gebhart/patrepeval huggingface dataset:
Vector Saliva in Vaccines for Visceral Leishmaniasis: A Brief Encounter of High Consequence? (2014)

Visceral leishmaniasis (VL) is a vector-borne disease transmitted by phlebotomine sand flies and remains the most serious form of the disease with no available human vaccine. Repeatedly, studies have demonstrated the immunogenicity and protective efficacy of a number of sand fly salivary proteins against cutaneous and visceral leishmaniasis. All Leishmania species including agents of VL are co-deposited into the skin together with vector saliva. Generally, the immune response to a protective salivary protein in vaccinated animals is rapid and possibly acts on the parasites soon after delivery into the skin by the bite of an infective sand fly. This is followed by the development of a stronger Leishmania-specific immunity in saliva-vaccinated animals compared to controls. Considering that several of the most efficacious protective molecules were identified from a proven vector of VL, we put forward the notion that a combination vaccine that includes a Leishmania antigen and a vector salivary protein has the potential to improve vaccine efficacy by targeting the parasite at it most vulnerable stage just after transmission.
Cardiac image reconstruction on a 16-slice CT scanner using a retrospectively ECG-gated multicycle 3D back-projection algorithm (2003)

Fast 16-slice spiral CT delivers superior cardiac visualization in comparison to older generation 2- to 8-slice scanners due to the combination of high temporal resolution along with isotropic spatial resolution and large coverage. The large beam opening of such scanners necessitates the use of adequate algorithms to avoid cone beam artifacts. We have developed a multi-cycle phase selective 3D back projection reconstruction algorithm that provides excellent temporal and spatial resolution for 16-slice CT cardiac images free of cone beam artifacts.
Isolating Potentiated Hsp104 Variants Using Yeast Proteinopathy Models (2014)

Many protein-misfolding disorders can be modeled in the budding yeast Saccharomyces cerevisiae. Proteins such as TDP-43 and FUS, implicated in amyotrophic lateral sclerosis, and α-synuclein, implicated in Parkinson’s disease, are toxic and form cytoplasmic aggregates in yeast. These features recapitulate protein pathologies observed in patients with these disorders. Thus, yeast are an ideal platform for isolating toxicity suppressors from libraries of protein variants. We are interested in applying protein disaggregases to eliminate misfolded toxic protein conformers. Specifically, we are engineering Hsp104, a hexameric AAA+ protein from yeast that is uniquely capable of solubilizing both disordered aggregates and amyloid and returning the proteins to their native conformations. While Hsp104 is highly conserved in eukaryotes and eubacteria, it has no known metazoan homologue. Hsp104 has only limited ability to eliminate disordered aggregates and amyloid fibers implicated in human disease. Thus, we aim to engineer Hsp104 variants to reverse the protein misfolding implicated in neurodegenerative disorders. We have developed methods to screen large libraries of Hsp104 variants for suppression of proteotoxicity in yeast. As yeast are prone to spontaneous nonspecific suppression of toxicity, a two-step screening process has been developed to eliminate false positives. Using these methods, we have identified a series of potentiated Hsp104 variants that potently suppress the toxicity and aggregation of TDP-43, FUS, and α-synuclein. Here, we describe this optimized protocol, which could be adapted to screen libraries constructed using any protein backbone for suppression of toxicity of any protein that is toxic in yeast.
MicroRNA-29 in Aortic Dilation: Implications for Aneurysm Formation (2011)

Rationale: Aging represents a major risk factor for coronary artery disease and aortic aneurysm formation. MicroRNAs (miRs) have emerged as key regulators of biological processes, but their role in age-associated vascular pathologies is unknown. Objective: We aim to identify miRs in the vasculature that are regulated by age and play a role in age-induced vascular pathologies. Methods and Results: Expression profiling of aortic tissue of young versus old mice identified several age-associated miRs. Among the significantly regulated miRs, the increased expression of miR-29 family members was associated with a profound downregulation of numerous extracellular matrix (ECM) components in aortas of aged mice, suggesting that this miR family contributes to ECM loss, thereby sensitizing the aorta for aneurysm formation. Indeed, miR-29 expression was significantly induced in 2 experimental models for aortic dilation: angiotensin II-treated aged mice and genetically induced aneurysms in Fibulin-4 R/R mice. More importantly, miR-29b levels were profoundly increased in biopsies of human thoracic aneurysms, obtained from patients with either bicuspid ( n =79) or tricuspid aortic valves ( n =30). Finally, LNA-modified antisense oligonucleotide-mediated silencing of miR-29 induced ECM expression and inhibited angiotensin II-induced dilation of the aorta in mice. Conclusion: In conclusion, miR-29-mediated downregulation of ECM proteins may sensitize the aorta to the formation of aneurysms in advanced age. Inhibition of miR-29 in vivo abrogates aortic dilation in mice, suggesting that miR-29 may represent a novel molecular target to augment matrix synthesis and maintain vascular wall structural integrity.
Concatenated phoneme models for text-variable speaker recognition (1993)

Methods that create models to specify both speaker and phonetic information accurately by using only a small amount of training data for each speaker are investigated. For a text-dependent speaker recognition method, in which arbitrary key texts are prompted from the recognizer, speaker-specific phoneme models are necessary to identify the key text and recognize the speaker. Two methods of making speaker-specific phoneme models are discussed: phoneme-adaptation of a phoneme-independent speaker model and speaker-adaptation of universal phoneme models. The authors also investigate supplementing these methods by adding a phoneme-independent speaker model to make up for the lack of speaker information. This combination achieves a rejection rate as high as 98.5% for speech that differs from the key text and a speaker verification rate of 100.0%.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Calibration of source level, expected transmitted power, and reverberation for long-range sonar in fluctuating range-dependent ocean waveguides (2007)

The ocean waveguide is temporally and spatially varying. An acoustic signal transmitted through the ocean or scattered from objects will get randomized. Estimating parameters of sonar, the environment, and scatterers requires a statistical approach that incorporates medium uncertainties into the signal analysis. Here we discuss source level, transmission loss (TL), and reverberation model calibration using data acquired with a long-range sonar on the New Jersey STRATAFORM. Broadband acoustic data measured by a desensitized hydrophone in a towed horizontal receiving array at numerous locations from a vertical source array are analyzed. The match-filtered data are compared to the expected TL output from a parabolic equation model that accounts for bathymetric variations. A maximum likelihood estimator is implemented to provide a global inversion of the data for source level, attenuation due to scattering, and match-filter degradation in the multi-modal ocean waveguide. An estimate is also provided of the coherence bandwidth for broadband acoustic signal transmission in this environment. A challenge in calibrating bottom reverberation models with sonar data lies in separating the scattered intensity from moving objects, such as fish groups, and distinguishing them from the statistically stationary background reverberation. An approach is presented for this purpose.
Active acoustic attenuation system for higher order mode non-uniform sound field in a duct (1990)

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Tetrahydro-2-naphthyl and 2-Indanyl Triazolopyrimidines Targeting <i>Plasmodium falciparum</i> Dihydroorotate Dehydrogenase Display Potent and Selective Antimalarial Activity (2016)

Malaria persists as one of the most devastating global infectious diseases. The pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (DHODH) has been identified as a new malaria drug target, and a triazolopyrimidine-based DHODH inhibitor 1 (DSM265) is in clinical development. We sought to identify compounds with higher potency against Plasmodium DHODH while showing greater selectivity toward animal DHODHs. Herein we describe a series of novel triazolopyrimidines wherein the p-SF5-aniline was replaced with substituted 1,2,3,4-tetrahydro-2-naphthyl or 2-indanyl amines. These compounds showed strong species selectivity, and several highly potent tetrahydro-2-naphthyl derivatives were identified. Compounds with halogen substitutions displayed sustained plasma levels after oral dosing in rodents leading to efficacy in the P. falciparum SCID mouse malaria model. These data suggest that tetrahydro-2-naphthyl derivatives have the potential to be efficacious for the treatment of malaria, but due to higher metabolic clearance than 1, they most likely would need to be part of a multidose regimen.
Implicit computation of minimum-cost feedback-vertex sets for partial scan and other applications (1994)

The contribution of this paper is an implicit method for computing the minimum cost feedback vertex set for a graph. For an arbitrary graph, we efficiently derive a Boolean function whose satisfying assignments directly correspond to feedback vertex sets of the graph. Importantly, cycles in the graph are never explicitly enumerated, but rather, are captured implicitly in this Boolean function. This function is then used to determine the minimum cost feedback vertex set. Even though computing the minimum cost satisfying assignment for a Boolean function remains an NP-hard problem, we can exploit the advances made in the area of Boolean function representation in logic synthesis to tackle this problem efficiently in practice for even reasonably large sized graphs. The algorithm has obvious application in flip-flop selection for partial scan. Our algorithm was the first to obtain the MFVS solutions for many benchmark circuits.
Predictive Flux Control for Induction Motor Drives With Modified Disturbance Observer for Improved Transient Response (2020)

This paper proposes an extended model based predictive flux control (MPFC) with modified disturbance observer speed loop for induction motors. The main advantages of the proposed method are the improvement of load estimation, the suppression of current overshoot at step changes in reference speed and the removal of weighting factor in the newly formulated cost function. Weighting factor is removed by using extended reference transformation which translates reference torque, generated by the speed controller, into equivalent stator flux vector eliminating the challenging task of gain tuning at different points of operation. Then, the load torque is considered as an unknown disturbance and the accuracy of load estimation during speed jumps is improved by using a reduced order PI observer (ROPIO) with low-pass filter (LPF) for improved integration. The observer is combined with disturbance rejection based control to design a composite speed controller replacing conventional PI loop. The effectiveness of the proposed method is validated on a two-level three-phase inverter fed induction motor drive using dSpace DS1104 controller board. The dynamic response of the proposed method is compared to previously proposed disturbance observer based controller (DOBC) for predictive torque control method. The load estimation error of the proposed method at speed jumps is reduced by 66% while current surges are also suppressed effectively.
Enhancements to Linear Least Squares Localization Through Reference Selection and ML Estimation (2008)

Linear least squares (LLS) estimation is a low complexity but sub-optimum method for estimating the location of a mobile terminal (MT) from some distance measurements. It requires selecting one of the fixed terminals (FTs) as a reference FT for obtaining a linear set of expressions. However, selection of the reference FT is commonly performed arbitrarily in the literature. In this paper, a method for selection of the reference FT is proposed, which improves the location accuracy compared to a fixed selection of the reference FT. Moreover, a covariance- matrix based LLS estimator is proposed in line of sight (LOS) and non-LOS (NLOS) environments which further improves accuracy since the correlations between the observations are exploited. Simulation results prove the effectiveness of the proposed techniques.
Aromatic Polymer with Pendant Perfluoroalkyl Sulfonic Acid for Fuel Cell Applications (2009)

Novel proton exchange membranes were prepared and investigated as polymer electrolyte membranes (PEMs) for polymer electrolyte membrane fuel cells (PEMFCs). Polymers having poly(arylene ether sulfone) in the main chain and −CF2CF2OCF2CF2SO3H in the side chain (PES-PSA) were synthesized by dehalogen coupling of poly{oxy-4,4′-(3,3′-dibromobiphenylene)oxy-4,4′-diphenylsulfone} (PES-Br) and potassium 1,1,2,2-tetrafluoro-2-(1,1,2,2-tetrafluoro-2- iodoethoxy)ethanesulfonate (PSA-K) using copper metal, followed by treatment with aqueous HCl. The proton conductivity of PES-PSA with an ion exchange capacity (IEC) of 1.58 mmol/g was 0.12 S/cm at 80 °C under 90% relative humidity. PES-PSA with an IEC of 1.34 mmol/g was used as the membrane for PEMFC, and the maximum power output at 80 °C was 805 mW/cm2 when fully humidified hydrogen and air were provided. A DMA measurement and a tensile test revealed that PES-PSA had a higher α-relaxation temperature than Nafion and higher flexibility than sulfonated polyethersulfone (SPES).
Sampling and Analysis of Particulate Matter by Glow Discharge Atomic Emission and Mass Spectrometries (1999)

The direct introduction of particulate matter into glow discharge atomic emission and mass spectrometry sources through a particle beam/momentum separator apparatus is described. Vacuum action through a narrow (0.0625 in. i.d.) stainless steel tube allows the introduction of discrete samples of NIST SRM 1648 urban particulate matter (UPM) and caffeine in powder form. Introduction of "ambient" airborne particulate matter is also possible. Particles passing through the aerodynamic momentum separator impinge on the heated (∼200-250 °C) inner surface of the glow discharge plasma volume and are flash-vaporized. The resultant atoms/molecules are subjected to excitation/ionization collisions within the low-pressure (0.5-5 Torr of He or Ar) plasma, producing characteristic photon emission and/or signature ionic species. In this way, atomic emission and mass spectrometry identification of particle constituents is possible. Basic design aspects of the apparatus are presented, and demonstrations of atomic emission detection of the constituents in the NIST SRM illustrate the general characteristics of the approach. Transient atomic emission signals are captured for the introduction of preweighed, discrete samples, with the integrated areas used to construct analytical response curves. Limits of detection using this relatively simple atomic emission system are on the order of tens of nanograms for sample masses of ∼50 μg. Mass spectrometric monitoring of introduced caffeine particles and a mixture of polycyclic aromatic hydrocarbons (PAHs) illustrates the ability of the glow discharge plasma to produce high-quality, library (electron impact) searchable mass spectra of molecular species while also yielding isotopic identification of elemental components of the UPM. Limits of detection for Fe in the NIST SRM are on the order of 175 ng of material, equivalent to ∼7 ng of analyte Fe. It is believed that the small size, low power consumption, ease of operation, and multimode sampling capabilities (AES/MS) of the particle beam-glow discharge (PB-GD) apparatus hold promise for applications in continuous monitoring and discrete particle sampling.
Brain-Derived Neurotrophic Factor Enhances Periodontal Tissue Regeneration (2005)

To address whether brain-derived neurotrophic factor (BDNF) could be involved in periodontal tissue regeneration, we examined the effects of BDNF on proliferation and the expression of bone (cementum)- related proteins (osteopontin, bone morphogenetic protein [BMP]-2, type I collagen, alkaline phosphatase [ALPase], and osteocalcin) in cultures of human periodontal ligament (HPL) cells, which are thought to be prerequisite for periodontal tissue regeneration, and on proliferation and angiogenesis in human endothelial cells. Furthermore, we examined the effect of BDNF on the regeneration of periodontal tissues in experimentally induced periodontal defects in dogs. BDNF elevated the expression of ALPase and osteocalcin mRNAs and increased the synthesis of osteopontin, BMP-2, and type I collagen DNA in HPL cells. BDNF stimulated mRNA expression of vascular endothelial growth factor-B and tenascin-X, and proliferation and angiogenesis in human endothelial cells. In vivo studies showed that BDNF stimulated the formation of new alveolar bone cementum and connective new fibers, which were inserted into the newly formed cementum and bone. BDNF also stimulated blood capillary formation. These findings suggest that the regulation of functioning of periodontal ligament cells and endothelial cells by BDNF results in the promotion of periodontal tissue regeneration.
Fractional Order Proportional-Resonant Controller (2018)

In this paper, a fractional order synchronous frame controller and its equivalent model, stationary frame control named fractional order proportional resonant controller, have been introduced using fractional order theory. Compared conventional proportional resonant controller, the proposed controller troller not only ensures a zero steady-state error for AC control systems, but also provides more robustness against fluctuations of resonant (center) frequency. Having a wider bandwidth and higher gain in the neighborhood of resonant frequency enhance the capability of this controller to deal with resonant frequency variations and furthermore, improve the time domain transient performance of these systems. Analog and digital implementions of this novel controller have been discussed. In addition, stability of the proposed controller has been investigated. Finally, the proposed fractional order control strategy is successfullyapplied to a grid-connected system as current regulator.
High throughput docking for library design and library prioritization (2001)

The prioritization of the screening of combinatorial libraries is an extremely important task for the rapid identification of tight binding ligands and ultimately pharmaceutical compounds. When structural information for the target is available, molecular docking is an approach that can be used for prioritization. Here, we present the initial validation of a new rapid approach to molecular docking developed for prioritizing combinatorial libraries. The algorithm is tested on 103 individual cases from the protein data bank and in nearly 90% of these cases docks the ligand to within 2.0 A of the observed binding mode. Because the mean CPU time is <5 s/mol, this approach can process hundreds of thousands of compounds per week. Furthermore, if a somewhat less thorough search is performed, the search time drops to 1 s/mol, thus allowing millions of compounds to be docked per week and tested for potential activity. Proteins 2001;43:113-124.
BlueSky (1999)

Palmtop computers are rapidly becoming the popular platform of choice for running personal productivity applications, but their networking capabilities are still lagging behind user expectations. Due to memory size, cost, and power considerations most palmtop computers support only limited form of point-to-point communication, namely, connection via a PSTN modem or a serial RS-232 cable. Due to wired point-to-point nature of these interfaces, satisfactory solutions for multi-point communication and direct LAN connection do not yet exist..
<title>Early fair drop: a new buffer management policy</title> (1998)

In this paper, we investigate the effectiveness of packet- drop mechanisms in conjunction with fair queuing link scheduling and hierarchical link sharing. Under fair queuing, the link share of a flow changes dynamically due to the arrivals and departures of flows and their bursts. This phenomenon becomes more pronounced in the case of hierarchical link sharing. Packet-drop mechanisms play an integral role for bandwidth-adaptive flows, such as TCP, that are expected to adjust their rates to the flows' changing fair share of the link bandwidth. We show experimentally that, under the existing drop policies (including random early detection and per-flow schemes such as the longest-queue drop) implemented with fair scheduling policies, TCP flows are slow to adjust their rates to their changing share of the link bandwidth. To overcome this problem, we propose a new packet-drop policy that simultaneously exploits two dimensions--when to drop and what to drop. We demonstrate that, under our packet-drop policy and with fair queuing, TCP flows adapt to their changing fair share of the link bandwidth when competing with different types of cross-traffic (e.g., bandwidth adaptive, rate controlled, greedy and on-off). We also illustrate that our drop policy provides isolation and fairness to flows other than TCP (e.g., rate controlled, on- off).
Bridged tetrahydroisoquinolines as selective NADPH oxidase 2 (Nox2) inhibitors (2013)

(1<i>SR</i>,4<i>RS</i>)-3,3-Dimethyl-1,2,3,4-tetrahydro-1,4-(epiminomethano)naphthalenes were synthesized in 2-3 steps from commercially available materials and assessed for specificity and effectiveness across a range of Nox isoforms. The <i>N</i>-pentyl and <i>N</i>-methylenethiophene substituted analogs 11g and 11h emerged as selective Nox2 inhibitors with cellular IC<sub>50</sub> values of 20 and 32 μM, respectively.
Mid-infrared quantum dot barrier photodetectors with extended cutoff wavelengths (2010)

A method to extend the cutoff wavelength of mid-infrared barrier photodetectors by incorporating self-assembled InSb quantum dots into the active area of the detector is demonstrated. This approach enables the extension of the cutoff wavelength of barrier photodetectors from 4.2 to 6 µm, demonstrating infrared response at temperatures up to 225 K.
Automatic Generation and Recommendation for API Mashups (2017)

Until today, finding the most suitable APIs to use in an application was burdensome, requiring manual and time-consuming searches across a diverse set of websites, in particular regarding how multiple APIs could be combined and worked together (i.e. API mashups). In this paper, we propose a new method to automatically generate API mashups through real-world data collection, text mining and natural language processing (NLP ) techniques. The generated API mashups are further ranked and recommended to developers based on a quantitative indicator of whether the given API mashup is plausible. To evaluate the overall accuracy of the proposed method, we use the generated API mashups to train several machine learning and deep learning models, and then use an independent mashup dataset collected from Github projects for testing. The experimental results show that our proposed method is feasible and accurate for automatic API mashup generation and recommendation.