gebhart/patrepeval huggingface dataset:
Beam Mass Spectrometer (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
P1‐021: Neuropathological evaluation of the nonhuman primate microcebus murinus immunized with K6Aβ1–30, an Aβ derivative peptide (2008)

Amyloid-β (Aβ) accumulation in senile plaques is a hallmark of Alzheimer's disease (AD). AD immunotherapy is a leading approach for amyloid clearance, despite the early termination of the Elan clinical trial because of a few cases of meningoencephalitis. Due to their phylogenetic proximity to humans, and their propensity to develop amyloid plaques, we evaluated the effects of K6Aβ1–30 immunization in old mouse lemurs. Six mouse lemurs, ranging from 6 to 9 years old, were immunized with K6Aβ1–30 peptide, and six others received alum adjuvant alone. The IgM and IgG titers were evaluated. Cognitive assessment was performed during the immunization protocol with a three panel runway task which evaluates working memory. At the end of the protocol, the animals were euthanized, and quantitative neuropathological evaluation was done of amyloid plaques, neurofibrillary tangles, gliosis, and microhemorrhages. Old immunized animals showed a relatively low titer of IgG against Aβ40 and Aβ42, which was several fold higher than in control animals. The groups had similar levels of IgM antibodies that recognized Aβ40/42 which indicates the presence of autoantibodies. The cognitive test did not detect significant difference between immunized and control groups. However, 63% of the immunized primates completed the test whereas only 33% of the controls. No toxicity of the vaccine was observed. Amyloid plaques were detected in one control and one immunized animal. Interestingly, six-fold more plaques were observed in the control primate. Furthermore, in that animal, amyloid deposits were characterized by a strong immunoreactivity with multicentric plaques whereas in the immunized primate, the plaques were diffuse. No differences were observed in abnormal tau protein deposits or astrocytosis in control and treated animals. No microhemorrhages were detected. These preliminary findings indicate that immunotherapy with K6Aβ1–30 is safe for old primates and it may reduce their amyloid burden without increasing microhemorrhages. For further clarification, we have repeated this study in 20 old mouse lemurs. Behavioral, biochemical and histological analyses are underway.
Novel Peptidomimetic Cysteine Protease Inhibitors as Potential Antimalarial Agents (2006)

The synthesis of a new class of peptidomimetics 1a-j, based on a 1,4-benzodiazepine scaffold and on a C-terminal aspartyl aldehyde building block, is described. Compounds 1a-j provided significant inhibitory activity against falcipains 2A and 2B (FP-2A and FP-2B), two cysteine proteases from Plasmodium falciparum.
Investigation on Combustion, Performance and Emissions of Automotive Engine Fueled with Ethanol Blended Gasoline (2016)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;To tackle the problems associated with the volatility of crude oil prices and ever stringent emission norms, oil industries and automobiles manufacturers are experimenting with various alternative fuels to increase its percentage share in the energy mix and to reduce the vehicular emissions. Alcohols are preferred choice of alternative fuels for the gasoline engines as it does not require any major engine modification and new infrastructure for the fuel distribution network. Ethanol as sole fuel or blending component for gasoline for use in spark ignition engines has been investigated many decades. Currently, 10% ethanol is blended in motor gasoline in India and the ethanol concentration may be further increased in future. In order to study the effect of higher blends of ethanol (upto 20%) on engine in-cylinder combustion, performance and emission, investigations were carried out on a latest generation passenger car engine in a climatic controlled test cell. Engine combustion, performance and emissions were analyzed at full throttle condition at regular speed intervals. Higher octane number and oxygen in the ethanol blends improved the combustion and thereby increased the power and torque marginally. Ethanol blends reduced the specific energy consumption of the engine for the all speeds at full throttle opening. E20 blends decreased CO emission by 65%; HC emission by 38% with the penalty of doubling the NOx emission at rated power condition. Increase in combustion duration was observed with ethanol blends compared to gasoline. Indicated mean effective pressure and maximum peak pressure of the engine were increased with engine speed for the all test fuels and the ethanol blends increased these values marginally. Ethanol as blending component for gasoline improved the combustion and thereby marginally enhanced the engine performance and significantly reduced the exhaust emissions.&lt;/div&gt;&lt;/div&gt;
Sonoelectrochemistry in Highly Resistive Media:Mass Transport Effects (1998)

Sonovoltammetry methodology is studied for the enhancement of electrochemical processes in highly resistive media. As model systems the reduction of [FeCp*2]PF6 (with Cp* = η5–C5Me5) and the oxidation of FeCp*2 in acetonitrile are examined at a 25 μm diameter Pt microdisk electrode. Both in the presence and in the absence of supporting electrolyte ultrasound induces a strong increase in the observed limiting current in agreement with an increase in mass transport or, associated with this, a change in the average diffusion layer thickness. However, iR drop effects cause distortion of voltammetric waves, potential fluctuation, and ultrasonically induced current decrease under conditions of extremely low ionic strength.
Comparison of the Viper Pulsed Fusion Rocket to Prior Fu-sion Space Propulsion Design Studies (2012)

– Fusion power systems have the potential to provide unparalleled power budgets to a spacecraft’s propulsion system, life support system, and electronics. Fusion power can be used directly to super heat propellant for thrust or, the energetic fusion products can be used as propellant. Some of these systems are operated strictly under steady-state conditions for long-duration continuous power out-put. Others are designed for shortburst pulsed operation and hence are known as nuclear pulsed propulsion. A series of these fusion bursts can be used to propel the spacecraft, charge power systems, or both. There are also fusion propulsion concepts that utilize a combination of these mechanisms. A preliminary design study of a new nuclear pulsed propulsion concept called the Viper Pulsed Fusion Rocket [ Orcutt, et. al.]. In this presentation VIPER will be compared to previously published fusion space propulsion concepts. The process identifies the requirements of fusion-class systems, and discusses operational parameters such as specific power, specific impulse, and nozzle jet efficiency.
A framework for the iterative dynamic optimisation of diesel engines: numerical methods, experimental setup, and first results (2014)

Owing to the many degrees of freedom provided by current engine systems and to the need to consider transient operation, deriving an engine calibration has become a tedious task. Control trajectories resulting from the solution of an optimal-control problem provide a guideline to the calibration engineer, serve as a benchmark, and might be used for a partial automation of the calibration procedure. The common approach to dynamic optimisation consists of solving a single optimal-control problem. However, this approach requires the availability of models that are valid throughout the whole engine operating range and actuator ranges. In addition, the result of the optimisation is meaningful only if the model is very accurate. We propose a methodology to circumvent those demanding requirements: an iteration between transient measurements to refine a purpose-built model and a dynamic optimisation which is constrained to the model-validity region. This paper presents all numerical methods required to implement this procedure. The crucial steps are analysed in detail, and the most important caveats are indicated. Finally, an experimental validation demonstrates the applicability of the method and reveals the components that require further development.
3D integration by wafer-level aligned wafer bonding (2015)

Wafer bonding is an attractive technology enabling manufacturing of complex wafer-level 3D architectures. The continuous demand for device size shrinking and performance improvement pushed for the development of new manufacturing technologies. This work reviews the main challenging raised for the wafer bonding processes and presents new developments in the aligned wafer bonding processes.
Augmentation of Stagnation Region Heat Transfer Due to Turbulence From an Advanced Dual-Annular Combustor (2002)

Heat transfer measurements have been made in the stagnation region of a flat plate with an elliptical leading edge. The radius of curvature at the stagnation point was similar to that of a first stage turbine vane airfoil used in a large commercial high-bypass turbofan engine. The airfoil was mounted downstream of an arc segment of a dual-annular combustor similar to the type used in an advanced turbine engine. Testing was done in air at atmospheric temperature and at pressures up to 376 kPa to simulate the vane leading edge Reynolds number seen in the engine. Spanwise average stagnation region heat transfer was measured with an electrically heated aluminum strip. Turbulence intensity, length scale and isotropy were measured using standard 2-wire hot wire probes. The combustor contained two annular rows of fuel-air swirlers which were aligned in the radial direction. Both heat transfer and hot wire data were taken at two circumferential positions; one directly downstream of a pair of swirlers and one half way between two pairs of swirlers. Reynolds number based on vane leading edge diameter was varied from 51000 to 160000. The maximum Reynolds number for turbulence measurements was limited to 87000. Turbulence intensity averaged over all test conditions was found to be 31.6%. Average axial, integral length scale was 1.29 cm, which gave a length scale-to-leading edge diameter ratio of 1.08. The turbulence was found to be nearly isotropic with the average ratio of axial to circumferential fluctuating components of 1.15. Heat transfer augmentation above laminar levels was found to vary from 34 to almost 59% depending on the Reynolds number. No effect of circumferential position was found. The heat transfer augmentation was found to be well predicted by a correlation derived from grid generated turbulence.
Frequency Spectrum of Spontaneous and Stimulated Line-Narrowing Effects Induced by Laser Radiation (1968)

Received 12 December 1967DOI:https://doi.org/10.1103/PhysRevLett.20.578©1968 American Physical Society
3D view synthesis with inter-view consistency (2013)

In this paper, we propose a new pipeline to synthesize virtual views by extrapolation. It allows us to generate virtual views far away from each other, each presenting the exact same level of quality. This inter-view consistency is key to seamlessly navigate between viewpoints. Its computational cost is also lower than that of existing approaches. We compare the proposed approach with state-of-the-art methods and show the effectiveness of this new view synthesis pipeline.
Comparison of Neutralizing Antibody Responses Elicited from Highly Diverse Polyvalent Heterotrimeric HIV-1 gp140 Cocktail Immunogens versus a Monovalent Counterpart in Rhesus Macaques (2014)

Eliciting neutralizing antibodies capable of inactivating a broad spectrum of HIV-1 strains is a major goal of HIV-1 vaccine design. The challenge is that envelopes (Envs) of circulating viruses are almost certainly different from any Env used in a vaccine. A novel immunogen composed of a highly diverse set of gp140 Envs including subtypes A, B, C, D and F was developed to stimulate a more cross-neutralizing antibody response. Env heterotrimers composed of up to 54 different gp140s were produced with the aim of focusing the response to the conserved regions of Env while reducing the dominance of any individual hypervariable region. Heterotrimeric gp140 Envs of inter- and intra-subtype combinations were shown to bind CD4 and a panel of neutralizing monoclonal antibodies with similar affinity to monovalent UG37 gp140. Macaques immunized with six groups of heterotrimer mixtures showed slightly more potent neutralizing antibody responses in TZM-BL tier 1 and A3R5 tier 2 pseudovirus assays than macaques immunized with monovalent Env gp140, and exhibited a marginally greater focus on the CD4-binding site. Carbopol enhanced neutralization when used as an adjuvant instead of RIBI in combination with UG37 gp140. These data indicate that cross-subtype heterotrimeric gp140 Envs may elicit some improvement of the neutralizing antibody response in macaques compared to monovalent gp140 Env.
Reproducible Science (2010)

The reproducibility of an experimental result is a fundamental assumption in science. Yet, results that are merely confirmatory of previous findings are given low priority and can be difficult to publish. Furthermore, the complex and chaotic nature of biological systems imposes limitations on the replicability of scientific experiments. This essay explores the importance and limits of reproducibility in scientific manuscripts.
Fine Mapping and Genetic Interactions of Nearly-Isogenic Allelic Series Representing Yield and Quality QTLs Derived from Wild Tomato Species (2002)

Wild germplasm represents a rich source of QTLs capable of enhancing productivity of crop plants. Using the molecular linkage map of tomato in conjunction with novel population structures, we have identified QTLs from five Lycopersicon species that improve key yield and quality associated traits of processing tomatoes. In this research we employed multi-testing sites for fine mapping analysis of the different components of the affected traits combined with genetic interaction studies. Our results demonstrate that 'exotic libraries', which comprise of marker-defined genomic regions taken from wild species and introgressed onto the background of elite crop lines, provide an important opportunity for improving of the agricultural performance of modem crop varieties. Furthermore, we showed that these genetic resources can also serve as reagents for the discovery and characterization of genes that underlie traits of agricultural value. The results set the stage for using the QTLs in marker assisted programs and for applying map-based cloning of the targeted QTL/genes. The cloning of QTLs revealed genes that control pathways for agricultural yield in tomato that may be common for other crop species.
Tunable all-optical pulse compression and stretching via doublet Brillouin gain lines in an optical fiber (2009)

We demonstrate tunable all-optical pulse compression and stretching via doublet Brillouin gain lines in an optical fiber. Tunable pulse compression or a stretching ratio of 1.47-0.43 accompanying a time delay is achieved by controlling the separation between two gain lines, for an input pulse train with a 40 ns width and a repetition rate of 5 MHz, in a 4 km silica fiber with a fixed pump power of 88.1 mW. The limitation of this pulse compressor or stretcher is also discussed.
Rate of diffusion-limited reactions in dispersions of spherical traps via multipole scattering (1991)

The effective reaction rate is calculated for a random array of reactive, stationary spherical traps in a medium containing a highly mobile reactant. Multipole scattering up to the quadrupole level, properly accounting for the conditionally convergent long-range interactions, plus direct addition of exact two-body interactions is employed. It is found that the addition of two-body interactions has a negligible effect on the effective reaction rates computed, in contrast to the case of the effective conductivity. Our results closely match the random walker simulation results of Lee, Kim, Miller, and Torquato [Phys. Rev. B 39, 11833 (1989)] up to 30% trap volume fraction, after which they underpredict the effective reaction rate. To accurately compute the effective reaction rate at high volume fractions, higher order many-body multipole interactions are required.
Fine-grained Angular Contrastive Learning with Coarse Labels (2021)

Few-shot learning methods offer pre-training techniques optimized for easier later adaptation of the model to new classes (unseen during training) using one or a few examples. This adaptivity to unseen classes is especially important for many practical applications where the pre-trained label space cannot remain fixed for effective use and the model needs to be "specialized" to support new categories on the fly. One particularly interesting scenario, essentially overlooked by the few-shot literature, is Coarse-to-Fine Few-Shot (C2FS), where the training classes (e.g. animals) are of much ‘coarser granularity’ than the target (test) classes (e.g. breeds). A very practical example of C2FS is when the target classes are sub-classes of the training classes. Intuitively, it is especially challenging as (both regular and few-shot) supervised pre-training tends to learn to ignore intra-class variability which is essential for separating sub-classes. In this paper, we introduce a novel ’Angular normalization’ module that allows to effectively combine supervised and self-supervised contrastive pre-training to approach the proposed C2FS task, demonstrating significant gains in a broad study over multiple baselines and datasets. We hope that this work will help to pave the way for future research on this new, challenging, and very practical topic of C2FS classification.
Adjustable nanostructure of synthetic geopolymers enables tunable and sustained release of oxycodone (2010)

Adjustable nanostructure of synthetic geopolymers enables tunable and sustained release of oxycodone
Design and Preparation of Organic−Inorganic Hybrid Catalysts (2002)

Solid catalysts provide numerous opportunities for&#13;\nrecovering and recycling catalysts from reaction&#13;\nenvironments. These features can lead to improved&#13;\nprocessing steps, better process economics, and environmentally&#13;\nfriendly industrial manufacturing.&#13;\nThus, the motivating factors for creating recoverable&#13;\ncatalysts are large.
Phase I Trial of a Combination of the Multikinase Inhibitor Sorafenib and the Farnesyltransferase Inhibitor Tipifarnib in Advanced Malignancies (2009)

Our study shows that the combination of tipifarnib and sorafenib is well tolerated. Activity was seen, especially in patients with medullary thyroid cancer, a tumor characterized by RET mutations.
Dimethyl Fumarate Blocks Tumor Necrosis Factor-Alpha-Driven Inflammation and Metabolic Rewiring in the Retinal Pigment Epithelium (2022)

The retinal pigment epithelium (RPE) acts as a metabolic gatekeeper between photoreceptors and the choroidal vasculature to maintain retinal function. RPE dysfunction is a key feature of age-related macular degeneration (AMD), the leading cause of blindness in developed countries. Inflammation is a key pathogenic mechanism in AMD and tumor necrosis factor-alpha (TNFα) has been implicated as a pro-inflammatory cytokine involved in AMD. While mitochondrial dysfunction has been implicated in AMD pathogenesis, the interplay between inflammation and cellular metabolism remains elusive. The present study explores how the pro-inflammatory cytokine, TNFα, impacts mitochondrial morphology and metabolic function in RPE. Matured human primary RPE (H-RPE) were treated with TNFα (10 ng/ml) for up to 5 days. TNFα-induced upregulation of IL-6 secretion and inflammatory genes (IL-6, IL-8, MCP-1) was accompanied by increased oxidative phosphorylation (OXPHOS) and reduced glycolysis, leading to an increase in cellular adenosine triphosphate (ATP) content. Transmission electron microscopy (TEM) revealed defects in mitochondrial morphology with engorged mitochondria and loss of cristae integrity following TNFα treatment. Pre-treatment with the anti-inflammatory drug, 80 μM dimethyl fumarate (DMFu), blocked TNFα-induced inflammatory activation of RPE (IL-6, IL-8, MCP-1, CFH, CFB, C3) and normalized their bioenergetic profile to control levels by regulating PFKFB3 and PKM2 gene expression. Furthermore, DMFu prevented TNFα-induced mitochondrial dysfunction and morphological anomalies. Thus, our results indicate that DMFu serves as a novel therapeutic avenue for combating inflammatory activation and metabolic dysfunction of RPE in AMD.
Fate of Litomosoides carinii Adults Transplanted into the Pleural or Peritoneal Cavity of Infected and Naive Multimammate Rats (Mastomys natalensis) (1976)

In each of 4 experiments, 58 multimammate rats (Mastomys natalensis) were subdivided into 5 groups. Thirty-four rats were infected with Litomosoides carinii and infections were allowed to become patent. Ten days after patency adult worms were surgically transferred from donor rats to each of 1 group of infected rats and 1 group of naive rats. Groups of infected and naive rats served as controls. Transfers were made either intrapleurally or intraperitoneally. Samples of blood and tissues were taken from each of 2 animals necropsied from each group at intervals to 31 days. At necropsy, the transferred worms and the original population (if any) were examined and samples were fixed. Infected rats accepted new worms with a minimum of reaction while naive rats rejected worms beginning at day 10 (intrapleural) of 17 (intraperitoneal). Rejections were complete leaving a white fibrous mass by day 24 or 31, respectively. Hemagglutination antibody titers fell into 2 groups: infected and naive. IHA titers of naive recipient rats increased into the infected range by day 3 (intrapleural) or day 10 (intraperitoneal). Microfilaria counts presented a more varied pattern but a similar lag in the intraperitoneal recipient group was observed. It was concluded that a preparation period is necessary for successful residence of adult worms, and that this preparation is not restricted to the pleural cavity.