identification (2016)

This work studies the usage of the Deep Neural Network (DNN) Bottleneck (BN) features together with the traditional MFCC features in the task of i-vector-based speaker recognition. We decouple the sufficient statistics extraction by using separate GMM models for frame alignment, and for statistics normalization and we analyze the usage of BN and MFCC features (and their concatenation) in the two stages. We also show the effect of using full-covariance GMM models, and, as a contrast, we compare the result to the recent DNN-alignment approach. On the NIST SRE2010, telephone condition, we show 60% relative gain over the traditional MFCC baseline for EER (and similar for the NIST DCF metrics), resulting in 0.94% EER.
Thoracoscopic Resection of Painful Multiple Rib Fractures: Case Report (2002)

Sing, Ronald F. DO, FACS; Mostafa, Gamal MD, FRCS; Matthews, Brent D. MD; Kercher, Kent W. MD; Heniford, B. Todd MD, FACS Author Information
Real-time Obstacle Avoidance for Underactuated Autonomous Underwater Vehicles in Unknown Vortex Sea Flow by the MDP Approach (2006)

A method for real-time collision avoidance for underactuated autonomous underwater vehicles (AUVs) in the sea environment with unknown obstacle configurations and unknown vortex sea flow is proposed. The proposed method is an application of the Markov-decision-process- (MDP) based motion planning method. It is essential to adopt the MDP-based method for managing both the kinematics and dynamics of an AUV affected by sea flow. The real-time obstacle avoidance needs replanning when a new obstacle is discovered so that the AUV can find a suitable path around concave obstacles; however, MDP-based re-planning calculations require high computational power and are hard to be used in real time. In addition, it is impossible to know the whole distribution of the changing sea flow velocity in real time. Therefore, MDP-based re-planning calculation during the mission is not efficient. As a solution, the proposed method combines a rough re-planning considering only the geometrical properties of obstacles with rough target path tracking considering the kinematical and dynamical property of the AUV. Because there is no guarantee that the AUV can track the target path with high accuracy, the AUV is controlled to avoid collisions with obstacles at the same time. The rough target path tracking and obstacle avoidance is done using the result of off-line MDP based motion planning. The performance of the proposed method is examined by simulation of an AUV cruising in a vortex sea flow
A Compressive Sensing Codec Architecture for ECG Signals with Adaptive Quantization and Stream Entropy Coding (2022)

&lt;p&gt;Compressive sensing (CS) is quite appealing as a low-complexity method for the compression of ECG data in resource-limited wearable devices. We propose a codec architecture comprising adaptive quantization and asymmetric numeral systems (ANS) based entropy coding of compressive measurements that can boost the compression ratio without sacrificing reconstruction performance. The quantized Gaussian entropy model for the compressive measurements is estimated directly from the data and is adapted dynamically to achieve better compression. We have tested our encoder with Block Sparse Bayesian learning as well as CS-NET sparse recovery algorithms on the MIT-BIH Arrhythmia database. Our encoder can achieve 5-25\% of additional space savings over compressive sensing.&lt;/p&gt; &lt;p&gt;The software code implementing this codec and all scripts for the experimental studies conducted in this work have been released as opensource software on GitHub.&lt;/p&gt;
Conducting composites of polypyrrole with polytetramethylbisphenol A carbonate (1996)

A new conducting composite of polypyrrole (PPy) has been prepared electrochemically where polytetramethylbisphenol A carbonate is used as the insulating matrix polymer. Characterization of the freestanding films of the composites were based on scanning electron microscopy, differential scanning calorimetry, and Fourier transform infrared studies as well as electrical conductivity measurements and solubility. Electrical conductivities were measured by a four-probe technique. Spectroscopic methods, together with conductivity and solubility studies, indicate that the synthesized composite is a homogeneous blend of the two polymers. No evidence of hydrogen bonding in the composite or grafting of the two polymers has been found, contrary to the PPy-polybisphenol A carbonate case. © 1996 John Wiley & Sons, Inc.
SUBWAVELENGTH PERIODIC RIPPLE FORMATION ON GaN SURFACE BY FEMTOSECOND LASER PULSES (2005)

The formation of femtosecond pulsed laser-induced periodic surface structure on GaN is reported for the first time (to our knowledge) in this paper. It has been found that the formation of the laser-induced ripples is very much dependent and quite sensitive to the laser conditions of the incident laser beam energy fluence and pulse numbers. Possibly due to the unique property of high-defect density of GaN material, the process window for laser-induced ripple formation is quite narrow compared to other materials such as InP , GaP , Al 2 O 3 etc. Nevertheless, through finely adjusting laser beam fluence and pulse number, subwavelength periodic ripples could be formed on the GaN surface. The formation of such periodic two-dimensional structures was attributed to optical interference of the incident laser light with scattered waves from a surface disturbance. Photoluminescence emission could still be detected on the GaN ripple area, indicating little degradation of GaN optical property after femtosecond laser processing. The femtosecond laser-induced ripple structure has potential applications in the fabrication of nanostructures for the GaN -based devices.
Effect of interleukin 1 on the expression of interleukin 2 receptor (Tac antigen) on human natural killer cells and natural killer-like cell line (YT cells). (1986)

The effect of interleukin 1 (IL 1) on the expression of interleukin 2 receptor (IL 2R/Tac antigen) on human natural killer (NK) cells and the NK-like cell line, YT was studied with the use of a fluoresceinated anti-IL 2R monoclonal antibody and a Spectrum III flow cytofluorometer. IL 2R was expressed on approximately 10% of NK cells. The expression of IL 2R on NK cells was increased to approximately 25% by the in vitro culture with monocytes or IL 1 and to a less extent by the culture with IL 2 or interferon-gamma (IFN-gamma). IL 2R was expressed on approximately 50% of YT cells without any stimulations. The expression of IL 2R on YT cells was increased up to almost 100% by the culture with IL 1 or monocytes, but not with IL 2, IFN-alpha, IFN-beta, IFN-gamma, or lectins such as concanavalin A and phytohemagglutinin-P. IL 1 absorbed with YT cells or murine thymocytes lost both IL 1 activity detected by the stimulation of murine thymocyte proliferative response and enhancing activity of IL 2R expression on YT cells, suggesting that IL 1 has both activities. However, the assay system of the expression of IL 2R on YT cells is much more sensitive than the stimulation of murine thymocyte proliferative response. By the kinetic study, the enhancement of IL 2R expression was induced by only a 2-hr incubation of YT cells with IL 1. This enhancement did not proceed at 4 degrees C or by the treatment of YT cells with actinomycin D or cycloheximide, suggesting that this enhancement is energy dependent and requires the synthesis of RNA and protein but not DNA. Thus IL 1 plays an important role for the regulation of the expression of IL 2R on NK cells, and IL 1-dependent IL 2R expression on YT cells may give us a good model for the study of the molecular mechanism of the regulation of IL 2R expression.
Analysis of Photovoltaic Power Yield Curtailment in Day-ahead Unit Commitment (2017)

High penetration of variable renewable energy (VRE) systems will impact power system operations because generation of VRE systems depends on weather conditions. We analyzed the operational situation and photovoltaic power yield curtailment for the Tokyo Electric Power Company area in 2030 using day-ahead unit commitment (UC) model when a high penetration of VRE systems is expected. At first, we updated our UC model to optimize PV curtailment keeping power system's security (load frequency control reserve) and minimizing operational cost. Using the updated model, we found that in case of 53GW and 100GW of PV penetration, around 0.34% and 4.83% of PV curtailment would be required throughout the year. High curtailment rate would be required only in spring and autumn seasons when power demand is small and PV yield is large. Regarding the other seasons, high curtailment rate would not be needed in any of the high PV penetration scenarios.
High cell density cultivation of Escherichia coli K4 in a microfiltration bioreactor: a step towards improvement of chondroitin precursor production (2011)

The increase of capsular polysaccharide titre confirmed the validity of the proposed fermentation strategy and opened the way to the use of the microfiltration bioreactor for the biotechnological production of chondroitin.
Temporin-SHf, a New Type of Phe-rich and Hydrophobic Ultrashort Antimicrobial Peptide (2010)

Because issues of cost and bioavailability have hampered the development of gene-encoded antimicrobial peptides to combat infectious diseases, short linear peptides with high microbial cell selectivity have been recently considered as antibiotic substitutes. A new type of short antimicrobial peptide, designated temporin-SHf, was isolated and cloned from the skin of the frog Pelophylax saharica. Temporin-SHf has a highly hydrophobic sequence (FFFLSRIFa) and possesses the highest percentage of Phe residues of any known peptide or protein. Moreover, it is the smallest natural linear antimicrobial peptide found to date, with only eight residues. Despite its small size and hydrophobicity, temporin-SHf has broad-spectrum microbicidal activity against Gram-positive and Gram-negative bacteria and yeasts, with no hemolytic activity. CD and NMR spectroscopy combined with restrained molecular dynamics calculations showed that the peptide adopts a well defined non-amphipathic alpha-helical structure from residue 3 to 8, when bound to zwitterionic dodecyl phosphocholine or anionic SDS micelles. Relaxation enhancement caused by paramagnetic probes showed that the peptide adopts nearly parallel orientations to the micelle surface and that the helical structure is stabilized by a compact hydrophobic core on one face that penetrates into the micelle interior. Differential scanning calorimetry on multilamellar vesicles combined with membrane permeabilization assays on bacterial cells indicated that temporin-SHf disrupts the acyl chain packing of anionic lipid bilayers, thereby triggering local cracks and microbial membrane disintegration through a detergent-like effect probably via the carpet mechanism. The short length, compositional simplicity, and broad-spectrum activity of temporin-SHf make it an attractive candidate to develop new antibiotic agents.
Comparative study of SiOCH low-k films with varied porosity interacting with etching and cleaning plasma (2002)

The interaction between conventional and highly porous SiOCH with CF4, O2, and H2 plasma has been investigated. The highly porous SiOCH film has porosity about 40% and a k value about 2.2. The pristine SiOCH film has 19% of porosity and k value of 2.7. All experiments were performed at room temperature in a downstream plasma reactor. It was found that (i) the CF4 plasma etches the SiOCH film without bulk material modification (however, the etch rate was higher in the case of the SiOCH film with increased porosity); (ii) the O2 plasma oxidizes the SiOCH film converting the top layer to a hydrophilic SiO2-like porous material, the SiOCH film with increased porosity suffers more severely from this kind of plasma; (iii) the CF4/O2 plasma mixture has an optimal O2 concentration at which the etch rate is maximal; and (iv) the H2 plasma does not interact with the SiOCH film and can be a promising candidate for the resist stripping.
A Case of The Reduction of Symptoms, But No Change on The CT Scanning in HNP by Oriental Medical Treatment Added Mori cortex-Bee Venom Acupuncture (2001)

By process of treatment for a case which diagnosed as HNP of left posterolateral aspect of L4/5 disc and treated from the 10th, May 2001 to the 23rd, Jun 2001, the results are as follows. Method & Results : This patient was medicated Hwallaktang-gami, taken acupuncture, phototherapy, TENS, electric acupuncture, exercises, Mori Cortex-bee venom acupuncture. As a result, the patient's clinical symptom were improved but a computed tomagraphy confirmed L4/5 and L5/S1 HNP was not changed as seen on repeated CT scanning. Conclusion : These results suggest that among conservative therapies the oriental medical treatments including Mori Cortex-bee venom acupuncture improve clinical symptom effectively. But in this case, the structure of herniated disc was not changed.
Brief announcement (2005)

Many overlay multicast protocols have been designed and deployed across the Internet to support content distribution. To our knowledge, however, none have provided a rigorous analysis of the problem or the effectiveness of their proposed solutions. We define the Overlay Network Content Distribution (OCD) problem to allow such analyses.