gebhart/patrepeval huggingface dataset:
Observing monomer: dimer transitions of neurotensin receptors 1 in single SMALPs by homoFRET and in an ABELtrap (2019)

G protein-coupled receptors (GPCRs) are a large superfamily of membrane proteins that are activated by extracellular small molecules or photons. Neurotensin receptor 1 (NTSR1) is a GPCR that is activated by neurotensin, i.e. a 13 amino acid peptide. Binding of neurotensin induces conformational changes in the receptor that trigger the intracellular signaling processes. While recent single-molecule studies have reported a dynamic monomer – dimer equilibrium of NTSR1 in vitro, a biophysical characterization of the oligomerization status of NTSR1 in living mammalian cells is complicated. Here we report on the oligomerization state of the human NTSR1 tagged with mRuby3 by dissolving the plasma membranes of living HEK293T cells into 10 nm-sized soluble lipid nanoparticles by addition of styrene-maleic acid copolymers (SMALPs). Single SMALPs were analyzed one after another in solution by multi-parameter single molecule spectroscopy including brightness, fluorescence lifetime and anisotropy for homoFRET. Brightness analysis was improved using single SMALP detection in a confocal ABELtrap for extended observation times in solution. A bimodal brightness distribution indicated a significant fraction of dimeric NTSR1 in SMALPs or in the plasma membrane, respectively, before addition of neurotensin.
Preparation and In-Vitro Dissolution of Ibuprofen: Soluplus Solid Dispersion (2016)

Introduction: Ibuprofen is widely used in treatment of mild to moderated pain and fever. However, according to Biopharmaceutical Classification System (BCS) it is classified as Class II compound having high permeability and low solubility, thus the rate limiting step to avoid delaying in analgesic effect is to be available in soluble state. Objective: To prepares and characterize Ibuprofen:Souplus solid dispersion using co-evaporation technique. Methods: Various ration of Soluplus (0, 10, 30, 50, 70, 80, 90, and 100 %) was first dissolved in a common solvent followed by adding the complementing ratio of Ibuprofen. The solvent was removed under fume hood overnight. The thin film formed after evaporation was collected, compressed and tested for in-vitro dissolution at phosphate buffer pH 7.2. The physical appearance of the film also was tested. Results:At 40% Soluplus the dissolution of Ibuprofen was around 25 % at 30 min compared with 15% Soluplus showed around 80% resales at the same time interval. 10% soluplus released 100% at 30 min. Interestingly, after 8-10 hr. The release profile was more sustained until 24 hr. Regardless the % of Soluplus. Conclusion: Sustained release profile of Ibuprofen:Soluplus solid dispersion can be achieved at lower % of Soluplus.
hnRNP L regulates the tumorigenic capacity of lung cancer xenografts in mice via caspase-9 pre-mRNA processing (2010)

Caspase-9 is involved in the intrinsic apoptotic pathway and suggested to play a role as a tumor suppressor. Little is known about the mechanisms governing caspase-9 expression, but post-transcriptional pre-mRNA processing generates 2 splice variants from the caspase-9 gene, pro-apoptotic caspase-9a and anti-apoptotic caspase-9b. Here we demonstrate that the ratio of caspase-9 splice variants is dysregulated in non-small cell lung cancer (NSCLC) tumors. Mechanistic analysis revealed that an exonic splicing silencer (ESS) regulated caspase-9 pre-mRNA processing in NSCLC cells. Heterogeneous nuclear ribonucleoprotein L (hnRNP L) interacted with this ESS, and downregulation of hnRNP L expression induced an increase in the caspase-9a/9b ratio. Although expression of hnRNP L lowered the caspase-9a/9b ratio in NSCLC cells, expression of hnRNP L produced the opposite effect in non-transformed cells, suggesting a post-translational modification specific for NSCLC cells. Indeed, Ser52 was identified as a critical modification regulating the caspase-9a/9b ratio. Importantly, in a mouse xenograft model, downregulation of hnRNP L in NSCLC cells induced a complete loss of tumorigenic capacity that was due to the changes in caspase-9 pre-mRNA processing. This study therefore identifies a cancer-specific mechanism of hnRNP L phosphorylation and subsequent lowering of the caspase-9a/9b ratio, which is required for the tumorigenic capacity of NSCLC cells.
Few-atom effects in atom optics (1998)

Despite the many advances and achievements in the fields of atom optics and atom cooling, there remains a wealth of dynamical detail to be filled in. While the main features of the important phenomena of atomic cooling, trapping and manipulation by electromagnetic fields are well understood, there are interesting subsidiary effects that are worth our attention. An example, which we discuss in Ch. 5 is the discovery that atomic diffusion in optical lattices may not follow the normal diffusion equation. The work reported in this dissertation represents an investigation into possible few-body effects in some atom optical configurations of interest. The effects of indistinguishability, through the exchange force, on atomic diffraction by standing wave light fields is considered in Ch. 2. In Ch. 3, after a brief overview of atomic collisions in light fields, we look at the role that the dipole-dipole interaction might play, again in atomic diffraction. Chapters 4 and 5 are concerned with optical lattices, and lay the ground work for a study of the effect of the dipole-dipole interaction on the dynamics of atoms confined in such lattices.
Architecting an Energy-Efficient DRAM System for GPUs (2017)

This paper proposes an energy-efficient, high-throughput DRAM architecture for GPUs and throughput processors. In these systems, requests from thousands of concurrent threads compete for a limited number of DRAM row buffers. As a result, only a fraction of the data fetched into a row buffer is used, leading to significant energy overheads. Our proposed DRAM architecture exploits the hierarchical organization of a DRAM bank to reduce the minimum row activation granularity. To avoid significant incremental area with this approach, we must partition the DRAM datapath into a number of semi-independent subchannels. These narrow subchannels increase data toggling energy which we mitigate using a static data reordering scheme designed to lower the toggle rate. This design has 35% lower energy consumption than a die-stacked DRAM with 2.6% area overhead. The resulting architecture, when augmented with an improved memory access protocol, can support parallel operations across the semi-independent subchannels, thereby improving system performance by 13% on average for a range of workloads.
Optical Frequency Comb Generation in Monolithic Microresonators ................... Kippenberg (2018)

Optical frequency combs [1-3] provide equidistant frequency markers in the infrared, visible and extreme ultra-violet [4,5]. Early work by T.W. Hansch recognized that the periodic 
pulse train of a mode-locked laser [6,7], which intrinsically provides in Fourier domain 
an output spectrum that constitutes an optical frequency comb, can be used to measure 
unknown optical frequencies. An optical frequency comb is generally characterized by 
its two degrees of freedom, the mode spacing frep, which in a pulsed laser is given by the 
pulse repetition rate [8], as well as the carrier envelope offset frequency fceo, which determines the frequency offset of the comb teeth from integer multiples of the repetition rates.In time domain, fceo describes the phase slippage of the pulse envelope with respect to 
the carrier. Thus, any comb line of the resulting output spectrum can be expressed by 
fm  =  fceo  + mfrep, where m is an integer. Measurement and control of frep and fceo allows 
to phase-coherently link optical frequencies across the entire spectrum spanned by the 
comb [8,9]. In this case, every comb tooth is uniquely determined by the experimentally 
controlled quantities fceo and frep. Therefore, any arbitrary optical frequency within the 
spectrum of the comb may be synthesized, or, vice versa, any given optical frequency 
within this spectrum may be phase-coherently compared to the frequencies fceo and frep in 
the RF domain, which can be referenced to microwave time standard [10,11]. This unique 
ability has made the frequency comb a revolutionary tool in metrology and laser spectroscopy, and, serving as a clockwork mechanism, has enabled the development and 
practical use of time standards in the optical domain [2,3,12,13]. Beyond these advances 
in metrology and precision measurements, frequency combs have given new impetus 
to applications such as broadband laser-based gas sensing [14-16] or cavity ring down 
spectroscopy [17].
Articulated Pose Estimation Using Hierarchical Exemplar-Based Models (2016)

Exemplar-based models have achieved great success on localizing the parts of semi-rigid objects. However, their efficacy on highly articulated objects such as humans is yet to be explored. Inspired by hierarchical object representation and recent application of Deep Convolutional Neural Networks (DCNNs) on human pose estimation, we propose a novel formulation that incorporates both hierarchical exemplar-based models and DCNNs in the spatial terms. Specifically, we obtain more expressive spatial models by assuming independence between exemplars at different levels in the hierarchy; we also obtain stronger spatial constraints by inferring the spatial relations between parts at the same level. As our method strikes a good balance between expressiveness and strength of spatial models, it is both effective and generalizable, achieving state-of-the-art results on different benchmarks: Leeds Sports Dataset and CUB-200-2011.
Alimentar a los gatos como carnívoros (y II). (2007)

Los gatos domesticos, igual que los perros, pertenecen al orden de los carnivoros. No obstante, la evaluacion comparativa de sus requerimientos nutricionales, caracteristicas anatomicas y adaptaciones metabolicas, demuestra que estas dos especies han evolucionado de forma distinta.
A Framework for MPEG-4 Contents Delivery over DMB (2004)

Digital Multimedia Broadcasting (DMB) is an upcoming standard in Korea used to provide mobile multimedia broadcasting service based on the Eureka-147 Digital Audio Broadcasting (DAB) system. The current dominant multimedia coding standard, MPEG-4, is foreseen to play an important role in forthcoming DMB services. However, the current approaches for transporting MPEG-4 content over DMB networks are not optimized. To address this issue we propose a novel MPEG-4 stream multiplexer, called M4SMux, which provides better stream multiplexing and delivery over DMB networks. M4SMux features an MPEG-4 elementary-stream interleaving mechanism that reduces the multiplexing overhead and a multiplex configuration mechanism that utilizes M4SLinkTable for easy content access. In addition, we propose an error correction method which enhances transport efficiency.
A Novel Efficient Deoxygenation Process for N-Heteroarene N-Oxides (2005)

A novel deoxygenation process for N-heteroarene N-oxides is described. The deoxygenation process has been carried out by utilizing some short C-chain alcohols, benzyl alcohol, or 1-phenylethanol as the solvent in the presence of a base, such as sodium alkoxide or sodium hydroxide. A series of N-heteroarene N-oxides was submitted to the developed conditions to provide the corresponding N-heteroarenes with high yield and excellent selectivity. When the deoxygenation is carried out with benzyl alcohol or 1-phenylethanol as the reaction medium, the process can be performed under very mild conditions, at only 30 degrees C. The deoxygenation process is in contrast to several other methods performed without the presence of any transition metal as a catalyst or stoichiometric reagent. DFT calculations suggest that the alkoxide performs a nucleophilic attack on the N-heteroarene in the ortho or para position. This bond is cleaved homolytically with the overall result being that a single electron-transfer step has occurred. The products of this process are an N-heteroarene N-oxide radical anion and an alkoxyl or benzyloxy radical, depending on the solvent that has been used. Successive steps of the mechanism result in an oxygen transfer from the N-oxide to give the deoxygenated N-heteroarene and 1 equiv of the aldehyde, which is the oxidation product of the solvent alcohol.
Our obsession with saturated fats: is it time to rethink their role in the coronary artery disease? (2014)

Abstract“WHO emphasizes physical inactivity as one of the five major targets to attack the onslaught of noncommunicable diseases around the world. It is time to replace the ‘war on fats’ with a ‘war on unhealthy lifestyle’.”Keywords: coronary artery diseasefood synergylifestyle synergysaturated fatstrans-fats
Improvement of nattokinase production by Bacillus subtilis using an optimal feed strategy in fed-batch fermentation (2017)

Nattokinase is an enzyme with strong fibrinolytic activity that can be used for preventing hypertension and cardiovascular diseases. In this study, Bacillus subtilis K-C3 was cultured in fed-batch fermentation for the production of nattokinase. In a first step the enzyme production was optimized by testing substrates for their influence on the enzyme activity. Experiments revealed glycerol as the best substrate with the highest enzyme yield and less by-product formation compared to other substrates. The optimal process parameters were then applied to fed-batch fermentation. An optimal feed strategy for fed-batch that allowed for maximum enzyme production was designed based on fed-batch kinetic model. During fed-bath operation a specific growth rate of 0.2 h-1was controlled using a glycerol feed rate predetermined from the model. With the designed feed strategy, a high cell density of 73.47±2.63 g/l and a nattokinase activity of 9,198.51±268.09 units/ml were achieved at 28 hours of cultivation. An overall enzyme yield of 61.36±1.80 units/g was obtained. Productivity of nattokinase in fed-batch fermentation was 545.95±27.88 units/h, a 20-fold higher than that in batch fermentation. High titer and high productivity of nattokinase achieved in this study has indicated the efficiency of the designed feed strategy used for fed-batch process. The same strategy may also be applied to other processes to increase production of other enzymes.
Space-based autonomous reconfigurable protocol chip (2005)

In this paper, we present an architecture for a reconfigurable protocol chip for space-based applications. We present a model for examining various stimuli for reconfiguration in space, and identify some approaches to operating on the stimuli. In particular, we examine fault tolerant schemes and reconfiguration based on detection of a link layer framing format.
A Bidirectional Knudsen Pump with a 3D-Printed Thermal Management Platform (2021)

This paper reports on a bidirectional Knudsen pump (KP) with a 3D-printed thermal management platform; the pump is intended principally for microscale gas chromatography applications. Knudsen pumps utilize thermal transpiration, where non-viscous flow is created against a temperature gradient; no moving parts are necessary. Here, a specialized design leverages 3D direct metal laser sintering and provides thermal management that minimizes loss from a joule heater located on the outlet side of KP, while maintaining convective cooling on the inlet side. The 3D-KP design is integrative and compact, and is specifically intended to simplify assembly. The 3D-KP pumping area is ≈1.1 cm2; with the integrated heat sink, the structure has a footprint of 64.2 × 64.2 mm2. Using mixed cellulose ester (MCE) membranes with a 25 nm average pore diameter and 525 μm total membrane thickness as the pumping media, the 3D-KP achieves a maximum flow rate of 0.39 sccm and blocking pressure of 818.2 Pa at 2 W input power. The operating temperature is 72.2 °C at ambient room temperature. In addition to MCE membranes, anodic aluminum oxide (AAO) membranes are evaluated as the pumping media; these AAO membranes can accommodate higher operating temperatures than MCE membranes. The 3D-KP with AAO membranes with 0.2 μm average pore diameter and 531 μm total membrane thickness achieves a maximum flow rate of 0.75 sccm and blocking pressure of 496.1 Pa at 9.8 W at an operating temperature of 191.2 °C.
Development of a quantitative fluorescence lateral flow immunoassay (LFIA) prototype for point-of-need detection of anti-Müllerian hormone (2023)

A panel of commercial calibrators was used to develop a standard curve to determine the analytical sensitivity (LOD = 0.41 ng/ml) and the analytical range (0.41-15.6 ng/ml) of the LFIA. Commercial controls were then tested to perform an initial evaluation of the prototype performance and showed a high degree of precision (Control I CV 2.18%; Control II CV 3.61%) and accuracy (Control I recovery 126%; Control II recovery 103%). <i>Conclusions</i>: This initial evaluation suggests that, in future clinical testing, the AMH LFIA will likely have the capability of distinguishing women with low ovarian reserve (<1 ng/ml AMH) from women with normal (1-4 ng/ml AMH) ovarian reserve. Furthermore, the LFIA demonstrated a wide linear range, indicating the assay's applicability to the detection of other health conditions such as PCOS, which requires AMH measurement at higher concentrations (>6 ng/ml).
Mechanisms underlying activation of retinal bipolar cells through targeted electrical stimulation: a computational study (2021)

<i>Objective</i>. Retinal implants have been developed to electrically stimulate healthy retinal neurons in the progressively degenerated retina. Several stimulation approaches have been proposed to improve the visual percept induced in patients with retinal prostheses. We introduce a computational model capable of simulating the effects of electrical stimulation on retinal neurons. Leveraging this computational platform, we delve into the underlying mechanisms influencing the sensitivity of retinal neurons' response to various stimulus waveforms.<i>Approach</i>. We implemented a model of spiking bipolar cells (BCs) in the magnocellular pathway of the primate retina, diffuse BC subtypes (DB4), and utilized our multiscale admittance method (AM)-NEURON computational platform to characterize the response of BCs to epiretinal electrical stimulation with monophasic, symmetric, and asymmetric biphasic pulses.<i>Main results</i>. Our investigations yielded four notable results: (a) the latency of BCs increases as stimulation pulse duration lengthens; conversely, this latency decreases as the current amplitude increases. (b) Stimulation with a long anodic-first symmetric biphasic pulse (duration > 8 ms) results in a significant decrease in spiking threshold compared to stimulation with similar cathodic-first pulses (from 98.2 to 57.5<i>µ</i>A). (c) The hyperpolarization-activated cyclic nucleotide-gated channel was a prominent contributor to the reduced threshold of BCs in response to long anodic-first stimulus pulses. (d) Finally, extending the study to asymmetric waveforms, our results predict a lower BCs threshold using asymmetric long anodic-first pulses compared to that of asymmetric short cathodic-first stimulation.<i>Significance</i>. This study predicts the effects of several stimulation parameters on spiking BCs response to electrical stimulation. Of importance, our findings shed light on mechanisms underlying the experimental observations from the literature, thus highlighting the capability of the methodology to predict and guide the development of electrical stimulation protocols to generate a desired biological response, thereby constituting an ideal testbed for the development of electroceutical devices.
Experimental performance assessment of the sub-band minimum variance beamformer for ultrasound imaging (2017)

Recent progress in adaptive beamforming techniques for medical ultrasound has shown that current resolution limits can be surpassed. One method of obtaining improved lateral resolution is the Minimum Variance (MV) beamformer. The frequency domain implementation of this method effectively divides the broadband ultrasound signals into sub-bands (MVS) to conform with the narrow-band assumption of the original MV theory. This approach is investigated here using experimental Synthetic Aperture (SA) data from wire and cyst phantoms. A 7MHz linear array transducer is used with the SARUS experimental ultrasound scanner for the data acquisition. The lateral resolution and the contrast obtained, are evaluated and compared with those from the conventional Delay-and-Sum (DAS) beamformer and the MV temporal implementation (MVT). From the wire phantom the Full-Width-at-Half-Maximum (FWHM) measured at a depth of 52mm, is 16.7μm (0.08λ) for both MV methods, while the corresponding values for the DAS case are at least 24 times higher. The measured Peak-Side-lobe-Level (PSL) may reach -41dB using the MVS approach, while the values from the DAS and MVT beamforming are above -24dB and -33dB, respectively. From the cyst phantom, the power ratio (PR), the contrast-to-noise ratio (CNR), and the speckle signal-to-noise ratio (sSNR) measured at a depth of 30mm are at best similar for MVS and DAS, with values ranging between -29dB and -30dB, 1.94 and 2.05, and 2.16 and 2.27 respectively. In conclusion the MVS beamformer is not suitable for imaging continuous targets, and significant resolution gains were obtained only for isolated targets.
H-2Ld Antigen Encoded by a Recombinant Retrovirus Genome Is Expressed on the Surface of Infected Cells (1985)

A recombinant murine retrovirus was constructed which contains, within its genome, a truncated version of the gene encoding the murine H-2Ld major histocompatibility antigen. The H-2Ld gene, which was inserted 3' of the env splice acceptor site in the recombinant retrovirus MSV-neo, lacked the 5' promoter and TATA sequences and the 3' transcription termination and polyadenylate addition sites of the normal H-2Ld gene. Transfection of the MSV-neo/H-2Ld plasmid (pLTV-11) into Y-2 cells resulted in the production of the transmissible recombinant retrovirus LTV-11. Cells infected with LTV-11 virus were resistant to the eucaryotic antibiotic G418 and expressed H-2Ld on the cell surface. These infected cells contained a viral RNA species which possessed both the H-2Ld and the neomycin resistance gene sequences but did not contain significant levels of the smaller H-2Ld-specific mRNA. The H-2Ld antigen expressed on the surface of infected cells functioned as a target for cytolytic T cells specific for the H-2Ld antigen.
Multiantenna Analog Network Coding for Multihop Wireless Networks (2010)

This paper proposes a two-phase minimum mean-square-error bidirectional amplify-and forward (MMSE-BAF) relaying protocol to allow two sources exchange independent messages via a relay node equipped with multiple antennas. MMSE-BAF performs a joint linear MMSE filtering of the received signal after the multiple access phase before amplifying and forwarding the filtered signal using a single transmit antenna, possibly through a specific antenna selection procedure, during the broadcast phase. The proposed protocol extends upon the so-called analog network coding schemes in the literature in that it inherently exploits the multiple antennas at the relay station to reduce the noise enhancement typical of an AF protocol, and can also compensate for link imbalances between the relay and the sources and is agnostic to sources' modulation and coding schemes. We derive the instantaneous signal-to-noise ratio expressions for the received signal by the sources in the downlink and provide extensive link-level simulations for the MMSE-BAF protocol subject to both frequency flat and selective fading. Furthermore, we pinpoint the modifications to be incorporated into the IEEE 802.16e orthogonal-frequency-division multiple access (OFDMA) cellular standard (mobile WiMax) to enable support of multiantenna bidirectional communications and show that MMSE-BAF is a viable solution within that framework.