gebhart/patrepeval huggingface dataset:
Effects of serum starvation and re-cloning on the efficiency of nuclear transfer using bovine fetal fibroblasts (1999)

The developmental potential of bovine fetal fibroblasts was evaluated using nuclear transfer. Fibroblasts from a 37-day-old fetus were fused to enucleated oocytes before activation. Nuclei of starved (cultured for 8 days in medium containing 0.5% serum) fibroblasts supported the development of reconstructed embryos to the blastocyst stage significantly better than those of non-starved fibroblasts (39% versus 20%; P < 0.05). When nuclear transfer morulae derived from starved or non-starved fibroblasts were used for re-cloning, the proportion of blastocysts (52 and 55%, respectively) obtained with these embryonic nuclei was significantly higher than it was with fibroblast nuclei used in the first round of nuclear transfer (P < 0.05 and P < 0.001, respectively). After transfer of blastocysts derived from non-starved and starved fibroblasts, respectively, 33% (1/3) and 78% (7/9) of recipients were pregnant on day 30 as assessed by ultrasonography. On day 90, the corresponding pregnancy rates were 33% (1/3) and 63% (5/8). Two live male twin calves, derived from non-starved fibroblasts, were delivered by Caesarean section at day 281 of gestation. This study demonstrates a positive effect of serum starvation on the efficiency of nuclear transfer using bovine fetal fibroblasts. The efficiency of nuclear transfer could be further increased by recloning.
Tuning the Porphyrin Building Block in Self‐Assembled Cages for Branched‐Selective Hydroformylation of Propene (2017)

Unprecedented regioselectivity to the branched aldehyde product in the hydroformylation of propene was attained on embedding a rhodium complex in supramolecular assembly L2, formed by coordination-driven self-assembly of tris(meta-pyridyl)phosphine and zinc(II) porpholactone. The design of cage L2 is based on the ligand-template approach, in which the ligand acts as a template for cage formation. Previously, first-generation cage L1, in which zinc(II) porphyrin units were utilized instead of porpholactones, was reported. Binding studies demonstrate that the association constant for the formation of second-generation cage L2 is nearly an order of magnitude higher than that of L1. This strengthened binding allows cage L2 to remain intact in polar and industrially relevant solvents. As a consequence, the unprecedented regioselectivity for branched aldehyde products can be maintained in polar and coordinating solvents by using the second-generation assembly.
Whole-body humanoid control from upper-body task specifications (2010)

This paper introduces a very efficient, modified resolved acceleration control algorithm for dynamic filtering and control of whole-body humanoid motion in response to upper-body task specifications. The dynamic filter is applicable for general upper-body motions when standing in place. It is characterized by modification of the commanded torso acceleration based on a geometric solution to produce a ZMP which is inside the support. The resulting feasible modified motion is synchronized to the reference motion when the computed ZMP for the reference motion again falls within the support. Contact forces at each foot are controlled through a dedicated force distribution module which optimizes the ankle roll and pitch torques. The proposed approach uses time-local information and is therefore targeted for online control. The effectiveness of the algorithm is demonstrated by means of simulated experiments on a model of the Honda humanoid robot ASIMO using a highly dynamic upper-body reference motion.
AADvac1, an Active Immunotherapy for Alzheimer's Disease and Non Alzheimer Tauopathies: An Overview of Preclinical and Clinical Development (2019)

Neurofibrillary tau protein pathology is closely associated with the progression and phenotype of cognitive decline in Alzheimer's disease and other tauopathies, and a high-priority target for disease-modifying therapies. Herein, we provide an overview of the development of AADvac1, an active immunotherapy against tau pathology, and tau epitopes that are potential targets for immunotherapy. The vaccine leads to the production of antibodies that target conformational epitopes in the microtubule-binding region of tau, with the aim to prevent tau aggregation and spreading of pathology, and promote tau clearance. The therapeutic potential of the vaccine was evaluated in transgenic rats and mice expressing truncated, non mutant tau protein, which faithfully replicate of human tau pathology. Treatment with AADvac1 resulted in reduction of neurofibrillary pathology and insoluble tau in their brains, and amelioration of their deleterious phenotype. The vaccine was highly immunogenic in humans, inducing production of IgG antibodies against the tau peptide in 29/30 treated elderly patients with mild-to-moderate Alzheimer's. These antibodies were able to recognise insoluble tau proteins in Alzheimer patients' brains. Treatment with AADvac1 proved to be remarkably safe, with injection site reactions being the only adverse event tied to treatment. AADvac1 is currently being investigated in a phase 2 study in Alzheimer's disease, and a phase 1 study in non-fluent primary progressive aphasia, a neurodegenerative disorder with a high tau pathology component.
Kinematic and Workspace Comparison of Four and Five Degree of Freedom Miniature In Vivo Surgical Robot (2011)

The adoption of laparoendoscopic single-site surgery (LESS) provides potential for surgical procedures to be performed with the use of a single incision into the peritoneal cavity. Benefits of this technique include faster recovery times, decreased chance of infection, and improved cosmetic results as compared with traditional surgery. Current technology in this area relies on multiple laparoscopic tools, which are inserted into the peritoneal cavity through a specialized port. Because of this, poor visualization, limited dexterity, and unintuitive controls occur. To mitigate these problems, this research group is developing a multifunctional, two-armed miniature in vivo surgical robot with a remote user interface for use in LESS. While this platform’s feasibility has been demonstrated in multiple nonsurvival surgeries in porcine models, including four cholecystectomies, previous prototypes have been too large to be inserted through a single incision. Work is currently being performed to reduce the overall size of the robot while increasing dexterity. Using the knowledge gained from the development of a four degree of freedom (DOF) miniature in vivo surgical robot, another robot prototype was designed, which was smaller, yet was able to utilize 5DOFs instead 4. The decreased size of the 5DOF robot allows it to be completely inserted into the peritoneal cavity through a single incision for use in LESS. Each arm of the surgical robot is inserted independently before being mated together and attached to a central control rod. Once inserted, this platform allows for gross repositioning of the robot to provide surgical capabilities in all four quadrants of the abdominal cavity by rotating the control rod. The additional degree of freedom allows for reaching positions in the surgical workspace from varied angles. This paper will provide a comparison of the 4DOF and 5DOF miniature in vivo surgical robots. The implications of the added degree of freedom on the forward and inverse kinematics will be discussed and the workspace of each robot will be compared. Additionally, the increased complexity of the control system for the remote surgical interface in moving from 4DOFs to 5DOFs will be demonstrated. Finally, results from nonsurvival procedures using a porcine model will be presented for both robots. This comparison will provide useful information for further development of miniature in vivo surgical robots as the goals of decreased size and improved dexterity are approached.
Optimization and performance analysis of SERS-active suspended core photonic crystal fibers (2020)

Recently, surface enhanced Raman spectroscopy (SERS)-active photonic crystal fiber (PCFs) probes have gained great interest for biosensing applications due to the tremendous advantages it has over the conventional planar substrate based SERS measurements, with improvements on the detection sensitivity and reliability in measurements. So far, two main approaches were employed to get the analyte molecule in the vicinity of nanoparticles (NPs) inside PCFs in order to achieve the SERS effect. In the first case, analyte and NPs are pre-mixed and injected inside the holes of the PCF prior to the measurement. In the second approach, controlled anchoring of the NPs inside the inner walls of the PCF was achieved prior to the incorporation of the analyte. Although many studies have been conducted using one configuration or the other, no clear trend is emerging on which one would be the best suited for optimizing the biosensing properties offered by SERS active-PCF. In this paper, we investigate the performances of both configurations along with their interplays with the core size of the PCF probe. We have fabricated several samples of a standard PCF design with different core sizes, and SERS measurements of a standard Raman-active molecule are realized in the same conditions for enabling direct comparisons of the SERS intensity and measurement reliabilities between each configuration, yielding clear directions on the optimization of the SERS-active PCF probe. We envision that this study will pave the way for next-generation clinical biosensors for body fluid analysis, as it exhibits high sensitivity and excellent reliability.
Improved Inter-Layer Prediction for the Scalable Extensions of HEVC (2014)

Summary form only given. Upon the completion of the single-layer H.265/HEVC, scalable extensions of the H.265/HEVC standard, called Scalable High Efficiency Video Coding (SHVC), are currently under development. Compared to the simulcast solution that simply compresses each layer separately, SHVC offers higher coding efficiency by means of inter-layer prediction which is implemented by inserting inter-layer reference (ILR) pictures generated from reconstructed base layer (BL) pictures into the enhancement layer (EL) decoded picture buffer (DPB) for motion-compensated prediction of the collocated pictures in the EL. If the EL has a higher resolution than that of the BL, the reconstructed BL pictures need to be up-sampled to form the ILR pictures. Given that the ILR picture is generated based on the reconstructed BL picture, its suitability for an efficient inter-layer prediction may be limited due to the following reasons. Firstly, quantization is usually applied when coding the BL pictures. Quantization causes the BL reconstructed texture to contain undesired coding artifacts, such as blocking artifacts, ringing artifacts, and color artifacts. Secondly, in case of spatial scalability, a down-sampling process is used to create the BL pictures. To reduce aliasing, the high frequency information in the video signal is typically removed by the down-sampling process. As a result, the texture information in the ILR picture lacks certain high frequency information. In contrast to the ILR picture, the EL temporal reference pictures contain plentiful high frequency information, which could be extracted to enhance the quality of the ILR picture. To further improve the efficiency of inter-layer prediction, a low pass filter may be applied to the ILR picture to alleviate the quantization noise introduced by the BL coding process. In this paper, an ILR enhancement method is proposed to improve the quality of the ILR picture by combining the high frequency information extracted from the EL temporal reference pictures together with the low frequency information extracted from the ILR picture. Experimental results show that the proposed method can significantly increase the ILR efficiency for EL coding, under the Common Test Condition of SHVC, which defines a number of temporal prediction structures called Random Access (RA), Low-delay B (LD-B) and Low-delay P (LD-P), on average the proposed method provides {Y, U, V} BD-rate (BL+EL) gains of {2.0%, 7.1%, 8.2%}, {2.2%, 6.7%, 7.6%} and {4.0%, 7.4%, 8.4%} for RA, LD-B, and LD-P, respectively, in comparison to the performance of the SHVC reference software SHM-2.0.
Plasmonic Imaging and Detection of Single DNA Molecules (2014)

The capability of imaging and detecting single DNA molecules is critical in the study, analysis, and applications of DNA. Fluorescence imaging is a widely used method, but it suffers from blinking and photobleaching, and fluorescence tags may block or affect binding sites on DNA. We report on label-free imaging of single DNA molecules with a differential plasmonic imaging technique. The technique produces high contrast images due to the scattering of surface plasmonic waves by the molecules and the removal of background noises and interference patterns, allowing for quantitative analysis of individual DNA molecules. Simulation of the images based on a scattering model shows good agreement with the experiment. We further demonstrate optical mapping of single DNA molecules.
Novel natural plant protein and mimetic peptides rescues aberrant brain‐energy metabolism and Alzheimer’s disease pathology (2020)

Abstract Background Extensive evidence has indicated that a high rate of cholesterol biogenesis and abnormal neuronal energy metabolism play key roles in Alzheimer’s disease (AD) pathogenesis. Here, for the first time, we used protein and peptide, a plant protein homolog of mammalian adiponectin, to determine its therapeutic efficacy in different AD models. Method Mice were grouped before treatment as follows: WT and Transgenic mice (APP/PS1 and Adipo ‐/‐ mice) were administered via intraperitoneal injection with 3 types of solution (saline, osmotin and osmotin mimetic peptide). Mice were decapitated at the age of 5, 9, 12 or 16 months. Protein samples were analyzed by immunobloting as well as immunofluorescence. Brain sections were analyzed by immune histochemistry. LTP was measured by mEPSC. Result Osmotin, natural plant protein, and its mimetic peptide treatment modulated adiponectin receptor 1 (AdipoR1), significantly induced AMPK/SIRT1 activation, and reduced SREBP2 expression in both in vivo and in vitro AD and Adiponectin deficient mice. Osmotin acts Via AdipoR1/AMPK/SIRT1/SREBP2 and TNFR1 signaling pathway, Osmotin and its mimetic peptide significantly diminished amyloidogenic Aβ production, abundance and aggregation, accompanied by improved pre‐ and post‐synaptic dysfunction, cognitive impairment, memory deficits. Most importantly, it reversed the suppression of long‐term potentiation (LTP) in AD mice. Interestingly, AdipoR1, AMPK, and SIRT1 silencing not only abolished Osmotin capability but also further enhanced AD pathology by increasing SREBP2, APP, and β‐secretase (BACE1) expression and the levels of toxic Aβ production. Likewise, mimetic peptide mechanistically instigates AdipoR1/AMPK signaling and consequently suppressed the hyperactivated TNF‐α/TNFR1 signaling in both in vivo and in vitro models of AD. Conclusion Osmotin and its mimetic peptide mitigate aberrant brain‐energy metabolism and AD pathology in in vivo and in vitro AD models via regulating AdipoR1/AMPK/SIRT1/SREBP2/TNFR1 signaling pathway. These results suggest that Osmotin and peptide‐based mimetics can be a potential candidate for AD treatment.
Dynamic Spectrum Management System Aggregating Non-Contiguous Spectrum over TVWS (2012)

This paper proposes a wireless communication system comprising a DSM (Dynamic Spectrum Management) Engine and DSM clients that can dynamically and opportunistically use and aggregate TVWS spectrum when deployed in a local area such as a home or a small office. Operation in TVWS spectrum requires tec
SS-CDC (2019)

Data deduplication has been widely used in storage systems to improve storage efficiency and I/O performance. In particular, content-defined variable-size chunking (CDC) is often used in data deduplication systems for its capability to detect and remove duplicate data in modified files. However, the CDC algorithm is very compute-intensive and inherently sequential. Efforts on accelerating it by segmenting a file and running the algorithm independently on each segment in parallel come at a cost of substantial degradation of deduplication ratio.
Identification of Mutations Contributing to the Temperature-Sensitive, Cold-Adapted, and Attenuation Phenotypes of the Live-Attenuated Cold-Passage 45 ( <i>cp</i> 45) Human Parainfluenza Virus 3 Candidate Vaccine (1999)

The live-attenuated human parainfluenza virus 3 (PIV3) cold-passage 45 (cp45) candidate vaccine was shown previously to be safe, immunogenic, and phenotypically stable in seronegative human infants. Previous findings indicated that each of the three amino acid substitutions in the L polymerase protein of cp45 independently confers the temperature-sensitive (ts) and attenuation (att) phenotypes but not the cold-adaptation (ca) phenotype (29). cp45 contains 12 additional potentially important point mutations in other proteins (N, C, M, F, and hemagglutinin-neuraminidase [HN]) or in cis-acting sequences (the leader region and the transcription gene start [GS] signal of the N gene), and their contribution to these phenotypes was undefined. To further characterize the genetic basis for the ts, ca, and att phenotypes of this promising vaccine candidate, we constructed, using a reverse genetics system, a recombinant cp45 virus that contained all 15 cp45-specific mutations mentioned above, and found that it was essentially indistinguishable from the biologically derived cp45 on the basis of plaque size, level of temperature sensitivity, cold adaptation, level of replication in the upper and lower respiratory tract of hamsters, and ability to protect hamsters from subsequent wild-type PIV3 challenge. We then constructed recombinant viruses containing the cp45 mutations in individual proteins as well as several combinations of mutations. Analysis of these recombinant viruses revealed that multiple cp45 mutations distributed throughout the genome contribute to the ts, ca, and att phenotypes. In addition to the mutations in the L gene, at least one other mutation in the 3' N region (i.e., including the leader, N GS, and N coding changes) contributes to the ts phenotype. A recombinant virus containing all the cp45 mutations except those in L was more ts than cp45, illustrating the complex nature of this phenotype. The ca phenotype of cp45 also is a complex composite phenotype, reflecting contributions of at least three separate genetic elements, namely, mutations within the 3' N region, the L protein, and the C-M-F-HN region. The att phenotype is a composite of both ts and non-ts mutations. Attenuating ts mutations are located in the L protein, and non-ts attenuating mutations are located in the C and F proteins. The presence of multiple ts and non-ts attenuating mutations in cp45 likely contributes to the high level of attenuation and phenotypic stability of this promising vaccine candidate.
Cell Membrane Coating Nanotechnology (2018)

Nanoparticle-based therapeutic, prevention, and detection modalities have the potential to greatly impact how diseases are diagnosed and managed in the clinic. With the wide range of nanomaterials available, the rational design of nanocarriers on an application-specific basis has become increasingly commonplace. Here, a comprehensive overview is provided on an emerging platform: cell-membrane-coating nanotechnology. As a fundamental unit of biology, cells carry out a wide range of functions, including the remarkable ability to interface and interact with their surrounding environment. Instead of attempting to replicate such functions via synthetic techniques, researchers are now directly leveraging naturally derived cell membranes as a means of bestowing nanoparticles with enhanced biointerfacing capabilities. This top-down technique is facile, highly generalizable, and has the potential to greatly augment existing nanocarriers. Further, the introduction of a natural membrane substrate onto nanoparticles surfaces has enabled additional applications beyond those traditionally associated with nanomedicine. Despite its relative youth, there exists an impressive body of literature on cell membrane coating, which is covered here in detail. Overall, there is still significant room for development, as researchers continue to refine existing workflows while finding new and exciting applications that can take advantage of this developing technology.
ANTIFREEZE ADMIXTURES FOR COLD WEATHER CONCRETING (1991)

Based on a literature survey, a laboratory study was begun to evaluate promising antifreeze compounds. Laboratory tests were performed to study the beneficial and detrimental effects of antifreeze admixturues on concrete properties such as strength gain at low temperature, freeze-thaw durability, workability and corrosion of embedded metal. It was found that antifreeze concrete can be cured at temperatures significantly below 0 deg C without harming its performance compared to that of normal concrete cured at room temperature. Of the antifreeze concrete mixes tested, those containing sodium nitirite/calcium nitrite and sodium nitrite/potassium carbonate performed the best. Even for those concretes whose strength lagged behind that of the control mix, the prognosis is that they will eventually recover full strength when thawed.
gSketch (2011)

Many dynamic applications are built upon large network infrastructures, such as social networks, communication networks, biological networks and the Web. Such applications create data that can be naturally modeled as graph streams , in which edges of the underlying graph are received and updated sequentially in a form of a stream. It is often necessary and important to summarize the behavior of graph streams in order to enable effective query processing. However, the sheer size and dynamic nature of graph streams present an enormous challenge to existing graph management techniques. In this paper, we propose a new graph sketch method, gSketch, which combines well studied synopses for traditional data streams with a sketch partitioning technique, to estimate and optimize the responses to basic queries on graph streams. We consider two different scenarios for query estimation: (1) A graph stream sample is available; (2) Both a graph stream sample and a query workload sample are available. Algorithms for different scenarios are designed respectively by partitioning a global sketch to a group of localized sketches in order to optimize the query estimation accuracy. We perform extensive experimental studies on both real and synthetic data sets and demonstrate the power and robustness of gSketch in comparison with the state-of-the-art global sketch method.
New Method of Voltage Application for Improving Response Time of a Liquid Crystal Lens (2005)

ABSTRACT A new method of rapid driving of a liquid crystal lens is proposed. High external voltages are initially applied to the liquid crystal cell accompanied with an in-plane electric field. The occurring of disclination lines is prevented and the response of the lens becomes more than two times faster.