gebhart/patrepeval huggingface dataset:
Allosteric effects of chromophore interaction with dimeric near-infrared fluorescent proteins engineered from bacterial phytochromes (2016)

Fluorescent proteins (FPs) engineered from bacterial phytochromes attract attention as probes for in vivo imaging due to their near-infrared (NIR) spectra and use of available in mammalian cells biliverdin (BV) as chromophore. We studied spectral properties of the iRFP670, iRFP682 and iRFP713 proteins and their mutants having Cys residues able to bind BV either in both PAS (Cys15) and GAF (Cys256) domains, in one of these domains, or without these Cys residues. We show that the absorption and fluorescence spectra and the chromophore binding depend on the location of the Cys residues. Compared with NIR FPs in which BV covalently binds to Cys15 or those that incorporate BV noncovalently, the proteins with BV covalently bound to Cys256 have blue-shifted spectra and higher quantum yield. In dimeric NIR FPs without Cys15, the covalent binding of BV to Сys256 in one monomer allosterically inhibits the covalent binding of BV to the other monomer, whereas the presence of Cys15 allosterically promotes BV binding to Cys256 in both monomers. The NIR FPs with both Cys residues have the narrowest blue-shifted spectra and the highest quantum yield. Our analysis resulted in the iRFP713/Val256Cys protein with the highest brightness in mammalian cells among available NIR FPs.
T‐cell‐receptor dose and the time of treatment during murine retrovirus infection for maintenance of immune function (1996)

C57BL/6 mice were injected with different doses of human T-cell receptor (TCR) V beta 8.1 CDR1 peptide at different times after murine retrovirus (LP-BM5) infection. Injection with TCR V beta 8.1 CDR1 peptide largely prevented the retrovirus-induced reduction in B- and T-cell proliferation, and T-helper 1 (Th1) cytokines [interleukin-2 (IL-2) and interferon-gamma (IFN-gamma)] secretion. It also suppressed T-helper 2 (Th2) cytokines (IL-6 and IL-10) production, which was stimulated by retrovirus infection. These effects were accomplished using at least 100 micrograms of peptide per mouse and the most effective dose of peptide had to be given within 4 weeks after retrovirus infection. Immunization with doses above 100 micrograms/mouse as long as 4 weeks postinfection maintained natural killer (NK) cell activity during retrovirus infection. Reducing the dose of peptide or delaying it until the disease progressed towards early murine acquired immune deficiency syndrome (AIDS) allowed development of immune dysfunction. These studies provide data suggesting that immune dysfunction, induced by murine retrovirus infection, was largely prevented by TCR V beta CDR1 peptide injection.
Multi-Tone Millimeter-Wave Frequency Synthesizer for Atmospheric Propagation Studies (2014)

The design and test results of a multi-tone millimeter-wave frequency synthesizer, based on a solid-state frequency comb generator is presented. The intended applications of the synthesizer is in a space-borne transmitter for radio wave atmospheric studies at Q-band (37 to 43 GHz). These studies would enable the design of robust high data rate space-to-ground satellite communication links.
Graphite Intercalation Compounds as Actuation Materials (2004)

The intrinsic electrochemical behavior of Graphite Intercalated Compounds (GICs) during formation offers the potential for high-force, high-strain solid-state actuation applications. To explore this behavior we submitted a “model” system, highly-oriented pyrolytic graphite (HOPG)/sulfuric acid (H2SO4), to axial compressive loads from 0 to 8 MPa, and measured the intercalation response in terms of voltage and displacement. We observed strains greater than 30% between 2 and 6 MPa, confirming the potential of GIC formation as a viable actuating mechanism. Further studies are planned in order to perform more precise analysis and examine alternate GICs.
Underground Anomaly Detection by Electromagnetic Shock Waves (2010)

A method for the detection of underground anomalies by electromagnetic (EM) shock waves is presented. Following Grischkowsky [Phys. Rev. Lett., vol. 59, pp. 1663-1666, 1987], an EM shock wave will develop in a dielectric medium by exciting a pulse which leaks into the dielectric bulk from a transmission line. A shock wave occurs when the group velocity in the line exceeds the phase velocity in the dielectric. This mechanism is similar to Cherenkov radiation. In this paper the transmission and reception of the EM shock wave between two identical leaky transmission lines is introduced. For underground detection, the two lines are placed in boreholes and are made in a manner in which the speed of propagation in the line is faster than the speed of propagation in the ground. The effect on the shock wave by an underground anomaly such as a dielectric or metallic pipeline located between the two boreholes is studied. The anomaly scatters the shock wave, resulting in a detectable disturbance in the received signal. The time delay of this disturbance, with respect to the time when the pulse was transmitted, is correlated with the location of the object. Numerical examples are presented by using a two-dimensional finite-difference time-domain algorithm.
Optical trapping, manipulation, and sorting of cells and colloids in microfluidic systems with diode laser bars (2004)

We demonstrate a new technique for trapping, sorting, and manipulating cells and micrometer-sized particles within microfluidic systems, using a diode laser bar. This approach overcomes the scaling limitations of conventional scanned laser traps, while avoiding the computational and optical complexity inherent to holographic optical trapping schemes. The diode laser bar enables us to control a large trapping zone, 1 microm by 100 microm, without the necessity of scanning or altering the phase of the beam.
Design of a polyepitope construct for the induction of HLA-A0201-restricted HIV 1-specific CTL responses usingHLA-A*0201 transgenic,H-2 class I KO mice (2001)

HLA-A*0201 transgenic, H-2D(b)/mouse beta2-microglobulin double-knockout mice were used to compare and optimize the immunogenic potential of 17HIV 1-derived,HLA-A0201-restricted epitopic peptides. A tyrosine substitution in position 1 of the epitopic peptides, which increases both their affinity for and their HLA-A0201 molecule stabilizing capacity, was introduced in a significant proportion, having verified that such modifications enhance their immunogenicity in respect of their natural antigenicity. Based on these results, a 13-polyepitope construct was inserted in the pre-S2 segment of the hepatitis B middle glycoprotein and used for DNA immunization. Long-lasting CTL responses against most of the inserted epitopes could be elicited simultaneously in a single animal with cross-recognition in several cases of their most common natural variants.
Pulmonary Phototherapy for Treating Carbon Monoxide Poisoning (2015)

Future development and scaling up of lung phototherapy for patients with CO exposure may provide a significant advance for treating and preventing CO poisoning.
Dialogue Learning with Human Teaching and Feedback in End-to-End Trainable Task-Oriented Dialogue Systems (2018)

In this work, we present a hybrid learning method for training task-oriented dialogue systems through online user interactions. Popular methods for learning task-oriented dialogues include applying reinforcement learning with user feedback on supervised pre-training models. Efficiency of such learning method may suffer from the mismatch of dialogue state distribution between offline training and online interactive learning stages. To address this challenge, we propose a hybrid imitation and reinforcement learning method, with which a dialogue agent can effectively learn from its interaction with users by learning from human teaching and feedback. We design a neural network based task-oriented dialogue agent that can be optimized end-to-end with the proposed learning method. Experimental results show that our end-to-end dialogue agent can learn effectively from the mistake it makes via imitation learning from user teaching. Applying reinforcement learning with user feedback after the imitation learning stage further improves the agent's capability in successfully completing a task.
Truthful Stochastic and Deterministic Auctions for Sponsored Search (2008)

Incentive compatibility is a central concept in auction theory, and a desirable property of auction mechanisms. In a celebrated result, Aggarwal, Goel and Motwani presented the first truthful deterministic auction for sponsored search (i.e., in a setting where multiple distinct slots are auctioned). Stochastic auctions present several advantages over deterministic ones, as they are less prone to strategic bidding, and increase the diversity of the winning bidders. Meek, Chickering and Wilson presented a family of truthful stochastic auctions for multiple identical items. We present the first class of incentive compatible stochastic auctions for the sponsored search setting. This class subsumes as special cases the laddered auctions and the stochastic auctions with the condex pricing rule, consolidating these two seemingly disconnected mechanisms in a single framework. Moreover, when the price per click depends deterministic ally on the bids the auctions in this class are unique. Accordingly, we give a precise characterization of all truthful auctions for sponsored search, in terms of the expected price that each bidder will pay per click. We also introduce randomized algorithms and pricing rules to derive, given an allocation mechanism for the single- or multiple-identical-slots scenarios, a new mechanism for the multislot framework with distinct slots. These extensions have direct practical applications.
Estimation of in vivo cancellous bone elasticity (2008)

Effect of decreasing bone density (a symptom of osteoporosis) is greater for cancellous bone than for dense cortical bone, because cancellous bone is metabolically more active. Therefore, bone density or bone mineral density at cancellous bone is generally used to estimate the onset of osteoporosis. Elasticity or elastic constant is one of fundamental mechanical parameters and directly related to the mechanical strength of bone. Accordingly, elasticity is a preferable parameter to assess the fracture risk. A novel ultrasonic bone densitometer LD-100 has been developed to obtain mass density and elasticity of cancellous bone with a spatial resolution comparable to that of the peripheral quantitative computed tomography system. Bone mass density and bone elasticity are evaluated using ultrasonic parameters based on fast and slow waves in cancellous bone using a modeling of ultrasonic wave propagation path. Elasticity is deduced from measured bone mass density and propagation speed of fast wave. Thus, elasticity of cancellous bone is approximately expressed by a cubic equation of bone mass density.
Optical Fiber Splicing (1977)

Presently available techniques for splicing optical fibers are reviewed. Methods for aligning fibers for splicing include the use of tubes, grooved substrates and precision pins. After the fibers are aligned, they are either held together by adhesives or fixtures, or they are welded by melting and fusing the ends together. In the case of cables with a large number of fibers, multi-fiber splicing considerations will impact heavily on cable design. Several multi-fiber splicing techniques achieve losses of only a few tenths dB indicating that early efforts directed at obtaining small transverse offsets and low loss have been successful. In order to obtain low splice loss in practical fiber optic systems, close attention will need to be directed toward fiber manufacturing tolerances. Indeed, mismatch in fiber parameters due to manufacturing variations may turn out to be a significant source of splice loss, thereby causing splicing requirements to impact on fiber design and fiber manufacturing. Future investigators will undoubtedly focus on the long term environmental stability of splices to determine which materials and methods provide practical fiber splices with adequate service life in the field.
Relationship Between Electrode-to-Modiolus Distance and Current Levels for Adults With Cochlear Implants (2015)

Our results suggest that electrode distance minimally contributes to the current level required for suprathreshold stimulation.
Novel waveguide MSM photodetectors on SOI substrates using silicides (2001)

Novel Si waveguide MSM photodetector suitable for high speed/high quantum efficiency applications is proposed and demonstrated. Silicides are formed on a silicon-on-insulator (SOI) substrate through metal/Si reaction under heat treatment, in two areas separated by a narrow gap. The silicide sidewalls on the two sides of the narrow gap provide lateral waveguide confinement, and also serve as electrodes. The silicide/Si interface forms a Schottky junction, making the structure a MSM diode. The waveguide structure provides a long optical path length to increase the quantum efficiency at near infrared wavelengths. The distance between electrodes can be changed easily through photolithography, and can be made very small to reduce the transit time between electrodes for high-speed operation. Since the devices are made on SOI substrates, the drift component of the photocurrent can be eliminated, further facilitating high-speed operation. First set of photodetectors was made using PtSi on commercially available SOI substrates with 0.34micrometers Si layer. Initial experiments have demonstrated a responsivity of near 200mA/W at (lambda) equals980 nm for a detector with 486micrometers long electrodes and 2 micrometers gap size. The dark current was on the order of 0.1 nA/micrometers <SUP>2</SUP> at 5V bias.
Tuning Hsp104 specificity to selectively detoxify α-synuclein (2020)

Summary Hsp104 is an AAA+ protein disaggregase that solubilizes and reactivates proteins trapped in aggregated states. We have engineered potentiated Hsp104 variants to mitigate toxic misfolding of α-synuclein, TDP-43, and FUS implicated in fatal neurodegenerative disorders. Though potent disaggregases, these enhanced Hsp104 variants lack substrate specificity, and can have unfavorable off-target effects. Here, to lessen off-target effects, we engineer substrate-specific Hsp104 variants. By altering Hsp104 pore loops that engage substrate, we disambiguate Hsp104 variants that selectively suppress α-synuclein toxicity but not TDP-43 or FUS toxicity. Remarkably, α-synuclein-specific Hsp104 variants emerge that mitigate α-synuclein toxicity via distinct ATPase-dependent mechanisms, involving α-synuclein disaggregation or detoxification of α-synuclein conformers without disaggregation. Importantly, both types of α-synuclein-specific Hsp104 variant reduce dopaminergic neurodegeneration in a C. elegans model of Parkinson’s disease more effectively than non-specific variants. We suggest that increasing the substrate specificity of enhanced disaggregases could be applied broadly to tailor therapeutics for neurodegenerative disease.
Multi-heterodyne two dimensional coherent spectroscopy using frequency combs (2017)

Optical multi-dimensional coherent spectroscopy is a powerful technique for studying the structure, properties and ultrafast dynamics of atoms, molecules, semiconductor materials and complex systems. Current implementations of multi-dimensional coherent spectroscopy have long acquisition times and/or limited spectral resolution. In addition, most of the techniques utilize complex geometries or phase cycling schemes to isolate non-linear signals. We demonstrate a novel approach of using frequency combs to perform rapid, high resolution and background free multi-dimensional coherent spectroscopy of semiconductor materials. Our approach is inspired by dual-comb spectroscopy, which has been proven to be a versatile tool for obtaining one dimensional absorption spectra with high resolution in a short acquisition time. We demonstrate the method using a GaAs multi-quantum well sample.
Constitutive expression of a rice GTPase‐activating protein induces defense responses (2008)

G-proteins (guanine nucleotide-binding proteins that usually exhibit GTPase activities) and related signal transduction processes play important roles in mediating plant defense responses; here, a rice (Oryza sativa) cDNA clone, OsGAP1, encoding a GTPase-activating protein (GAP) that also contains a protein kinase C conserved region 2 (C2) domain is reported. An interacting G-protein partner for the OsGAP1 protein was identified by yeast two-hybrid library screening and confirmed by co-immunoprecipitation; the GTPase-activation activity of OsGAP1 on this interacting G-protein was demonstrated using in vitro assays. OsGAP1 was induced by wounding in rice and the presence of the R locus Xa14 enhances such induction. Gain-of-function tests in transgenic rice and Arabidopsis thaliana showed that constitutive expression of OsGAP1 led to increased resistance to bacterial pathogens in both monocots and dicots.
Proteomic profiling of cancer of the gingivo‐buccal complex: Identification of new differentially expressed markers (2009)

Tobacco-related oral cancer is the most common cancer among Indian males, gingivo-buccal complex (GBC) being the most affected subsite due to the habit of chewing tobacco. Proteins from the lysates of microdissected normal and transformed epithelium from clinically well-characterized tissue samples of the GBC were separated by two-dimensional gel electrophoresis to identify differentially expressed proteins. Eleven protein spots showed differential expression, which could withstand the stringency of statistical evaluation. The observations were confirmed with additional tissues. Nine of these differentiators were identified by MS as lactate dehydrogenase B, α-enolase, prohibitin, cathepsin D, apolipoprotein A-I, tumor protein translationally controlled-1, an SFN family protein, 14-3-3σ and tropomyosin. Cluster analysis indicated that these proteins, as a coexpressed set, could distinguish normal and transformed epithelium. Functionally, these differentiator molecules are relevant to the pathways and processes that have been previously implicated in oral carcinogenesis and could therefore be investigated further as a panel of markers for management of cancer of the GBC.
Prostate surface segmentation from 3D ultrasound images (2003)

Segmenting, or outlining, the prostate boundary is a very important task in diagnosing and treating cancer. In this paper, an algorithm is described for semiautomatic segmentation of the prostate from 3D ultrasound images. The algorithm uses model-based initialization and mesh refinement using an efficient deformable model. Initialization requires the user to select only six points from which the outline of the prostate is estimated using shape information. The estimated outline is then automatically deformed to better fit the prostate boundary. The performance of the algorithm with a single user was compared to manual outlining by the same user. The average distance between semiautomatically and manually outlined boundaries was found to be 1.19 mm, and the average difference in volumes was 7.2%.
Silicon Photonic Crystal Open Sensors for High Sensitivity Multiplexed Chem-Bio Sensing (2013)

Photonic crystal nanophotonic open sensors are demonstrated in applications for highly sensitive chip-integrated optical absorption spectroscopy (down to 1ppb) for environmental pollution detection and biosensing microarrays (down to 50femto-molar) for fundamental medical research.
The Geometry of Differential Privacy: the Sparse and Approximate Cases (2012)

In this work, we study trade-offs between accuracy and privacy in the context of linear queries over histograms. This is a rich class of queries that includes contingency tables and range queries, and has been a focus of a long line of work. For a set of $d$ linear queries over a database $x \in \R^N$, we seek to find the differentially private mechanism that has the minimum mean squared error. For pure differential privacy, an $O(\log^2 d)$ approximation to the optimal mechanism is known. Our first contribution is to give an $O(\log^2 d)$ approximation guarantee for the case of $(\eps,δ)$-differential privacy. Our mechanism is simple, efficient and adds correlated Gaussian noise to the answers. We prove its approximation guarantee relative to the hereditary discrepancy lower bound of Muthukrishnan and Nikolov, using tools from convex geometry. We next consider this question in the case when the number of queries exceeds the number of individuals in the database, i.e. when $d > n \triangleq \|x\|_1$. It is known that better mechanisms exist in this setting. Our second main contribution is to give an $(\eps,δ)$-differentially private mechanism which is optimal up to a $\polylog(d,N)$ factor for any given query set $A$ and any given upper bound $n$ on $\|x\|_1$. This approximation is achieved by coupling the Gaussian noise addition approach with a linear regression step. We give an analogous result for the $\eps$-differential privacy setting. We also improve on the mean squared error upper bound for answering counting queries on a database of size $n$ by Blum, Ligett, and Roth, and match the lower bound implied by the work of Dinur and Nissim up to logarithmic factors. The connection between hereditary discrepancy and the privacy mechanism enables us to derive the first polylogarithmic approximation to the hereditary discrepancy of a matrix $A$.
Whitening effect of novel peptide mixture by regulating melanosome biogenesis, transfer and degradation (2020)

Peptides are short chain of amino acids linked by peptide bonds. They are widely used as effective and biocompatible active ingredients in cosmetic industry. In this study, we developed novel peptide mixture and identified its anti-pigmentation effect on melanocytes and keratinocytes. Our results revealed that peptide mixture inhibited melanosome biogenesis through the regulation of microphthalmia-associated transcription factor, a key factor of melanogenesis in melanocytes. And we observed that peptide mixture inhibited melanosome uptake through the reduction of protease-activated receptor 2, a phagocytosis-related receptor in keratinocytes. Furthermore, peptide mixture activated autophagy system resulting in degradation of transferred melanosomes in keratinocytes. The anti-pigmentation effect of multi-targeting peptide mixture was assessed in a human skin equivalent model (MelanoDerm). Melanin contents in epidermal layer were significantly decreased by topical treatment of peptide mixture, suggesting that it can be applied as a novel cosmetics material having a whitening function.
Design of modified pyrroline N-oxide derivatives as spin traps specific for hydroxyl radical (1992)

NRC publication: Yes