gebhart/patrepeval huggingface dataset:
Negative Role of RIG-I Serine 8 Phosphorylation in the Regulation of Interferon-β Production (2010)

RIG-I (retinoic acid-inducible gene I) and TRIM25 (tripartite motif protein 25) have emerged as key regulatory factors to induce interferon (IFN)-mediated innate immune responses to limit viral replication. Upon recognition of viral RNA, TRIM25 E3 ligase binds the first caspase recruitment domain (CARD) of RIG-I and subsequently induces lysine 172 ubiquitination of the second CARD of RIG-I, which is essential for the interaction with downstream MAVS/IPS-1/CARDIF/VISA and, thereby, IFN-beta mRNA production. Although ubiquitination has emerged as a major factor involved in RIG-I activation, the potential contribution of other post-translational modifications, such as phosphorylation, to the regulation of RIG-I activity has not been addressed. Here, we report the identification of serine 8 phosphorylation at the first CARD of RIG-I as a negative regulatory mechanism of RIG-I-mediated IFN-beta production. Immunoblot analysis with a phosphospecific antibody showed that RIG-I serine 8 phosphorylation steady-state levels were decreased upon stimulation of cells with IFN-beta or virus infection. Substitution of serine 8 in the CARD RIG-I functional domain with phosphomimetic aspartate or glutamate results in decreased TRIM25 binding, RIG-I ubiquitination, MAVS binding, and downstream signaling. Finally, sequence comparison reveals that only primate species carry serine 8, whereas other animal species carry an asparagine, indicating that serine 8 phosphorylation may represent a primate-specific regulation of RIG-I activation. Collectively, these data suggest that the phosphorylation of RIG-I serine 8 operates as a negative switch of RIG-I activation by suppressing TRIM25 interaction, further underscoring the importance of RIG-I and TRIM25 connection in type I IFN signal transduction.
An Original Setup for Power Amplifier AM-AM and AM-PM Characterization (2008)

An original measurement system for nonlinear RF power amplifier characterization is presented. This new setup enables AM-AM and AM-PM measurements using one six-port reflectometer as a traveling wave ratio calculator. Experimental results of a commercial power amplifier at 2 GHz are presented and compared to those performed using a vector network analyzer.
Molecularly Imprinted Polymers: A New Generation of Affinity Matrices (2006)

The increased use of pharmaceutical drugs for human and veterinary applications provides an important clinical solution to the treatment of disease; however, there are technical challenges involved in monitoring these drugs in biological and environmental matrices. Quantitation of pharmaceutically active compounds and their metabolites in blood, serum, or urine is difficult, often requiring tedious analytical procedures. A further complication is that certain pharmacologically useful compounds, such as the antibiotic chloramphenicol or the group of beta-agonists that are used as growth promoters in animals, are frequently banned in foodstuffs of animal origin to be used for human consumption. For these types of compounds, the extremely low detection limits set by various organizations (i.e., EU, FDA, and U.S. EPA) place pressure on the analytical detection methods and demand labor-intensive preparation and analysis steps. One area of particular concern is the release of active pharmaceuticals into the environment. Their persistence in various environmental matrices is not always mitigated by the standard wastewater treatment processes. Since such compounds can persist in ground and surface waters at levels below the sensitivity limit of many existing analytical methods, they may remain undetected in sources of drinking water used for human and animal consumption, emphasizing the importance of
Analysis of gene networks in white adipose tissue development reveals a role for ETS2 in adipogenesis (2011)

Obesity is characterized by an expansion of white adipose tissue mass that results from an increase in the size and the number of adipocytes. However, the mechanisms responsible for the formation of adipocytes during development and the molecular mechanisms regulating their increase and maintenance in adulthood are poorly understood. Here, we report the use of leptin-luciferase BAC transgenic mice to track white adipose tissue (WAT) development and guide the isolation and molecular characterization of adipocytes during development using DNA microarrays. These data reveal distinct transcriptional programs that are regulated during murine WAT development in vivo. By using a de novo cis-regulatory motif discovery tool (FIRE), we identify two early gene clusters whose promoters show significant enrichment for NRF2/ETS transcription factor binding sites. We further demonstrate that Ets transcription factors, but not Nrf2, are regulated during early adipogenesis and that Ets2 is essential for the normal progression of the adipocyte differentiation program in vitro. These data identify ETS2 as a functionally important transcription factor in adipogenesis and its possible role in regulating adipose tissue mass in adults can now be tested. Our approach also provides the basis for elucidating the function of other gene networks during WAT development in vivo. Finally these data confirm that although gene expression during adipogenesis in vitro recapitulates many of the patterns of gene expression in vivo, there are additional developmental transitions in pre and post-natal adipose tissue that are not evident in cell culture systems.
Overcoming Insolubility Towards Thin Films (2010)

The authors transform the film of the soluble cycloadduct 1 into insoluble 2 via ­thermal annealing. This known strategy aims to ­increase the ease of processability for thin films.
ChemInform Abstract: BENZAZEPINONE, DIE SYNTH. VON MONOAZAANALOGA DES DIAZEPAMS UND DIE KORREKTE STRUKTUR DES BENZOYLPROPIONANILID‐CYCLISIERUNGSPRODUKTES (1971)

Abstract Bei der Umlagerung des Oxims (I) in Polyphosphorsäure entsteht das Dihydrobenzazepinon (II), das sich mit Dicyandichlorchinon (DDQ) zu dem Benzazepinon (III) dehydrieren läßt, mit N‐Chlorsuccinimid (NCS) zu dem Chlorderivat (IV) chloriert werden kann und mit Methyljodid am Stickstoffatom methyliert wird.
Defective CD8+ T Cell Peripheral Tolerance in Nonobese Diabetic Mice (2001)

Nonobese diabetic (NOD) mice develop spontaneous autoimmune diabetes that involves participation of both CD4+ and CD8+ T cells. Previous studies have demonstrated spontaneous reactivity to self-Ags within the CD4+ T cell compartment in this strain. Whether CD8+ T cells in NOD mice achieve and maintain tolerance to self-Ags has not previously been evaluated. To investigate this issue, we have assessed the extent of tolerance to a model pancreatic Ag, the hemagglutinin (HA) molecule of influenza virus, that is transgenically expressed by pancreatic islet beta cells in InsHA mice. Previous studies have demonstrated that BALB/c and B10.D2 mice that express this transgene exhibit tolerance of HA and retain only low-avidity CD8+ T cells specific for the dominant peptide epitope of HA. In this study, we present data that demonstrate a deficiency in peripheral tolerance within the CD8+ T cell repertoire of NOD-InsHA mice. CD8+ T cells can be obtained from NOD-InsHA mice that exhibit high avidity for HA, as measured by tetramer (K(d)HA) binding and dose titration analysis. Significantly, these autoreactive CD8+ T cells can cause diabetes very rapidly upon adoptive transfer into NOD-InsHA recipient mice. The data presented demonstrate a retention in the repertoire of CD8+ T cells with high avidity for islet Ags that could contribute to autoimmune diabetes in NOD mice.
Neural Control of the Urethra (2001)

Coordination between the urinary bladder and the urethra is mediated by multiple reflex pathways organized in the brain and spinal cord. Some reflexes promote urine storage; whereas other reflexes facilitate voiding. During bladder filling, activation of mechanoreceptor afferent nerves in the bladder wall triggers firing in the cholinergic efferent pathways to the external urethral sphincter (EUS) and in sympathetic adrenergic pathways to the urethral smooth muscle. These storage reflexes are dependent upon interneuronal circuitry in the spinal cord. During voiding the spinal storage reflexes are inhibited by supraspinal mechanisms which originate in the pontine micturition center. Glutamatergic, serotonergic and alpha, adrenergic excitatory transmission as well as GABAergic/glycinergic inhibitory transmission have been implicated in the central control of sphincter reflexes. During voiding, a parasympathetic nitrergic inhibitory input to the urethral smooth is activated. This reflex mechanism which is triggered by bladder afferents persists in paraplegic rats and therefore must be mediated at least in part by spinal interneuronal circuitry. In female rats, the parasympathetic nitrergic pathway is prominent; but in male rats it is obscured by a dominant parasympathetic cholinergic excitatory input to the urethral smooth muscle. The function of the cholinergic pathway in voiding is uncertain. Stimulation of urethral afferents can also influence bladder activity. Contraction of the external urethral sphincter activates afferents that inhibit reflex bladder contractions; whereas infusion of fluid through the urethra facilitates bladder contractions. These reflexes are also organized in the spinal cord and presumably play a role in urine storage and elimination. Alterations in primitive bladder-to-urethra and urethra-to-bladder reflex mechanisms may contribute to neurogenic bladder dysfunction.
Coherent optical wireless communication link employing orbital angular momentum multiplexing in a ballistic and diffusive scattering medium (2019)

We experimentally investigate the scattering effect on an 80 Gbit/s orbital angular momentum (OAM) multiplexed optical wireless communication link. The power loss, mode purity, cross talk, and bit error rate performance are measured and analyzed for different OAM modes under scattering levels from ballistic to diffusive regions. Results show that (i) power loss is the main impairment in the ballistic scattering, while the mode purities of different OAM modes are not significantly affected; (ii) in the diffusive scattering, however, the performance of an OAM-multiplexed link further suffers from the increased cross talk between the different OAM modes.
Molecular interactions in the priming complex of bacteriophage T7 (2012)

The lagging-strand DNA polymerase requires an oligoribonucleotide, synthesized by DNA primase, to initiate the synthesis of an Okazaki fragment. In the replication system of bacteriophage T7 both DNA primase and DNA helicase activities are contained within a single protein, the bifunctional gene 4 protein (gp4). Intermolecular interactions between gp4 and T7 DNA polymerase are crucial for the stabilization of the oligoribonucleotide, its transfer to the polymerase, and its extension by DNA polymerase. We have identified conditions necessary to assemble the T7 priming complex and characterized its biophysical properties using fluorescence anisotropy. In order to reveal molecular interactions that occur during delivery of the oligoribonucleotide to DNA polymerase, we have used four genetically altered gp4 to demonstrate that both the RNA polymerase and the zinc-finger domains of DNA primase are involved in the stabilization of the priming complex and in sequence recognition in the DNA template. We find that the helicase domain of gp4 contributes to the stability of the complex by binding to the ssDNA template. The C-terminal tail of gp4 is not required for complex formation.
Submicro-pillars and holes from the depth-wise Talbot images of a conical phase mask (2015)

We construct two-dimensional arrays of submicro-pillars and holes from the depth-wise Talbot images of a conical phase mask in a photoactive layer prepared on a quartz substrate. In contrast to the conventional Talbot lithography employing only one image in the photoactive layer, two images of the phase mask are produced in a depth-wise manner such that the pillar patterns are in the primary image plane while the hole patterns in the secondary image plane according to the penetration depth of the exposure energy. The conical symmetry plays a critical role in producing the covariant patterns of the phase mask in the photoactive layer through the suppression of higher orders of diffraction. Our two image-type approach is simple and versatile for producing different kinds of periodic structures for photonic applications and surface engineering on a micrometer-to-nanometer scale.
Growth evolution and characterization of ultra-thin CoGe2 films synthesized via a catalytic solid–vapour reaction technique (2013)

A low temperature process, relying on the catalytic chemical vapor reaction of GeH4 with solid Co layers, is developed to synthesize ultra-thin CoGe2 layers (10–20 nm) on 300 mm Si wafers. The selective reaction of Co with GeH4 results in the direct formation of CoGe2 films crystallizing in the orthorhombic structure. Detailed studies under germanidation reaction conditions show that the optimal temperature (325 °C vs. 400 °C) to obtain low resistive, defect free and continuous CoGe2 films depends on the initial Co thickness. Investigation on various stages of cobalt germanide growth evolution demonstrates that the complete conversion of Co, leading to closed and stoichiometric CoGe2 films, occurs after 60 s of GeH4 exposure as evidenced by atomic force microscopy (AFM), Rutherford back scattering (RBS) and sheet resistance (Rs) analysis. The CoGe2 formation is found to exhibit self-limiting growth. The layers demonstrate constant film properties (phase purity, resistivity, composition homogeneity, uniformity, and smooth morphology with insignificant rms roughness increase) within a large process window, negligibly influenced by excessive GeH4 exposure conditions. Independent of the post-deposition annealing employed (RTA or furnace annealing), results showed the CoGe2 layers to be thermally stable up to 500 °C without phase or morphological degradation or film roughening. Resistivity values in the range of 70–50 μΩ cm were observed for 10–20 nm CoGe2 films.
Biological breakdown of RDX in slurry reactors proceeds with multiple kinetically distinguishable paths (1997)

Biotransformation of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) in slurry reactors was studied to determine the importance of supplementation of known biodegraders and the type of nutrient source required. Although addition of bacteria to the system increased the biotransformation rates, the increase may not justify the additional work and cost needed to grow the organisms in a laboratory and mix them into the soil. An inexpensive, rich nutrient source, corn steep liquor, was shown to provide sufficient nutrients to allow for the cometabolic biotransformation of RDX. The rate of RDX transformation was not constant throughout the course of the experiment due to the heterogeneous microbial population. Three kinetically distinct phases were observed. Regardless of the process, RDX biotransformation in slurry reactors was reaction rate limited under the test conditions. Model simulations based on experimental results demonstrate that, at cell densities of 5 g/L, bioremediation of RDX-contaminated soil is an attractive clean-up alternative.
Thermally Stable Ohmic Contacts on Silicon Carbide Developed for High- Temperature Sensors and Electronics (2001)

The NASA aerospace program, in particular, requires breakthrough instrumentation inside the combustion chambers of engines for the purpose of, among other things, improving computational fluid dynamics code validation and active engine behavioral control (combustion, flow, stall, and noise). This environment can be as high as 600 degrees Celsius, which is beyond the capability of silicon and gallium arsenide devices. Silicon-carbide- (SiC-) based devices appear to be the most technologically mature among wide-bandgap semiconductors with the proven capability to function at temperatures above 500 degrees Celsius. However, the contact metalization of SiC degrades severely beyond this temperature because of factors such as the interdiffusion between layers, oxidation of the contact, and compositional and microstructural changes at the metal/semiconductor interface. These mechanisms have been proven to be device killers. Very costly and weight-adding packaging schemes that include vacuum sealing are sometimes adopted as a solution.
IDH1 Mutations Alter Citric Acid Cycle Metabolism and Increase Dependence on Oxidative Mitochondrial Metabolism (2014)

Oncogenic mutations in isocitrate dehydrogenase 1 and 2 (IDH1/2) occur in several types of cancer, but the metabolic consequences of these genetic changes are not fully understood. In this study, we performed13C metabolic flux analysis on a panel of isogenic cell lines containing heterozygous IDH1/2 mutations. We observed that under hypoxic conditions, IDH1-mutant cells exhibited increased oxidative tricarboxylic acid metabolism along with decreased reductive glutamine metabolism, but not IDH2-mutant cells. However, selective inhibition of mutant IDH1 enzyme function could not reverse the defect in reductive carboxylation activity. Furthermore, this metabolic reprogramming increased the sensitivity of IDH1-mutant cells to hypoxia or electron transport chain inhibition in vitro. Lastly, IDH1-mutant cells also grew poorly as subcutaneous xenografts within a hypoxic in vivo microenvironment. Together, our results suggest therapeutic opportunities to exploit the metabolic vulnerabilities specific to IDH1 mutation. Â©2014 AACR.
Exploiting User Patience for Scaling Resource Capacity in Cloud Services (2014)

An important feature of cloud computing is its elasticity, that is, the ability to have resource capacity dynamically modified according to the current system load. Auto-scaling is challenging because it must account for two conflicting objectives: minimising system capacity available to users and maximising QoS, which typically translates to short response times. Current auto-scaling techniques are based solely on load forecasts and ignore the perception that users have from cloud services. As a consequence, providers tend to provision a volume of resources that is significantly larger than necessary to keep users satisfied. In this article, we propose a scheduling algorithm and an auto-scaling triggering technique that explore user patience in order to identify critical times when auto-scaling is needed and the appropriate volume of capacity by which the cloud platform should either extend or shrink. The proposed technique assists service providers in reducing costs related to resource allocation while keeping the same QoS to users. Our experiments show that it is possible to reduce resource-hour by up to approximately 8% compared to auto-scaling based on system utilisation.
Adaptive and scalable color correction for stereoscopic 3D displays (2012)

This paper presents a color correction algorithm on a stereo video using a locality-based color correspondence search. The adaptive and iterative refinement process ensures the robust color correction. It is real-time on a single-core CPU.
Investigation of two-branch boron diffusion from vapor phase in n-type 4H-SiC (2008)

Boron diffusion from gas phase was implemented for p-type doping of 4H-SiC at temperatures in the range of 1800–2000°C. A two-branch diffusion associated with two different diffusion mechanisms was observed. The activation energy Ea and prefactor D0 were calculated for each diffusion branch, that are Ea=7.258eV∕D0=1.931×106cm2∕s and Ea=8.742eV∕D0=2.126×107cm2∕s for fast and slow diffusion, respectively. It has been confirmed that the surface layer of diffused boron mostly consists of shallow boron acceptors, while the tail of diffusion profile has mostly deep level D centers.
Highly Potent and Subtype Selective Ligands Derived byN-Methyl Scan of a Somatostatin Antagonist (2001)

The search for synthetic peptide analogues of somatostatin (SRIF) which exhibit selective affinities for the five known receptor subtypes (sst1-5) has generated a large number of potent agonists. Some of these agonists display good subtype selectivities and affinities for the subtypes 1, 2, 3, and 5, including analogues created by N-methyl amino acid substitutions in a standard octapeptide analogue format. We have now extended this peptide backbone N-methylation approach to a potent somatostatin receptor antagonist series using the antagonist Cpa-cyclo(DCys-Pal-DTrp-Lys-Thr-Cys)-Nal-NH2 9 reported from this laboratory as the lead structure. Synthetic analogues were tested for their ability to inhibit somatostatin-stimulated GH release from rat pituitary cells in culture and to displace 125I-labeled somatostatin from CHO cells transfected with the five known human somatostatin receptors. Several interesting observations resulted from the study. N-Methylation at the Lys(9) residue (5) increased the rat GH release inhibitory potency nearly 4-fold to 0.73 nM but resulted in little change in the binding affinity for human type 2 receptor. This analogue also had a high affinity of 5.98 nM for sst5 receptor (compared to 1.4 nM for somatostatin itself) and is the first antagonist analogue to be reported with high affinity for sst5. It also had high potency on in vitro inhibition of sst5 mediated intracellular calcium mobilization. These results were considered surprising, since the Lys(9) residue has long been considered to constitute the active center of somatostatin, important both for receptor binding and activation, and suggests important conformational differences between D-Cys(9) somatostatin antagonists and normal agonist structures. More modifications were carried out on this analogue with the aim of improving antagonist potency and/or specificity. Tyr(7) substitution of 5 resulted in an analogue, which had the highest affinity in the series for hsst2 (K(I) 5.51 nM) and an extraordinarily low IC50 of 0.53 nM in the rat pituitary cell assay. However, this analogue lost considerable affinity for sst5 relative to analogue 5. Analogue 16 with DTrp(12) at C-terminus had the highest affinity for hsst2, however, the IC50 in the rat GH release assay was only 11.6 nM. Replacement of Lys(9) in 9 with Dab(9) gave 11 which displayed high binding affinity for sst3, and it was also quite selective for that receptor. Both the sst3 and sst5 antagonists should be of value in assigning the physiological roles to type 3 and 5 receptor, respectively.
On the globalization of English (2016)

This article discusses the globalization of English and suggests that the changing role and nature of English in the expanding circle requires new methodological approaches and new empirical materials which better represent non-native global English(es), that is, when English is used as an additional linguistic resource alongside L1s. Our case study investigates how ongoing grammatical changes are adapted in global use, and focuses on a specific use of the progressive: the subjective sense with an intervening adverbial. Our findings corroborate those of Hundt &amp; Vogel (2011) on the progressive in general, but also show that stretched, special uses of progressives are fully established in non-native global usage. We conclude that as the globalization of English continues to blur the neat division of the English varieties, better data is needed to take into account the diversity of texts emerging in the expanding circle and to represent a variety of text types from natural, non-instructional settings.