gebhart/patrepeval huggingface dataset:
Hybrid Anthracyclines from a Genetically Engineered<i>Streptomyces</i><i>g</i><i>alilaeus</i>Mutant (2000)

The genetic engineering of antibiotic-producing Streptomyces strains is an approach that is emerging and ready to become established as a successful methodology in developing analogues of the original, pharmaceutically important, natural products obtained from the organisms. The current report highlights this succes by demonstrating the high-level production of novel anthracyclines. The biosynthetic pathways of the nogalamycin-producing Streptomyces nogalater and the aclacinomycin-producing S. galilaeus were combined by transferring the genes of S. nogalater polyketide synthetase into a nonproducing S. galilaeus mutant. The resulting anthracycline antibiotics that were produced possessed structural features characteristic of compounds from both of the undoctored Streptomycesstrains.
Treating the metabolic syndrome: acetyl-CoA carboxylase inhibition (2005)

Metabolic syndrome is defined as a clustering of cardiovascular risk factors (abdominal obesity, hyperinsulinaemia, atherogenic dislipidaemia, hypertension, hypercoagulability) that together increase the risk of developing coronary heart disease and Type-2 diabetes. Inhibition of acetyl-CoA carboxylase (ACC), with its resultant inhibition of fatty acid synthesis and stimulation of fatty acid oxidation, has the potential to favourably affect, in a concerted manner, a multitude of cardiovascular risk factors associated with metabolic syndrome. Studies in ACC2 knockout mice and in experimental animals treated with isozyme-nonselective ACC inhibitors have demonstrated the potential for treating metabolic syndrome through this modality. A variety of structurally diverse, mechanistically distinct classes of ACC inhibitors have been disclosed in the scientific and patent literature. Isozyme-nonselective ACC inhibitors may provide the optimal therapeutic potential for beneficially affecting metabolic syndrome. However, demonstration of the full potential of isozyme-selective inhibitors, once identified, should reveal advantages and liabilities associated with single isozyme inhibition. Whereas demonstrating clinical efficacy of an ACC inhibitor should be straightforward, the heterogeneity of the patient population and absence of established guidelines regarding approval end points for agents simultaneously affecting multiple aspects of metabolic syndrome will pose developmental challenges for initial market entries.
Bulk Process for Enrichment of Capsinoids from Capsicum Fruit (2022)

Various methods to synthesize capsinoids (the nonpungent analogs of capsaicinoids) from precursor molecules have been reported. Capsinoids are also naturally present, at typically low concentrations, in the fruit of many Capsicum species and genotypes. However, they are also present in the fruit of select genotypes at high concentrations. The fruit of high-capsiate genotypes represents a commercial source of these compounds. To date, no method has been published that efficiently extracts and purifies capsinoids from Capsicum fruit in a rapid and simple bulk process. This study evaluated the efficacy of various organic solvents for the extraction of capsinoids from dried Capsicum annuum fruit. Among the organic solvents evaluated, pentane appeared to provide a good combination of both recovery and purity. A subsequent liquid/liquid extraction step, utilizing pentane and acetonitrile, resulted in 26.3% (wt/wt) capsiate and 19.4% (wt/wt) dihydrocapsiate for a combined capsinoids yield of 45.7% (wt/wt). A third step, involving a rapid hp20ss chromatography column using a water/acetonitrile gradient, resulted in a combined capsinoids yield of 96.6% (wt/wt).
Gamma frequency entrainment attenuates amyloid load and modifies microglia (2016)

Abstract Changes in gamma oscillations (20–50 Hz) have been observed in several neurological disorders. However, the relationship between gamma oscillations and cellular pathologies is unclear. Here we show reduced, behaviourally driven gamma oscillations before the onset of plaque formation or cognitive decline in a mouse model of Alzheimer’s disease. Optogenetically driving fast-spiking parvalbumin-positive (FS-PV)-interneurons at gamma (40 Hz), but not other frequencies, reduces levels of amyloid-β (Aβ)1–40 and Aβ 1–42 isoforms. Gene expression profiling revealed induction of genes associated with morphological transformation of microglia, and histological analysis confirmed increased microglia co-localization with Aβ. Subsequently, we designed a non-invasive 40 Hz light-flickering regime that reduced Aβ1–40 and Aβ1–42 levels in the visual cortex of pre-depositing mice and mitigated plaque load in aged, depositing mice. Our findings uncover a previously unappreciated function of gamma rhythms in recruiting both neuronal and glial responses to attenuate Alzheimer’s-disease-associated pathology.
Efficiency of Database Search for Identification of Mutated and Modified Proteins via Mass Spectrometry (2001)

Although protein identification by matching tandem mass spectra (MS/MS) against protein databases is a widespread tool in mass spectrometry, the question about reliability of such searches remains open. Absence of rigorous significance scores in MS/MS database search makes it difficult to discard random database hits and may lead to erroneous protein identification, particularly in the case of mutated or post-translationally modified peptides. This problem is especially important for high-throughput MS/MS projects when the possibility of expert analysis is limited. Thus, algorithms that sort out reliable database hits from unreliable ones and identify mutated and modified peptides are sought. Most MS/MS database search algorithms rely on variations of the Shared Peaks Count approach that scores pairs of spectra by the peaks (masses) they have in common. Although this approach proved to be useful, it has a high error rate in identification of mutated and modified peptides. We describe new MS/MS database search tools, MS-CONVOLUTION and MS-ALIGNMENT, which implement the spectral convolution and spectral alignment approaches to peptide identification. We further analyze these approaches to identification of modified peptides and demonstrate their advantages over the Shared Peaks Count. We also use the spectral alignment approach as a filter in a new database search algorithm that reliably identifies peptides differing by up to two mutations/modifications from a peptide in a database.
Moving in stereo: Efficient structure and motion using lines (2009)

We present a fast and robust system for estimating structure and motion using a stereo pair, with straight lines as features. Our first set of contributions are efficient algorithms to perform this estimation using a few (two or three) lines, which are well-suited for use in a hypothesize-and-test framework. Our second contribution is the design of an efficient structure from motion system that performs robustly in complex indoor environments. By using infinite lines rather than line segments, our approach avoids the issues arising due to uncertain determination of end-points. Our cost function stems from a rank condition on planes backprojected from corresponding image lines. We propose a framework that imposes orthonormality constraints on the rigid body motion and can perform estimation using only two or three lines, through efficient solution of an overdetermined system of polynomials. This is in contrast to simple approaches which first reconstruct 3D lines and then align them, but perform poorly in real-world scenes with narrow baseline stereo. Experiments using synthetic as well as real data demonstrate the speed, accuracy and reliability of our system.
Microwave Moisture Sensor for Grain and Seed (2008)

A low-cost microwave sensor for nondestructive, rapid sensing of moisture content in granular and particulate materials has been built and tested. The sensor operates at a single frequency of 5.8 GHz and uses the principle of free-space transmission for moisture determination from measurement of the dielectric properties of the material. A unified calibration algorithm was used for moisture determination independent of bulk density and independent of the material type. Results for wheat and soybeans show that moisture content can be determined in either material from a single moisture calibration equation with a standard error of calibration of 0.5%. The low price, simplicity of use, and level of accuracy of the proposed sensor can provide an opportunity for widespread integration of microwave sensing technology in numerous industries dealing with granular and particulate materials, including food and agriculture, pharmaceuticals, mining, and construction.
Encapsulation shape with non-rotational symmetry designed for extraction of polarized light from unpolarized sources (2007)

A non-rotationally symmetric encapsulation shape - which takes advantage of the low reflection coefficient for transverse magnetic polarized light near Brewster's angle - designed to enhance extraction of a particular desired linear polarization from an unpolarized source is reported. The algorithm for optimization of the shape is described. Numerical ray-tracing simulations of the encapsulation shape are performed and predict an integrated enhancement of 8.3% in the ratio of desired polarization to undesired polarization when the refractive index of the encapsulant is 1.5. Experimental measurements of fabricated encapsulant shapes agree well with numerical predictions.
Note: Reflection-type micro multipoint laser Doppler velocimeter for measuring velocity distributions in blood vessels (2011)

We have developed a laser Doppler velocimeter (LDV) for measuring velocity distributions in blood vessels. We converted a transmission-based LDV into a reflection-based LDV to make it suitable for clinical applications. The velocity distribution image of a serpentine flow channel obtained could be qualitatively explained by the numerical results. Finally, we evaluated the system by using it to measure injection of blood into a glass tube by a syringe pump. The results obtained demonstrate that erythrocytes can be used as seeding particles for the reflection-type micro multipoint LDV. The results obtained are useful as basic data for clinical applications.
Personalization via Probabilistic Adaptation (2013)

We present a new approach for personalizing Web search results to a specific user. Ranking functions for Web search engines are typically trained by machine learn-ing algorithms using either direct human relevance judgments or indirect judg-ments obtained from click-through data from millions of users. The rankings are thus optimized to this generic population of users, not to any specific user. We propose a generative model of relevance which can be used to infer the relevance of a document to a specific user for a search query, and show how to learn these profiles from a user’s long-term search history. Our algorithm for computing the personalized ranking is simple and has little computational overhead. We evaluate our personalization approach using historical search data from thousands of users of a major Web search engine.1 1
Grafting of Molecularly Imprinted Polymer Films on Silica Supports Containing Surface-Bound Free Radical Initiators (2001)

Silica particles containing surface-bound free radical initiators have been used as supports for the grafting of thin films of molecularly imprinted polymers (MIPs). This technique offers a means of fine-tuning the layer thickness for improved kinetic properties or enhanced capacity in chromatographic or sensor applications. Thus prepared MIPs imprinted with l-phenylalanine anilide, have been characterized by FT-IR spectroscopy, thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), elemental analysis, fluorescence microscopy, and scanning electron microscopy (SEM), providing evidence concerning the reproducibility in each step and the quantity and quality of the grafted films. The chromatographic properties of the materials have been investigated with respect to the average layer thickness of the polymer on the surface, the solvent, the support pore diameter, the cross-linker concentration, and the composition of the mobile phase. For the porous particles, the column efficiency depended strongly on the amount of grafted polymer. Thus, polymers grafted as thin films (ca. 0.8 nm as average film thickness) on silica with 10 nm average pore diameter showed the highest column efficiency giving plate numbers (N) for the imprinted enantiomer of ca. 700 m-1 and for the antipode ca. 24 000 m-1. This resulted in baseline resolutions on a 33 mm long column in less than 5min. On the other hand the sample load capacity and separation factor increased up to 7.0 nm layer thickness and dropped again for larger amounts of grafted polymer. A support with an average pore diameter of 100 nm and a 3.8 nm layer thickness showed a far higher saturation capacity than values previously determined for the conventional monolithic materials.
Self‐biasing memristor crossbar used for string matching and ternary content‐addressable memory implementation (2017)

A memristor crossbar‐based technique for highly parallel string matching is presented. An input string can be simultaneously compared against a bank of stored words, each having a different length, due to the self‐biasing nature of the crossbar circuit. This string matching system essentially acts as a ternary content‐addressable memory (TCAM). Owing to the high‐density nature of nanoscale memristor crossbars, this system can provide a significant area reduction when compared alternative TCAM designs while remaining competitive in terms of timing and energy.
<title>Preparation of the SnO<formula><inf><roman>2</roman></inf></formula> gate pH-ISFET by sol gel technology</title> (2001)

In this paper, the sol-gel prepared SnO<SUB>2</SUB> thin film is first applied for the pH sensing. We use the SnCl<SUB>2</SUB>(DOT)2H<SUB>2</SUB>O as the precursor. It is cheaper than other methods. The resulting solution is dropped on the gate of the SiO<SUB>2</SUB> gate pH-ISFET (ion sensitive field effect transistor). After baking, the thin film will convert to SnO<SUB>2</SUB>. We also use the thermal evaporation system to prepare the SnO<SUB>2</SUB> gate MOSFET. Then, we use the Keithley 236 instrument to measure the I<SUB>DS</SUB>-V<SUB>G</SUB> curves of the SnO<SUB>2</SUB> gate MOSFET and pH-ISFET for the different pH buffer solutions. Since the MOSFET and pH-ISFET are fabricated on the same silicon wafer, the properties of these devices are identical. Therefore, we can use the experimental results and theoretical model of the pH-ISFET to find the pH sensitivity and pH<SUB>PZC</SUB> (pH at the point of zero charge) of the sol-gel prepared SnO<SUB>2</SUB> gate pH-ISFET, which are about 57.36 mV/pH and 11.3, respectively.
Fly ash-enhanced aluminum composites for automotive parts. Report for program startup to September 30, 1997 (1997)

To produce and evaluate the use of aluminum ''ashalloys''--metal matrix composites that incorporate coal fly ash--in the commercial manufacture of cast automotive parts. The use of fly ash as an additive will help reduce the weight and cost of automotive parts, improve selected material properties, and reduce energy consumption and pollution.
Benefit of Complete Response in Multiple Myeloma Limited to High-Risk Subgroup Identified by Gene Expression Profiling (2007)

Access to gene expression information permitted the recognition of a small very high-risk subgroup of 13% of patients, in whom prolonged survival critically depended on achieving CR. Absence of such benefit in the remainder should lead to a reassessment of clinical trial designs that rely on this end point as a surrogate for long-term prognosis.
Monotonic counters: a new mechanism for thread synchronization (2002)

Only a handful of fundamental mechanisms for synchronizing the access of concurrent threads to shared memory are widely implemented and used. These include locks, condition variables, semaphores, barriers, and monitors. In this paper, we introduce a new synchronization mechanism-monotonic counters-and make a case for its addition to this group. Unlike most other synchronization mechanisms, monotonic counters were designed primarily for multiprocessing, rather than for systems programming. Counters have a very simple definition: a counter object has a nonnegative value, an Increment operation, and a Check operation. Increment atomically increases the counter, and Check suspends until the counter reaches a specified level. We demonstrate that many practical thread synchronization patterns can be expressed more elegantly using counters than with other synchronization mechanisms. Of particular importance, the monotonicity of counters can be used to guarantee deterministic synchronization and the equivalence of multithreaded and sequential execution. In terms of implementation, counters are distinguished from traditional synchronization mechanisms, in that they have a dynamically varying number of thread suspension queues. We give several examples of multithreaded programs that use counter synchronization, and give an implementation of counters on top of locks and condition variables.
Aggregate flow control: improving assurances for differentiated services network (2002)

The differentiated services architecture is a simple, but novel, approach for providing service differentiation in an IP network. However, there are various issues to be addressed before any sophisticated end-to-end services can be offered. This work proposes an aggregate flow control (AFC) technique with a Diffserv traffic conditioner to improve the bandwidth and delay assurance of differentiated services. A prototype has been developed to study the end-to-end behavior of customer aggregates. In particular, this new approach improves performance in the following manner: (1) fairness issues among aggregated customer traffic with different number of micro-flows in an aggregate, interaction of non-responsive traffic (UDP) and responsive traffic (TCP), and the effect of different packet sizes in aggregates; (2) improved transactions per second for short TCP flows; and (3) reduced inter-packet delay variation for streaming UDP traffic. Experiments are also performed in a topology with multiple congestion points to show an improved treatment of conformant aggregates, and the ability of AFC to handle multiple aggregates and differing target rates.
Electrodeposition for Low-Cost, Water-Based Electrode Manufacturing. Research Performance Progress Report, Jan. 1, 2016 - Dec. 31, 2019 (2020)

The viability of electrocoat to fabricate battery electrodes at commercially relevant formulations has been demonstrated using both bench-scale equipment and a small pilot-scale roll-to-roll system (mini-coater). Through this, we show that an electrodeposited lithium-ion battery electrode coating system and manufacturing process is capable of reducing cell costs. Specifically, >60% decrease in capital costs is expected when transitioning from slot-die to electrocoat-based coating systems due to the removal of a solvent recovery system. In addition, a 50% reduction in operating costs in also expected as we enable 2-coat/2-cure processing of cathode electrodes.
Travel assistance device: utilising global positioning system-enabled mobile phones to aid transit riders with special needs (2010)

Recent advancements in mobile technology allow global positioning system (GPS)-enabled cell phones to provide a variety of real-time location-based services. This study reports on the design, implementation and testing of such a service, the travel assistance device (TAD), that aids transit riders with special needs in using public transportation. TAD is a program that provides the rider with customised real-time audio, visual and tactile prompts for exiting the transit vehicle by announcing ‘Get ready ’ and ‘Pull the cord now!’ Additionally, TAD provides alerts to riders, their caretakers and travel trainers if a rider deviates from the planned route. A website allows easy access for the creation of new trip itineraries and allows authorised personnel to monitor the rider's location in real-time from any computer. While the TAD was designed to aid transit riders with special needs to increase their level of independence and their care-takers' level of security, any rider new to a transit system can use TAD for planning and executing trips with confidence and ease.
A mathematical model of the systemic circulatory system with logistically defined nervous system regulatory mechanisms (2006)

A mathematical model is developed that accurately describes the pressure, volume and flow dynamics of the systemic circulatory system over the full physiological range of human pressures and volumes. At the heart of this model are mathematical representations for the autonomic and central nervous system reflexes which maintain arterial pressure, cardiac output and cerebral blood flow. These representations involve functions in which a maximum effect and a minimum effect are smoothly connected by a logistic transition. A new approach to modelling the pressure -- volume relationship in a vessel with smooth muscle contraction is also presented. To test the model, simulations of cardiac arrest and various haemorrhagic situations were conducted, and predicted results were compared with clinical observations. Near-perfect agreement was obtained between predicted and observed values of the mean circulatory filling pressure, cardiac output and arterial pressure decay in the face of significant haemorrhage, and the critical values delineating progressive from non-progressive hypovolaemic shock.
Fast scanning transmissive delay line for optical coherence tomography (2005)

A novel Fourier domain fast scanning optical delay line is proposed in which the walk-off is eliminated by only two passes through a diffraction grating. Working in transmission, the novel delay line is ideal for balanced optical coherence tomography configurations with recirculation of the reference beam. We evaluate theoretically and experimentally its walk-off and dispersion compensation capabilities.
Soluble 2-Substituted Aminopyrido[2,3-<i>d</i>]pyrimidin-7-yl Ureas. Structure−Activity Relationships against Selected Tyrosine Kinases and Exploration of in Vitro and in Vivo Anticancer Activity (2001)

In continuing our search for medicinal agents to treat proliferative diseases, we have discovered 2-substituted aminopyrido[2,3-d]pyrimidin-7-yl ureas as a novel class of soluble, potent, broadly active tyrosine kinase (TK) inhibitors. An efficient route was developed that enabled the synthesis of a wide variety of analogues with substitution on several positions of the template. From the lead structure 1, several series of analogues were made that examined the C-6 aryl substituent, a variety of water solublizing substitutents at the C-2 position, and urea or other acyl functionality at the N-7 position. Compounds of this series were competitive with ATP and displayed submicromolar to low nanomolar potency against a panel of TKs, including receptor (platelet-derived growth factor, PDGFr; fibroblast growth factor, FGFr;) and nonreceptor (c-Src) classes. Several of the most potent compounds displayed submicromolar inhibition of PDGF-mediated receptor autophosphorylation in rat aortic vascular smooth muscle cells and low micromolar inhibition of cellular growth in five human tumor cell lines. One of the more thoroughly evaluated members, 32, with IC50 values of 0.21 microM (PDGFr), 0.049 microM (bFGFr), and 0.018 microM (c-Src), was evaluated in in vivo studies against a panel of five human tumor xenografts, with known and/or inferred dependence on the EGFr, PDGFr, and c-Src TKs. Compound 32 produced a tumor growth delay of 14 days against the Colo-205 colon xenograft model.