gebhart/patrepeval huggingface dataset:
Structural Optimization and De Novo Design of Dengue Virus Entry Inhibitory Peptides (2010)

Viral fusogenic envelope proteins are important targets for the development of inhibitors of viral entry. We report an approach for the computational design of peptide inhibitors of the dengue 2 virus (DENV-2) envelope (E) protein using high-resolution structural data from a pre-entry dimeric form of the protein. By using predictive strategies together with computational optimization of binding "pseudoenergies", we were able to design multiple peptide sequences that showed low micromolar viral entry inhibitory activity. The two most active peptides, DN57opt and 1OAN1, were designed to displace regions in the domain II hinge, and the first domain I/domain II beta sheet connection, respectively, and show fifty percent inhibitory concentrations of 8 and 7 microM respectively in a focus forming unit assay. The antiviral peptides were shown to interfere with virus:cell binding, interact directly with the E proteins and also cause changes to the viral surface using biolayer interferometry and cryo-electron microscopy, respectively. These peptides may be useful for characterization of intermediate states in the membrane fusion process, investigation of DENV receptor molecules, and as lead compounds for drug discovery.
Joint frequency-domain adaptive equalization and interference cancellation for multi-user space-time block-coded systems (2004)

We develop an efficient adaptive receiver for joint equalization and interference cancellation for multi-user space-time block-coded transmissions. The receiver exploits the rich code structure and allows multiple user transmissions over frequency-selective fading channels with reduced complexity and lower system overhead. The adaptation scheme is based on a recursive least-squares implementation for faster convergence; nevertheless, it exploits the code structure to attain RLS performance at LMS complexity.
Novel Markers for Alternative Activation of Macrophages: Macrophage Galactose‐Type C‐Type Lectins 1 and 2 (2004)

In parallel with the Th1/Th2 dichotomy, macrophages are capable of developing into functionally and molecularly distinct subpopulations, due to differences in, for example cytokine environment and pathological conditions. While the best‐studied, classically activated macrophage is induced by type I stimuli such as IFN‐γ, a type II cytokine environment antagonizes the classical activation of macrophages and is capable of alternatively activating macrophages. However, molecular markers associated with these type II cytokine‐dependent, alternatively activated macrophages remain scarce. Besides the earlier documented markers macrophage mannose receptor and arginase 1, we recently demonstrated that murine alternatively activated macrophages are characterized by increased expression of FIZZ1 and Ym. We now report that expression of the two members of the mouse macrophage galactose‐type C‐type lectin gene family, termed mMGL1 and mMGL2, is induced in diverse populations of alternatively activated macrophages, including peritoneal macrophages elicited during infection with the protozoan Trypanosoma brucei or the Helminth Taenia crassiceps , and alveolar macrophages elicited in a mouse model of allergic asthma. We also demonstrate that, in vitro , interleukin‐4 and interleukin‐13 upregulate mMGL1 and mMGL2 expression and that, in vivo , induction of mMGL1 and mMGL2 is dependent on interleukin‐4 receptor signalling. Moreover, we show that regulation of MGL expression is similar in human monocytes and monocyte‐derived macrophages. Hence, macrophage galactose‐type C‐type lectins represent novel markers for both murine and human alternatively activated macrophages; thus, paving the way for further characterization of the phenotype of macrophages occurring in Th2 conditions.
Dopant-selective etch stops in 6H and 3C SiC (1997)

A novel photoelectrochemical etching process for 6H– and 3C–SiC is described. This method enables n-type material to be etched rapidly (up to 25 μm/min), while a buried p-type layer acts as an etch stop. Dissolution of SiC takes place through hole–catalyzed surface dissolution. The holes are supplied either from the bulk (e.g., p-SiC) or by UV photogeneration (in n- or p-SiC). The differing flatband potentials of n- and p-type SiC in HF solutions allow the selection of a potential range for which hole current injection occurs only in n-type materials, facilitating dopant-selective etching. This process can be utilized in controlled etching of deep features, as well as in precise patterning of multilayer films.
Hybridization chain reaction enables a unified approach to multiplexed, quantitative, high-resolution immunohistochemistry and in situ hybridization (2021)

ABSTRACT RNA in situ hybridization (RNA-ISH) based on the mechanism of hybridization chain reaction (HCR) enables multiplexed, quantitative, high-resolution RNA imaging in highly autofluorescent samples including whole-mount vertebrate embryos, thick brain slices, and formalin-fixed paraffin-embedded (FFPE) tissue sections. Here, we extend the benefits of 1-step, multiplexed, quantitative, isothermal, enzyme-free HCR signal amplification to immunohistochemistry (IHC), enabling accurate and precise protein relative quantitation with subcellular resolution in an anatomical context. More-over, we provide a unified framework for simultaneous quantitative protein and RNA imaging with 1-step HCR signal amplification performed for all target proteins and RNAs simultaneously. SUMMARY Signal amplification based on the mechanism of hybridization chain reaction enables multiplexed, quantitative, high-resolution imaging of protein and RNA targets in highly autofluorescent tissues.
Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors (2022)

CRISPR-Cas systems are host-encoded pathways that protect microbes from viral infection using an adaptive RNA-guided mechanism. Using genome-resolved metagenomics, we find that CRISPR systems are also encoded in diverse bacteriophages, where they occur as divergent and hypercompact anti-viral systems. Bacteriophage-encoded CRISPR systems belong to all six known CRISPR-Cas types, though some lack crucial components, suggesting alternate functional roles or host complementation. We describe multiple new Cas9-like proteins and 44 families related to type V CRISPR-Cas systems, including the Casλ RNA-guided nuclease family. Among the most divergent of the new enzymes identified, Casλ recognizes double-stranded DNA using a uniquely structured CRISPR RNA (crRNA). The Casλ-RNA-DNA structure determined by cryoelectron microscopy reveals a compact bilobed architecture capable of inducing genome editing in mammalian, Arabidopsis, and hexaploid wheat cells. These findings reveal a new source of CRISPR-Cas enzymes in phages and highlight their value as genome editors in plant and human cells.
Double Synchronous Unified Virtual Oscillator Control for Asymmetrical Fault Ride-Through in Grid-Forming Voltage Source Converters (2021)

A double synchronous unified virtual oscillator controller (dsUVOC) is proposed for grid-forming voltage source converters to achieve synchronization to the fundamental frequency positive- and negative-sequence components of unbalanced or distorted grids. The proposed controller leverages a positive- and a negative-sequence virtual oscillator, a double-sequence current reference generator, and a double-sequence vector limiter. Under fault conditions, the controller enables to clamp the converter output current below the maximum value limited by the converter hardware while retaining synchronization without a phase-locked-loop (PLL) regardless of the balanced or unbalanced nature of grid faults. Consequently, balanced and unbalanced fault ride-through can be achieved without the need for switching to a back-up controller. The paper presents the systematic development of the double-synchronous structure along with detail design and implementation guidelines. Validation of the proposed controller is provided through extensive control-hardware-in-the-loop (CHIL) and laboratory hardware experiments.
Efficient Gaussian mixture model evaluation in voice conversion (2006)

Voice conversion refers to the adaptation of the characteristics of a source speaker's voice to those of a target speaker. Gaussian mixture models (GMM) have been found to be efficient in the voice conversion task. The GMM parameters are estimated from a training set with the goal to minimize the mean squared error (MSE) between the transformed and target vectors. Obviously, the quality of the GMM model plays an important role in achieving better voice conversion quality. This paper presents a very efficient approach for the evaluation of GMM models directly from the model parameters without using any test data, facilitating the improvement of the transformation performance especially in the case of embedded implementations. Though the proposed approach can be used in any application that utilizes GMM based transformation, we take voice conversion as an example application throughout the paper. The proposed approach is experimented with in this context and evaluated against an MSE based evaluation method. The results show that the proposed method is in line with all subjective observations and MSE results.
Buffered Clos-network packet switch with per-output flow queues (2011)

Proposed is a buffered Clos-network switch with per-output flow queues in the middle-stage modules to avoid head-of-line blocking of the queues in the middle stage that occurs in Clos-network switches using simple crosspoint-buffered switch modules. It is shown that the proposed switch achieves higher performance than a conventional buffered Clos-network packet switch.
Proxy-based accelerated discovery of Fischer–Tropsch catalysts (2014)

Development of heterogeneous catalysts for complex reactions such as Fischer-Tropsch synthesis of fuels is hampered by difficult reaction conditions, slow characterisation techniques such as chemisorption and temperature-programmed reduction and the need for long term stability. High-throughput (HT) methods may help, but their use has until now focused on bespoke micro-reactors for direct measurements of activity and selectivity. These are specific to individual reactions and do not provide more fundamental information on the materials. Here we report using simpler HT characterisation techniques (XRD and TGA) along with ageing under Fischer-Tropsch reaction conditions to provide information analogous to metal surface area, degree of reduction and thousands of hours of stability testing time for hundreds of samples per month. The use of this method allowed the identification of a series of highly stable, high surface area catalysts promoted by Mg and Ru. In an advance over traditional multichannel HT reactors, the chemical and structural information we obtain on the materials allows us to identify the structural effects of the promoters and their effects on the modes of deactivation observed.
Immunomodulation of Atherosclerosis (2004)

A number of studies have shown activation of the immune system throughout various stages of atherosclerosis. Recent observations have suggested that activation of immune responses may promote atherosclerosis on one hand by inducing and perpetuating arterial inflammation, whereas on the other hand, selective activation of certain immune functions may inhibit atherosclerosis and arterial inflammation. These observations suggest the possibility that selective suppression of proatherogenic immune responses or selective activation of antiatherogenic immune responses may provide new approaches for atherosclerosis prevention and treatment. Several antigens activating immune responses affecting development of atherosclerosis have been identified. These immune responses may be modulated by presenting the antigens together with different types of adjuvants as well as through the route of administration. In this review, we summarize recent experimental studies using immunomodulatory approaches for treatment of atherosclerosis.
Technique and uses for absorbable barbed sutures (2006)

The author describes barbed sutures as a unique wound closure tool. Their advantages include the closure of wounds without any knots or the need for a third hand. They are also capable of shifting tissues differentially along the suture to redistribute tensile and compressive forces. The author discusses the development of these tools and their application.
Realtime setpoint optimization with time-varying extremum seeking for vapor compression systems (2015)

In many formulations of controller architectures for variable-speed vapor compression machines, evaporator superheat temperature is commonly selected as a regulated variable due to its correlation with cycle efficiency. Further, the superheat temperature setpoint is conveniently taken as a constant value over the wide range of operating conditions. However, direct measurement of superheat is not always available, and estimates of superheat have limited robustness. Therefore identifying alternate signals in the control of vapor compression machines that correlate to efficiency is desired. In this paper, we consider a model-free extremum seeking algorithm that adjusts compressor discharge temperature setpoints in order to optimize energy efficiency. While perturbation-based extremum seeking methods have been known for some time, they suffer from slow convergence rates-a problem emphasized in application by the long time constants associated with thermal systems. Our method uses a new algorithm (time-varying extremum seeking), which has dramatically faster and more reliable convergence properties. In particular, we regulate the compressor discharge temperature using setpoints selected from a model-free time-varying extremum seeking algorithm. We show that the relationship between compressor discharge temperature and power consumption is convex (a requirement for this class of realtime optimization), and use time-varying extremum seeking to drive these setpoints to values that minimize power. The results are compared to the traditional perturbation-based extremum seeking approach. Experiments are performed demonstrating discharge temperature optimization from 72°C to 62°C for a particular set of experimental conditions where the power consumption is decreased from 525 W to 450 W, resulting in an increase in observed coefficient of performance (COP) of 14%.
Mono-Substituted Phthalonitriles and Phthalocyanines. (1979)

Abstract : Iodophthalonitrile is prepared by mixing aminophthalonitrile with sulfuric acid at a temperature below 25 C, reacting that product with sodium nitrite at a temperature below 15 C, and reacting that product with potassium iodide at a temperature below 20 C. A fluoroalkyl phthalonitrile is prepared by mixing fluoroalkyl iodide, activated copper, iodophthalonitrile, and a solvent under an inert atmosphere at a temperature from 110 C to 125 C at least until the solution turns green. Both compounds are useful in synthesizing phthalocyanines and polyphthalocyanines. (Author)
Toward Fast Reliable Communication at Rates Near Capacity with Gaussian Noise (2010)

For the additive Gaussian noise channel with average codeword power constraint, sparse superposition codes and adaptive successive decoding is developed. Codewords are linear combinations of subsets of vectors, with the message indexed by the choice of subset. A feasible decoding algorithm is presented. Communication is reliable with error probability exponentially small for all rates below the Shannon capacity.
High temperature operation of 1.3 μm GaInAsP/Inp GRINSCH strained-layer quantum well lasers (1993)

The well number of 1.3 μm GaInAsP/InP strained-layer GRINSCH quantum well lasers has been experimentally investigated in terms of the temperature dependence of the threshold current. A very high CW operating temperature of 170°C with a threshold current of 46.2 mA was obtained for an HR coated laser with eight wells.
Cardiac output and stroke volume estimation using a hybrid of three models (2010)

Cardiac output (CO) and stroke volume (SV) are the key hemodynamic parameters to be monitored and assessed in ambulatory and critically ill patients. The purpose of this study was to introduce and validate a new algorithm to continuously estimate, within a proportionality constant, CO and SV by means of mathematical analysis of peripheral arterial blood pressure (ABP) waveforms. The algorithm combines three variants of the Windkessel model. Input parameters to the algorithm are the end-diastolic pressure, mean arterial pressures, inter-beat interval, and the time interval from end-diastolic to peak systolic pressure. The SV estimates from the three variants of the Windkessel model were weighted and integrated to provide beat-to-beat SV estimation. In order to validate the new algorithm, the estimated CO and SV were compared to those obtained through surgically implanted Transonic™ aortic flow probes placed around the aortic roots of six Yorkshire swine. Overall, estimation errors in CO and SV derived from radial ABP were 10.1% and 14.5% respectively, and 12.7% and 16.5% from femoral ABP. The new algorithm demonstrated statistically significant improvement in SV estimation compared with previous methods.
Enhanced multi-protocol analysis via intelligent supervised embedding (EMPrAvISE): detecting prostate cancer on multi-parametric MRI (2011)

Currently, there is significant interest in developing methods for quantitative integration of multi-parametric (structural, functional) imaging data with the objective of building automated meta-classifiers to improve disease detection, diagnosis, and prognosis. Such techniques are required to address the differences in dimensionalities and scales of individual protocols, while deriving an integrated multi-parametric data representation which best captures all disease-pertinent information available. In this paper, we present a scheme called Enhanced Multi-Protocol Analysis via Intelligent Supervised Embedding (EMPrAvISE); a powerful, generalizable framework applicable to a variety of domains for multi-parametric data representation and fusion. Our scheme utilizes an ensemble of embeddings (via dimensionality reduction, DR); thereby exploiting the variance amongst multiple uncorrelated embeddings in a manner similar to ensemble classifier schemes (e.g. Bagging, Boosting). We apply this framework to the problem of prostate cancer (CaP) detection on 12 3 Tesla pre-operative <i>in vivo</i> multi-parametric (T2-weighted, Dynamic Contrast Enhanced, and Diffusion-weighted) magnetic resonance imaging (MRI) studies, in turn comprising a total of 39 2D planar MR images. We first align the different imaging protocols via automated image registration, followed by quantification of image attributes from individual protocols. Multiple embeddings are generated from the resultant high-dimensional feature space which are then combined intelligently to yield a single stable solution. Our scheme is employed in conjunction with graph embedding (for DR) and probabilistic boosting trees (PBTs) to detect CaP on multi-parametric MRI. Finally, a probabilistic pairwise Markov Random Field algorithm is used to apply spatial constraints to the result of the PBT classifier, yielding a per-voxel classification of CaP presence. Per-voxel evaluation of detection results against ground truth for CaP extent on MRI (obtained by spatially registering pre-operative MRI with available whole-mount histological specimens) reveals that EMPrAvISE yields a statistically significant improvement (AUC=0.77) over classifiers constructed from individual protocols (AUC=0.62, 0.62, 0.65, for T2w, DCE, DWI respectively) as well as one trained using multi-parametric feature concatenation (AUC=0.67).
Clinical evaluation of a direct fluorescent monoclonal antibody test for detection of Pseudomonas aeruginosa in blood cultures (1989)

A direct fluorescent monoclonal antibody test (DFA; Genetic Systems Corp., Seattle, Wash.) was evaluated for the detection of Pseudomonas aeruginosa in 178 blood culture broths obtained from 128 patients. The DFA identified 44 (98%) of 45 blood cultures positive for P. aeruginosa and was negative in 131 (98%) of 133 blood cultures which grew gram-negative rods other than P. aeruginosa. Upon further investigation, saline suspensions of the organism from the false-negative blood culture were strongly (4+) DFA positive. The false-positive reactions were not due to cross-reactivity, as shown by lack of DFA staining of the non-P. aeruginosa isolates following subculture to agar media. The specificity of the reagent was further demonstrated by directly staining culture isolates including 10 serotypes of P. aeruginosa (all positive) and 57 selected gram-negative bacilli including eight species of Pseudomonas that were not P. aeruginosa (all negative). DFA staining of blood culture broths was easy to perform and read with minimal background fluorescence. The DFA method can be performed in 50 min and appears promising as a rapid method for the identification of P. aeruginosa bacteremia.
Therapy Prospects for Mitochondrial DNA Maintenance Disorders (2021)

Mitochondrial DNA depletion and multiple deletions syndromes (MDDS) constitute a group of mitochondrial diseases defined by dysfunctional mitochondrial DNA (mtDNA) replication and maintenance. As is the case for many other mitochondrial diseases, the options for the treatment of these disorders are rather limited today. Some aggressive treatments such as liver transplantation or allogeneic stem cell transplantation are among the few available options for patients with some forms of MDDS. However, in recent years, significant advances in our knowledge of the biochemical pathomechanisms accounting for dysfunctional mtDNA replication have been achieved, which has opened new prospects for the treatment of these often fatal diseases. Current strategies under investigation to treat MDDS range from small molecule substrate enhancement approaches to more complex treatments, such as lentiviral or adenoassociated vector-mediated gene therapy. Some of these experimental therapies have already reached the clinical phase with very promising results, however, they are hampered by the fact that these are all rare disorders and so the patient recruitment potential for clinical trials is very limited.
Dynamic Label-free Imaging of Live-cell Adhesion Using Photonic Crystal Enhanced Microscopy (PCEM) (2015)

We demonstrate label-free imaging of cell attachment upon a photonic-crystal biosensor surface. Newly-implemented PCEM image-analysis software is used to dynamically visualize individual live-cell movement and demonstrate the spatiotemporal-distribution of cellular material during adhesion and motion.
Low-temperature magnetic characterization of optimum and etch-damaged in-plane magnetic tunnel junctions (2013)

We describe low-temperature characterization of magnetic tunnel junctions (MTJs) patterned by reactive ion etching for spin-transfer-torque magnetic random access memory. Magnetotransport measurements of typical MTJs show increasing tunneling magnetoresistance (TMR) and larger coercive fields as temperature is decreased down to 10 K. However, MTJs selected from the high-resistance population of an MTJ array exhibit stable intermediate magnetic states when measured at low temperature and show TMR roll-off below 100 K. These non-ideal low-temperature behaviors arise from edge damage during the etch process and can have negative impacts on thermal stability of the MTJs.