gebhart/patrepeval huggingface dataset:
Cytomegalovirus vaccines and methods of production (WO20009049138): the emerging recognition of the importance of virus neutralization at the epithelial/endothelial interface (2010)

Human cytomegalovirus (CMV) is the most common cause of congenital viral infection in the developed world. Approximately 40,000 congenitally infected infants are born in the US each year. Congenital CMV infection is responsible for a wide range of neurodevelopmental disabilities and is the most common infectious cause of hearing loss in children. The significant public health impact of congenital CMV has led the Institute of Medicine to rank development of a CMV vaccine as a top priority. Vaccine development has been ongoing; however, there is no licensed CMV vaccine currently available. Before vaccines can be optimized, a better understanding of how CMV infects the host is required. Recently, it has been demonstrated that CMV enters epithelial and endothelial cells by different pathways than those used for entry into fibroblasts, and that a recently described complex of CMV proteins, the gH/gL/UL128/130/131 complex, is essential for this process to occur. This discovery has allowed identification of a novel, heretofore unexplored, potential CMV vaccine targets, and provides the basis for the patent, 'Cytomegalovirus Vaccines and Methods of Production - WO2009049138.' In this patent evaluation, the basis for this patent is reviewed. The potential application of this discovery for future CMV vaccine design is discussed.
Comparative study of hydrogen and methane production in the human colon using caecal and faecal homogenates. (1990)

Rates of hydrogen and methane production were compared in caecal and faecal homogenates in six methane producers. Faecal homogenates produced hydrogen and methane in the absence of and after the addition of lactulose, whereas caecal homogenates produced hydrogen but little methane.
The Strength of Interaction at the Raf Cysteine-Rich Domain Is a Critical Determinant of Response of Raf to Ras Family Small GTPases (1999)

To be fully activated at the plasma membrane, Raf-1 must establish two distinct modes of interactions with Ras, one through its Ras-binding domain and the other through its cysteine-rich domain (CRD). The Ras homologue Rap1A is incapable of activating Raf-1 and even antagonizes Ras-dependent activation of Raf-1. We proposed previously that this property of Rap1A may be attributable to its greatly enhanced interaction with Raf-1 CRD compared to Ras. On the other hand, B-Raf, another Raf family member, is activatable by both Ras and Rap1A. When interactions with Ras and Rap1A were measured, B-Raf CRD did not exhibit the enhanced interaction with Rap1A, suggesting that the strength of interaction at CRDs may account for the differential action of Rap1A on Raf-1 and B-Raf. The importance of the interaction at the CRD is further supported by a domain-shuffling experiment between Raf-1 and B-Raf, which clearly indicated that the nature of CRD determines the specificity of response to Rap1A: Raf-1, whose CRD is replaced by B-Raf CRD, became activatable by Rap1A, whereas B-Raf, whose CRD is replaced by Raf-1 CRD, lost its response to Rap1A. Finally, a B-Raf CRD mutant whose interaction with Rap1A is selectively enhanced was isolated and found to possess the double mutation K252E/M278T. B-Raf carrying this mutation was not activated by Rap1A but retained its response to Ras. These results indicate that the strength of interaction with Ras and Rap1A at its CRD may be a critical determinant of regulation of the Raf kinase activity by the Ras family small GTPases.
Recovery from Acute Kidney Injury: Determinants and Predictors (2010)

Predicting recovery of renal function following acute kidney injury (AKI) is one of the top ten questions in the field of AKI research. Accurate prediction would help physicians distinguish patients with poor renal prognosis in whom further therapy is likely to be futile from those who are likely to have good renal prognosis. Proper stratification of patients with AKI is also critical to design clinical trials to target patients with poor prognosis. Unfortunately, current general clinical severity scores (APACHE, SOFA, etc.) and AKI-specific severity scores (Mehta's score, Liano's score, Chertow's score, etc.) are not the good predictors of renal recovery. Recent progress on the pathophysiology of renal injury and recovery is encouraging. Repopulation of surviving renal tubular epithelial cell with the assistance of certain renal epithelial cell and specific growth factors such as neutrophil gelatinase-associated lipocalin (NGAL), hepatocyte growth factor (HGF), epidermal growth factor, and insulin-like growth factor-1, etc., play a major role in the recovery process. Such findings provide a great opportunity to test and validate these potential biomarkers as candidate markers of renal recovery. This review will describe the current understanding of the renal recovery process, and the role of clinical severity scores and novel biomarkers such as NGAL, HGF, and cystatin C in predicting renal recovery.
Multiwavelength diffraction and apodization using binary superimposed gratings (1998)

The binary superimposed grating (BSG), consisting of equal-size segments of two possible values of refractive index and capable of effecting multiwavelength reflection, offers ease of fabrication and great versatility in guided-wave wavelength-division-multiplexing (WDM) applications. We present an analytical formula for the coupling strength of a BSG as a function of segment size, and verify it with numerical transfer matrix simulations of the grating reflectance spectra. Perfect agreement is found for a single grating, and values /spl sim/10%-12% less than predicted for 2-11 superimposed gratings. Subdividing the grating into sections of grouped segments permits step-like apodization, while maintaining binary index and base segment size. Sidemode suppression ratios (SMSRs) of 27 and 16 dB are computed for single-peak and 11-peak BSGs respectively.
Sustained Release of Multiple Growth Factors from Injectable Polymeric System as a Novel Therapeutic Approach Towards Angiogenesis (2009)

Sequential delivery of VEGF and PDGF using an injectable, biodegradable platform resulted in stable and sustained improvements in perfusion. This sustained, control-released, injectable alginate polymer system is a promising approach for multiple growth factor delivery in clinical application.
Feature identification: a novel approach and a case study (2005)

Feature identification is a well-known technique to identify subsets of a program source code activated when exercising a functionality. Several approaches have been proposed to identify features. We present an approach to feature identification and comparison for large object-oriented multi-threaded programs using both static and dynamic data. We use processor emulation, knowledge filtering, and probabilistic ranking to overcome the difficulties of collecting dynamic data, i.e., imprecision and noise. We use model transformations to compare and to visualise identified features. We compare our approach with a naive approach and a concept analysis-based approach using a case study on a real-life large object-oriented multi-threaded program, Mozilla, to show the advantages of our approach. We also use the case study to compare processor emulation with statistical profiling.
High-resolution x-ray study of deoxy recombinant human hemoglobins synthesized from .beta.-globins having mutated amino termini (1992)

The crystal structures of three mutant hemoglobins reconstituted from recombinant beta chains and authentic human alpha chains have been determined in the deoxy state at 1.8-A resolution. The primary structures of the mutant hemoglobins differ at the beta-chain amino terminus. One mutant, beta Met, is characterized by the addition of a methionine at the amino terminus. The other two hemoglobins are characterized by substitution of Val 1 beta with either a methionine, beta V1M, or an alanine, beta V1A. All the mutation-induced structural perturbations are small intrasubunit changes that are localized to the immediate vicinity of the beta-chain amino terminus. In the beta Met and beta V1A mutants, the mobility of the beta-chain amino terminus increases and the electron density of an associated inorganic anion is decreased. In contrast, the beta-chain amino terminus of the beta V1M mutant becomes less mobile, and the inorganic anion binds with increased affinity. These structural differences can be correlated with functional data for the mutant hemoglobins [Doyle, M. L., Lew, G., DeYoung, A., Kwiatkowski, L., Noble, R. W., & Ackers, G. K. (1992) Biochemistry preceding paper is this issue] as well as with the properties of ruminant hemoglobins and a mechanism [Perutz, M., & Imai, K. (1980) J. Mol. Biol. 136, 183-191] that relates the intrasubunit interactions of the beta-chain amino terminus to changes in oxygen affinity. Since the structures of the mutant deoxyhemoglobins show only subtle differences from the structure of deoxyhemoglobin A, it is concluded that any of the three hemoglobins could probably function as a surrogate for hemoglobin A.(ABSTRACT TRUNCATED AT 250 WORDS)
Structure and growth of the interface of Pd ona−Si:H (1981)

The structure of the $\mathrm{Pd}$ --- $a\ensuremath{-}\mathrm{S}\mathrm{i}$:$\mathrm{H}$ interface is probed using interference-enhanced Raman scattering. It was found that \ensuremath{\sim} 2 nm of Pd was initially consumed to form a crystalline silicide at the $\mathrm{Pd}$ --- $a\ensuremath{-}\mathrm{S}\mathrm{i}$:$\mathrm{H}$ interface. Annealing to 300\ifmmode^\circ\else\textdegree\fi{}C caused a spectroscopic change, which is associated with a structural change, and additional annealing at 500\ifmmode^\circ\else\textdegree\fi{}C caused the formation of crystalline Si.
ABOUT A PROMPT STRATEGY FOR ESTIMATING MISSING DATA IN LONG TIME SERIES (2024)

A quick practical strategy is proposed for estimating missing data in time series that obey low-order ARIMA models and whose length is greater than that supported by current statistical computer programs. The proposed methodology is based on the idea of identifying the series model from its subseries. To obtain these subseries, a minimal number of data points following a missing observation are deduced to achieve numerical stabilization in its recursive prediction.
T cell recognition of endogenous IgG2a expressed in B lymphoma cells (1988)

We recently characterized a panel of C57BL/6J T cell clones specific for IgG2a of the a allotype in association with I-Ab. Several of the clones gave surprisingly strong responses in the presence of normal spleen cells from several H-2b strains, including C3H.SW, A.BY, D1.LP and BALB.B, without the addition of exogenous antigen. Experiments using Igh-congenic mouse strains demonstrated that this response was directed towards shared allotypic determinants expressed on endogenously synthesized IgG2a molecules in various strains. Here we present evidence that the cell(s) responsible for this stimulation are conventional low density splenic accessory cells. Presentation of endogenously synthesized IgG2a by this population of dendritic cells, macrophages, and/or activated B cells was chloroquine sensitive. Thus, we conclude that this response is probably directed towards secreted IgG2a molecules that are internalized, processed and re-expressed at the cell surface in association with class II molecules. We also tested the ability of T cell clone B61-34 to respond in the presence of the B lymphoma cell line M12.C3.A2. A strong response was again observed in the absence of exogenous antigen. Northern gel analysis of M12.C3.A2 messenger RNA provided evidence that these cells synthesize IgG2a in both a secreted and a membrane form. The response directed towards endogenous IgG2a expressed in M12.C3.A2 lymphoma cells is chloroquine resistant and considerably more efficient than that stimulated by IgG2a added as exogenous soluble antigen. These results demonstrate for the first time that B cells have the capacity to present antigenic determinants expressed on endogenously synthesized immunoglobulins to class II-restricted T cells. The implications of these findings with respect to network models of immune regulation are discussed.
Synthesis of 1′-C-Fluoromethyladenosine (2007)

In search for new antiviral agents, we have been interested in 1'-C-fluoromethyl branched ribonucleosides. In this paper, we describe the synthesis of 1'-C-fluoromethyladenosine via electrophilic fluorination of exo-glycal.
Intracellular Kinase Inhibitors Selected from Combinatorial Libraries of Designed Ankyrin Repeat Proteins (2005)

The specific intracellular inhibition of protein activity at the protein level allows the determination of protein function in the cellular context. We demonstrate here the use of designed ankyrin repeat proteins as tailor-made intracellular kinase inhibitors. The target was aminoglycoside phosphotransferase (3')-IIIa (APH), which mediates resistance to aminoglycoside antibiotics in pathogenic bacteria and shares structural homology with eukaryotic protein kinases. Combining a selection and screening approach, we isolated 198 potential APH inhibitors from highly diverse combinatorial libraries of designed ankyrin repeat proteins. A detailed analysis of several inhibitors revealed that they bind APH with high specificity and with affinities down to the subnanomolar range. In vitro, the most potent inhibitors showed complete enzyme inhibition, and in vivo, a phenotype comparable with the gene knockout was observed, fully restoring antibiotic sensitivity in resistant bacteria. These results underline the great potential of designed ankyrin repeat proteins for modulation of intracellular protein function.
Smart Clothing (2009)

GPS-embedded clothing for finding children or skiers when they are lost, bio-monitoring smart shirts, and vests that monitor a patient's vital signs are no longer science fiction but science fact. It is quite likely that within 20 or 30 years, computers, telephones, and televisions will be a part of our intimate clothing. Covering the whole design
Promiscuous Glycan Site Recognition by Antibodies to the High-Mannose Patch of gp120 Broadens Neutralization of HIV (2014)

Broadly neutralizing monoclonal antibodies (bnmAbs) that target the high-mannose patch centered around the glycan at position 332 on HIV Env are promising vaccine leads and therapeutic candidates because they effectively protect against mucosal SHIV challenge and strongly suppress SHIV viremia in established infection in macaque models. However, these antibodies demonstrate varying degrees of dependency on the N332 glycan site, and the origins of their neutralization breadth are not always obvious. By measuring neutralization on an extended range of glycan site viral variants, we found that some bnmAbs can use alternate N-linked glycans in the absence of the N332 glycan site and therefore neutralize a substantial number of viruses lacking the site. Furthermore, many of the antibodies can neutralize viruses in which the N332 glycan site is shifted to the 334 position. Finally, we found that a combination of three antibody families that target the high-mannose patch can lead to 99% neutralization coverage of a large panel of viruses containing the N332/N334 glycan site and up to 66% coverage for viruses that lack the N332/N334 glycan site. The results indicate that a diverse response against the high-mannose patch may provide near-equivalent coverage as a combination of bnmAbs targeting multiple epitopes. Additionally, the ability of some bnmAbs to use other N-linked glycan sites can help counter neutralization escape mediated by shifting of glycosylation sites. Overall, this work highlights the importance of promiscuous glycan binding properties in bnmAbs to the high-mannose patch for optimal antiviral activity in either protective or therapeutic modalities.
Intelligent Hospital Space Platform Combined with RFID and Wireless Sensor Network (2008)

In this paper, the Radio Frequency Identification (RFID) system has also been applied in telemedicine, which employs wired or wireless communications to provide hospital information and services. The RFID systems can be used to manage medicine and hospital equipment, track patients care, and help doctors and nursers to keep tabs on their patients frequently and remotely. We use the sensor location and management for Wireless Sensor Networks (WSNs) and RFID important technologies.
Flow cytometric analysis of the in situ hybridization of cyclooxygenase isoforms in mesangial cells treated with cyclosporine A (2006)

"In situ" hybridization by flow cytometry is an useful method to detect mRNA. We observed an increased COX-2 expression in a time-dependent manner in parallel with Reactive Oxygen Species synthesis. COX-1 expression increased only at 10 days.
Continuous Glucose Monitoring and Intensive Treatment of Type 1 Diabetes (2008)

Continuous glucose monitoring can be associated with improved glycemic control in adults with type 1 diabetes. Further work is needed to identify barriers to effectiveness of continuous monitoring in children and adolescents. (ClinicalTrials.gov number, NCT00406133.)
Sampling and Retention Efficiencies of Batch-Type Liquid-Based Bioaerosol Samplers (2010)

Four commercially available batch-type bioaerosol samplers, which collect time-integrated samples in liquids, were evaluated. Sampling efficiency was characterized as a function of particle size using near-monodisperse polystyrene spheres (sizes of 1–5 μ m) and oleic acid droplets (3–10 μ m). Results show the sampling efficiency of AGI-30 impingers range from 4–67% for particle sizes of 1 to 5.1 μ m with significant variations between units; those of SKC BioSampler impingers range from 34–105% for particle sizes from 1 to 9 μ m; those of a batch-type wetted wall cyclone with compensation for evaporation (BWWC-EC) range from 5 to 65% for particle sizes 1 to 10 μ m; and, those of a batch-type wetted wall cyclone with no evaporation compensation (BWWC-NC) range of 55 to 88% for particle sizes of 1–8 μ m. Retention efficiency was measured for 1 and 10 μ m polystyrene spheres. For the AGI-30 and BWWC-EC, the retention efficiency of 1 μ m particles after 1 h was less than 30%, while that of the SKC BioSampler was 59%. Due to liquid evaporation, the BWWC-NC could not be operated for 1 h. Retention efficiencies for Bacillus atrophaeus spores and Pantoea agglomerans vegetative cells were measured for the AGI-30 and the SKC BioSampler. Results for the spores were about the same as those for 1 μ m non-viable polystyrene particles; however, the vegetative bacteria lose culturability and consequently show lower retention efficiencies. For the impingers, significant performance differences were observed in units delivered by vendors at different times.
Estimating the Number of Classes via Sample Coverage (1992)

Abstract Assume that a random sample is drawn from a population with unknown number of classes and possibly unequal class probabilities. A nonparametric estimation technique is proposed to estimate the number of classes using the idea of sample coverage, which is defined as the sum of the cell probabilities of the observed classes. Since expected sample coverage can be well estimated, we were motivated to find its role in the estimation of the number of classes. This work generalizes the result of Esty to a nonparametric approach and extends Darroch and Ratcliff to incorporate the heterogeneity of the class probabilities. The coefficient of variation of the class sizes is shown to play an important role in the recommended estimation procedures. The performance of the proposed estimators is investigated by means of Monte Carlo simulations.
Sleep‐disordered breathing in 3,680 Greek children (2004)

The goal of the present investigation was to describe the prevalence of and clinical factors associated with sleep-disordered breathing in children and adolescents. Children and adolescents (3,680 in all, 1-18 years old) attending schools in central Greece were surveyed by questionnaires distributed to parents. We found a similar prevalence of habitual snoring (present every night) among three different age groups (5.3%, 4%, and 3.8% in 1-6-, 7-12-, and 13-18-year-old subjects, P = NS). Several children with an adenoidectomy and/or tonsillectomy were snoring every night (6.1%), whereas sleepiness at school was more common in habitual snorers than in nonhabitual snorers (4.6 vs. 2%, P = 0.03). Seventy randomly selected subjects among 307 snorers without adenoidectomy and/or tonsillectomy underwent polysomnography. The estimated frequency of obstructive sleep apnea-hypopnea among children without adenoidectomy and/or tonsillectomy was 4.3%. Factors associated with snoring were: male gender (odds ratio 1.5 (confidence interval, 1.2-1.9)); chronic rhinitis (2.1 (1.6-2.7)); snoring in father (1.5 (1.2-1.9)), mother (1.5 (1.1-2.0)), or siblings (1.7 (1.2-2.4)); adenoidectomy in mother (1.5 (1.0-2.2)); and passive smoking (1.4 (1.1-1.8)). In conclusion, snoring every night was equally prevalent in younger and older ages, more frequent in males, and present even in some children with a history of adenoidectomy and/or tonsillectomy. Chronic rhinitis, family history of snoring, and exposure to cigarette smoke were associated with an increased frequency of habitual snoring.
The MexGHI-OpmD multidrug efflux pump controls growth, antibiotic susceptibility and virulence in Pseudomonas aeruginosa via 4-quinolone-dependent cell-to-cell communication (2005)

In Pseudomonas aeruginosa the production of multiple virulence factors depends on cell-to-cell communication through the integration of N-acylhomoserine lactone (AHL)- and 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS)- dependent signalling. Mutation of genes encoding the efflux protein MexI and the porin OpmD from the MexGHI-OpmD pump resulted in the inability to produce N-(3-oxododecanoyl)-L-homoserine lactone (3-oxo-c12-hsl) and pqs and a marked reduction in n-butanoyl-L-homoserine lactone levels. Both pump mutants were impaired in growth and exhibited enhanced rather than reduced antibiotic resistance. Provision of exogenous PQS improved growth and restored AHL and virulence factor production as well as antibiotic susceptibility, indicating that the pump mutants retained their capacity to respond to PQS. RT-PCR analysis indicated that expression of the PQS biosynthetic genes, phnA and pqsA, was inhibited when the mutants reached stationary phase, suggesting that the pleiotropic phenotype observed may be due to intracellular accumulation of a toxic PQS precursor. To explore this hypothesis, double mexI phnA (unable to produce anthranilate, the precursor of PQS) and mexI pqsA mutants were constructed; the improved growth of the former suggested that the toxic compound is likely to be anthranilate or a metabolite of it. Mutations in mexI and opmD also resulted in the attenuation of virulence in rat and plant infection models. In plants, addition of PQS restored the virulence of mexI and opmD mutants. Collectively, these results demonstrate an essential function for the MexGHI-OpmD pump in facilitating cell-to-cell communication, antibiotic susceptibility and promoting virulence and growth in P. aeruginosa.