gebhart/patrepeval huggingface dataset:
Specific interaction between eEF1A and HIV RT is critical for HIV-1 reverse transcription and a potential anti-HIV target (2015)

Reverse transcription is the central defining feature of HIV-1 replication. We previously reported that the cellular eukaryotic elongation factor 1 (eEF1) complex associates with the HIV-1 reverse transcription complex (RTC) and the association is important for late steps of reverse transcription. Here we show that association between the eEF1 and RTC complexes occurs by a strong and direct interaction between the subunit eEF1A and reverse transcriptase (RT). Using biolayer interferometry and co-immunoprecipitation (co-IP) assays, we show that association between the eEF1 and RTC complexes occurs by a strong (KD ~3–4 nM) and direct interaction between eEF1A and reverse transcriptase (RT). Biolayer interferometry analysis of cell lysates with titrated levels of eEF1A indicates it is a predominant cellular RT binding protein. Both the RT thumb and connection domains are required for interaction with eEF1A. A single amino acid mutation, W252A, within the thumb domain impaired co-IP between eEF1A and RT, and also significantly reduced the efficiency of late reverse transcription and virus replication when incorporated into infectious HIV-1. Molecular modeling analysis indicated that interaction between W252 and L303 are important for RT structure, and their mutation to alanine did not impair heterodimerisation, but negatively impacted interaction with eEF1A. Didemnin B, which specifically binds eEF1A, potently inhibited HIV-1 reverse transcription by greater than 2 logs at subnanomolar concentrations, especially affecting reverse transcription late DNA synthesis. Analysis showed reduced levels of RTCs from HIV-1-infected HEK293T treated with didemnin B compared to untreated cells. Interestingly, HIV-1 with a W252A RT mutation was resistant to didemnin B negative effects showing that didemnin B affects HIV-1 by targeting the RT-eEF1A interaction. The combined evidence indicates a direct interaction between eEF1A and RT is crucial for HIV reverse transcription and replication, and the RT-eEF1A interaction is a potential drug target.
Quantification of Hepatitis B Virus Covalently Closed Circular DNA in Infected Cell Culture Models by Quantitative PCR (2019)

Persistence of the human hepatitis B virus (HBV) requires the maintenance of covalently closed circular (ccc)DNA, the episomal genome reservoir in nuclei of infected hepatocytes. cccDNA elimination is a major aim in future curative therapies currently under development. In cell culture based <i>in vitro</i> studies, both hybridization- and amplification-based assays are currently used for cccDNA quantification. Southern blot, the current gold standard, is time-consuming and not practical for a large number of samples. PCR-based methods show limited specificity when excessive HBV replicative intermediates are present. We have recently developed a real-time quantitative PCR protocol, in which total cellular DNA plus all forms of viral DNA are extracted by silica column. Subsequent incubation with T5 exonuclease efficiently removes cellular DNA and all non-cccDNA forms of viral DNA while cccDNA remains intact and can reliably be quantified by PCR. This method has been used for measuring kinetics of cccDNA accumulation in several <i>in vitro</i> infection models and the effect of antivirals on cccDNA. It allowed detection of cccDNA in non-human cells (primary macaque and swine hepatocytes, <i>etc</i>.) reconstituted with the HBV receptor, human sodium taurocholate cotransporting polypeptide (NTCP). Here we present a detailed protocol of this method, including a work flowchart, schematic diagram and illustrations on how to calculate "cccDNA copies per (infected) cell".
Microstructure and Optical Properties of Black Chrome Befor and After Exposure to High Temperatures (1979)

the chemical and microstructural stability of the CHROM-ONYX type of black chrome solar coating was investigated at different temperatures and atmospheres. This was done to give a better understanding of the mechanism of solar energy selectivity and its variability when subjected to short term heat treatments. The as-plated structure was found to consist of a suspension of metallic chromium particles within the size range of 100A in a amorphous oxide matrix. this assembly was in turn formed into larger particles within the size range of 0.05 to 0.30 microns. Short term high temperature heat treatments were used to simulate stagnation conditions. Samples were annealed in both air and vacuum, which resulted in similar characteristics. Annealing in air appeared to mildly accelerate optical degradation at high temperatures. For short term heat treatments below 300/sup 0/C the reflective and microstructural properties appeared to be unchanged. By in situ vacuum annealing of the coating above 400/sup 0/C microscrystalline Cr/sub 2/O/sub 3/ was identified. By observation of diffraction patterns it was concluded that a-Cr/sub 2/O/sub 3/ was transformed into crystalline Cr/sub 2/O/sub 3/. The Cr/sub 2/O/sub 3/ phase continued to grow at higher temperatures at the expense of chromium content. At temperatures above 500/sup 0/C in vacuum, a new phase identified as Cr/sub 3/O/sub 4/ formed. It was found that black chrome failed optically between 500 to 600/sup 0/C for 1 hour heat treatments in both air and vacuum; also the coating heated in air failed mechanically by peeling at 600/sup 0/C.
CAR T cells and checkpoint inhibition for the treatment of glioblastoma (2020)

<b>Introduction</b>: Glioblastoma (GBM) is a highly aggressive brain tumor and is one of the most lethal human cancers. Chimeric antigen receptor (CAR) T cell therapy has markedly improved survival in previously incurable disease; however, this vanguard treatment still faces challenges in GBM. Likewise, checkpoint blockade therapies have not enjoyed the same victories against GBM. As it becomes increasingly evident that a mono-therapeutic approach is unlikely to provide anti-tumor efficacy, there evolves a critical need for combined treatment strategies.<b>Areas covered</b>: This review highlights the clinical successes observed with CAR T cell therapy as well the current efforts to overcome its perceived limitations. The review also explores employed combinations of CAR T cell approaches with immune checkpoint blockade strategies, which aim to potentiate immunotherapeutic benefits while restricting the impact of tumor heterogeneity and T cell exhaustion.<b>Expert opinion</b>: Barriers such as tumor heterogeneity and T cell exhaustion have exposed the weaknesses of various mono-immunotherapeutic approaches to GBM, including CAR T cell and checkpoint blockade strategies. Combining these potentially complementary strategies, however, may proffer a rational means of mitigating these barriers and advancing therapeutic successes against GBM and other solid tumors.
B26 Multiple Magnetic Suspension Systems : 3rd report : Proof of Basic Theorems (2009)

The controllability of parallel multiple magnetic suspension systems is discussed based on their basic analytical models. The multiple magnetic suspension systems are classified according to power amplifier and coil connection. This paper focuses on the voltage-controlled multiple suspension system with parallel connected coils. The conditions are clarified under which the system becomes controllable.
A fast learning algorithm for neural network applications (2002)

Describes the use of the ALOPEX algorithm for solving nonlinear learning tasks by multilayer feedforward networks. ALOPEX is a stochastic parallel process. They demonstrate the use of ALOPEX for modifying the weights in a multilayer perception using a measure of global performance of the network. It estimates the weight changes by using only a scalar cost function which is a measure of global performance. The results of computer simulations of applying ALOPEX to nonrecurrent networks which include any feedforward architecture, in addition to multilayer perceptrons, are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Pump in Parallel—Mechanical Assistance of Partial Cavopulmonary Circulation Using a Conventional Ventricular Assist Device (2017)

Mechanical assistance of systemic single ventricle is effective in pulling blood through a cavopulmonary circuit. In patients with superior cavopulmonary connection, this strategy can lead to arterial desaturation secondary to increased inferior caval flow. We hypothesized that overall augmentation in cardiac output with mechanical assistance compensates for the drop in oxygen saturation thereby maintaining tissue oxygen delivery (DO2). Bidirectional Glenn (BDG) was established in seven swine (25 kg) after a common atrium had been established by balloon septostomy. Mechanical circulatory assistance of the single ventricle was achieved using an axial flow pump with ventricular inflow and aortic outflow. Cardiac output, mean pulmonary artery pressure (PAP), common atrial pressure (left atrial pressure [LAP]), arterial oxygen saturation (SaO2), partial pressure of arterial oxygen (PaO2), and DO2 were compared between assisted and nonassisted circulation. Significant augmentation of cardiac output was achieved with mechanical assistance in BDG circulation (BDG: median [interquartile range {IQR}], 0.8 [0.9-1.15] L/min versus assisted BDG: median [IQR], 1.5 [1.15-1.7] L/min; p = 0.05). Although oxygen saturations and PaO2 trended to be lower with assistance (SaO2; BDG: median [IQR], 43% [32-57%]; assisted BDG: median [IQR], 32% [24-35%]; p = 0.07) (PaO2; BDG: median [IQR], 24 [20-30] mm Hg; assisted BDG: median [IQR], 20 [17-21] mm Hg; p = 0.08), DO2 was unchanged with mechanical assistance (BDG: median [IQR], 94 [35-99] ml/min; assisted BDG: median [IQR], 79 [63-85] ml/min; p = 0.81). No significant change in the LAP or PAP was observed. In the setting of superior cavopulmonary connection/single ventricle, the systemic ventricular assistance with a ventricular assist device (VAD) leads to increase in cardiac output. Arterial oxygen saturations however may be lower with mechanical assistance, without any change in DO2.
Manipulating anion intercalation enables a high-voltage aqueous dual ion battery (2021)

Aqueous graphite-based dual ion batteries have unique superiorities in stationary energy storage systems due to their non-transition metal configuration and safety properties. However, there is an absence of thorough study of the interactions between anions and water molecules and between anions and electrode materials, which is essential to achieve high output voltage. Here we reveal the four-stage intercalation process and energy conversion in a graphite cathode of anions with different configurations. The difference between the intercalation energy and hydration energy of bis(trifluoromethane)sulfonimide makes the best use of the electrochemical stability window of its electrolyte and delivers a high intercalation potential, while BF<sub>4</sub><sup>-</sup> and CF<sub>3</sub>SO<sub>3</sub><sup>-</sup> do not exhibit a satisfactory potential because the graphite intercalation potential of BF<sub>4</sub><sup>-</sup> is inferior and the graphite intercalation potential of CF<sub>3</sub>SO<sub>3</sub><sup>-</sup> exceeds the voltage window of its electrolyte. An aqueous dual ion battery based on the intercalation behaviors of bis(trifluoromethane)sulfonimide anions into a graphite cathode exhibits a high voltage of 2.2 V together with a specific energy of 242.74 Wh kg<sup>-1</sup>. This work provides clear guidance for the voltage plateau manipulation of anion intercalation into two-dimensional materials.
Role of Us9 Phosphorylation in Axonal Sorting and Anterograde Transport of Pseudorabies Virus (2013)

Alphaherpes viruses, such as pseudorabies virus (PRV), undergo anterograde transport in neuronal axons to facilitate anterograde spread within hosts. Axonal sorting and anterograde transport of virions is dependent on the viral membrane protein Us9, which interacts with the host motor protein Kif1A to direct transport. Us9-Kif1A interactions are necessary but not sufficient for these processes, indicating that additional cofactors or post-translational modifications are needed. In this study, we characterized two conserved serine phosphorylation sites (S51 and S53) in the PRV Us9 protein that are necessary for anterograde spread in vivo. We assessed the subcellular localization of phospho-Us9 subspecies during infection of neurons and found that the phospho-form is detectable on the majority, but not all, of axonal vesicles containing Us9 protein. In biochemical assays, phospho-Us9 was enriched in lipid raft membrane microdomains, though Us9 phosphorylation did not require prior lipid raft association. During infections of chambered neuronal cultures, we observed only a modest reduction in anterograde spread capacity for diserine mutant Us9, and no defect for monoserine mutants. Conversely, mutation of the kinase recognition sequence residues adjacent to the phosphorylation sites completely abrogated anterograde spread. In live-cell imaging analyses, anterograde transport of virions was reduced during infection with a recombinant PRV strain expressing GFP-tagged diserine mutant Us9. Phosphorylation was not required for Us9-Kif1A interaction, suggesting that Us9-Kif1A binding is a distinct step from the activation and/or stabilization of the transport complex. Taken together, our findings indicate that, while not essential, Us9 phosphorylation enhances Us9-Kif1A-based transport of virions in axons to modulate the overall efficiency of long-distance anterograde spread of infection.
Neurotensin in Plasma: Immunochemical and Chromatographic Character of Acid/Acetone-Soluble Material* (1980)

Using a RIA, we have examined the character of the neurotensin-like (NT-like) peptides present in acid/acetone extracts of animal and human plasma. Plasma immunoreactivity was measured using four antisera with different specificities. Antisera which were directed against the COOH-terminus of NT measured higher levels of plasma immunoreactivity than did antisera with NH2-terminal or mixed specificity. Chromatographic fractionation of bovine plasma extracts revealed the presence of multiple substances, one of which was chromatographically and immunochemically indistinguishable from NT. We estimate the plasma level of this component to be about 15-25 fmol/ml, which is 30-50% of the measurement obtained on unfractionated extracts using antiserum HC-8. Several other components were also identified which behaved as though they were smaller than NT and seemed to share with NT four to eight of its COOH-terminal amono acids. One eluted from Sephadex G-25 in the region of the NT-like peptide previously identified in extracts of gastric mucosa. Infusion of synthetic NT into rats for 30 min did not result in the formation of these COOH-terminal relatives of NT. Our results argue strongly for the presence of NT in plasma and also indicate that other peptides, sharing COOH-terminal homologies with NT, appear in plasma, possibly from the stomach, liver, and other as yet unidentified source(s).
Acoustic Doppler velocimetry (ADV) data on flow-vegetation interaction with natural-like and rigid model plants in hydraulic flumes (2020)

Vegetation, generally present along river margins and floodplains, governs key hydrodynamic processes in riverine systems. Despite the flow-influencing mechanisms exhibited by natural vegetation and driven by its complex morphology and flexibility, vegetation has been conventionally simulated by using rigid cylinders. This article presents a dataset obtained from hydraulic experiments performed for investigating the flow-vegetation interaction in partly vegetated channels. Vegetation was simulated by using both natural-like and rigid model plants. Specifically, two sets of experiments are described: in the first, vegetation was simulated with natural-like flexible foliated plants standing on a grassy bed; in the second, rigid cylinders were used. Experiments with rigid cylinders were designed to be compared against tests with natural-like plants, as to explore the effects of vegetation representation. The following experimental data were produced: 3D instantaneous velocity measured by acoustic Doppler velocimetry, vegetation motion video recordings, and auxiliary data including detailed vegetation characterization. These experiments are unique both for the use of natural-like flexible woody vegetation in hydraulic experiments and for the similarity achieved between the resulting observed vegetated shear layers. These data are expected to be useful in vegetated flows model development and validation, and represent a unique benchmark for the interpretation of the flow-vegetation interaction in partly vegetated channels.
Optical coherence tomography assessment of capsule closure after cataract surgery (2005)

Optical coherence tomography produced cross-sectional tomograms of capsule-IOL contact in the early postoperative period. There was no significant difference in the time to capsule bend formation between the 3 IOLs. However, capsule bend formation at the optic edge occurred earlier with the 1-piece acrylic IOL than with the 3-piece silicone IOL.
1,3-Dipolar Cycloadditions of Substituted Vinylphosphonate with Nitrile Oxides or Nitrones (2007)

1,3-dipolar cycloaddition reactions are among the most important synthetic manipulations allowing the construction of five-membered ring carbocycles and heterocycles. Vinylphosphonates and its analogues have found wide application in organic chemistry during the last two decades and have become very useful for the construction of functionalised organophosphorous compounds. In this report, we have developed a method for the synthesis of β-Substituted vinylphosphonates and the novel structural heterocyclic compound containing a phosphonyl group.
What is this link doing here? Beginning a fine-grained process of identifying reasons for academic hyperlink creation (2003)

The purpose of this paper is to begin a [fine-grained] process of differentiating between creation motivations for links in academic Web sites and citations in journals on the basis that they are very different phenomena.
Autonomic QoS-Aware resource management in grid computing using online performance models (2007)

As Grid Computing increasingly enters the commercial domain, performance and Quality of Service (QoS) issues are becoming a major concern. The inherent complexity, heterogeneity and dynamics of Grid computing environments pose some challenges in managing their capacity to ensure that QoS requirements are continuously met. In this paper, an approach to autonomic QoS-aware resource management in Grid computing based on online performance models is proposed. The paper presents a novel methodology for designing autonomic QoS-aware resource managers that have the capability to predict the performance of the Grid components they manage and allocate resources in such a way that service level agreements are honored. The goal is to make the Grid middleware self-configurable and adaptable to changes in the system environment and workload. The approach is subjected to an extensive experimental evaluation in the context of a real-world Grid environment and its effectiveness, practicality and performance are demonstrated.
Pitx2a Binds to Human Papillomavirus Type 18 E6 Protein and Inhibits E6-mediated P53 Degradation in HeLa Cells (2005)

Binding of high risk human papillomavirus (HPV) E6 protein to E6-associated protein (E6AP), a cellular ubiquitin-protein ligase, enables E6AP to ubiquitinate p53, leading to p53 degradation in cervical cancer cells such as HeLa cells. Here we report that Pitx2a, a bicoid-type homeodomain transcription factor, can bind to HPV E6 protein and inhibit E6/E6AP-mediated p53 degradation. Deletion of the Pitx2a homeodomain abrogates its ability to bind to HPV E6 protein and to induce p53 accumulation in HeLa cells, suggesting that the homeodomain of Pitx2a is essential for inhibition of E6/E6AP-mediated p53 degradation. Recombinant Pitx2a can also block E6/E6AP-mediated p53 degradation in vitro, indicating that this function of Pitx2a is independent of its transcription activity. Pitx2a does not regulate Hdm2-mediated p53 degradation, because Pitx2a does not affect p53 protein levels in HPV-negative cells, such as HCT116, U2OS, and C33A cells. In addition, Pitx2a-induced p53 is transcriptionally active and maintains its specific DNA binding activity in HeLa cells. Taken together, these findings suggest that, by binding to E6, Pitx2a interferes with E6/E6AP-mediated p53 degradation, leading to the accumulation of functional p53 protein in HeLa cells.
Early Postoperative Plasma Transforming Growth Factor-β1 is a Strong Predictor of Biochemical Progression After Radical Prostatectomy (2008)

Postoperative interleukin-6 and interleukin-6 soluble receptor have limited clinical usefulness in prostate cancer. In contrast, postoperative plasma transforming growth factor-beta1 measured 6 to 8 weeks after surgery is a strong predictor of biochemical progression, presumably due to an association with early low volume occult metastases that are at the threshold of clinical progression.
A 2.048 Mb/s Full-Duplex Free-Space Optical Transceiver IC for a Real-Time <italic>In Vivo</italic> Brain–Computer Interface Mouse Experiment Under Social Interaction (2017)

This paper presents the first free-space optical transceiver IC for social, psychological brain–computer interface experiments with multiple mice. The proposed IC embedded in a head-mounted module (HMM) includes 8-channel neural recorder and a neural stimulator in order to record extracellular action potentials and local field potentials while injecting diverse waveforms of monophasic intracranial stimulation current into the medial forebrain bundle for the activation of the nervous system. The HMM implanted on a mouse transmits the neural recording data to an optical base station by using a mandatory 591/624-nm (amber/red) visible behavior tracking LED as an optical transmitter to save power. The HMM is controlled simultaneously via a 940 nm infrared optical downlink to reduce interference to the visible optical uplink. The proposed IC fabricated in a 0.18- <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> HV BCDMOS process consumes 90 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mu \text{W}$ </tex-math></inline-formula> while achieving a 2.048-Mb/s transmission rate.
Chelate Bonding Mechanism in a Novel Magnesium Phosphate Bone Cement (2015)

A novel approach to harden magnesium phosphate cements was tested using phytic acid (C 6 H 18 O 24 P 6 ) solutions as chelation agent. In addition to complex formation, a cementitious dissolution and precipitation reaction led to the formation of newberyite (Mg HPO 4 ·3H 2 O) as the hydrated form of the farringtonite [Mg 3 ( PO 4 ) 2 ] raw powder. The set cements showed good mechanical properties (up to 65 MPa in compression) displaying a doubling of the compressive strength of conventional newberyite forming cements despite of a significantly lower degree of cement conversion. An increasing phytic acid concentration from 10% to 30% had a retarding effect on the setting time (11–16 min), decreased the pH close to acidic conditions ( pH = 5–4) and increased the maximum setting temperature (26°C–31°C), but none of these factors reached critical values. The presented strategy was successful in fabricating a good workable, novel mineral biocement with promising characteristics for biomedical applications.