gebhart/patrepeval huggingface dataset:
Role of Transmembrane Domain and Cytoplasmic Tail Amino Acid Sequences of Influenza A Virus Neuraminidase in Raft Association and Virus Budding (2004)

Influenza virus neuraminidase (NA), a type II transmembrane glycoprotein, possesses receptor-destroying activity and thereby facilitates virus release from the cell surface. Among the influenza A viruses, both the cytoplasmic tail (CT) and transmembrane domain (TMD) amino acid sequences of NA are highly conserved, yet their function(s) in virus biology remains unknown. To investigate the role of amino acid sequences of the CT and TMD on the virus life cycle, we systematically mutagenized the entire CT and TMD of NA by converting two to five contiguous amino acids to alanine. In addition, we also made two chimeric NA by replacing the CT proximal one-third amino acids of the NA TMD [NA(1T2N)NA] and the entire NA TMD (NATRNA) with that of human transferrin receptor (TR) (a type II transmembrane glycoprotein). We rescued transfectant mutant viruses by reverse genetics and examined their phenotypes. Our results show that all mutated and chimeric NAs could be rescued into transfectant viruses. Different mutants showed pleiotropic effects on virus growth and replication. Some mutants (NA2A5, NA3A7, and NA4A10) had little effect on virus growth while others (NA3A2, NA5A27, and NA5A31) produced about 50- to 100-fold-less infectious virus and still some others (NA5A14, NA4A19, and NA4A23) exhibited an intermediate phenotype. In general, mutations towards the ectodomain-proximal sequences of TMD progressively caused reduction in NA enzyme activity, affected lipid raft association, and attenuated virus growth. Electron microscopic analysis showed that these mutant viruses remained aggregated and bound to infected cell surfaces and could be released from the infected cells by bacterial NA treatment. Moreover, viruses containing mutations in the extreme N terminus of the CT (NA3A2) as well as chimeric NA containing the TMD replaced partially [NA(1T2N)NA] or fully (NATRNA) with TR TMD caused reduction in virus growth and exhibited the morphological phenotype of elongated particles. These results show that although the sequences of NA CT and TMD per se are not absolutely essential for the virus life cycle, specific amino acid sequences play a critical role in providing structural stability, enzyme activity, and lipid raft association of NA. In addition, aberrant morphogenesis including elongated particle formation of some mutant viruses indicates the involvement of NA in virus morphogenesis and budding.
VAr reserve concept applied to a wind power plant (2011)

Larger percentages of wind power penetration translate into more demanding requirements from the grid codes; for example voltage support at the point of connection has been introduced recently by several grid codes from around the world, making it important to analyze this control when applied to wind power plants. This paper proposes two different VAr reserve control strategies for a wind power plant. The amount of dynamic VAr available most of the operation time, makes the wind power plant (WPP) a good candidate to include a VAr reserve management system. Two different ways of implementing a VAr management system are proposed and analyzed. Such a reactive power reserve may be provided by the wind power plant since the amount of reactive power installed for most active power working points exceeds the demand required by the grid operator. Basically, this overrated reactive power capacity is a consequence of sizing wind turbine facilities for maximum active power level. The reactive power losses, due to active power transportation inside the plant (normally two transformers), and P-Q wind turbine characteristics define the P-Q reserve chart. By utilizing the intrinsic overrated reactive power capacity, additional devices, such as for example SVCs and STATCOMs, can be avoided in other locations of the grid.
Escherichia coli as a cause of diarrhea (2002)

Escherichia coli is the best-known member of the normal microbiota of the human intestine and a versatile gastrointestinal pathogen. The varieties of E. coli that cause diarrhea are classified into named pathotypes, including enterotoxigenic, enteroinvasive, enteropathogenic and enterohemorrhagic E. coli. Individual strains of each pathotype possess a distinct set of virulence-associated characteristics that determine the clinical, pathological and epidemiological features of the diseases they cause. In the present brief review, we summarize the key distinguishing features of the major pathotypes of diarrheagenic E. coli. Knowledge of the pathogenic mechanisms of these bacteria has led to the development of rational interventions for the treatment and prevention of E. coli-induced diarrhea. In addition, investigations into E. coli virulence are providing useful insights into the origins and evolution of bacterial pathogens more generally.
A Survey on Multicarrier Communications: Prototype Filters, Lattice Structures, and Implementation Aspects (2014)

Due to their numerous advantages, communications over multicarrier schemes constitute an appealing approach for broadband wireless systems. Especially, the strong penetration of orthogonal frequency division multiplexing (OFDM) into the communications standards has triggered heavy investigation on multicarrier systems, leading to re-consideration of different approaches as an alternative to OFDM. The goal of the present survey is not only to provide a unified review of waveform design options for multicarrier schemes, but also to pave the way for the evolution of the multicarrier schemes from the current state of the art to future technologies. In particular, a generalized framework on multicarrier schemes is presented, based on what to transmit, i.e., symbols, how to transmit, i.e., filters, and where/when to transmit, i.e., lattice. Capitalizing on this framework, different variations of orthogonal, bi-orthogonal, and non-orthogonal multicarrier schemes are discussed. In addition, filter designs for various multicarrier systems are reviewed considering four different design perspectives: energy concentration, rapid decay, spectrum nulling, and channel/hardware characteristics. Subsequently, evaluation tools which may be used to compare different filters in multicarrier schemes are studied. Finally, multicarrier schemes are evaluated from the perspective of practical implementation aspects, such as lattice adaptation, equalization, synchronization, multiple antennas, and hardware impairments.
Perioperative and Long-term Clinical Outcomes for Bone Morphogenetic Protein Versus Iliac Crest Bone Graft for Lumbar Fusion in Degenerative Disk Disease (2014)

BMP, in particular rhBMP-2, is a good alternative to autogenous bone graft, especially in cases when harvesting of autologous bone is contraindicated or undesirable, operation time is limited, and there are no contraindications for BMP use.However, the current study did not reveal evidence robust enough to develop strong medical recommendations concerning BMP use for lumbar arthrodesis in degenerative disk disease.
Glycomics‐based analysis of chicken red blood cells provides insight into the selectivity of the viral agglutination assay (2011)

Agglutination of red blood cells (RBCs), including chicken RBCs (cRBCs), has been used extensively to estimate viral titer, to screen glycan-receptor binding preference, and to assess the protective response of vaccines. Although this assay enjoys widespread use, some virus strains do not agglutinate RBCs. To address these underlying issues and to increase the usefulness of cRBCs as tools for studying viruses, such as influenza, we analyzed the cell surface N-glycans of cRBCs. On the basis of the results obtained from complementary analytical strategies, including MS, 1D and 2D-NMR spectroscopy, exoglycosidase digestions, and HPLC profiling, we report the major glycan structures present on cRBCs. By comparing the glycan structures of cBRCs with those of representative human upper respiratory cells, we offer a possible explanation for the fact that certain influenza strains do not agglutinate cRBCs, using specific human-adapted influenza hemagglutinins as examples. Finally, recent understanding of the role of various glycan structures in high affinity binding to influenza hemagglutinins provides context to our findings. These results illustrate that the field of glycomics can provide important information with respect to the experimental systems used to characterize, detect and study viruses.
A flexible 5G RAN architecture with dynamic baseband split distribution and configurable optical transport (2017)

In a Cloud Radio Access Network (C-RAN) architecture, different baseband processing functions (BPFs) splits options are available on the interface between the central unit (CU) and the radio units (RUs) [1]. A lower layer split, e.g., low-physical (PHY), can support advanced radio coordination techniques, for example Joint Reception (JR) Coordinated MultiPoint (JR-CoMP) [2]. However, the interface between low-PHY and the rest of the BPF chain (i.e., referred to as enhanced Common Public Radio Interface - eCPRI [3]) requires a high-capacity transport. With a higher layer split, e.g., between the Packet Data Convergence Protocol (PDCP) and the Radio Link Control layer (RLC), the transport capacity required on the interface between RLC and PDCP (i.e., referred to as F1 [1][4]) is lower than for eCPRI. However, with this split it is difficult to implement advanced radio coordination functions. The choice of BPF split and consequently the transport capacity requirements are determined by the RUs' radio coordination needs [1][5].
A Nanoscale Optical Biosensor:  The Long Range Distance Dependence of the Localized Surface Plasmon Resonance of Noble Metal Nanoparticles (2003)

The elucidation of the long range distance dependence of the localized surface plasmon resonance (LSPR) of surface-confined noble metal nanoparticles is the aim of this work. It was suspected that the linear distance dependence found in CH3(CH2)xSH self-assembled monolayer (SAM) formation was the thin shell limit of a longer range, nonlinear dependence. To verify this, multilayer SAM shells based on the interaction of HOOC(CH2)10SH and Cu2+ were assembled onto surface-confined noble metal nanoparticles and were monitored using UV−visible spectroscopy. Measurement of the LSPR extinction peak shift versus number of layers and adsorbate thickness is nonlinear and has a sensing range that is dependent on the composition, shape, in-plane width, and out-of-plane height of the nanoparticles. Theoretical calculations based on an accurate electrodynamics description of the metal nanoparticle plus surrounding layered material indicate plasmon resonance wavelength shifts that are in excellent agreement with the measurements. The calculations show that the sensing range is determined by falloff of the average induced electric field around the nanoparticle. This detailed set of experiments coupled with an excellent theory versus experiment comparison prove that the sensing capabilities of noble metal nanoparticles can be size tuned to match the dimensions of biological and chemical analytes by adjusting the aforementioned properties. The optimization of the LSPR nanosensor for a specific analyte will significantly improve an already sensitive nanoparticle-based sensor.
High-Level Transgene Expression in Nonhuman Primate Liver with Novel Adeno-Associated Virus Serotypes Containing Self-Complementary Genomes (2006)

Adeno-associated virus (AAV) vectors are being considered for in vivo applications of gene therapy in the treatment of a variety of disorders. This study evaluates the biology of second-generation vectors based on the novel serotypes AAV7 and AAV8 and containing self-complementary genomes in the nonhuman primate liver. Stable levels of transgene expression were achieved in cynomolgus macaques and suggest efficiencies at least 2 log higher than what could be achieved with AAV2 vectors using traditional single-stranded genomes. Analysis of DNAs from tissues revealed high levels of vector in the liver that appeared proportional to the relative amounts of transgene expression.
A Kinetic and Mechanistic Study of the Amino Acid Catalyzed Aldol Condensation of Acetaldehyde in Aqueous and Salt Solutions (2008)

The amino acid catalyzed aldol condensation is of great interest in organic synthesis and natural environments such as atmospheric particles. However, kinetic and mechanistic information on these reactions is limited. In this work the kinetics of the aldol condensation of acetaldehyde in water and aqueous salt solutions (NaCl, CaCl2, Na2SO4, MgSO4) catalyzed by five amino acids (glycine, alanine, serine, arginine, and proline) at room temperature (295 +/- 2 K) has been studied. Monitoring the formation of three products, crotonaldehyde, 2,4-hexadienal, and 2,4,6-octatrienal, by UV-vis absorption over 200-1100 nm revealed two distinct kinetic regimes: at low amino acid concentrations (in all cases, below 0.1 M), the overall reaction was first-order with respect to acetaldehyde and kinetically limited by the formation of the enamine intermediate. At larger amino acid concentrations (at least 0.3 M), the kinetics was second order and controlled by the C-C bond-forming step. The first-order rate constants increased linearly with amino acid concentration consistent with the enamine formation. Inorganic salts further accelerated the enamine formation according to their pKb plausibly by facilitating the iminium or enamine formation. The rate constant of the C-C bond-forming step varied with the square of amino acid concentration suggesting the involvement of two amino acid molecules. Thus, the reaction proceeded via a Mannich pathway. However, the contribution of an aldol pathway, first-order in amino acid, could not be excluded. Our results show that the rate constant for the self-condensation of acetaldehyde in aqueous atmospheric aerosols (up to 10 mM of amino acids) is identical to that in sulfuric acid 10-15 M (kI approximately 10-7-10-6 s-1) clearly illustrating the potential importance of amino acid catalysis in natural environments. This work also demonstrates that under usual laboratory conditions and in natural environments aldol condensation is likely to be kinetically controlled by the enamine formation. Notably, kinetic investigations of the C-C bond-forming addition step would only be possible with high concentrations of amino acids.
325292 Molecular Recognition Using Nanotube-Adsorbed Polymer Complexes (2013)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, February 2013.
Neonatal administration of β-endorphin produces “chronic” insensitivity to thermal stimuli (1979)

Male and female rat pups were injected with β-endorphin, naloxone or a saline control solution during days 2–7 postnatally. At 90 days of age the rats were tested for analgesia with the tail flick test. Testing was conducted during the first 2 hours of the light and the dark cycle. In both sexes and during both phases of the light cycle rats treated with β-endorphin as infants evidenced a significant elevation in threshold for painful thermal stimuli. Early treatment with naloxone also resulted in elevated threshold for thermal stimuli. Administration of naloxone to these rats as adults did not reverse the analgesic effect. It was concluded that early exposure to β-endorphin results in permanent changes in behavior perhaps by altering the interaction of endogenous opiates with their binding sites during a ciritcal period of opiate receptor development.
Two-year outcomes after dextrose gel prophylaxis for neonatal hypoglycaemia (2020)

Objective To determine the effect of prophylactic dextrose gel for prevention of neonatal hypoglycaemia on neurodevelopment and executive function at 2 years’ corrected age. Design Prospective follow-up of a randomised trial. Setting New Zealand. Patients Participants from the pre-hypoglycaemia Prevention with Oral Dextrose (pre-hPOD) trial randomised to one of four dose regimes of buccal 40% dextrose gel or equivolume placebo. Main outcome measures Coprimary outcomes were neurosensory impairment and executive function. Secondary outcomes were components of the primary outcomes, neurology, anthropometry and health measures. Results We assessed 360 of 401 eligible children (90%) at 2 years’ corrected age. There were no differences between dextrose gel dose groups, single or multiple dose groups, or any dextrose and any placebo groups in the risk of neurosensory impairment or low executive function (any dextrose vs any placebo neurosensory impairment: relative risk (RR) 0.77, 95% CI 0.50 to 1.19, p=0.23; low executive function: RR 0.50, 95% CI 0.24 to 1.06, p=0.07). There were also no differences between groups in any secondary outcomes. There was no difference between children who did or did not develop neonatal hypoglycaemia in the risk of neurosensory impairment (RR 1.05, 95% CI 0.68 to 1.64, p=0.81) or low executive function (RR 0.73, 95% CI 0.34 to 1.59, p=0.43). Conclusion Prophylactic dextrose gel did not alter neurodevelopment or executive function and had no adverse effects to 2 years’ corrected age, but this study was underpowered to detect potentially clinically important effects on neurosensory outcomes.
Designing MacPherson Suspension Architectures using Bayesian Optimization (2022)

Engineering design is traditionally performed by hand: an expert makes design proposals based on past experience, and these proposals are then tested for compliance with certain target specifications. Testing for compliance is performed first by computer simulation using what is called a discipline model. Such a model can be implemented by a finite element analysis, multibody systems approach, etc. Designs passing this simulation are then considered for physical prototyping. The overall process may take months, and is a significant cost in practice. We have developed a Bayesian optimization system for partially automating this process by directly optimizing compliance with the target specification with respect to the design parameters. The proposed method is a general framework for computing a generalized inverse of a high-dimensional non-linear function that does not require e.g. gradient information, which is often unavailable from discipline models. We furthermore develop a two-tier convergence criterion based on (i) convergence to a solution optimally satisfying all specified design criteria, or (ii) convergence to a minimum-norm solution. We demonstrate the proposed approach on a vehicle chassis design problem motivated by an industry setting using a state-of-the-art commercial discipline model. We show that the proposed approach is general, scalable, and efficient, and that the novel convergence criteria can be implemented straightforwardly based on existing concepts and subroutines in popular Bayesian optimization software packages.
Interaction between chicken TRIM25 and MDA5 and their role in mediated antiviral activity against IBDV infection (2022)

Infectious Bursal Disease Virus (IBDV) is the causative agent of an immunosuppressive disease that affects domestic chickens (<i>Gallus gallus</i>) severely affecting poultry industry worldwide. IBDV infection is characterized by a rapid depletion of the bursal B cell population by apoptosis and the atrophy of this chief lymphoid organ. Previous results from our laboratory have shown that exposure of infected cells to type I IFN leads to an exacerbated apoptosis, indicating an important role of IFN in IBDV pathogenesis. It has been described that recognition of the dsRNA IBDV genome by MDA5, the only known cytoplasmic pattern recognition receptor for viral RNA in chickens, leads to type I IFN production. Here, we confirm that TRIM25, an E3 ubiquitin ligase that leads to RIG-I activation in mammalian cells, significantly contributes to positively regulate MDA5-mediated activation of the IFN-inducing pathway in chicken DF-1 cells. Ectopic expression of chTRIM25 together with chMDA5 or a deletion mutant version exclusively harboring the CARD domains (chMDA5 2CARD) enhances IFN-β and NF-ĸB promoter activation. Using co-immunoprecipitation assays, we show that chMDA5 interacts with chTRIM25 through the CARD domains. Moreover, chTRIM25 co-localizes with both chMDA5 and chMDA5 2CARD, but not with chMDA5 mutant proteins partially or totally lacking these domains. On the other hand, ablation of endogenous chTRIM25 expression reduces chMDA5-induced IFN-β and NF-ĸB promoter activation. Interestingly, ectopic expression of either wild-type chTRIM25, or a mutant version (chTRIM25 C59S/C62S) lacking the E3 ubiquitin ligase activity, restores the co-stimulatory effect of chMDA5 in chTRIM25 knockout cells, suggesting that the E3-ubiquitin ligase activity of chTRIM25 is not required for its downstream IFN-β and NF-ĸB activating function. Also, IBDV-induced expression of <i>IFN-β</i>, <i>Mx</i> and <i>OAS</i> genes was reduced in chTRIM25 knockout as compared to wild-type cells, hence contributing to the enhancement of IBDV replication. Enhanced permissiveness to replication of other viruses, such as avian reovirus, Newcastle disease virus and vesicular stomatitis virus was also observed in chTRIM25 knockout cells. Additionally, chTRIM25 knockout also results in reduced MAVS-induced IFN-β promoter stimulation. Nonetheless, similarly to its mammalian counterpart, chTRIM25 overexpression in wild-type DF-1 cells causes the degradation of ectopically expressed chMAVS.
Design, manufacturing, and measurements of a metal-less V-groove RXI collimator (2011)

A metal-less RXI collimator has been designed. Unlike to the conventional RXI collimators, whose back surface and central part of the front surface have to be metalized, this collimator does not include any mirrored surface. The back surface is designed as a grooved surface providing two TIR reflections for all rays impinging on it. The main advantage of the presented design is lower manufacturing cost since there is no need for the expensive process of metalization. Also, unlike to the conventional RXI collimators this design performs good colour mixing. The first prototype of V-groove RXI collimator has been made of PMMA by direct cutting using a five axis diamond turning machine. The experimental measurements of the first prototype are presented.
Microscopy with Ultraviolet Surface Excitation (MUSE) for Rapid Intraoperative Pathology of Breast Surgical Margins (2019)

Comprehensive pathology of fresh breast specimen surfaces has been achieved with a fluorescent analogue of H&amp;E and a fully-automated MUSE system that incorporates 3D deconvolution to improve image quality.
An autonomously folding β‐hairpin derived from the human YAP65 WW domain: Attempts to define a minimum ligand‐binding motif (2005)

WW domains are broadly distributed among natural proteins; these modules play a role in bringing specific proteins together. The ligands recognized by WW domains are short segments rich in proline residues. We have tried to identify the minimum substructure within a WW domain that is required for ligand binding. WW domains typically comprise ca. 40 residues and fold to a three-stranded beta-sheet. Structural data for several WW domain/ligand complexes suggest that most or all of the intermolecular contacts involve beta-strands 2 and 3. We have developed a 16-residue peptide that folds to a beta-hairpin conformation that appears to mimic beta-strands 2 and 3 of the human YAP65 WW domain, but this peptide does not bind to known ligands. Thus, the minimum binding domain is larger than the latter two strands of the WW domain beta-sheet.