gebhart/patrepeval huggingface dataset:
A novel two-step genome editing strategy with CRISPR-Cas9 provides new insights into telomerase action and TERT gene expression (2015)

We develop a two-step CRISPR-Cas9 genome editing strategy to introduce precise modifications at the endogenous TERT locus in human cell lines. This method provides a useful tool for studying telomerase biology, and suggests a general approach to edit loci with low targeting efficiency and to purify and visualize low abundance proteins.
Doubly differential cross sections for electron-loss in ion-atom collisions (1976)

The doubly differential cross section for electron loss from the projectile in fast atomic collisions is obtained from a transformation to the laboratory frame of the corresponding Born cross section for ionization of electrons in the projectile frame. The ejected-electron velocity distribution is always centred close to the projectile speed but the character of the ejected electrons is different in forward and backward directions. In forward directions a cusp-shaped velocity distribution arises. In backward directions the description of the distribution as due to elastic scattering of the ejected electrons from the target nucleus is justified.
Anxiolytic-like effects of metabotropic glutamate antagonist (RS)-alpha-methylserine-O-phosphate in rats. (1997)

Using the conflict drinking Vogel test in rats as a model we examined the anxiolytic-like activity of (RS)-alpha-methylserine-O-phosphate (MSOP) and (RS)-alpha-methylserine-O-phosphate-monophenyl ester (MSOPPE), the antagonists of group III and II of mGluR, respectively, after their intrahippocampal administration. The results indicated that MSOP produced a dose dependent anticonflict effect in rats.
Optical and structual characterization of InP nanorods (2005)

InP nanorods were chemically synthesized. We investigated the structures of InP nanorods and their optical properties by using UV-VIS spectroscopy, photoluminescence study, powder X-ray diffractometer and transmission electron microscopy. Also, we suggested their photonic applications.
Recombinant Herpesvirus Vectors: Durable Immune Responses and Durable Protection against Simian Immunodeficiency Virus SIVmac239 Acquisition (2021)

A prophylactic vaccine that confers durable protection against human immunodeficiency virus (HIV) would provide a valuable tool to prevent new HIV/AIDS cases. As herpesviruses establish lifelong infections that remain largely subclinical, the use of persistent herpesvirus vectors to deliver HIV antigens may facilitate the induction of long-term anti-HIV immunity. We previously developed recombinant (r) forms of the gamma-herpesvirus rhesus monkey rhadinovirus (rRRV) expressing a replication-incompetent, near-full-length simian immunodeficiency virus (SIVnfl) genome. We recently showed that 8/16 rhesus macaques (RMs) vaccinated with a rDNA/rRRV-SIVnfl regimen were significantly protected against intrarectal (i.r.) challenge with SIVmac239. Here we investigated the longevity of this vaccine-mediated protection. Despite receiving no additional booster immunizations, the protected rDNA/rRRV-SIVnfl vaccinees maintained detectable cellular and humoral anti-SIV immune responses for more than 1.5 years after the rRRV boost. To assess if these responses were still protective, the rDNA/rRRV-SIVnfl vaccinees were subjected to a second round of marginal-dose i.r. SIVmac239 challenges, with eight SIV-naive RMs serving as concurrent controls. After three SIV exposures, 8/8 control animals became infected, compared to 3/8 vaccinees. This difference in SIV acquisition was statistically significant (<i>P = </i>0.0035). The three vaccinated monkeys that became infected exhibited significantly lower viral loads than those in unvaccinated controls. Collectively, these data illustrate the ability of rDNA/rRRV-SIVnfl vaccination to provide long-term immunity against stringent mucosal challenges with SIVmac239. Future work is needed to identify the critical components of this vaccine-mediated protection and the extent to which it can tolerate sequence mismatches in the challenge virus. <b>IMPORTANCE</b> We report on the long-term follow-up of a group of rhesus macaques (RMs) that received an AIDS vaccine regimen and were subsequently protected against rectal acquisition of simian immunodeficiency virus (SIV) infection. The vaccination regimen employed included a live recombinant herpesvirus vector that establishes persistent infection in RMs. Consistent with the recurrent SIV antigen expression afforded by this herpesvirus vector, vaccinees maintained detectable SIV-specific immune responses for more than 1.5 years after the last vaccination. Importantly, these vaccinated RMs were significantly protected against a second round of rectal SIV exposures performed 1 year after the first SIV challenge phase. These results are relevant for HIV vaccine development because they show the potential of herpesvirus-based vectors to maintain functional antiretroviral immunity without the need for repeated boosting.
613 Mitigation of Ethephon Injury to Tomato Plants by a Natural Lipid Lysophosphatidylethanolamine (LPE): Influence on the Activity of Phospholipase D (PLD) (2000)

Ethephon [2-(chloroethyl) phoshonic acid] is used widely to maximize the yield of ripe tomato fruits. However, ethephon causes rapid and extensive defoliation, overripening, and promotes sunscald damage to the fruit. Recent studies from our laboratory have provided evidence that lysophosphatidylethanolamine (LPE) can reduce leaf senescence. We investigated the potential use of LPE to reduce damaging effect of ethephon on tomato foliage and influence on the activity of phospholipase D (PLD). Disruption of membrane integrity has been suggested as a primary cause of senescence in plants. PLD is known to be a key enzyme, which initiates the selective degradation of membrane phospholipids in senescing tissues. Two-month-old tomato plants (`Mountain Spring') grown in greenhouse condition were sprayed with water, 200 ppm LPE, and 1000 ppm ethephon. In addition, LPE spray prior to ethephon or mixture with ethephon were also tested. Leaves were sampled after 0, 2, 5, 24, 72, and 168 h of spray application, for PLD activity measurements. Spray of LPE prior to ethephon spray or inclusion of LPE in the ethephon spray reduced foliar injury by ethephon. Activity of soluble PLD was increased dramatically in leaves sprayed with ethephon initially and than dropped by 7 days. We also found that LPE-treated leaves had lower PLD activity than the ethephon-treated leaves. Plants treated with LPE-ethephon mixture also showed significantly lower PLD activity. These results suggest that LPE treatments mitigate ethephon injury to tomato plants. Furthermore, it appears that this mitigation involves modulation of the activity of PLD.
The ‘Valve Racket’: a new and different concept of atrioventricular valve repair (2006)

This initial experience confirmed the efficacy and simplicity of the technique.
Carbon-Dot/Silver-Nanoparticle Flexible SERS-Active Films (2016)

Development of effective platforms for surface enhanced Raman scattering (SERS) sensing has mostly focused on fabrication of colloidal metal surfaces and tuning of their surface morphologies, designed to create "hot spots" in which plasmonic fields yield enhanced SERS signals. We fabricated distinctive SERS-active flexible films comprising polydimethylsiloxane (PDMS) embedding carbon dots (C-dots) and coated with silver nano-particles (Ag NPs). We show that the polymer-associated Ag NPs and C-dots intimately affected the physical properties of each other. In particular, the C-dot-Ag-NP-polymer films exhibited SERS properties upon deposition of versatile targets, both conventional SERS-active dyes as well as bacterial samples. We show that the SERS response was correlated to the formation C-dots within the polymer film and the physical proximity between the C-dots and Ag NPs, indicating that coupling between the plasmonic fields of the Ag NPs and C-dots' excitons constituted a prominent factor in the SERS properties.
GPU in-Memory Processing Using Spark for Iterative Computation (2017)

Due to its simplicity and scalability, MapReduce has become a de facto standard computing model for big data processing. Since the original MapReduce model was only appropriate for embarrassingly parallel batch processing, many follow-up studies have focused on improving the efficiency and performance of the model. Spark follows one of these recent trends by providing in-memory processing capability to reduce slow disk I/O for iterative computing tasks. However, the acceleration of Spark's in-memory processing using graphics processing units (GPUs) is challenging due to its deep memory hierarchy and host-to-GPU communication overhead. In this paper, we introduce a novel GPU-accelerated MapReduce framework that extends Spark's in-memory processing so that iterative computing is performed only in the GPU memory. Having discovered that the main bottleneck in the current Spark system for GPU computing is data communication on a Java virtual machine, we propose a modification of the current Spark implementation to bypass expensive data management for iterative task offloading to GPUs. We also propose a novel GPU in-memory processing and caching framework that minimizes host-to-GPU communication via lazy evaluation and reuses GPU memory over multiple mapper executions. The proposed system employs message-passing interface (MPI)-based data synchronization for inter-worker communication so that more complicated iterative computing tasks, such as iterative numerical solvers, can be efficiently handled. We demonstrate the performance of our system in terms of several iterative computing tasks in big data processing applications, including machine learning and scientific computing. We achieved up to 50 times speed up over conventional Spark and about 10 times speed up over GPU-accelerated Spark.
Thermomechanical properties in a thin film of shape memory polymer of polyurethane series (1996)

The thermomechanical properties of a thin film of shape memory polymer of polyurethane series were investigated experimentally. The results were summarized as follows: (1) Modulus of elasticity and yield stress are high below glass transition temperature T<SUB>g</SUB> and low above T<SUB>g</SUB>. The value of loss tangent is large in the vicinity of T<SUB>g</SUB>. (2) The stress-strain curves vary significantly in the early cycles but slightly thereafter under cyclic deformation above T<SUB>g</SUB>. (3) During the heating process after loading above T<SUB>g</SUB> followed by unloading below T<SUB>g</SUB>, strain is recovered in the vicinity of T<SUB>g</SUB>. (4) Shape fixity with loading above T<SUB>g</SUB> followed by unloading below T<SUB>g</SUB> does not vary under thermomechanical cycling. (5) Creep strain is recovered after unloading above T<SUB>g</SUB>. Creep residual strain below T<SUB>g</SUB> is recovered in the vicinity of T<SUB>g</SUB> during the heating process. (6) About a half of initial stress relaxes after a certain duration of time. Several applications of the polymers were introduced.
Integral-Slot Versus Fractional-Slot Concentrated-Winding Axial-Flux Permanent-Magnet Machines: Comparative Design, FEA, and Experimental Tests (2012)

In slotted axial-flux permanent-magnet (PM) (AFPM) machines, two possible concentrated-winding arrangements can be used: integral slot and fractional slot. Integral-slot concentrated windings (ISCWs) have a number of slots/pole/phase equal to one and have long been a preferred choice with machine designers due to their simple layout. On the other hand, fractional-slot concentrated windings (FSCWs) have a number of slots/pole/phase less than one and have been the focus of a significant amount of international research in the past decade. This paper presents an original comparison between two 10-kW AFPM machine prototypes with concentrated windings: a 20-pole 60-slot ISCW machine and a 20-pole 24-slot FSCW machine. The design of both machines is described, highlighting the constraints that have been set to allow a fair comparison between them. Static and time-stepped finite-element-analysis results are presented. Comparative no-load and load experimental tests are performed on full-scale prototypes, and the results are reported: Important tradeoffs in key aspects such as peak cogging torque, constant power speed range, and additional losses are demonstrated. Finally, conclusions are made regarding the performances and required tradeoffs for both machines.
Principles and practice of functional MRI of the human brain (2003)

Conventional MRI is used extensively for radiological diagnosis and produces spatial maps of the properties of mobile hydrogen nuclei (single protons) that are contained mainly in water molecules. Conventional magnetic resonance images portray anatomic details with exquisite resolution (on the order of 1 mm or better), in three dimensions, and differentiate soft tissues very well. The contrast within images results from variations mainly in the density of water within tissues and in the manner in which water interacts with macromolecules. Functional MRI (fMRI) is now also well established in many centers and uses similar imaging techniques and the same equipment as conventional MRI. fMRI relies on detecting small changes in the signals used to produce magnetic resonance images that are associated with neuronal activity in the brain, and it is producing unique and valuable information for applications in both basic and clinical neuroscience. fMRI is safe, noninvasive, and repeatable in adults and children and thus has widespread potential uses. This short overview will attempt to illustrate the physical basis of fMRI, how it is performed in practice, some of the limitations of the technique, and some of the types of application that have been exploited to date. fMRI detects the blood oxygen level‐dependent
Inductively coupled plasma etch damage in (-201) Ga2O3 Schottky diodes (2017)

Bulk, single-crystal Ga2O3 was etched in BCl3/Ar inductively coupled plasmas as a function of ion impact energy. For pure Ar, the etch rate (R) was found to increase with ion energy (E) as predicted from a model of ion enhanced sputtering by a collision-cascade process, R ∝(E0.5 – ETH0.5), where the threshold energy for Ga2O3, ETH, was experimentally determined to be ∼75 eV. When BCl3 was added, the complexity of the ion energy distribution precluded, obtaining an equivalent threshold. Electrically active damage introduced during etching was quantified using Schottky barrier height and diode ideality factor measurements obtained by evaporating Ni/Au rectifying contacts through stencil masks onto the etched surfaces. For low etch rate conditions (∼120 Å min−1) at low powers (150 W of the 2 MHz ICP source power and 15 W rf of 13.56 MHz chuck power), there was only a small decrease in reverse breakdown voltage (∼6%), while the barrier height decreased from 1.2 eV to 1.01 eV and the ideality factor increased from 1.00 to 1.06. Under higher etch rate (∼700 Å min−1) and power (400 W ICP and 200 W rf) conditions, the damage was more significant, with the reverse breakdown voltage decreasing by ∼35%, the barrier height was reduced to 0.86 eV, and the ideality factor increased to 1.2. This shows that there is a trade-off between the etch rate and near-surface damage.
Homogeneous immunofluorometric assays of alpha-fetoprotein with macroporous, monosized particles and flow cytometry (1993)

We evaluated two homogeneous immunofluorometric assays (IFMAs) of alpha-fetoprotein (AFP) based on new macroporous acrylate particles combined with flow cytometry. The standard IFMA, requiring 1 h of incubation, provided a working range from 1.8 to > 900 kIU/L (CV < 10%) and a detection limit of 0.6 kIU/L. Use of overnight incubation and a lower particle concentration extended the working range by 1 decade in the lower end. Analytical recoveries for the standard IFMA varied between 97% and 108%. The slope and y-intercept of the regression line correlating measurements by the standard IFMA and a routine immunoradiometric assay were not significantly different from 1 and 0, respectively (P > 0.5), and the correlation coefficient was 0.996. High precision and warning of spuriously high measurements were obtained by including in each sample separate particle types for detecting instrument instability and measuring nonspecific binding only.
High-Capacity Adenoviral Vectors: Expanding the Scope of Gene Therapy (2020)

The adaptation of adenoviruses as gene delivery tools has resulted in the development of high-capacity adenoviral vectors (HC-AdVs), also known, helper-dependent or "gutless". Compared with earlier generations (E1/E3-deleted vectors), HC-AdVs retain relevant features such as genetic stability, remarkable efficacy of in vivo transduction, and production at high titers. More importantly, the lack of viral coding sequences in the genomes of HC-AdVs extends the cloning capacity up to 37 Kb, and allows long-term episomal persistence of transgenes in non-dividing cells. These properties open a wide repertoire of therapeutic opportunities in the fields of gene supplementation and gene correction, which have been explored at the preclinical level over the past two decades. During this time, production methods have been optimized to obtain the yield, purity, and reliability required for clinical implementation. Better understanding of inflammatory responses and the implementation of methods to control them have increased the safety of these vectors. We will review the most significant achievements that are turning an interesting research tool into a sound vector platform, which could contribute to overcome current limitations in the gene therapy field.
Stimulation of the pituitary-adrenocortical axis by saikosaponin of Bupleuri radix. (1981)

The effects of saikosaponin-a, -c and -d, isolated from the roots of Bupleurum falcatum L., on plasma adrenccotrcotropin (ACTH) and corticosterone concentrations in unanesthetized or pentobarbital-anesthetized rats were determined by radioimmunoassay and by the competitive protein binding method. A single dose of saikosaponin-a (5 mg/kg, i. p.) or -d (2.5 mg/kg, i. p.) significantly increased plasma ACTH and corticosterone levels 30 and 60 min after the treatment, but saikosaponin-c at a dose of 100 mg/kg had no effect. Intraperitoneal administration of saikosaponin-a or -d, but not -c, induced a transient hyperglycemia and a transient hypoinsulinemia. Dexamethasone pretreatment depressed the saponin-induced increase of both corticosterone and glucose. Treatment with hexamethonium partially depressed the saponin-induced responses in plasma corticosterone, but treatment with diphenhydramine did not.
Impact of an EHR-generated NICU rounding report on residents’ workflow and quality of care. (2019)

Background: Physicians’ computer time in the U.S. is increasing. Over the years we have observed in our NICU a decrease in the amount of bedside time before rounds and an increase in the time performing computer tasks that have high administrative but low academic value for our residents. An EHR-generated rounding report is an informatics tool that can save time by gathering data from the patients’ electronic record and organizing it into one report. NICUs are a data dense service with lots of calculations and numbers to collect every day. We conducting …
Localized travelling waves in the asymptotic suction boundary layer (2016)

We present two spanwise-localized travelling-wave solutions in the asymptotic suction boundary layer, obtained by continuation of solutions of plane Couette flow. One of the solutions has the vortical structures located close to the wall, similar to spanwise-localized edge states previously found for this system. The vortical structures of the second solution are located in the free stream far above the laminar boundary layer and are supported by a secondary shear gradient that is created by a large-scale low-speed streak. The dynamically relevant eigenmodes of this solution are concentrated in the free stream, and the departure into turbulence from this solution evolves in the free stream towards the walls. For invariant solutions in free-stream turbulence, this solution thus shows that the source of energy of the vortical structures can be a dynamical structure of the solution itself, instead of the laminar boundary layer.
Resource allocation for multicarrier cooperative cognitive radio networks with imperfect channel state information (2014)

In this paper we consider a decode-and-forward cooperative network, which is active in the same bandwidth as a primary user network. The cooperative or secondary user network applies a dynamic resource allocation algorithm to maximize its own performance while limiting the interference caused at the primary user receivers. The main contribution of this paper is the proposition of a new accurate approximation for the outage probability, which takes into account that the channel state information available at the transmitter is imperfect and outdated. The accuracy of the approximation and the performance of the resource allocation scheme are validated through numerical simulations.
Histidine 39 in the dengue virus type 2 M protein has an important role in virus assembly (2004)

The mature flavivirus particle comprises a nucleocapsid core surrounded by a lipid bilayer containing the membrane (M) (derived from the precursor prM) and envelope (E) proteins. The formation of intracellular prM/E heterodimers occurs rapidly after translation and is believed to be important for the assembly and secretion of immature virus particles. In this study, the role of the His residue at position 39 in the M protein (M39) of dengue virus type 2 (DENV-2) in the virus life cycle was investigated. Mutations encoding basic (Arg), non-polar (Leu and Pro) and uncharged polar (Asn, Gln and Tyr) amino acids at M39 were introduced into a DENV-2 genomic-length cDNA clone and their effects on virus replication were examined. Substitution of the His residue with non-polar amino acids abolished virus replication, whereas substitution with basic or uncharged polar amino acids decreased virus replication moderately ( approximately 2 log(10) p.f.u. ml(-1) decrease in viral titre for Arg and Asn) or severely (>3.5 log(10) p.f.u. ml(-1) decrease in viral titre for Gln and Tyr). Selected mutations were introduced into a prM-E gene cassette and expressed transiently in COS cells to investigate whether the mutations impaired prM/E association or secretion. None of the mutations was found to disrupt the formation of intracellular prM/E heterodimers. However, the mutations that abolished virus replication prevented secretion of prM/E complexes. The results of this study pinpoint a critical residue in the M protein that potentially plays a role in viral morphogenesis, secretion and entry.