gebhart/patrepeval huggingface dataset:
Prokaryotic Utilization of the Twin-Arginine Translocation Pathway: a Genomic Survey (2003)

The twin-arginine translocation (Tat) pathway, which has been identified in plant chloroplasts and prokaryotes, allows for the secretion of folded proteins. However, the extent to which this pathway is used among the prokaryotes is not known. By using a genomic approach, a comprehensive list of putative Tat substrates for 84 diverse prokaryotes was established. Strikingly, the results indicate that the Tat pathway is utilized to highly varying extents. Furthermore, while many prokaryotes use this pathway predominantly for the secretion of redox proteins, analyses of the predicted substrates suggest that certain bacteria and archaea secrete mainly nonredox proteins via the Tat pathway. While no correlation was observed between the number of Tat machinery components encoded by an organism and the number of predicted Tat substrates, it was noted that the composition of this machinery was specific to phylogenetic taxa.
Tetrakis(thione)platinum(II) complexes: synthesis, spectroscopic characterization, crystal structures, and <i>in vitro</i> cytotoxicity (2015)

A new series of platinum(II) complexes based on thione ligands with general formula [Pt(thione)4]X2 (X− = Cl−, NO3−) has been synthesized and characterized using CHNS elemental analysis, infrared, 1H and 13C solution-state NMR as well as 13C and 15N solid-state NMR spectroscopy, and X-ray crystallography. The spectroscopic methods confirm the coordination of Pt(II) with thiocarbonyl groups via sulfur of the thione ligands. The X-ray structures showed a distorted square planar geometry for 1, [Pt(MeImt)4]Cl2 (MeImt = N-Methylimidazolidine-2-thione) while the hydrogen bonding interactions in 7, [Pt(iPrImt)4](NO3)2·0.6(H2O) induce a bent see-saw distortion relative to the ideal square planar geometry. The in vitro cytotoxicity studies showed that 2, [Pt(EtImt)4]Cl2 is generally the most effective, a two-fold better cytotoxic agent than cisplatin and carboplatin against MCF7 (human breast cancer).
Quantification of liver function by linearization of a two‐compartment model of gadoxetic acid uptake using dynamic contrast‐enhanced magnetic resonance imaging (2018)

Dynamic gadoxetic acid-enhanced magnetic resonance imaging (MRI) allows the investigation of liver function through the observation of the perfusion and uptake of contrast agent in the parenchyma. Voxel-by-voxel quantification of the contrast uptake rate (k<sub>1</sub> ) from dynamic gadoxetic acid-enhanced MRI through the standard dual-input, two-compartment model could be susceptible to overfitting of variance in the data. The aim of this study was to develop a linearized, but more robust, model. To evaluate the estimated k<sub>1</sub> values using this linearized analysis, high-temporal-resolution gadoxetic acid-enhanced MRI scans were obtained in 13 examinations, and k<sub>1</sub> maps were created using both models. Comparison of liver k<sub>1</sub> values estimated from the two methods produced a median correlation coefficient of 0.91 across the 12 scans that could be used. Temporally sparse clinical MRI data with gadoxetic acid uptake were also employed to create k<sub>1</sub> maps of 27 examinations using the linearized model. Of 20 scans, the created k<sub>1</sub> maps were compared with overall liver function as measured by indocyanine green (ICG) retention, and yielded a correlation coefficient of 0.72. In the 27 k<sub>1</sub> maps created via the linearized model, the mean liver k<sub>1</sub> value was 3.93 ± 1.79 mL/100 mL/min, consistent with previous studies. The results indicate that the linearized model provides a simple and robust method for the assessment of the rate of contrast uptake that can be applied to both high-temporal-resolution dynamic contrast-enhanced MRI and typical clinical multiphase MRI data, and that correlates well with the results of both two-compartment analysis and independent whole liver function measurements.
Parallel operation of microhollow cathode discharges (2002)

Summary form only given. Microhollow cathode discharges (MHCDs) are high pressure gas discharges between a cathode, which contains a circular opening and an arbitrarily shaped anode. The diameter of the cathode hole as well as the electrode gap is approximately 100 /spl mu/m. Operation on such a small spatial scale enables stable direct current glow discharge operation even at high pressure. Microhollow cathode discharges have been operated at atmospheric pressure in rare gases (e.g., argon, xenon), rare gas halogen mixtures (e.g., argon fluoride, xenon chloride) and in air. Stable dc high pressure glow discharge operation is of interest in lighting, plasma processing, and as plasma cathodes for air plasma ramparts. The required plasma size for these applications exceeds that of a single microhollow cathode discharge and therefore requires their arrangement in arrays. Parallel operation of up to sixteen micro discharges has been reported using distributed ballast. A simpler way to generate arrays is to operate the glow discharges in a range where the voltage current characteristic has a positive slope, e.g. In the abnormal glow region. This can be achieved by limiting the cathode surface to a small value such that even at low currents it is completely covered by the plasma. In order to reduce the cathode area, the cathode surface was covered with a dielectric, such that only the cylindrical surface area of the cathode opening was available as cathode.
A generic visualization framework for understanding missing links in bipartite networks (2018)

The analysis of bipartite networks is critical in many application domains, such as studying gene expression in bio-informatics. One important task is missing link prediction, which infers the existence of new links based on currently observed ones. However, in practice, analysts need to utilize their domain knowledge based on the algorithm outputs in order to make sense of the results. We propose a novel visual analysis framework, MissBi, which allows for examining and understanding missing links in bipartite networks. Some initial feedback from a management school professor has demonstrated the effectiveness of the tool.
Deep Siamese Networks with Bayesian non-Parametrics for Video Object\n Tracking (2018)

We present a novel algorithm utilizing a deep Siamese neural network as a\ngeneral object similarity function in combination with a Bayesian optimization\n(BO) framework to encode spatio-temporal information for efficient object\ntracking in video. In particular, we treat the video tracking problem as a\ndynamic (i.e. temporally-evolving) optimization problem. Using Gaussian Process\npriors, we model a dynamic objective function representing the location of a\ntracked object in each frame. By exploiting temporal correlations, the proposed\nmethod queries the search space in a statistically principled and efficient\nway, offering several benefits over current state of the art video tracking\nmethods.\n
A TOPSAR Processing Algorithm Based on Extended Chirp Scaling: Evaluation with TerraSAR-X Data (2008)

This paper presents an efficient phase preserving processor for the TOPS (Terrain Observation by Progressive Scans) imaging mode. TOPS has been proposed as a new wide swath imaging mode, which solves the problems of scalloping and azimuth-varying ambiguities introduced by the conventional ScanSAR mode by means of steering the antenna along the azimuth direction. The TOPS signal includes particularities of both ScanSAR and Spotlights modes, but existing processing algorithms do not provide an efficient processing of TOPS data. This paper presents an algorithm based on Extended Chirp Scaling (ECS) together with a new azimuth scaling step. The proposed solution allows also the selection of the final azimuth image sampling without the need of interpolations, hence easing the forthcoming mosaicking of the different subswaths. Real data acquired by TerraSAR-X are used to validate the processor.
Fabrication and Dark-Field Scattering Characterization of Deterministic Aperiodic Plasmonic Spirals (2010)

Plasmonic aperiodic spirals with various geometries have been designed, fabricated and characterized for the first time. These new structures could result in the engineering of novel plasmonic devices for plasmonic-enhanced, polarization-insensitive broadband photo-detectors.
Multirate signal processing for multiple listener low frequency room acoustic equalization (2005)

Low frequency room acoustic equalization is a challenging problem to solve with realizable low order digital equalization filters. In this paper we address the problem of low frequency room equalization for multiple listeners, simultaneously, using multirate filtering with a pattern recognition approach. The pattern recognition model captures the variabilities in room acoustics between different listening positions, whereas multirate processing allows effective filtering, of low frequency room responses, at low rates. An important feature of the proposed filter is its ability to perform simultaneous equalization of responses at low frequencies at multiple locations with a reduced computational requirement. A comparison of equalization performance between the proposed filter and a lower order filter, designed using a popular warping technique, is also presented.
Design and implementation of an automated artificial urinary sphincter (2015)

Abstract—Severe urinary incontinence is defined as an involuntary urine loss in great quantity. Implantation of an artificial urinary sphincter can overcome this handicap and make the patient recover a normal social life. Today, the prosthesis (AMS 800™) implanted is manufactured by the American Medical System company. It provides good results on human incontinence and has demonstrated its reliability on about 80 % of implanted patients. However, surgical revision rate linked to mechanical breakdowns or urethral atrophy, secondary to continuous high pressures exerted on the urethra, remains high. Moreover, the use of this prosthesis is difficult and, then, not adapted to all patients. The purpose of this study is an improvement upon the AMS 800 ™ system by dynamically regulating the pressure within the cuff in order to maintain an optimum pressure applied on the urethra. Ergonomics is aimed to be improved as well. I.
Optical Parametric Oscillator with Bi-noncolinear, Porro Prism Cavity (1997)

Optical parametric oscillators (OPOs) have become accepted in recent years as useful, reliable sources of tunable coherent light, particulary those pumped by Q-switched, nanosecond-pulse-length pump lasers.
Local SAR, global SAR, transmitter power and excitation accuracy trade-offs in low flip-angle parallel transmit pulse design (2013)

Purpose\nWe propose a constrained optimization approach for designing parallel transmit (pTx) pulses satisfying all regulatory and hardware limits. We study the trade-offs between excitation accuracy, local and global specific absorption rate (SAR), and maximum and average power for small flip-angle pTx (eight channels) spokes pulses in the torso at 3 T and in the head at 7 T.\nMethods\nWe compare the trade-offs between the above-mentioned quantities using the L-curve method. We use a primal-dual algorithm and a compressed set of local SAR matrices to design radio-frequency (RF) pulses satisfying all regulatory (including local SAR) and hardware constraints.\nResults\nLocal SAR can be substantially reduced (factor of 2 or more) by explicitly constraining it in the pulse design process compared to constraining global SAR or pulse power alone. This often comes at the price of increased pulse power.\nConclusion\nSimultaneous control of power and SAR is needed for the design of pTx pulses that are safe and can be played on the scanner. Constraining a single quantity can create large increase in the others, which can then rise above safety or hardware limits. Simultaneous constraint of local SAR and power is fast enough to be applicable in a clinical setting.
Modeling Artistic Workflows for Image Generation and Editing (2020)

People often create art by following an artistic workflow involving multiple stages that inform the overall design. If an artist wishes to modify an earlier decision, significant work may be required to propagate this new decision forward to the final artwork. Motivated by the above observations, we propose a generative model that follows a given artistic workflow, enabling both multi-stage image generation as well as multi-stage image editing of an existing piece of art. Furthermore, for the editing scenario, we introduce an optimization process along with learning-based regularization to ensure the edited image produced by the model closely aligns with the originally provided image. Qualitative and quantitative results on three different artistic datasets demonstrate the effectiveness of the proposed framework on both image generation and editing tasks.
A field splicing system for single-mode optical fiber (1983)

Abstract : This paper discusses a field splicing ssystem for single-mode optical fiber. The system consists of a specialized single-mode fusion splicing set and an optical power monitoring system used to assist in aligning the fibers. The prerequisites for fusion splicing of single-mode fiber are discussed. The fusion equipment and optical power monitoring system are described in detail and their operation is discussed. Finally, the performance of system is reported. (Author)
A Flexible Surgical Robotic System for Removal of Early-Stage Gastrointestinal Cancers by Endoscopic Submucosal Dissection (2016)

Endoscopic submucosal dissection (ESD) is an effective and less invasive treatment for early gastric and colorectal cancers. Nevertheless, performing ESD through a flexible endoscope is technically challenging due to the limited controllability of the endoscopic instruments. Therefore, a surgical robotic system with high dexterity and better ergonomics is much needed. A master-slave dual-arm robot with customizing workspace for ESD is proposed for this study. The design is such that the procedure is completed without the need for changing the instrument. Our robot is mainly driven by tendon-sheath (TS) mechanism. Modeling and use of a controller for elongation compensation of tendon due to friction to increase position control accuracy are presented. Experiment shows that the controller greatly enhances the controllability of the robot. We have demonstrated that the design of the robot arm allows it to lift up to 48 g, which is sufficient for ESD. Six subjects, including three endoscopists and upper gastrointestinal surgeons, were invited to evaluate the system in an ex vivo experiment. Experienced surgeons were able to complete a dissection within 30 min. We have demonstrated a prototype robot that can facilitate the ESD procedure with bimanual tissue dissection. The system is competent to remove a lesion area precisely. Further studies are needed to evaluate the system in vivo.
Enhancing intracranial delivery of clinically relevant non-viral gene vectors (2016)

Gene therapy is a promising strategy for the management of various neurological disorders that do not respond adequately to conventional therapeutics. The development of gene vectors with favorable safety profiles that can achieve uniform distribution and high-level transgene expression in the brain remains challenging. The rod-shaped, non-viral gene delivery platform based on poly-L-lysine (PLL) conjugated to a single segment of polyethylene glycol (PEG) has shown safe transfection in human nares and mouse brains <i>in vivo</i>. However, we have previously demonstrated that a denser PEG coating is required for rapid diffusion of nanoparticles in the brain extracellular space. Here, we engineered a densely PEGylated version of this platform based on PLL polymers conjugated to branched PEG via alkyne-azide cycloaddition. We found that the newly developed gene vectors rapidly diffused in the brain parenchyma, providing significantly improved vector distribution and overall transgene expression <i>in vivo</i> compared to the previously developed platform. These brain-penetrating DNA nanoparticles exhibited enhanced cellular uptake presumably due to their ellipsoidal morphology. By simultaneously improving delivery to target cells and subsequent transfection, our densely PEGylated PLL DNA nanoparticles can provide widespread, high levels of transgene expression, essential for effective targeting of highly disseminated brain diseases.
A Framework for Representing and Manipulating Tonal Music (2000)

This paper describes a novel set of tools, collectively known as “Smart Harmony”, that allows the composer to control and manipulate music at a high level, while constraining the music to conform to a designated functional tonal framework. The Smart Harmony system permits two essential types of operations. First, it allows musical material to be taken from one context and used in a new context – that is, with a new key and/or chord progression – and automatically transforms the material to sound appropriate in that context. Second, it enables musical material to be reshaped, pulling notes higher or lower in pitch, while constraining the material to sound appropriate within a given harmony. An important benefit of our mechanism derives from its relaxation of a strict interpretation of harmonic function, by which means we gain the flexibility to perform these manipulations. We describe data structures and algorithms to implement this mechanism, and offer motivation steeped in traditional functional harmony for its behavior. Lastly, we present musical examples. 1.
Evaluation of Aminohydantoins as a Novel Class of Antimalarial Agents (2013)

Given the threat of drug resistance, there is an acute need for new classes of antimalarial agents that act via a unique mechanism of action relative to currently used drugs. We have identified a set of druglike compounds within the Tres Cantos Anti-Malarial Set (TCAMS) which likely act via inhibition of a Plasmodium aspartic protease. Structure-activity relationship analysis and optimization of these aminohydantoins demonstrate that these compounds are potent nanomolar inhibitors of the Plasmodium aspartic proteases PM-II and PM-IV and likely one or more other Plasmodium aspartic proteases. Incorporation of a bulky group, such as a cyclohexyl group, on the aminohydantion N-3 position gives enhanced antimalarial potency while reducing inhibition of human aspartic proteases such as BACE. We have identified compound 8p (CWHM-117) as a promising lead for optimization as an antimalarial drug with a low molecular weight, modest lipophilicity, oral bioavailability, and in vivo antimalarial activity in mice.
Study and characterization of mutated antigen specific T cells isolated from fresh tumor and peripheral lymphocytes in cancer patients (2015)

Meeting abstracts T cell-based immunotherapy shows promise for the successful treatment of advanced cancer. Indeed, adoptively transferred tumor infiltrating T lymphocytes (TIL) that mediated complete regression of metastatic melanoma have been shown to recognize neoantigens/mutated epitopes
Targeting Migration inducting gene-7 inhibits carcinoma cell invasion, early primary tumor growth, and stimulates monocyte oncolytic activity (2009)

Expression of Migration inducting gene-7 (Mig-7) is limited to tumor cells and to date not found in normal tissues. Multiple tumor microenvironment factors, such as epidermal and hepatocyte growth factors, in concert with alphavbeta5 integrin ligation, induce Mig-7 mRNA expression. Gain or loss of Mig-7 protein studies shows that Mig-7 promotes invasion of colon and endometrial carcinoma cells. These data led us to hypothesize that targeting Mig-7 through various methods could decrease invasion, enhance monocyte cell killing of tumor cells, and inhibit disease progression. To begin testing this hypothesis, an in vitro chemoinvasion assay of endometrial carcinoma cells treated with Mig-7-specific or control antibodies was used. Mig-7 antibody significantly reduced invasion by >60% compared with controls. In another approach to test this hypothesis, an in vitro analysis of peptide-stimulated human peripheral blood monocyte cells and their killing of MCF-7 breast carcinoma cells was used. Mig-7 peptide treatment increased monocyte cell tumor necrosis factor expression and killing of MCF-7 cells 30-fold over no peptide stimulation and 3-fold over MUC-1 or control peptide treatments. Furthermore, stably expressing Mig-7-specific short hairpin RNA resulted in significantly reduced Mig-7 protein levels and early primary tumor growth in a xenograft nude mouse model. Reduced phosphorylation of ERK1/2, Akt, and S6 kinase as well as decreased membrane-type 1 matrix metalloproteinase activity were mechanisms through which Mig-7 protein caused these effects. Based on these collective data, Mig-7 expression could be a potential candidate for future targeted cancer therapies.
Bias-Compensated Informed Sound Source Localization Using Relative Transfer Functions (2018)

In this paper, we consider the problem of estimating the target sound direction of arrival (DoA) for a hearing aid (HA) system, which can connect to a wireless microphone worn by the talker of interest. The wireless microphone “informs” the HA system about the noise-free target speech. To estimate the DoA, we consider a maximum-likelihood approach, and we assume that a database of DoA-dependent relative transfer functions (RTFs) has been measured in advance and is available. The proposed DoA estimator is able to take the available noise-free target speech, ambient noise characteristics, and the shadowing effect of the user's head on the received signals into account, and it supports both monaural and binaural microphone array configurations. Moreover, we analytically analyze the bias in the proposed estimator and introduce a modified estimator, which has been compensated for the bias. We demonstrate that the proposed method has lower computational complexity and better performance than recent RTF-based estimators. Furthermore, to decrease the number of parameters required to be wirelessly exchanged between the HAs in binaural configurations, we propose an information fusion strategy, which avoids transmitting microphone signals between the HAs. An important benefit of the proposed IF strategy is that the number of parameters to be exchanged between the HAs is independent of the number of HA microphones. Finally, we investigate the performance of variants of the proposed estimator extensively in different noisy and reverberant situations.