gebhart/patrepeval huggingface dataset:
Neisseria gonorrhoeaestrain PID2 simultaneously expresses six chemically related lipooligosaccharide structures (2002)

Neisseria gonorrhoeae strain PID2 was isolated from a woman suffering from pelvic inflammatory disease. When LOS expressed by this strain is analyzed on SDS-PAGE gels, at least six different lipooligosaccharide (LOS) components are visualized. We characterized the LOSs made by this strain by exoglycosidase digestion, sugar composition analysis, mass spectrometry, and analysis of the genes needed for its synthesis. DNA sequence analysis showed that the lgt gene cluster in this strain has undergone a rearrangement and that it possesses two copies of lgtA, one copy of lgtB and lgtC, and a hybrid gene containing sequences from lgtB and lgtE. We determined that the hybrid lgtB/E gene retained the lgtE gene function. DNA sequence analysis of the gene organization suggested that an intramolecular recombination between lgtA and lgtD and lgtB and lgtE had occurred via homologous recombination between similar sequences. Our studies demonstrated that fluorophore-assisted carbohydrate electrophoresis can be utilized to rapidly determine the composition of LOS. By combining exoglycosidase digestion, in combination with mass spectrometry analysis and compositional analysis, the data indicate that all of the LOS components produced by PID2 extend off of the alpha chain. The longest alpha chain oligosaccharide structure is Gal-GlcNAc-Gal-GlcNAc-Gal-Glc-Heptose I, and the six LOS components are built up by sequentially adding sugars onto the first heptose. PID2 LOS is the first Neisserial LOS to be shown to be devoid of phosphoethanolamine modifications. Because PID2 can surface express its LOS, it indicates that the addition of phosphoethanolamine is not required for LOS surface expression.
Interference-Controlled Transmission Schemes for Cognitive Radio in Frequency-Selective Time-Varying Fading Channels (2011)

Interference control is crucial in cognitive radio networks and the existing related works focus on quasi-static channels. The expansion of wireless services and applications in everyday life has necessitated support of higher mobility, as evident from the emerging wireless standards. This results in time-varying fading channels within a transmission frame for which the interference power control schemes and power allocation strategies have not been developed yet. This paper proposes several interference control and power allocation strategies with different criteria for underlay cognitive radios in time-varying frequency-selective fading channels and extend the transmission schemes to multiple secondary systems. The transmission schemes are evaluated in terms of interference statistics at the primary receiver and the ergodic capacity of the secondary user link. Simulation results over the wide Doppler range show how the proposed schemes with different criteria shape the interference at the primary receiver and the capacity of the secondary user. The results also illustrate better interference control capability of the proposed approaches over the existing scheme.
Multivalent DNA Vaccines as a Strategy to Combat Multiple Concurrent Epidemics: Mosquito-Borne and Hemorrhagic Fever Viruses (2021)

The emergence of multiple concurrent infectious diseases localized in the world creates a complex burden on global public health systems. Outbreaks of Ebola, Lassa, and Marburg viruses in overlapping regions of central and West Africa and the co-circulation of Zika, Dengue, and Chikungunya viruses in areas with A. aegypti mosquitos highlight the need for a rapidly deployable, safe, and versatile vaccine platform readily available to respond. The DNA vaccine platform stands out as such an application. Here, we present proof-of-concept studies from mice, guinea pigs, and nonhuman primates for two multivalent DNA vaccines delivered using in vivo electroporation (EP) targeting mosquito-borne (MMBV) and hemorrhagic fever (MHFV) viruses. Immunization with MMBV or MHFV vaccines via intradermal EP delivery generated robust cellular and humoral immune responses against all target viral antigens in all species. MMBV vaccine generated antigen-specific binding antibodies and IFNγ-secreting lymphocytes detected in NHPs up to six months post final immunization, suggesting induction of long-term immune memory. Serum from MHFV vaccinated NHPs demonstrated neutralizing activity in Ebola, Lassa, and Marburg pseudovirus assays indicating the potential to offer protection. Together, these data strongly support and demonstrate the versatility of DNA vaccines as a multivalent vaccine development platform for emerging infectious diseases.
High speed graphene optoelectronic devices enabled through controlled molecularly doped graphene (2020)

Ultra-fast graphene optoelectronic devices require a stable voltage-free doped graphene that is achieved through meticulous molecular surface adsorption in this work. The graphene film resistance is significantly reduced from 40 to less than 10.
Physically Transient Field-Effect Transistors Based on Black Phosphorus (2018)

Black phosphorus (BP) has shown great potential as a semiconductor material beyond graphene and MoS<sub>2</sub> because of its intrinsic band gap and high mobility. Moreover, the biocompatibility of the final biodegradation products of BP has led to extensive research on biomedical applications. Herein, physically transient field-effect transistors (FETs) based on black phosphorus have been demonstrated using peptide insulator as a gate dielectric layer. The fabricated devices show high hole mobility up to 468 cm<sup>2</sup> V<sup>-1</sup> s<sup>-1</sup> and on-off current ratio over 10<sup>3</sup>. The combined use of black phosphorus, peptide, and molybdenum provides rapid disappearance of the devices within 36 h. Dissolution kinetics and cytotoxicity of black phosphorus are assessed to clarify its availability to be applied in transient electronics. This work provides transient FETs with high degradability and high performance based on biocompatible black phosphorus.
Scheduling of Soft Real-Time Systems for Context-Aware Applications (2005)

Context-aware applications pose new challenges, including a need for new computational models, uncertainty management, and efficient optimization under uncertainty. Uncertainty can arise at two levels: multiple and single tasks. When a mobile user changes environments, the context changes resulting in the possibility of the user requesting tasks which are specific for the new environment. However as the user moves these requested tasks may no longer be context relevant. Additionally, the runtime of each task is often highly dependent on the input data. We introduce an hierarchical multi-resolution statistical task model that captures relevant aspects at the task and intertask levels, and captures not only uncertainty, but also introduces the notion of utility for the user. We have developed a system of nonparametric statistical techniques for modeling the runtime of a specific task. This model is a framework where we define problems of design and optimization of statistical soft real-time systems (SSRTS). The main algorithmic novelty is a cumulative potential-based task scheduling heuristic for maximizing utility. The heuristic conducts global optimization and induces low runtime overhead. We demonstrate the effectiveness of the scheduling heuristic using a Trimaran-based evaluation platform.
Second harmonic generation from metamaterials strongly coupled to intersubband transitions in quantum wells (2014)

We theoretically analyze the second harmonic generation capacity of two-dimensional periodic metamaterials comprising sub-wavelength resonators strongly coupled to intersubband transitions in quantum wells (QWs) at mid-infrared frequencies. The metamaterial is designed to support a fundamental resonance at ∼30 THz and an orthogonally polarized resonance at the second harmonic frequency (∼60 THz), while the asymmetric quantum well structure is designed to provide a large second order susceptibility. Upon continuous wave illumination at the fundamental frequency we observe second harmonic signals in both the forward and backward directions, with the forward efficiency being larger. We calculate the overall second harmonic conversion efficiency of the forward wave to be ∼1.3 × 10−2 W/W2—a remarkably large value, given the deep sub-wavelength dimensions of the QW structure (about 1/15th of the free space wavelength of 10 μm). The results shown in this Letter provide a strategy for designing easily fabricated sources across the entire infrared spectrum through proper choice of QW and resonator designs.
Cool future fashion: Personal cooling as part of social adaptation to hotter climates (2019)

“Deadly heat waves: it’s only getting worse”, a headline from this summer, succinctly summarizes recent weather and predictions on its future patterns. According to World Metrological Organization,...
Advanced methods for the analysis, design, and optimization of SMA-based aerostructures (2011)

Engineers continue to apply shape memory alloys to aerospace actuation applications due to their high energy density, robust solid-state actuation, and silent and shock-free operation. Past design and development of such actuators relied on experimental trial and error and empirically derived graphical methods. Over the last two decades, however, it has been repeatedly demonstrated that existing SMA constitutive models can capture stabilized SMA transformation behaviors with sufficient accuracy. This work builds upon past successes and suggests a general framework by which predictive tools can be used to assess the responses of many possible design configurations in an automated fashion. By applying methods of design optimization, it is shown that the integrated implementation of appropriate analysis tools can guide engineers and designers to the best design configurations. A general design optimization framework is proposed for the consideration of any SMA component or assembly of such components that applies when the set of design variables includes many members. This is accomplished by relying on commercially available software and utilizing tools already well established in the design optimization community. Such tools are combined with finite element analysis (FEA) packages that consider a multitude of structural effects. The foundation of this work is a three-dimensional thermomechanical constitutive model for SMAs applicable for arbitrarily shaped bodies. A reduced-order implementation also allows computationally efficient analysis of structural components such as wires, rods, beams and shells. The use of multiple optimization schemes, the consideration of assembled components, and the accuracy of the implemented constitutive model in full and reduced-order forms are all demonstrated.
Mycetoma of the Foot due to <i>Fusarium </i>sp. Treated with Oral Ketoconazole (1992)

We report the case of a 30-year-old Nigerian patient with mycetoma of the foot without bone involvement caused by Fusarium sp..Long-term administration of ketoconazole produced a significant improvement with good clinical and biological tolerance.
Scalable Video Streaming over Fading Wireless Channels (2009)

We consider the transmission of multiple scalable video streams from a server to multiple users over a fading wireless channel. We first present a long-term resource allocation algorithm that determines the scheduling policy and the parameters used by the scheduling policy in order to maximize the weighted sum of PSNR of all video streams. We then present an online scheduling algorithm that utilizes the results obtained by the long-term resource allocation algorithm for user and packet scheduling as well as video frame dropping strategy. Simulation results show that our proposed scheduling scheme significantly improves the video quality compared to the best-known scheduling algorithms in the literature.
Phosphorescence of red Os(fptz)2(PPh2Me)2 doped organic light-emitting devices with n and p hosts (2006)

We have applied a stericly-hindered red phosphorescent dopant Os(fptz)2(PPh2Me)2 [fptz=3-trifluoromethyl-5-(2-pyridyl)-1,2,4-triazole, PPh2Me=phosphine ligand] in p-type 4,4′-N,N′-dicarbazole-biphenyl or n-type bis(2-methyl-8-quinolinolato)(p-phenylphenolato) aluminum host and found that the latter produced higher luminance efficiency at lower doping concentration. We present a model to rationalize this phenomenon in which the n-type host impedes hole transport, which leads to narrower recombination zone near the hole transport layer/emission layer interface than the p-type host, hence, more effective recombination.
Optimal‐cost repair in multi‐hop distributed storage systems with network coding (2016)

Abstract We study the transmission cost of repair in a distributed storage system, where storage nodes are connected together through an arbitrary network topology, and there is a cost in the use of the network link. Contrary to the classical model, where there exists a link between a pair of storage node, in our repair model there might not exist a link between some pairs of storage nodes or it might be expensive to use. For that, we propose surviving nodes cooperation in repair, meaning that the surviving nodes as the intermediate nodes combine their received packets with their own stored packets and then transmit coded packets towards the new node. We show that surviving node cooperation can reduce the repair‐cost, the sum of the costs for transmitting repairing data between the surviving nodes and the new node. For the system that allows surviving node cooperation, we find the minimum‐cost codes in repair by firstly deriving a lower bound of the repair‐cost through an optimization problem and then proposing achievable codes. We show the gain of the proposed codes in reducing the repair‐cost in some scenarios. Copyright © 2016 John Wiley &amp; Sons, Ltd.
<title>Nanoparticle optics: fabrication, surface-enhanced spectroscopy, and sensing</title> (2003)

Recently, nanoparticles have become the platform for many sensing schemes. In particular, the utilization of the optical response of nanoparticles to changes in their nanoenvironment has served as a signal transduction mechanism for these sensing events. For example, silver nanoparticle arrays synthesized using nanosphere lithography have served as an ultrasensitive detection platform for small molecules, proteins, and antibodies with the detection limit of 60,000 and less than 25 molecules/nanoparticle for hexadecanethiol and antibodies, respectively. While this approach is low cost and highly portable, one limitation of the array platform is that the signal arises from approximately 1x10<sup>6</sup> nanoparticles. A method to improve the overall number of molecules detected would be to decrease the number of nanoparticles probed. Recently, single nanoparticle sensing has been accomplished using dark-field microscopy. A 40 nm shift in the localized surface plasmon resonance induced from less than 60,000 small-molecule adsorbates has been monitored from a single Ag nanoparticle. Additionally, streptavidin sensing has also been demonstrated using a single Ag nanoparticle. Detection platforms based on nanoparticle arrays and single nanoparticles will be discussed and compared.
Material optimization for electro-optic modulation and cascading (2000)

A large effort has been devoted to the preparation of organic polymeric materials for electro-optic modulation and more recently for cascading based processes. These materials contain push-pull chromophores either incorporated as guest in a high T<SUB>g</SUB> polymeric matrix (doped polymers) or grafted onto the polymeric matrix. These systems present several advantages but require significant improvement at the molecular level- by designing optimized chromophores with very large molecular figure of merit specific to each application targeted. The sol-gel route was used to prepare hybrid organic-inorganic materials, for the fabrication of amorphous solids of various shapes (bulk, think films...). The results obtained on optimized chromophore-doped poled thin films emphasize that intermolecular interactions have to be taken into account, as already pointed out by Dalton and coworkers. By combining a molecular engineering strategy for getting large molecular figure of merit and by controlling the intermolecular dipole-dipole interactions via both tuning the push-pull chromophore concentration and the incorporation screening carbazole moieties in high concentration. This strategy allows us to obtain a r<SUB>33</SUB> of about 50 pm/V at 831 nm for a new optimized chromophore structure. In parallel, these thin films are being processed to be used as passive components for integrated optics.
Natural and Directed Evolution of Intrinsically Disordered Proteins (2014)

Directed Evolution: An Overview 320 Analysis of Protein-Protein Interactions 322 Introducing Disorder to Study Natural and Evolutionary Mechanisms 324 Examples of IDPs Studied Using Protein Engineering/Directed Evolution 325Increased Rigidity of Protein Domains Results in Increased Protein Stability 325An increase in the proportion of intrinsically disordered proteins (IDPs) concomitant with an increase in organism complexity (Tompa, Dosztanyi et al. 2006; Ward, Sodhi et al. 2004) suggests an important role for disorder in evolution. Uncovering details regarding the origin and changes that occurred in the evolution of IDPs may shed light on the evolution of more ordered proteins and the rise of complex protein functions in humans. Moreover, such information will provide insight to the role of disorder, IDP functionality, and their mechanisms of action at the molecular level. Such information for IDPs, however, is dicult to obtain using traditional biochemical and biophysical methods. Directed evolution can mimic such combinatorial processes that occur in natural evolution. Pairing directed evolution with detailed analyses of the biophysical properties of IDPs, therefore, could bring new understanding to protein disorder and evolution, as well as indicate novel strategies for engineering proteins for biotechnological and therapeutic purposes. In this chapter, we provide an overview of recent research concerning the natural evolution of IDPs, as well as advances in the use of directed evolution methods to gain insight to IDP function.
Convenios colectivos estatutarios: contenido, eficacia e inaplicación (2013)

El convenio colectivo para alcanzar eficacia personal general y directa (normativa) ha de cumplir un cuadro muy completo de requisitos, sustantivos y formales. De ahi el nombre de convenios colectivos estatutarios; o conforme al Estatuto de los Trabajadores. Una de las innovaciones fuertes de la ultima Reforma Laboral se concreta en la posibilidad del descuelgue de la vinculacion normativa de dichos convenios.
ChemInform Abstract: Molecular Belts. Part 2. Substrate‐Directed Syntheses of Belt‐Type and Cage‐Type Structures. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A hybrid least squares and principal component analysis algorithm for Raman spectroscopy (2011)

The least squares fitting algorithm is the most commonly used algorithm in Raman spectroscopy. In this paper, however, we show that it is sensitive to variations in the background signal when the signal of interest is weak. To address this problem, we propose a novel algorithm to analyze measured spectra in Raman spectroscopy. The method is a hybrid least squares and principal component analysis algorithm. It explicitly accounts for any variations expected in the reference spectra used in the signal decomposition. We compare the novel algorithm to the least squares method with a low-order polynomial residual model, and demonstrate the novel algorithm's superior performance by comparing quantitative error metrics. Our experiments use both simulated data and data acquired from an in vitro solution of Raman-enhanced gold nanoparticles.
Three Novel EPAS1/HIF2A Somatic and Germline mutations Associated with Polycythemia and Pheochromocytoma/Paraganglioma. (2012)

Abstract Abstract 2080 Congenital polycythemias have diverse etiologies, including mutations in the hypoxia sensing pathway leading to increased levels of hypoxia inducible factors (HIF) and erythropoietin. These include mutations of negative regulators of HIFs, such as germline von Hippel-Lindau (VHL) gene heterozygous mutations (Chuvash polycythemia), HIF-prolyl hydroxylase 2 (PHD2) gene mutations, and gain-of-function mutations of HIF-2-alpha (HIF2A) (exon 12). Mutation of the PHD2 gene in one family was associated with polycythemia and recurrent pheochromocytoma/paraganglioma (PHEO/PGL) a neuroendocrine tumor commonly found in so called VHL tumor predisposition syndrome. Over the past two decades, we have studied six unrelated patients with sporadic congenital polycythemia who subsequently developed PHEO/PGLs without till now discernible molecular basis. We now report on these three patients, two with different tumor somatic codon A530 HIF2A mutations in exon 12 and one with germline mutation F374Y inherited from his mother, in a unique domain (exon 9) of HIF2A, all three cases later developed multiple recurrent neuroendocrine tumors and were subjects of our study. In search of species homology, codons F374 and A530 of the HIF2A are highly conserved among man, chimpanzee, mouse, horse, cattle, chicken and zebrafish, suggesting this serves an important function for the gene. These mutations were identified in the vicinity of the primary hydroxylation site (exon 12) and novel domain (exon 9) of the HIF2A protein which affects VHL protein binding, Functional studies of the HIF2A mutants shown that three HIF2A variants have increased half-life consistent with gain-of-function of the HIF2A due to disruption in the VHL binding to these mutant residues impairing ubiquitination and proteasomal degradation. This results in increased transcription of genes downstream of HIF2A including erythropoietin. Further examination did not reveal any evidence of loss-of-heterozygosity, nor an additional mutation of HIF2A, or other HIF-pathway genes in their tumor tissues. The fact that two patients with polycythemia and PHEO/PGL had somatic and one germline HIF2A mutations, albeit at different locations, underscore the PHEO/PGL promoting potential of gain-of-function mutations of HIF2A that alone, either as somatic or germline mutations can contribute to, but are not sufficient for PHEO/PGL development but is sufficient for inducing polycythemic phenotype. Disclosures: No relevant conflicts of interest to declare.