gebhart/patrepeval huggingface dataset:
A Steady-State Biofilm Model for Simultaneous Reduction of Nitrate and Perchlorate, Part 2: Parameter Optimization and Results and Discussion (2011)

Part 1 of this work developed a steady-state, multispecies biofilm model for simultaneous reduction of nitrate and perchlorate in the H(2)-based membrane biofilm reactor (MBfR) and presented a novel method to solve it. In Part 2, the half-maximum-rate concentrations and inhibition coefficients of nitrate and perchlorate are optimized by fitting data from experiments with different combinations of influent nitrate and perchlorate concentrations. The model with optimized parameters is used to quantitatively and systematically explain how three important operating conditions (nitrate loading, perchlorate loading, and H(2) pressure) affect nitrate and perchlorate reduction and biomass distribution in these reducing biofilms. Perchlorate reduction and accumulation of perchlorate-reducing bacteria (PRB) in the biofilm are affected by four promotion or inhibition mechanisms: simultaneous use of nitrate and perchlorate by PRB and competition for H(2), the same resources in PRB, and space in a biofilm. For the hydrogen pressure evaluated experimentally, a low nitrate loading (<0.1 g N/m(2)-d) slightly promotes perchlorate removal, because of the beneficial effect from PRB using both acceptors. However, a nitrate loading of >0.6 g N/m(2)-d begins to inhibit perchlorate removal, as the competition effects become dominant.
Using Electric Water Heater Tanks as an Energy Storage Solution to Solve the Duck Curve Issue (2021)

The electricity production transition leads to the development of low-carbon content renewable energy resources, such as photovoltaic (PV) panels. Due to the later, utilities operators see a significant drop in mid-day net load, raising concerns that the conventional power system will be unable to accommodate the ramp rate and change needed to fully utilize solar energy. Also, this could result in overgeneration and curtailed renewable energy, increasing its cost and reducing its environmental benefit. This paper presents and quantifies a solution that has the potential to help solve this issue and help the development of more PV panels. It consists of using electric water heater tanks to store the excess energy produced by the PV panels by heating the water above the typical setpoint during mid-day hours. Simulations have been run through EnergyPlus (EP) using the average profile of hot water consumption in the US and modified scheduled of water heater to show the feasibility and impact of the methodology. Across California, it has been evaluated that up to 59 GWh of energy could be potentially stored per day during mi-day hours through this technique, reducing by 97% the current need to add expensive energy storage devices, such as batteries, to flatten the duck curve.
Tracking Network Events with Write Optimized Data Structures (2015)

Access to network traffic records is an integral part of recognizing and addressing network security breaches. Even with the increasing sophistication of network attacks, basic network events such as connections between two IP addresses play an important role in any network defense. Given the duration of current attacks, long-term data archival is critical but typically very little of the data is ever accessed. Previous work has provided tools and identified the need to trace connections. However, traditional databases raise performance concerns as they are optimized for querying rather than ingestion. The study of write-optimized data structures (WODS) is a new and growing field that provides a novel approach to traditional storage structures (e.g., B-trees). WODS trade minor degradations in query performance for significant gains in the ability to quickly insert more data elements, typically on the order of 10 to 100 times more inserts per second. These efficient, out-of-memory data structures can play a critical role in enabling robust, long-term tracking of network events. In this paper, we present TWIAD, the Write-optimized IP Address Database. TWIAD uses a write-optimized B-tree known as a B" tree to track all IP address connections in a network traffic stream. Our initial implementation focuses on utilizing lower cost hardware, demonstrating that basic long-term tracking can be done without advanced equipment. We tested TWIAD on a modest desktop system and showed a sustained ingestion rate of about 20,000 inserts per second.
Lost microbes of COVID-19: Bifidobacterium , Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity (2022)

NCT04031469 (PCR-) and 04359836 (PCR+).
The {110} reflection in X‐ray diffraction of MX ene films: Misinterpretation and measurement via non‐standard orientation (2017)

Abstract It has been claimed that disappearance of the {110} reflection in powder X‐ray diffraction of MX ene films and powders is indicative of shearing or general disorder of restacking of the flakes. Here we show this to be incorrect and provide experimental justification. The disappearance of this peak arises from a combination of sample texture and orientation. Furthermore, our methods provide a simple way to estimate a unit cell parameters when the relevant reflections are not present in most reports of MX ene films.
A Cross-Sectional Survey on Prevalence and Risk Factors for Persistent Postsurgical Pain 1 Year After Total Hip and Knee Replacement (2012)

Persistent postsurgical pain is common after THR and TKR and is associated with reduced health-related quality of life, although our survey may be biased by the low response rate and retrospective recall bias. Nonmodifiable risk factors may lead to risk stratification. Severity of acute postoperative pain may be a modifiable risk factor.
Oncolytic measles virus induces tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-mediated cytotoxicity by human myeloid and plasmacytoid dendritic cells (2016)

Attenuated measles virus (MV) is currently being evaluated in clinical trials as an oncolytic therapeutic agent. Originally used for its lytic activity against tumor cells, it is now admitted that the effectiveness of MV also lies in its ability to initiate antitumor immune responses through the activation of dendritic cells (DCs). In this study, we investigated the capacity of oncolytic MV to convert human blood myeloid CD1c<sup>+</sup> DCs and plasmacytoid DCs (pDCs) into cytotoxic effectors. We found that MV induces the expression of the cytotoxic protein TNF-related apoptosis-inducing ligand (TRAIL) on the surface of DCs. We demonstrate that the secretion of interferon-α (IFN-α) by DCs in response to MV is responsible for this TRAIL expression. Several types of PRRs (pattern recognition receptors) have been implicated in MV genome recognition, including RLRs (RIG-I-like receptors) and TLRs (Toll-like receptors). We showed that CD1c<sup>+</sup> DCs secrete modest amounts of IFN-α and express TRAIL in an RLR-dependent manner upon exposure to MV. In pDCs, MV is recognized by RLRs and also by TLR7, leading to the secretion of high amounts of IFN-α and TRAIL expression. Finally, we showed that MV-stimulated DCs induce TRAIL-mediated cell death of Jurkat cells, confirming their acquisition of cytotoxic functions. Our results demonstrate that MV can activate cytotoxic myeloid CD1c<sup>+</sup> DCs and pDCs, which may participate to the antitumor immune response.
Epitaxial Hybrid Silicon Technology (2011)

Abstract : We have investigated a wide range of conditions for MOCVD epitaxial layer overgrowth, and studies the impact on coalescence on the ELO patterns and orientations. We have found conditions that allow us to grow such that the coalesced regions are defect free. This is a first for MOCVD and it is the first for growth across a significantly wide field. The fundamental nucleation and growth of As and Sb based III-V semiconductors on SiO2 masked Si(100) and InP(100) surfaces were investigated via molecular beam epitaxy (MBE) to determine the best growth windows for nucleation and lateral overgrowth. Antimonides provide better lateral overgrowth than arsenides indicating transitions from layer-by-layer to step flow growth regimes in MBE may be critical for ELO.
Three‐dimensional structure and actions of immunosuppressants and their immunophilins (1995)

The use of the immunosuppressant drug cyclosporin A (CsA) as a biochemical tool to study the signal transduction pathway in T cells has led to the discovery of a first family of immunosuppressant-binding proteins or "immunophilins," the cyclophilins (Cyp). Another, chemically unrelated immunosuppressant molecule, FK506, was then found to be related to a second class of immunophilins, the FK506-binding proteins (FKBPs). This paper reviews the existing structural information on these immunophilins in the context of present knowledge of the biochemical mechanisms for immunosuppression. The formation of Cyp-CsA and FKBP-FK506 complexes, and the subsequent specific interaction of these complexes with the serine/threonine phosphatase calcineurin (CN), are key steps in the cascade of events that result in the desired immunosuppression. Knowledge of the conformation of the Cyp-CsA-CN and FKBP-FK506-CN ternary complexes is of significant biomedical interest, because mimics of the composite contact surfaces of, for example, Cyp-CsA or FKBP-FK506, could provide immunosuppressant drugs with improved pharmacological profiles.
Supplementary File 8 from Genome-Wide Functional Synergy between Amplified and Mutated Genes in Human Breast Cancer (2023)

Supplementary File 8 from Genome-Wide Functional Synergy between Amplified and Mutated Genes in Human Breast Cancer
A Convenient Synthesis of 1-(S)-[1’-(S)-(t-Butyloxycarbonylamino)-2’-phenylethyl]oxirane, a Versatile Intermediate for the Preparation of Hydroxyethylamine Based HIV Protease Inhibitors (1995)

A concise, stereocontrolled synthesis of N-protected (1S,1’S)-α-aminoepoxides, important intermediates for the preparation of hydroxyethylamine dipeptide isosteres, beginning with α-aminoesters is described.
Plasmid-Encoded Iron Uptake Systems (2014)

Plasmids confer genetic information that benefits the bacterial cells containing them. In pathogenic bacteria, plasmids often harbor virulence determinants that enhance the pathogenicity of the bacterium. The ability to acquire iron in environments where it is limited, for instance the eukaryotic host, is a critical factor for bacterial growth. To acquire iron, bacteria have evolved specific iron uptake mechanisms. These systems are often chromosomally encoded, while those that are plasmid-encoded are rare. Two main plasmid types, ColV and pJM1, have been shown to harbor determinants that increase virulence by providing the cell with essential iron for growth. It is clear that these two plasmid groups evolved independently from each other since they do not share similarities either in the plasmid backbones or in the iron uptake systems they harbor. The siderophores aerobactin and salmochelin that are found on ColV plasmids fall in the hydroxamate and catechol group, respectively, whereas both functional groups are present in the anguibactin siderophore, the only iron uptake system found on pJM1-type plasmids. Besides siderophore-mediated iron uptake, ColV plasmids carry additional genes involved in iron metabolism. These systems include ABC transporters, hemolysins, and a hemoglobin protease. ColV- and pJM1-like plasmids have been shown to confer virulence to their bacterial host, and this trait can be completely ascribed to their encoded iron uptake systems.
Automating and Validating Semantic Annotations (2006)

The present field study evaluated the safety and 3-month preventive efficacy of a novel spot-on endectocide containing emodepside 2.04% w/v, praziquantel 8.14% w/v and tigolaner 9.79% w/v (Felpreva®, Vetoquinol) when administered at the intended commercial dose of 0.15 ml/kg body weight to privately owned cats infested by fleas (<i>Ctenocephalides felis</i>) and/or ticks (<i>Ixodes ricinus</i>, <i>Ixodes hexagonus</i>, <i>Rhipicephalus</i> spp.). The efficacy of Felpreva® to reduce the clinical signs associated with flea allergy dermatitis was also evaluated. A total of 326 cats, i.e. 120 and 206 infested by ticks and fleas respectively, from 16 different sites located in Hungary and Portugal were included on Day 0 and allocated in two Groups at a ratio of 2:1 (T1:T2). Cats of T1 were treated with Felpreva®, while cats of T2 were dosed with a commercial Control Product (Bravecto®, MSD Animal Health) licensed for the same indications. Of the 120 tick-infested cats, 79 and 41 were treated with Felpreva® and Bravecto® respectively, while of the 206 flea-infested cats, 139 were treated with Felpreva® and 67 with Bravecto®. Cats were physically examined on Days 7, 28, 56, 75 and 90; when present, fleas and ticks were counted and collected. Efficacy evaluation was based on the mean percent reduction of live parasite counts for each of five visits <i>versus</i> the pre-treatment count. Percent reductions of live flea and tick counts over all post-baseline periods were 99.74% (T1) <i>versus</i> 98.56% (T2) and 97.50% (T1) <i>versus</i> 98.65% (T2), respectively. Non-inferiority for the Felpreva® compared with the Bravecto® treated group was statistically demonstrated for both fleas and ticks. Three adverse events were observed and considered unlikely related to the treatment. These results show that the new topical combination product Felpreva® is safe and highly efficacious in treating flea and tick infections in cats for at least three months (90 days) with a single administration. In 16 cats that were identified with flea allergy dermatitis, the clinical signs of flea allergy dermatitis improved following treatment in both groups.
Comparison of oxygen supplementation in very preterm infants: Variations of oxygen saturation features and their application to hypoxemic episode based risk stratification (2023)

Analysis of oxygen saturation signal routinely collected in the NICU, may have extensive applications in inferring subtle changes to cardiorespiratory dynamics under various conditions as well as in informing clinical decisions about infant care.
Leveraging sentence weights in a concept-based optimization framework for extractive meeting summarization (2009)

We adopt an unsupervised concept-based global optimization framework for extractive meeting summarization, where a subset of sentences is selected to cover as many important concepts as possible. We propose to leverage sentence importance weights in this model. Three ways are introduced to combine the sentence weights within the concept-based optimization framework: selecting sentences for concept extraction, pruning unlikely candidate summary sentences, and using joint optimization of sentence and concept weights. Our experimental results on the ICSI meeting corpus show that our proposed methods can significantly improve the performance for both human transcripts and ASR output compared to the concept-based baseline approach, and this unsupervised approach achieves results comparable with those from supervised learning approaches presented in previous work. Index Terms: global optimization, sentence weights, meeting summarization
TRIAL FOR MAKING THREE DIMENSIONAL PZT CAPACITOR FOR HIGH DENSITY FERROELECTRIC RANDOM ACCESS MEMORY (2006)

ABSTRACT Three dimensional capacitors of Pb(Zr,Ti)O3 [PZT] together with the Ru electrodes were tried to deposit by metal organic chemical vapor deposition for realizing high density ferroelectric random access memory (FeRAM). Good conformability was obtained for both of CVD-Ru and PZT layers on the trenched substrates by optimizing the deposition conditions. In addition, PZT films deposited on Ru bottom electrode showed the good compositional conformability. Finally we demonstrated the Ru/PZT/Ru three dimensional capacitor. These data accelerate the development of three dimensional PZT capacitors.
Covariance Eigenvector Sparsity for Compression and Denoising (2012)

Sparsity in the eigenvectors of signal covariance matrices is exploited in this paper for compression and denoising. Dimensionality reduction (DR) and quantization modules present in many practical compression schemes such as transform codecs, are designed to capitalize on this form of sparsity and achieve improved reconstruction performance compared to existing sparsity-agnostic codecs. Using training data that may be noisy a novel sparsity-aware linear DR scheme is developed to fully exploit sparsity in the covariance eigenvectors and form noise-resilient estimates of the principal covariance eigenbasis. Sparsity is effected via norm-one regularization, and the associated minimization problems are solved using computationally efficient coordinate descent iterations. The resulting eigenspace estimator is shown capable of identifying a subset of the unknown support of the eigenspace basis vectors even when the observation noise covariance matrix is unknown, as long as the noise power is sufficiently low. It is proved that the sparsity-aware estimator is asymptotically normal, and the probability to correctly identify the signal subspace basis support approaches one, as the number of training data grows large. Simulations using synthetic data and images, corroborate that the proposed algorithms achieve improved reconstruction quality relative to alternatives.
ChemInform Abstract: The Synthesis of Conformationally/Rotationally Restricted Analogues ( III) and (VIII) of the Neurotransmitter Serotonin. (1994)

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 Nonredundant Human Protein Chip for Antibody Screening and Serum Profiling (2003)

There is burgeoning interest in protein microarrays, but a source of thousands of nonredundant, purified proteins was not previously available. Here we show a glass chip containing 2413 nonredundant purified human fusion proteins on a polymer surface, where densities up to 1600 proteins/cm(2) on a microscope slide can be realized. In addition, the polymer coating of the glass slide enables screening of protein interactions under nondenaturing conditions. Such screenings require only 200-microl sample volumes, illustrating their potential for high-throughput applications. Here we demonstrate two applications: the characterization of antibody binding, specificity, and cross-reactivity; and profiling the antibody repertoire in body fluids, such as serum from patients with autoimmune diseases. For the first application, we have incubated these protein chips with anti-RGSHis(6), anti-GAPDH, and anti-HSP90beta antibodies. In an initial proof of principle study for the second application, we have screened serum from alopecia and arthritis patients. With analysis of large sample numbers, identification of disease-associated proteins to generate novel diagnostic markers may be possible.
ChemInform Abstract: Synthesis and Properties of New π‐Donor Sulfur Heterocycles. (1991)

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 widely tunable narrow linewidth RF source utilizing an integrated heterogeneous photonic module (2014)

Generating RF signals over the entire spectrum, from hundreds of MHz to the hundreds of GHz, typically requires the use of multiple oscillators which operate only for specific bands within that spectrum. By mixing two lasers together, it is possible to generate RF signals over that entire band. Through the use of a narrow linewidth low frequency oscillator, optical modulator, and injection locking, much higher frequency outputs can be produced that still retain the narrow linewidth of the low frequency oscillator. Here we present the results of our efforts to develop an integrated version of this system based on a silicon-photonic integrated circuit coupled to III-V semiconductor gain chips. Towards that effort, we have successfully demonstrated an integrated module and shown tunable RF generation with a 1 Hz linewidth.
Variation in cell surface hydrophobicity among Cryptococcus neoformans strains influences interactions with amoeba (2019)

ABSTRACT Cryptococcus neoformans and Cryptococcus gattii are pathogenic fungi that cause significant morbidity and mortality. Cell surface hydrophobicity (CSH) is a biophysical parameter that influences the adhesion of fungal cells or spores to biotic and abiotic surfaces. C. neoformans is encased by polysaccharide capsule that is highly hydrophilic and is a critical determinant of virulence. In this study, we report large differences in the CSH of some C. neoformans and C. gattii strains. The capsular polysaccharides of C. neoformans strains differ in repeating motifs, and therefore vary in the number of hydroxyl groups, which along with higher-order structure of the capsule, may contribute to the variation in hydrophobicity that we observed. For C. neoformans , CSH correlated with phagocytosis by natural soil predator Acanthamoeba castellani . Furthermore, capsular binding of the protective antibody (18B7), but not the non-protective (13F1) antibody altered the CSH of C. neoformans strains. Variability in CSH could be an important characteristic when comparing the biological properties of cryptococcal strains. IMPORTANCE The interaction of a microbial cell with its environment is influenced by the biophysical properties of a cell. The affinity of the cell surface for water, defined by the Cell Surface Hydrophobicity (CSH), is a biophysical parameter that varied amongst different strains of Cryptococcus neoformans . The CSH influenced the phagocytosis of the yeast by its natural predator in the soil, Amoeba. Studying variation in biophysical properties like CSH gives us insight into the dynamic host-predator interaction, and host-pathogen interaction in a damage-response framework.
Vaccine adjuvants – understanding molecular mechanisms to improve vaccines (2014)

Infectious pathogens are responsible for high utilisation of healthcare resources globally. Attributable morbidity and mortality remains exceptionally high. Vaccines offer the potential to prime a pathogen-specific immune response and subsequently reduce disease burden. Routine vaccination has fundamentally altered the natural history of many frequently observed and serious infections. Vaccination is also recommended for persons at increased risk of severe vaccine-preventable disease. Many current nonadjuvanted vaccines are poorly effective in the elderly and immunocompromised populations, resulting in nonprotective postvaccine antibody titres, which serve as surrogate markers for protection. The vaccine-induced immune response is influenced by: (i.) vaccine factors i.e., type and composition of the antigen(s), (ii.) host factors i.e., genetic differences in immune-signalling or senescence, and (iii.) external factors such as immunosuppressive drugs or diseases. Adjuvanted vaccines offer the potential to compensate for a lack of stimulation and improve pathogen-specific protection. In this review we use influenza vaccine as a model in a discussion of the different mechanisms of action of the available adjuvants. In addition, we will appraise new approaches using "vaccine-omics" to discover novel types of adjuvants.