gebhart/patrepeval huggingface dataset:
Untersuchung schwacher Protein‐Ligand‐Wechselwirkungen mithilfe langlebiger NMR‐Zustände: verbesserter Kontrast für das fragmentbasierte Wirkstoffscreening (2014)

Abstract Die vorteilhaften Eigenschaften langlebige Zustände (LLS, “long‐lived states”) in der NMR‐Spektroskopie ermöglichen ein effizientes Affinitätsscreening von Substanzbibliotheken. Wir beschreiben hier die Anwendung der LLS in kompetitiven Bindungsstudien, um präzise auch schwache Bindungskonstanten von Fragmenten an die ATP‐Bindungsstelle der N‐terminalen ATPase‐Domäne des Hitzeschockproteins 90 (Hsp90), einem therapeutischen Ansatzpunkt in der Krebstherapie, zu bestimmen. Der LLS‐Ansatz ermöglicht es, Liganden über einen außergewöhnlich weiten Bereich von Affinitäten aufzuspüren, denn er kann auch bei Ligandenkonzentrationen [L], die einige Größenordnungen kleiner als die Dissoziationskonstanten K D sind, verwendet werden. Diese Eigenschaft macht das LLS‐Experiment besonders für die erste Stufe des fragmentbasierten Screenings attraktiv, in dem kleine Moleküle (Fragmente) mit geringer Bindungsneigung identifiziert werden müssen, was mit allen anderen biophysikalischen Methoden nur schwer gelingt.
Broad spectrum capture of clinical pathogens using engineered Fc-Mannose-Binding Lectin (FcMBL) enhanced by antibiotic treatment (2018)

Abstract FcMBL, an engineered version of the blood opsonin mannose-binding lectin (MBL) that contains the carbohydrate recognition domain (CRD) and flexible neck regions of MBL fused to the Fc portion of human IgG1, has been shown to bind various microbes and pathogen-associated molecular patterns (PAMPs). FcMBL also has been used to create an enzyme-linked lectin sorbent assay (ELLecSA) for use as a rapid (&lt; 1 hr) diagnostic of bloodstream infections. Here we extended this work by using the ELLecSA to test FcMBL’s ability to bind to more than 200 different isolates from over 100 different pathogen species. FcMBL bound to 86% of the isolates and 110 of the 122 (90%) different pathogen species tested, including bacteria, fungi, viruses, and parasites. It also bound to PAMPs including, lipopolysaccharide endotoxin (LPS) and lipoteichoic acid (LTA) from Gram-negative and Gram-positive bacteria, as well as lipoarabinomannan (LAM) and phosphatidylinositol mannoside 6 (PIM 6 ) from Mycobacterium tuberculosis . The efficiency of pathogen detection and variation between binding of different strains of the same species also could be improved by treating the bacteria with antibiotics prior to FcMBL capture to reveal previously concealed binding sites within the bacterial cell wall. As FcMBL can bind to pathogens and PAMPs in urine as well as blood, its broad-binding capability could be leveraged to develop a variety of clinically relevant technologies, including infectious disease diagnostics, therapeutics, and vaccines.
Dynamic textures: modeling, learning, synthesis, animation, segmentation, and recognition (2005)

Dynamic textures are sequences of images of dynamic scenes that exhibit some temporal regularity properties, intended in a statistical sense; these include, for example, ocean waves, smoke, whirlwind, fire, foliage, but also moving objects with a “defined shape,” for instance flowers, or flags in wind etc. This work presents a characterization of this class of video sequences, and poses the problems of modeling, learning, synthesis, animation, recognition, and segmentation of dynamic textures. 
Since, in absence of any additional prior knowledge, the visual reconstruction problem from images alone is ill-posed, in this work we give up trying to infer the physical model that generated the images, and analyze sequences of images solely as visual signals. We do so by building a statistical framework, and draw on disciplines like time series analysis, system, control, and identification theory. 
We derive three generative models, the simplest possible, that are able to capture, respectively, the temporal second-order statistics, the spatio-temporal second-order statistics, and the higher-order temporal statistics of dynamic textures. We propose to learn model parameters in the maximum-likelihood sense, or minimum prediction error variance. We derive efficient closed-form inference procedures for learning the second-order statistics, and revert to non-linear optimization techniques for the higher-order ones. After learning a model, it can be used to extrapolate, or predict new image data both in the temporal and spatial domain. We analyze the meaning of the parameters of a model, and show how they can be manipulated to control, or animate the simulation. Using the geometry of subspaces, and statistical pattern recognition theory we derive a technique to discriminate between models, and assess the potential for building a recognition system. Finally, by combining these results with a variational framework, we design a region-based segmentation system able to partition a video sequence into regions characterized by different spatio-temporal statistics.
Magnetic resonance imaging-guided focal laser ablation for prostate cancer: A phase I trial. (2015)

e16128 Background: The majority of patients with low risk prostate cancer (CaP) harbor indolent disease and maybe safely observed on active surveillance (AS). However more than 30% of those on AS will ultimately receive definitive treatment. Focal therapy offers a treatment alternative that may provide oncologic control while avoiding treatment-related morbidity. The objective of this study was to determine the safety and feasibility of magnetic resonance (MR) image-guided focal laser ablation (FLA) of biopsy confirmed and MR visible prostate cancer. Methods: MR image-guided FLA was performed for men with Gleason < 7(3+4) when < 3 cores were positive in a standard 12 core biopsy corresponding to locations of MR lesions, or < 4 cores positive on MR image-guided biopsy. MR localization of biopsy-positive lesions were targeted via a transperineal approach and treated with a laser thermal ablation system. Validated quality of life questionnaires were completed pre-procedure and at each subsequent followup visit. MR-imaging was performed at 6 and 12 month followup with repeat fusion-guided biopsy perfomed at 12 months post-procedure. Results: 15 patients were treated with a mean preoperative PSA of 7.04 (Table 1). 14 patients had complete 1 year followup of which 6 patients had Gleason 6 and 8 patients had Gleason 6 disease. Mean operative time was 3.8 hours per treatment session for 1 lesion ablated. The mean (±Std Dev) IPSS and SHIM scores were 6.5±4.1 and 18.9±6.9 respectively, with no significant differences in SHIM or IPSS at 12 month followup. PSA was significantly lower at 1 year followup versus preoperatively (7.0 vs. 4.5, P = 0.0007).Five Grade 1 adverse events (AEs) were note in 4 patients, consisting of 4 incidences of hematuria and a pressure blister. Grade 2 AEs consisted of a UTI and epididymitis, one of which was unrelated to the procedure. Gleason 6 prostate cancer was identified in 2 prior treated lesions at repeat biopsy, of which 1 was observed and 1 underwent radical prostatectomy. Conclusions: MR-image guided FLA is safe and feasible for men with low risk CaP with acceptable oncologic outcomes at 1 year followup. Focal therapy is a promising alternate treatment that allows for preservation of functional outcomes. Clinical trial information: NCI-11-C-0158.
Cubic three-dimensional hybrid silica solids for nuclear hyperpolarization (2016)

Hyperpolarization of metabolites by dissolution dynamic nuclear polarization (D-DNP) for MRI applications often requires fast and efficient removal of the radicals (polarizing agents). Ordered mesoporous SBA-15 silica materials containing homogeneously dispersed radicals, referred to as HYperPolarizing SOlids (HYPSOs), enable high polarization - <i>P</i>(<sup>1</sup>H) = 50% at 1.2 K - and straightforward separation of the polarizing HYPSO material from the hyperpolarized solution by filtration. However, the one-dimensional tubular pores of SBA-15 type materials are not ideal for nuclear spin diffusion, which may limit efficient polarization. Here, we develop a generation of hyperpolarizing solids based on a SBA-16 structure with a network of pores interconnected in three dimensions, which allows a significant increase of polarization, <i>i.e. P</i>(<sup>1</sup>H) = 63% at 1.2 K. This result illustrates how one can improve materials by combining a control of the incorporation of radicals with a better design of the porous network structures.
Supplementary Figure Legends from Potentiation of antileukemic therapies by Smac mimetic, LBW242: effects on mutant FLT3-expressing cells (2023)

Supplementary Figure Legends from Potentiation of antileukemic therapies by Smac mimetic, LBW242: effects on mutant FLT3-expressing cells
EMI Filter Design for a 1 MHz, 10 kW Three-Phase/Level PWM Rectifier (2010)

The attenuation characteristics of electromagnetic interference (EMI) filters in practice often differ from theoretical predictions and minor changes can result in a significant improvement in performance. The performance of the differential-mode (DM) filter stage can usually be well predicted, but the common mode (CM) behavior is more difficult to handle. This is especially true for three-phase pulsewidth modulation (PWM) rectifier systems, which inherently show a large high-frequency CM voltage at the rectifier output. Possible CM noise current paths of a three-phase/level PWM rectifier are analyzed in this paper where parasitic capacitances to the heat sink and to earth are considered. In addition, a concept to significantly reduce CM emissions is discussed in detail. Based on the proposed models, an EMI filter design for a system with 1 MHz switching frequency is shown. Experimental verification of the designed EMI filter is presented by impedance and conducted emission (CE) measurements taken from a 10 kW prototype. Several practical aspects of filter implementation such as component arrangement, shielding layers, magnetic coupling, etc., are discussed and verified by measurements.
Reinforcement Learning for Controlling a Coupled Tank System Based on the Scheduling of Different Controllers (2010)

Reinforcement Learning has been an approach successfully applied for solving several problems available in literature. It is usually employed for solving complex problems, such as the ones involving systems with incomplete knowledge, time variant systems, non-linear systems, etc., but it does not mean that it cannot be applied for solving simple problems. Therefore, this paper proposes an alternative application, where RL could be applied to switch among controllers with a fixed tuning, in a system with a known non-linear dynamics, aiming to optimize its time response. It was shown, after the online training and test of the RL agent that it could take advantage of the best characteristics of the available controllers to improve the response of the coupled tank system.
History of the flextensional transducer (1989)

Although the invention of the flextensional acoustic transducer is usually attributed to William J. Toulis, it was actually invented at the U. S. Naval Research Laboratories, Washington DC, in 1929 by Harvey C. Hayes. It was intended as a foghorn for the Lighthouse Service. This paper will review Hayes' flextensional from invention to disappearance (c. 1936), and discuss its reinvention and development by Toulis and Frank R. Abbott in the 1950s.
Plug Loads Conservation Measures (2010)

This software requires inputs of simple plug loads inventory information and calculates the energy and cost benefits of various retrofit opportunities. This tool includes energy conservation measures for: Vending Machine Misers, Delamp Vending Machine, Desktop to Laptop retrofit, CRT to LCD monitors retrofit, Computer Power Management Settings, and Energy Star Refrigerator retrofit. This tool calculates energy savings, demand reduction, cost savings, building life cycle costs including: simple payback, discounted payback, net-present value, and savings to investment ratio. In addition this tool also displays the environmental benefits of a project.
A 3D wideband package solution using MCM-D BCB technology for tile TR module (2005)

This paper describes the works performed on a solution of packaging dedicated to 3D TR modules in the 2-20 GHz frequency range. The proposed solution is based on a non hermetic architecture involving organic and BCB substrates. The studied key bricks relative to assembly, vertical interconnections, passives integration are described and results consecutive to electrical and environmental evaluation are presented. A 3D TR module demonstrator taking benefit from the key bricks evaluated through test vehicles has been realised and its performances measured when submitted to airborne environmental constraints.
Research Note: Application of an Escherichia coli spray challenge model for neonatal broiler chickens (2021)

Avian pathogenic Escherichia coli (E. coli) is an opportunistic pathogen often introduced to neonatal chicks during the hatching process. This commensal bacterium, particularly as a pioneer colonizer of the gastrointestinal tract, can have substantial implications in the rearing of poultry because of reduced flock performance. In order to mimic the effects of the natural bacterial bloom present during the hatch, a seeder challenge model was developed to expose neonatal chicks to virulent E. coli. On day 20 of embryogenesis, selected early hatched chicks (n = 18/hatcher) were briefly removed and sprayed challenged with saline (vehicle) or E. coli at 1 × 10<sup>7</sup> colony-forming unit (CFU)/chick (exp 1) and 2.5 × 10<sup>7</sup> CFU/chick (exp 2). These challenged chicks were returned to the hatcher to serve as seeders to transmit the pathogen to the indirect challenged or contact chicks (n = 195/hatcher). For two 7-d experiments, the efficacy of transmission was evaluated via enteric bacterial recovery, body weight gain (BWG), and mortality. For exp 1 and exp 2, significantly (P < 0.0001) more gram-negative bacteria were recovered from the seeder and contact gastrointestinal samples than the negative control samples on day of hatch. In addition, there was a reduction (P < 0.05) in 7-d BWG and significantly (P < 0.0001) higher mortality in the contact-challenged chicks than the negative control chicks in both exp 1 and exp 2. These data suggest that this challenge model could be used to evaluate different methods of controlling the bacterial bloom that occurs in the hatching environment.
Systemic Amyloidosis Presenting with Angina Pectoris (1999)

Cardiac amyloidosis can present as angina pectoris associated with coronary flow reserve abnormalities despite normal coronary angiograms. This finding may have major therapeutic and prognostic implications in this patient population.
Polymorphic Control and Scale-Up Strategy for Antisolvent Crystallization Using a Sequential Supersaturation and Direct Nucleation Control Approach (2020)

In this work, a rapid direct design approach for crystallization processes was implemented using the novel Quality-by-Control (QbC) framework by sequentially applying antisolvent-based supersaturation control (AS-SSC) and temperature driven direct nucleation control (T-DNC) strategies. This novel strategy was used to optimize and scale up the batch crystallization of indomethacin (IMC) from a ternary solvents/antisolvent system, which enables the production of the desired polymorphic γ form with significantly increased process yield. Sequentially applying the supersaturation control (SSC) and direct nucleation control (DNC) led to a combination of the advantages of the two feedback control strategies. SSC-based direct design and scale-up strategy showed high efficiency in providing high productivity (high process yield and shorter batch time), whereas DNC is advantageous in ensuring reproducible particle size distribution from processes at different scales. The combined AS-SSC and T-DNC strategy presented in this work showed a promising synergy, which enabled a good balance between the high productivity of the crystallization process and reproducible crystal properties from the processes at different scales. The results provide a proof-of-concept showing that the proposed QbC approach based on the sequential SSC-DNC implementation can be applied for rapid and successful scale-up, leading to similar particulate properties across scales.
A Phase I Dose-Finding Study Using an Innovative Sequential Biweekly Schedule of Irinotecan Followed 24 Hours Later by Capecitabine (2007)

The suggested Phase II dose of this combination and schedule is irinotecan 100 mg/m(2) and capecitabine 1000 mg/m(2) BID. Some patients tolerated a capecitabine dose as high as 1250 mg/m(2) BID.
Robustness of space-time turbo codes (2002)

We consider the performance of a turbo code with 2 transmit antennas and 2 receive antennas for flat fading channels. We consider robustness within and among families of channels with the same singular values (SVs). When the two SVs are similar, the bit error rate performance is robust in terms of proximity to the channel capacity. When the 2 SVs differ significantly, robust performance can be achieved by a time-varying linear transformation (TVLT). Iterative decoding is the same as for standard parallel concatenated convolutional codes, except that the extrinsic information about encoder outputs are also exchanged.
Quantum paraelectric varactors for radio-frequency measurements at mK temperatures (2020)

Radio-frequency reflectometry allows for fast and sensitive electrical readout of charge and spin qubits hosted in quantum dot devices coupled to resonant circuits. Optimizing readout, however, requires frequency tuning of the resonators and impedance matching. This is difficult to achieve using conventional semiconductor or ferroelectric-based varactors in the detection circuit as their performance degrades significantly in the mK temperature range relevant for solid-state quantum devices. Here we explore a different type of material, strontium titanate, a quantum paraelectric with exceptionally large field-tunable permittivity at low temperatures. Using strontium titanate varactors we demonstrate perfect impedance matching and resonator frequency tuning at 6 mK and characterize the varactors at this temperature in terms of their capacitance tunability, dissipative losses and magnetic field sensitivity. We show that this allows us to optimize the radio-frequency readout signal-to-noise ratio of carbon nanotube quantum dot devices to achieve a charge sensitivity of 4.8 $μ$e/Hz$^{1/2}$ and capacitance sensitivity of 0.04 aF/Hz$^{1/2}$.
Activation and Regulation of the Pattern Recognition Receptors in Obesity-Induced Adipose Tissue Inflammation and Insulin Resistance (2013)

Obesity-associated chronic tissue inflammation is a key contributing factor to type 2 diabetes mellitus, and a number of studies have clearly demonstrated that the immune system and metabolism are highly integrated. Recent advances in deciphering the various immune cells and signaling networks that link the immune and metabolic systems have contributed to our understanding of the pathogenesis of obesity-associated inflammation. Other recent studies have suggested that pattern recognition receptors in the innate immune system recognize various kinds of endogenous and exogenous ligands, and have a crucial role in initiating or promoting obesity-associated chronic inflammation. Importantly, these mediators act on insulin target cells or on insulin-producing cells impairing insulin sensitivity and its secretion. Here, we discuss how various pattern recognition receptors in the immune system underlie the etiology of obesity-associated inflammation and insulin resistance, with a particular focus on the TLR (Toll-like receptor) family protein Radioprotective 105 (RP105)/myeloid differentiation protein-1 (MD-1).
Conformal Wideband Optically Addressed Transmitting Phased Array With Photonic Receiver (2014)

In this paper we present a wideband optically addressed transmitting phased array antenna, consisting of an ultra-wideband tunable RF synthesizer, an optical phase-feed network, and a high-speed photodetector-integrated conformal array antenna. RF source generation and the optical feed network are capable of covering a frequency range of up to 50 GHz. A conformal 4 × 4 Ka-band patch array antenna is designed, fabricated and characterized. The array is designed to sweep over ±40° from the broadside. An optically based detector is implemented to measure the far-field of the transmitting phased array. Embedded electronic control is developed for the RF synthesizer, optical feed network control, and photonic receiver. This system is consolidated into a portable cart for field testing. Extensive studies of the subsystems have been performed. Electrically controlled optical beam steering is demonstrated and characterized, and far-fields are measured, and compared with simulation results, showing excellent agreement.
The C Terminus of the Catalytic Domain of Type A Botulinum Neurotoxin May Facilitate Product Release from the Active Site (2013)

Botulinum neurotoxins are the most toxic of all compounds. The toxicity is related to a poor zinc endopeptidase activity located in a 50-kDa domain known as light chain (Lc) of the toxin. The C-terminal tail of Lc is not visible in any of the currently available x-ray structures, and it has no known function but undergoes autocatalytic truncations during purification and storage. By synthesizing C-terminal peptides of various lengths, in this study, we have shown that these peptides competitively inhibit the normal catalytic activity of Lc of serotype A (LcA) and have defined the length of the mature LcA to consist of the first 444 residues. Two catalytically inactive mutants also inhibited LcA activity. Our results suggested that the C terminus of LcA might interact at or near its own active site. By using synthetic C-terminal peptides from LcB, LcC1, LcD, LcE, and LcF and their respective substrate peptides, we have shown that the inhibition of activity is specific only for LcA. Although a potent inhibitor with a Ki of 4.5 μm, the largest of our LcA C-terminal peptides stimulated LcA activity when added at near-stoichiometric concentration to three versions of LcA differing in their C-terminal lengths. The result suggested a product removal role of the LcA C terminus. This suggestion is supported by a weak but specific interaction determined by isothermal titration calorimetry between an LcA C-terminal peptide and N-terminal product from a peptide substrate of LcA. Our results also underscore the importance of using a mature LcA as an inhibitor screening target.
Silicon nitride based planar integrated circuits for biophotonics applications (2016)

Biophotonic based sensing or imaging relies often on expensive and bulky equipment. Integrated optics solutions could alleviate both cost and equipment size, by integrating the optical functionality on chip. Even more so, it is beneficial to integrate this optical functionality directly on top of a CMOS chip, that can detect the light and process the information. We have developed a 200 mm CMOS compatible SiN waveguide platform with low losses at visible wavelengths. We have already demonstrated density controlled nanophotonic waveguide gratings for tailored out-coupling of light, and applied this to integrated excitation and detection of fluorescently tagged particles and cells. In addition, we have shown integrated excitation and collection of molecular fluorescence. In this talk we will discuss the current component library and the applications that are envisioned.