gebhart/patrepeval huggingface dataset:
Identification of a lytic-phase origin of DNA replication in human herpesvirus 6B strain Z29 (1993)

DNA sequences which have structural features suggestive of their functioning as an origin of lytic-phase DNA replication were previously identified in both human herpesvirus 6B strain Z29 [HHV-6B (Z29)] and in HHV-6A (U1102). Plasmid constructs containing the putative HHV-6B (Z29) oriLyt element were replicated after transfection into permissive T cells, when trans-acting factors were provided by HHV-6B (R-1) infection. By using this assay, the HHV-6B (Z29) oriLyt was mapped to a minimal region of approximately 400 bp which lies upstream of the gene that is homologous to herpes simplex virus UL29, a region that carries an origin in other betaherpesviruses and in some alphaherpesviruses.
Effect of liquid viscosity on mixing times in bubble columns (2016)

Mixing is a key parameter in bioreactors studies as it can intensify mass and heat transfer and can affect biological reactions. In the present work, mixing times are investigated in a 42 L vessel with water and various polyethylene glycol and carboxymethyl cellulose solutions. To improve the physical description of dispersion induced by bubbles, the first step of our study was to characterize dispersion of tracers inside bubbly flows at various gas volume fractions for different liquid viscosities. A colorimetric technique is used in order to record mixing times corresponding to 95 or 80% of homogeneity. Bubble size is also measured at the same time by image processing. It clearly appears that the liquid viscosity impacts the mixing time value, the bubble size and the tracer propagation.
Aryl‐Glycosidase Activities in Germinating Maize (2003)

ABSTRACT Soluble protein extracts of germinating maize seedlings exhibited a limited ability to hydrolyze purified xylans, and specific assays were unable to confirm the presence of endo‐β‐1,4‐xylanase activity. However, extracts contained a variety of aryl‐glycosidase activities, including β‐glucosidase, β‐xylosidase, and α‐ l ‐arabinofuranosidase. These activities peaked in three‐ to four‐day seedlings and were particularly concentrated in shoot and root tissues. Maximal levels of β‐glucosidase were two orders of magnitude greater than those of β‐xylosidase or α‐ l ‐arabinofuranosidase. Isoelectric focusing gels revealed multiple forms of these enzymes. The principal β‐glucosidase and α‐ l ‐arabinofuranosidase protein species were clustered at pI 4.8–4.9 and pI 5.8–6.0, respectively. β‐Xylosidase activity appeared to be associated with both of these enzymes, and no evidence was obtained for a distinct β‐xylosidase.
Dedication (1990)

This is the completely revised and updated version of the popular and highly regarded textbook, Applied Geophysics. It describes the physical methods involved in exploration for hydrocarbons and minerals, which include gravity, magnetic, seismic, electrical, electromagnetic, radioactivity, and well-logging methods. All aspects of these methods are described, including basic theory, field equipment, techniques of data acquisition, data processing and interpretation, with the objective of locating commercial deposits of minerals, oil, and gas and determining their extent. In the fourteen years or so since the first edition of Applied Geophysics, many changes have taken place in this field, mainly as the result of new techniques, better instrumentation, and increased use of computers in the field and in the interpretation of data. The authors describe these changes in considerable detail, including improved methods of solving the inverse problem, specialized seismic methods, magnetotellurics as a practical exploration method, time-domain electromagnetic methods, increased use of gamma-ray spectrometers, and improved well-logging methods and interpretation.
In Vivo Inhibition of RIPK2 Kinase Alleviates Inflammatory Disease (2014)

The RIPK2 kinase transduces signaling downstream of the intracellular peptidoglycan sensors NOD1 and NOD2 to promote a productive inflammatory response. However, excessive NOD2 signaling has been associated with numerous diseases, including inflammatory bowel disease (IBD), sarcoidosis and inflammatory arthritis, making pharmacologic inhibition of RIPK2 an appealing strategy. In this work, we report the generation, identification, and evaluation of novel RIPK2 specific inhibitors. These compounds potently inhibit the RIPK2 tyrosine kinase activity in in vitro biochemical assays and cellular assays, as well as effectively reduce RIPK2-mediated effects in an in vivo peritonitis model. In conjunction with the development of these inhibitors, we have also defined a panel of genes whose expression is regulated by RIPK2 kinase activity. Such RIPK2 activation markers may serve as a useful tool for predicting settings likely to benefit from RIPK2 inhibition. Using these markers and the FDA-approved RIPK2 inhibitor Gefitinib, we show that pharmacologic RIPK2 inhibition drastically improves disease in a spontaneous model of Crohn Disease-like ileitis. Furthermore, using novel RIPK2-specific inhibitors, we show that cellular recruitment is inhibited in an in vivo peritonitis model. Altogether, the data presented in this work provides a strong rationale for further development and optimization of RIPK2-targeted pharmaceuticals and diagnostics.
TruSDN: Bootstrapping Trust in Cloud Network Infrastructure (2017)

Software-Defined Networking (SDN) is a novel architectural model for cloud network infrastructure, improving resource utilization, scalability and administration. SDN deployments increasingly rely on virtual switches executing on commodity operating systems with large code bases, which are prime targets for adversaries attacking the net- work infrastructure. We describe and implement TruSDN, a framework for bootstrapping trust in SDN infrastructure using Intel Software Guard Extensions (SGX), allowing to securely deploy SDN components and protect communication between network endpoints. We introduce ephemeral flow-specific pre-shared keys and propose a novel defense against cuckoo attacks on SGX enclaves. TruSDN is secure under a powerful adversary model, with a minor performance overhead.
Study on fabrication of conductive antimony doped tin oxide thin films (SnO x :Sb) by 3rd generation mist chemical vapor deposition (2019)

Abstract Transparent conducing antimony doped tin oxide (SnO x :Sb) thin films were fabricated by solution-processed atmospheric-pressure 3rd generation mist chemical vapor deposition (3rd G mist CVD) system with two solution chambers and one mixing chamber to control the atmosphere in reaction area. To study how to reduce the resistivity, the effects of each additive component in dopant solution were investigated; this was followed by identification of components contributing to the fabrication of SnO x :Sb films. Experimentally, the HNO 3 clearly affected the resistivity and the formation of SnO 2 thin films through a change in the valence state of N derived from HNO 3 promoting the transformation of Sn (II) and Sb (III) to Sn (IV) and Sb (V). Moreover, the values of electron and hole effective mass were defined using the specified referred parameters to confirm the band diagram of SnO x :Sb thin films fabricated by 3rd G mist CVD system.
Improved Pen Alignment for Bidirectional Printing (2007)

The quality of the prints produced by an ink jet printer is highly dependent on the characteristics of the dots produced by the ink jet pens. While some literature discusses metrics for the objective evaluation of print quality, few of the efforts have combined automated quality tests with subjective assessment. The authors develop an algorithm for analyzing printed dots and study the effect of the dot characteristics on perceived print alignment. The authors establish the perceptual preferences of human observers via a set of psychophysical experiments.
Real-time system identification for load monitoring and transient handling of Dc-Dc supplies (2008)

Switching mode power supply (SMPS) behavior depends entirely upon known component values and often unknown load impedances. Load change produces voltage over- and undershoots and a design-point shift. In most cases, the controller is blind to these shifts. However, load knowledge is an essential design parameter and should precede optimal and adaptive control techniques. System identification algorithms implemented on digital processors open new opportunities in control and system performance. Typical studies in SMPS identification are based on offline steady-state measurements that form nonparametric frequency-domain models. This paper investigates real-time system identification algorithms that generate parametric models - a practical form for pole-placement and root-locus design. Two key metrics are introduced: parameter error and convergence time to describe algorithm accuracy and speed, respectively, after abrupt parameter changes - a common SMPS load scenario. Hardware and simulation results will show that an algorithm called recursive least squares, in its most basic form, could reasonable approximate the input-to-inductor current plant for static loads during startup, but not for abrupt load steps.
Expression of the murine interleukin 6 receptor in hepatoma cells: the intracytoplasmic domain is not required for interleukin 6 signal transduction (1992)

This paper reports on cDNA coding for the 80-kDa murine IL6 receptor (mIL6R) that was cloned from a mouse liver cDNA library. Human hepatoma Hep3B cells transfected transiently or stably with an expression vector carrying the entire coding region for mIL6R become responsive to mouse IL6 (mIL6). We monitored response to the cytokine through the transcriptional activation of a co-transfected IL6-inducible human C-reactive protein (CRP) promoter; response to mIL6 is lost upon treatment of the cells with increasing amounts of a monoclonal antibody to mIL6R. mIL6R mutants have been generated in the carboxy-terminal portion of the molecule. Their functional analysis in hepatoma cells shows that the intracytoplasmic domain of the receptor is not absolutely essential to IL6 signal transduction (i.e. CRP promoter activation), but that the last 40 amino acids contribute to maximal IL6 response in these cells.
Intraspinal stimulation with a silicon-based 3D chronic microelectrode array for bladder voiding in cats (2020)

<i>Objective.</i>Bladder dysfunction is a significant and largely unaddressed problem for people living with spinal cord injury (SCI). Intermittent catheterization does not provide volitional control of micturition and has numerous side effects. Targeted electrical microstimulation of the spinal cord has been previously explored for restoring such volitional control in the animal model of experimental SCI. Here, we continue the development of the intraspinal microstimulation array technology to evaluate its ability to provide more focused and reliable bladder control in the feline animal model.<i>Approach.</i>For the first time, a mechanically robust intraspinal multisite silicon array was built using novel microfabrication processes to provide custom-designed tip geometry and 3D electrode distribution. Long-term implantation was performed in eight spinally intact animals for a period up to 6 months, targeting the dorsal gray commissure area in the S2 sacral cord that is known to be involved in the coordination between the bladder detrusor and the external urethral sphincter.<i>Main results.</i>About one third of the electrode sites in the that area produced micturition-related responses. The effectiveness of stimulation was further evaluated in one of eight animals after spinal cord transection (SCT). We observed increased bladder responsiveness to stimulation starting at 1 month post-transection, possibly due to supraspinal disinhibition of the spinal circuitry and/or hypertrophy and hyperexcitability of the spinal bladder afferents.<i>Significance</i>. 3D intraspinal microstimulation arrays can be chronically implanted and provide a beneficial effect on the bladder voiding in the intact spinal cord and after SCT. However, further studies are required to assess longer-term reliability and safety of the developed intraspinal microstimulation array prior to eventual human translation.
Runtime-Controlled Energy Reduction Techniques for FPGAs (2012)

Green communications can only be as eﬃcient as the underlying technology used to implement protocols and algorithms. Over the past 50 years, advances in Integrated Circuit fabrication technology have provided system designers with unprecedented amounts of computing power. This has led to dramatic changes in feature sets of mobile devices along with the infrastructure required to support this new “mobile world”. The exponential growth in semiconductor technology, however, has led to a new problem: the cost of designing, verifying, and fabricating an integrated circuit has become so prohibitive, that today, very few enterprises are capable of creating state-of-the-art chips. This has led many designers to employ standard parts such as Field-Programmable Gate Arrays (FPGAs) to leverage advanced process technologies without the cost and risk of designing a custom integrated circuit. FPGAs are pre-designed substrates which can be conﬁgured, in seconds, to implement any digital circuit. By amortizing the fabrication cost over all FPGA users, these devices essentially provide large-scale integration without requiring access to a stateof-the-art chip fabrication plant.
Carcinoembryonic antigen-targeted photodynamic therapy in colorectal cancer models (2019)

Our findings suggest cells (and tumors) have different levels of susceptibility for tPDT even though they all express CEA. Furthermore, tPDT can effectively reduce tumor growth in vivo.
P.106: Magnetic Resonant Wireless Power Transmission to Thin OLED Lighting Panel (2013)

Abstract We used the magnetic resonant wireless power transmission technology to lit thin OLED lighting panels. For the magnetic resonant wireless power transmission, we used small and thin four layer printed circuit board for the receiver. The resonant frequency is lowered up to 457 kHz for the electromagnetic regulation.
Killer Artificial Antigen Presenting Cells (KaAPC) for Efficient <em>In Vitro</em> Depletion of Human Antigen-specific T Cells (2014)

Current treatment of T cell mediated autoimmune diseases relies mostly on strategies of global immunosuppression, which, in the long term, is accompanied by adverse side effects such as a reduced ability to control infections or malignancies. Therefore, new approaches need to be developed that target only the disease mediating cells and leave the remaining immune system intact. Over the past decade a variety of cell based immunotherapy strategies to modulate T cell mediated immune responses have been developed. Most of these approaches rely on tolerance-inducing antigen presenting cells (APC). However, in addition to being technically difficult and cumbersome, such cell-based approaches are highly sensitive to cytotoxic T cell responses, which limits their therapeutic capacity. Here we present a protocol for the generation of non-cellular killer artificial antigen presenting cells (KaAPC), which allows for the depletion of pathologic T cells while leaving the remaining immune system untouched and functional. KaAPC is an alternative solution to cellular immunotherapy which has potential for treating autoimmune diseases and allograft rejections by regulating undesirable T cell responses in an antigen specific fashion.
14-3-3 Interaction with Histone H3 Involves a Dual Modification Pattern of Phosphoacetylation (2008)

Histone modifications occur in precise patterns and are proposed to signal the recruitment of effector molecules that profoundly impact chromatin structure, gene regulation, and cell cycle events. The linked modifications serine 10 phosphorylation and lysine 14 acetylation on histone H3 (H3S10phK14ac), modifications conserved from Saccharomyces cerevisiae to humans, are crucial for transcriptional activation of many genes. However, the mechanism of H3S10phK14ac involvement in these processes is unclear. To shed light on the role of this dual modification, we utilized H3 peptide affinity assays to identify H3S10phK14ac-interacting proteins. We found that the interaction of the known phospho-binding 14-3-3 proteins with H3 is dependent on the presence of both of these marks, not just phosphorylation alone. This is true of mammalian 14-3-3 proteins as well as the yeast homologues Bmh1 and Bmh2. The importance of acetylation in this interaction is also seen in vivo, where K14 acetylation is required for optimal Bmh1 recruitment to the GAL1 promoter during transcriptional activation.
Role of tissue plasminogen activator in clinical aggravation of experimental autoimmune encephalomyelitis and its therapeutic potential (2020)

Tissue plasminogen activator (tPA), a component of the plasminogen activator (PA) system, is elevated in inflammatory neurological disorders. In the present study, we explored the immunomodulatory activity of tPA in experimental autoimmune encephalomyelitis (EAE). The EAE was treated with two catalytic inactive tPA variant proteins: S(481)A and S(481)A + KHRR(296-299)AAAA. EAE-induced tPA<sup>-/-</sup> mice presented with markedly more severe disease than wt EAE mice. Further, treatment with tPA variants, demonstrated a significant suppression of disease severity in tPA<sup>-/-</sup> and wt mice. Immunological evaluation showed that specific T-cell reactivity was markedly reduced in the tPA<sup>-/-</sup> animals, as indicated by decreased T-cell reactivity and reduction in T-regulatory cells. The current findings indicate that tPA plays a role in the pathogenesis of EAE. Moreover, successful amelioration of EAE was achieved by administration of tPA variant proteins. This might mean that these proteins have potential for the immunomodulation of neuroinflammation.
Habitual hip joint activity level of the penned EMU (Dromaius novaehollandie). (2007)

Orthopaedic management of femoral head osteonecrosis remains problematic, partly because of inability to systematically compare treatments in an animal model whose natural history parallels the human in terms of progression to femoral head collapse. Recently, it was determined that collapse could be consistently achieved for cryogenically induced osteonecrosis in the emu. Toward delineating the comparative hip joint biomechanics of emus versus humans, for purposes of establishing the emu as a model for human femoral head osteonecrosis, habitual hip joint activity level was quantified for a group of seven healthy adult emus housed in an outdoor research pen typical of those used in emu farming operations. The daily number of steps taken, and the time spent with the hips loaded (standing, or squatting/sitting) versus unloaded (recumbent), were quantified from 24-hour videotape recordings, analyzed by four independent observers. The average number of steps taken per day was 9563, which extrapolates to 1.8 million hip loadings per year, a value that falls in the same general range as seen in normal adult humans. On average, the emus spent 4:05 hours per day idly standing, 2:12 hours squatting/sitting, and 10:44 hours recumbent; they underwent an average of 37 transitions per day between the respective posture/activity states.
Statistical inference for the mean outcome under a possibly non-unique optimal treatment strategy (2016)

We consider challenges that arise in the estimation of the mean outcome under an optimal individualized treatment strategy defined as the treatment rule that maximizes the population mean outcome, where the candidate treatment rules are restricted to depend on baseline covariates. We prove a necessary and sufficient condition for the pathwise differentiability of the optimal value, a key condition needed to develop a regular and asymptotically linear (RAL) estimator of the optimal value. The stated condition is slightly more general than the previous condition implied in the literature. We then describe an approach to obtain root-<i>n</i> rate confidence intervals for the optimal value even when the parameter is not pathwise differentiable. We provide conditions under which our estimator is RAL and asymptotically efficient when the mean outcome is pathwise differentiable. We also outline an extension of our approach to a multiple time point problem. All of our results are supported by simulations.
Mixed-Lineage Kinase 1 and Mixed-Lineage Kinase 3 Subtype-Selective Dihydronaphthyl[3,4-a]pyrrolo[3,4-c]carbazole-5-ones: Optimization, Mixed-Lineage Kinase 1 Crystallography, and Oral in Vivo Activity in 1-Methyl-4-phenyltetrahydropyridine Models (2008)

The optimization of the dihydronaphthyl[3,4-a]pyrrolo[3,4-c]carbazole-5-one R(2) and R(12) positions led to the identification of the first MLK1 and MLK3 subtype-selective inhibitors within the MLK family. Compounds 14 (CEP-5104) and 16 (CEP-6331) displayed good potency for MLK1 and MLK3 inhibition with a greater than 30- to 100-fold selectivity for related family members MLK2 and DLK. Compounds 14 and 16 were orally active in vivo in a mouse MPTP biochemical efficacy model that was comparable to the first-generation pan-MLK inhibitor 1 (CEP-1347). The MLK1 structure-activity relationships were supported by the first-reported X-ray crystal structure of MLK1 bound with 16.
Bioprinting small-diameter vascular vessel with endothelium and smooth muscle by the approach of two-step crosslinking process (2021)

Three-dimensional (3D) bioprinting shows great potential for autologous vascular grafts due to its simplicity, accuracy, and flexibility. 6mm diameter vascular grafts are used in clinic. However, producing small-diameter vascular grafts are still an enormous challenge. Normally, sacrificial hydrogels are used as temporary lumen support to mold tubular structure which will affect the structure’s stability. In this study, we develop a new bioprinting approach to fabricating small-diameter vessel using two-step crosslinking process. ¼ lumen wall of bioprinted gelatin mechacrylate (GelMA) flat structure is exposed to ultraviolet (UV) light briefly for having certain strength, while ¾ lumen wall shows as concave structure remained uncrosslinked. Pre-crosslinked flat structure is merged towards the uncrosslinked concave structure. Two individual structures will be combined tightly into an intact tubular structure by receiving more UV exposure time. Complicated tubular structures are constructed by these method. Notably, the GelMA-based bioink loaded with smooth muscle cells (SMCs) are bioprinted as the outer layer and human umbilical vein endothelial cells (HUVECs) are seeded onto the inner surface. A bionic vascular vessel with dual layers is fabricated successfully and keeps good viability, and functionality. This study may provide a novel idea for fabricating biomimetic vascular network or other more complicated organs.
Filling factors, structural, and electronic properties ofC60molecules in single-wall carbon nanotubes (2002)

We report recent measurements of the electronic and structural properties of bulk samples of ${\mathrm{C}}_{60}$ molecules encapsulated in single-wall carbon nanotubes (so-called peapods) using electron-energy-loss spectroscopy in transmission. We demonstrate that ${\mathrm{C}}_{60}$ peapods with a single-wall carbon nanotube (SWNT) diameter distribution of $1.37\ifmmode\pm\else\textpm\fi{}0.08 \mathrm{nm}$ have an average fullerene filling of 60%. Regarding the electronic and optical properties, the overall shape of the response of the SWNT and the peapods is very similar, but with distinct differences in the fine structure. The interband transitions of the SWNT are slightly downshifted in the peapods, which can be explained by either a small increase of the SWNT diameter or by a change of the intertube interaction. The electronic and optical properties of the encapsulated ${\mathrm{C}}_{60}$ peas closely resemble those of solid fcc ${\mathrm{C}}_{60}$ showing small changes in the relative intensities, peak positions, and peak width, which point to a weak van der Waals interaction between the tubes and the encapsulated fullerenes.