gebhart/patrepeval huggingface dataset:
Measurements of resonance frequencies and damping of large encapsulated bubbles in a closed, water-filled tank (2012)

The ultimate goal of this work is to accurately predict the resonance frequencies of large (on the order of 10 cm radius) tethered encapsulated bubbles used in an underwater noise abatement system, and also to investigate ways to enhance the system’s efficacy over the use of air-filled bubbles alone. Toward that end, a closed water-filled tank was developed for the purpose of measuring the resonance frequency and damping of single large tethered encapsulated bubbles. The tank was designed to be operated in the long wavelength limit for frequencies below the lowest tank resonance, which was chosen to be 500 Hz, using the method described be Leighton, et al. [J. Acoust. Soc. Am. 112, 1366--1376 (2002)]. Individual bubble resonance frequencies and Q-factors were measured for encapsulated bubbles of various sizes. The effects of the encapsulating material and wall thickness were investigated, along with the effects of alternative fill gases and internal heat transfer materials. Experimental results are compared with an existing predictive model [J. Acoust. Soc. Am. 97, 1510--1521 (1995)] of bubble resonance and damping. [Work supported by Shell Global Solutions.]
Design, Synthesis, and Structure–Activity Relationship Studies of a Potent PACE4 Inhibitor (2013)

PACE4 plays an important role in the progression of prostate cancer and is an attractive target for the development of novel inhibitor-based tumor therapies. We previously reported the design and synthesis of a novel, potent, and relatively selective PACE4 inhibitor known as a Multi-Leu (ML) peptide. In the present work, we examined the ML peptide through detailed structure-activity relationship studies. A variety of ML-peptide analogues modified at the P8-P5 positions with leucine isomers (Nle, DLeu, and DNle) or substituted at the P1 position with arginine mimetics were tested for their inhibitory activity, specificity, stability, and antiproliferative effect. By incorporating d isomers at the P8 position or a decarboxylated arginine mimetic, we obtained analogues with an improved stability profile and excellent antiproliferative properties. The DLeu or DNle residue also has improved specificity toward PACE4, whereas specificity was reduced for a peptide modified with the arginine mimetic, such as 4-amidinobenzylamide.
Long term stabilization of the beam combination laser with a phase controlled stimulated Brillouin scattering phase conjugation mirrors for the laser fusion driver (2006)

Laser fusion requires very high energy/power output with high repetition rate over 10 Hz, which is very difficult with the current laser technologies. However, the recent research work on the phase controlling of the stimulated Brillouin scattering wave enables the realization of this kind of laser fusion driver. The recent progress of controlling the phase has been successfully demonstrated by the self-generated density modulation method proposed by one of the authors (Kong). Nevertheless, it showed a long-term fluctuation of the phase because of the long-term fluctuation of the density of the SBS medium due to the thermal fluctuation. This long-term thermal fluctuation is inevitable a fact in nature. The authors used a specially designed stabilizing system for the phase controlling system, which has the PZT control of the mirror for phase controlling SBS-PCM (the so-called feedback mirror). This system stabilizes the phase controlling system very well for more than 1 h. This technique will help the laser fusion driver to be realized sooner than expected. In addition, we propose a similar scheme to be applied to the ultra-fast pulse laser system, which must operate at high repetition rate for the laser fusion energy power plant.
Chemical Similarity Searches Using Latent Semantic Structural Indexing (LaSSI) and Comparison to TOPOSIM (2001)

Similarity searches based on chemical descriptors have proven extremely useful in aiding large-scale drug screening. Here we present results of similarity searching using Latent Semantic Structure Indexing (LaSSI). LaSSI uses a singular value decomposition on chemical descriptors to project molecules into a k-dimensional descriptor space, where k is the number of retained singular values. The effect of the projection is that certain descriptors are emphasized over others and some descriptors may count as partially equivalent to others. We compare LaSSI searches to searches done with TOPOSIM, our standard in-house method, which uses the Dice similarity definition. Standard descriptor-based methods such as TOPOSIM count all descriptors equally and treat all descriptors as independent. For this work we use atom pairs and topological torsions as examples of chemical descriptors. Using objective criteria to determine how effective one similarity method is versus another in selecting active compounds from a large database, we find for a series of 16 drug-like probes that LaSSI is as good as or better than TOPOSIM in selecting active compounds from the MDDR database, if the user is allowed to treat k as an adjustable parameter. Typically, LaSSI selects very different sets of actives than does TOPOSIM, so it can find classes of actives that TOPOSIM would miss.
Prevalence of capsular serotypes among Staphylococcus aureus isolates from cows with mastitis in the United States (1997)

Development of an appropriate Staphylococcus aureus vaccine for bovine mastitis has eluded researchers for decades. The ability of S. aureus to form a protective exopolysaccharide capsule has posed a major obstacle because of the multiple serotypes and the poor immune response elicited by exopolysaccharides. This study characterized S. aureus serotypes isolated from cases of bovine mastitis obtained from veterinary diagnostic laboratories that service 44% of the dairy cattle in the United States. Major milk producing areas of the northeast, north central, Pacific coast and southwest were proportionately represented. Sub-samples of mastitic milk that contained S. aureus were frozen and sent to our laboratory for strain serotyping. The only other regional serotyping of S. aureus from bovine mastitis to date was done in France. The primary serotypes found were types 5 (51%) and 8 (18%) and 31% were non-typeable. In the current study, serotype 5 accounted for 18% of the isolates and serotype 8 for 23%. More importantly 59% of the isolates were not typeable with either type 5 or 8 antisera. These data indicate that S. aureus vaccines employing serotypes 5 and 8 would only be marginally effective in the United States. These data also suggest that development of a S. aureus vaccine for bovine mastitis should take into account regional variation in S. aureus serotypes.
Traumatic Stress and Human DNA Methylation: A Critical Review (2015)

Animal studies have identified persistent and functional effects of traumatic stress on the epigenome. This review discusses the clinical evidence for trauma-induced changes in DNA methylation across the life span in humans. Studies are reviewed based on reports of trauma exposure during the prenatal period (13 studies), early life (20 studies), and adulthood (ten studies). Even though it is apparent that traumatic stress influences the human epigenome, there are significant drawbacks in the existing human literature. These include a lack of longitudinal studies, methodological heterogeneity, selection of tissue type, and the influence of developmental stage and trauma type on methylation outcomes. These issues are discussed in order to present a way in which future studies can gain more insight into the functional relevance of trauma-related DNA methylation changes. Epigenetic studies investigating the detrimental effects of traumatic stress have great potential for an improved detection and treatment of trauma-related psychiatric disorders.
Optical Modulator With a Near-Linear Field Response (2016)

The principle and characteristics of a linear optical modulator (LOM), which has a high field-response linearity, are discussed. A conventional Mach-Zehnder modulator (MZM) shows a nonlinear (sinusoidal) field response. This nonlinearity causes some problems in advanced digital coherent optical transmission systems that employ advanced multilevel modulation or pulse-shaping technologies. To solve this, we devised the LOM, which has a two-stage asymmetric lattice configuration with two MZMs driven with a pair of complementary voltage signals. The key idea of the LOM is to utilize the complementary output from the first MZM for generating the compensation signal. This enables us to improve the linearity without losing much optical power. Theoretical characteristics of the LOM are discussed in detail for the first time. To verify the LOM concept, we fabricated a linear in-phase-and-quadrature modulator (LIQM) with a hybrid configuration of silica planar lightwave circuits and a LiNbO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> chip with a high-speed phase-modulator array. Using the LIQM, we experimentally proved that the LOM provides a better loss-linearity trade-off than the conventional MZM does. The LIQM was also tested for 12.5-GBd 16-QAM modulation, and it generated a clear constellation where the nonlinearity of the MZM was compensated well.
A new on-chip ESD protection circuit with dual parasitic SCR structures for CMOS VLSI (2002)

A novel CMOS on-chip ESD (electrostatic discharge) protection circuit which consists of dual parasitic SCR structure is proposed. Experimental results show that it can successfully provide for negative and positive ESD protection with failure thresholds greater than +or-1 kV and +or-10 kV in machine-mode (MM) and human-body-mode (HBM) testing, respectively. Moreover, low triggering voltages in both SCRs can be readily achieved without involving device or junction breakdown.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Analysis of binding centers in nicotinic receptors with the aid of synthetic peptides (2016)

We studies the receptor-binding specificity of the synthetic peptide HAP (High Affinity Peptide) and its analogues, which are regarded as a model of the orthosteric site nicotinic acetylcholine receptors (nAChR). Using radioligand analysis, electrophysiology tests, and calcium imaging, we assessed the ability of HAP to interact with nAChR antagonists: long α-neurotoxins and α-conotoxins. A high affinity of HAP for α-bungarotoxin and the absence of its interaction with α-cobratoxin and α-conotoxins was found. The synthesized analogues of HAP in general retained the properties of the original peptide. Thus, HAP cannot be a model of a ligand-binding site.
Constraint-based design of optical transmission systems (2003)

The last decade has witnessed wide-scale deployment of optical networks to support the growing data traffic. This success can be traced back to advances in optical transmission systems such as dense wavelength-division multiplexing, Raman amplification, etc., which allow a single fiber to carry several wavelengths very far, while sharing expensive equipment. However, these cutting-edge technologies require careful placement of amplifiers and other network elements to ensure error-free propagation of the signal and to minimize costs. In practice, it is common to use a set of constraints to ensure valid configurations for deployment. It is nontrivial to identify the optimal configuration under all but the simplest constraints. In this paper, we consider a set of constraints with varying flexibilities and present algorithms for efficiently computing the cost-optimal configuration under them. We also present experimental and theoretical results to evaluate the various constraints and algorithms.
P<sup>1</sup>,P<sup>2</sup>-Diimidazolyl derivatives of pyrophosphate and bis-phosphonates – synthesis, properties, and use in preparation of dinucleoside tetraphosphates and analogs (2010)

P(1),P(2)-Diimidazolyl derivatives of pyrophosphate and halomethylene-bis-phosphonates have been synthesized and characterized, and the mechanism of their formation was studied. These reagents enable synthesis of dinucleoside tetraphosphates and tetraphosphonates conveniently and in high yields.
Tracking sustained chaos: A segmentation method (2000)

We introduce a segmentation control method to sustain chaotic transients in dynamical systems. The sustained transient can be tracked as a system parameter is substantially varied, allowing sustained chaotic transients far away from crisis parameter values. The method is applied to a chaotic CO2 laser as well as to a hyperchaotic continuum mechanics model.
Metathesis and Decomposition of Fischer Carbenes of Cyclometalated <i>Z</i>-Selective Ruthenium Metathesis Catalysts (2018)

The addition of vinyl ethers to Z-selective, cyclometalated ruthenium metathesis catalysts generates Fischer carbene complexes. Although Fischer carbenes are usually thought to be metathesis inactive, we show that Fischer carbenes are metathesis active under certain circumstances. These species were found to decompose facilely to Ru hydride complexes, as identified by both experiment and computation. Since vinyl ethers are often used to quench metathesis reactions implementing Ru-based metathesis catalysts, their decomposition to hydrides can have a deleterious effect on the desired stereochemistry of the olefin product.
Progress in Development of an Automated Mosquito Salivary Gland Extractor: A Step Forward to Malaria Vaccine Mass Production (2021)

Malaria causes more than 200 million clinical illnesses and 45 million deaths every year, making mass production of an effective vaccine increasingly urgent. A Plasmodium falciparum sporozoites (PfSPZ) based vaccine has been proved to be a promising choice to defend against the malaria pandemic. However, large scale industrial production of PfSPZ vaccine is currently sub-optimal as the process for sporozoite extraction from salivary glands of infected mosquitoes is performed by manual microdissection, a relatively inefficient process requiring many hours of training. This paper reports continued progress in our development of a robotic system for automating the extraction of salivary glands. Compared to our previous versions, the structure of the new system is optimized to be more compact and allows different steps in workflow to be performed in parallel. We also report continued progress in developing key subsystem components. Finally, experiments show encouraging results with success rates of 90% in robotic mosquito manipulation, 95.6% in salivary gland extraction and 92.7% in debris disposal.
Detection and recovery techniques for database corruption (2003)

Increasingly, for extensibility and performance, special purpose application code is being integrated with database system code. Such application code has direct access to database system buffers, and as a result, the danger of data being corrupted due to inadvertent application writes is increased. Previously proposed hardware techniques to protect from corruption require system calls, and their performance depends on details of the hardware architecture. We investigate an alternative approach which uses codewords associated with regions of data to detect corruption and to prevent corrupted data from being used by subsequent transactions. We develop several such techniques which vary in the level of protection, space overhead, performance, and impact on concurrency. These techniques are implemented in the Dali main-memory storage manager, and the performance impact of each on normal processing is evaluated. Novel techniques are developed to recover when a transaction has read corrupted data caused by a bad write and gone on to write other data in the database. These techniques use limited and relatively low-cost logging of transaction reads to trace the corruption and may also prove useful when resolving problems caused by incorrect data entry and other logical errors.
Large-Scale Synthesis of Uniform and Extremely Small-Sized Iron Oxide Nanoparticles for High-Resolution <i>T</i><sub>1</sub> Magnetic Resonance Imaging Contrast Agents (2011)

Uniform and extremely small-sized iron oxide nanoparticles (ESIONs) of < 4 nm were synthesized via the thermal decomposition of iron-oleate complex in the presence of oleyl alcohol. Oleyl alcohol lowered the reaction temperature by reducing iron-oleate complex, resulting in the production of small-sized nanoparticles. XRD pattern of 3 nm-sized nanoparticles revealed maghemite crystal structure. These nanoparticles exhibited very low magnetization derived from the spin-canting effect. The hydrophobic nanoparticles can be easily transformed to water-dispersible and biocompatible nanoparticles by capping with the poly(ethylene glycol)-derivatized phosphine oxide (PO-PEG) ligands. Toxic response was not observed with Fe concentration up to 100 μg/mL in MTT cell proliferation assay of POPEG-capped 3 nm-sized iron oxide nanoparticles. The 3 nm-sized nanoparticles exhibited a high r(1) relaxivity of 4.78 mM(-1) s(-1) and low r(2)/r(1) ratio of 6.12, demonstrating that ESIONs can be efficient T(1) contrast agents. The high r(1) relaxivities of ESIONs can be attributed to the large number of surface Fe(3+) ions with 5 unpaired valence electrons. In the in vivo T(1)-weighted magnetic resonance imaging (MRI), ESIONs showed longer circulation time than the clinically used gadolinium complex-based contrast agent, enabling high-resolution imaging. High-resolution blood pool MR imaging using ESIONs enabled clear observation of various blood vessels with sizes down to 0.2 mm. These results demonstrate the potential of ESIONs as T(1) MRI contrast agents in clinical settings.
Hemostatic effect of a monoclonal antibody mAb 2021 blocking the interaction between FXa and TFPI in a rabbit hemophilia model (2012)

Hemophilia is treated by IV replacement therapy with Factor VIII (FVIII) or Factor IX (FIX), either on demand to resolve bleeding, or as prophylaxis. Improved treatment may be provided by drugs designed for subcutaneous and less frequent administration with a reduced risk of inhibitor formation. Tissue factor pathway inhibitor (TFPI) down-regulates the initiation of coagulation by inhibition of Factor VIIa (FVIIa)/tissue factor/Factor Xa (FVIIa/TF/FXa). Blockage of TFPI inhibition may facilitate thrombin generation in a hemophilic setting. A high-affinity (K(D) = 25pM) mAb, mAb 2021, against TFPI was investigated. Binding of mAb 2021 to TFPI effectively prevented inhibition of FVIIa/TF/FXa and improved clot formation in hemophilia blood and plasma. The binding epitope on the Kunitz-type protease inhibitor domain 2 of TFPI was mapped by crystallography, and showed an extensive overlap with the FXa contact region highlighting a structural basis for its mechanism of action. In a rabbit hemophilia model, an intravenous or subcutaneous dose significantly reduced cuticle bleeding. mAb 2021 showed an effect comparable with that of rFVIIa. Cuticle bleeding in the model was reduced for at least 7 days by a single intravenous dose of mAb 2021. This study suggests that neutralization of TFPI by mAb 2021 may constitute a novel treatment option in hemophilia.
Monolithic integrated high-T.sub.c superconductor-semiconductor structure (2000)

A method for the fabrication of active semiconductor and high-temperature superconducting device of the same substrate to form a monolithically integrated semiconductor-superconductor (MISS) structure is disclosed. A common insulating substrate, preferably sapphire or yttria-stabilized zirconia, is used for deposition of semiconductor and high-temperature superconductor substructures. Both substructures are capable of operation at a common temperature of at least 77 K. The separate semiconductor and superconductive regions may be electrically interconnected by normal metals, refractory metal silicides, or superconductors. Circuits and devices formed in the resulting MISS structures display operating characteristics which are equivalent to those of circuits and devices prepared on separate substrates.
An N-Heterocyclic Amine Chelate Capable of Antioxidant Capacity and Amyloid Disaggregation (2012)

Alzheimer's disease is a neurodegenerative disorder characterized by the development of intracellular neurofibrillary tangles, deposition of extracellular amyloid beta (Aβ) plaques, along with a disruption of transition metal ion homeostasis in conjunction with oxidative stress. Spectroscopic, transmission electron microscopy, and scanning electron microscopy imaging studies show that 1 (pyclen) is capable of both preventing and disrupting Cu(2+) induced AB(1-40) aggregation. The pyridine backbone of 1 engenders antioxidant capacity, as shown by cellular DCFH-DA (dichlorodihydrofluorescein diacetate) assay in comparison to other N-heterocyclic amines lacking this aromatic feature. Finally, 1 prevents cell death induced by oxidative stress as shown by the Calcein AM assay. The results are supported using density functional theory studies which show that the pyridine backbone is responsible for the antioxidant capacity observed.
<i>IDH1</i>and<i>IDH2</i>Mutations in Gliomas (2009)

Mutations of NADP(+)-dependent isocitrate dehydrogenases encoded by IDH1 and IDH2 occur in a majority of several types of malignant gliomas.
IT-09 * PHASE I STUDY OF SAFETY, TOLERABILITY AND IMMUNOLOGIC EFFECTS OF A SURVIVIN PEPTIDE MIMIC VACCINE (SurVaxM) IN PATIENTS WITH RECURRENT MALIGNANT GLIOMA (2014)

BACKGROUND: Survivin is an inhibitor of apoptosis protein (IAP) that is highly expressed in malignant gliomas and other cancers. Induction of cytotoxic immunity against survivin is an attractive antitumor strategy. Preclinical studies demonstrated the ability of a KLH-conjugated survivin peptide mimic (SVN53-67/M57-KLH; SurVaxM) to induce an immune response capable of inhibiting the growth of gliomas in mice, and killing human glioma cells ex vivo. The vaccine is predicted to be immunogenic in humans with HLA-A*02, HLA-A*03, HLA-A*24 and other haplotypes and pre-clinical studies demonstrate potent and specific cytokine-supported antitumor CTL responses. METHODS: Nine patients with survivin-positive, recurrent malignant gliomas and either HLA-A*02 or HLA-A*03 haplotypes received a series of 4 subcutaneous injections of SurVaxM at 2 week intervals. MRIs were performed at baseline, week 8, and at subsequent intervals. RESULTS: SurVaxM was well tolerated with no SAE, and mostly grade one AE. 6 of 9 patients experienced grade 1 localized erythema at the injection site, likely related to the vaccine. 3 patients reported grades 1 or 2 fatigue, 2/9 experienced myalgia, possibly related to the study drug. Grade 1 lymphopenia was seen in 3/9 patients and grade 1 or 2 leukopenia was recorded in 3 patients. The only grade 3 AE, a seizure, was not related to the vaccine. The majority of patients developed specific cellular and humoral immune responses to survivin and 3 of 8 patients (all with GBM), who are evaluable for clinical response, have stable disease after more than 12 months of follow-up. All others have had progressive disease. Survival data will be described. CONCLUSION: This study demonstrated the safety and tolerability of SurVaxM in patients with recurrent or progressive malignant glioma following failure of standard therapy. SurVaxM proved to be immunogenic in most patients. A phase II clinical trial of SurVaxM is planned.