gebhart/patrepeval huggingface dataset:
Ligand-Doped Copper Oxo-hydroxide Nanoparticles are Effective Antimicrobials (2018)

Bacterial resistance to antimicrobial therapies is an increasing clinical problem. This is as true for topical applications as it is for systemic therapy. Topically, copper ions may be effective and cheap antimicrobials that act through multiple pathways thereby limiting opportunities to bacteria for resistance. However, the chemistry of copper does not lend itself to facile formulations that will readily release copper ions at biologically compatible pHs. Here, we have developed nanoparticulate copper hydroxide adipate tartrate (CHAT) as a cheap, safe, and readily synthesised material that should enable antimicrobial copper ion release in an infected wound environment.First, we synthesised CHAT and showed that this had disperse aquated particle sizes of 2-5 nm and a mean zeta potential of - 40 mV. Next, when diluted into bacterial medium, CHAT demonstrated similar efficacy to copper chloride against Escherichia coli and Staphylococcus aureus, with dose-dependent activity occurring mostly around 12.5-50 mg/L of copper. Indeed, at these levels, CHAT very rapidly dissolved and, as confirmed by a bacterial copper biosensor, showed identical intracellular loading to copper ions derived from copper chloride. However, when formulated at 250 mg/L in a topically applied matrix, namely hydroxyethyl cellulose, the benefit of CHAT over copper chloride was apparent. The former yielded rapid sustained release of copper within the bactericidal range, but the copper chloride, which formed insoluble precipitates at such concentration and pH, achieved a maximum release of 10 ± 7 mg/L copper by 24 h.We provide a practical formulation for topical copper-based antimicrobial therapy. Further studies, especially in vivo, are merited.
ChemInform Abstract: Water‐Soluble Conducting Polymers. (1987)

Abstract The sulfonates (II) and (IV) are converted into the analogous polymerizable methyl esters via the sulfonyl chlorides.
3D assessment of mechanical wave propagation in the crystalline eye lens using PhS-SSOCT (2011)

The stiffness of biological tissues could be assessed by measuring the propagation of mechanically induced waves on its surfaces that could help identifying various tissue pathologies. Here we present results for the volumetric assessment of mechanical waves propagating on both surfaces of the crystalline lens measured with the Phase-Sensitive Swept Source Optical Coherence Tomography (PhS-SSOCT) technique. The results indicate that the system could detect vibrations of as small as 0.03 μm in amplitude induced on the surface of crystalline lens, and hence, PhS-SSOCT could potentially be used to assess stiffness of a crystalline lens.
P135 BIOLOGICAL EVIDENCE OF TOFACITINIB EFFICACY IN CROHN’S DISEASE (2018)

While phase II-III trials clearly demonstrated efficacy of tofacitinib, an oral small molecule pan-JAK inhibitor, in patients with UC, in CD tofacitinib did not differ from placebo, raising questions about the design of those trials but also about tofacitinb elicited biological mechanisms that can be beneficial for only UC. Subsequently, second generation JAK-1 selective inhibitors such as filgotinib were found efficacious in CD, underscoring lack of understanding how JAK inhibitors work in IBD and which patients are more likely to benefit from their use. To overcome the limitations of current drug evaluation approaches using primarily mouse models of experimental colitis, we have developed a Therapeutic Response Predictor Assay-TheRPA, which is based on treatment of patient-derived tissue explants and has been validated using anti-TNF (45% patient response rate and 87% test accuracy). Punch biopsies obtained from the inflamed mucosa of 12 patients with CD were cultured with 100uM tofacitinib or vehicle. Culture supernatants were collected for multiplex cytokine analysis (16-plex) and tissues for RNA extraction followed by RNAseq analysis. TheRPA-based response rates to tofacitinib (ie inhibition of >2 cytokines) were comparable in CD (8/12) and UC (6/9) patients. TNFa, GM-CSF, MCP-1, IL-8 and IL-6 were inhibited more frequently, consistent with reports from the field of rheumatoid arthritis. IL-10 was also downregulated, which is in contrast to previous findings in mice, but in agreement with the effects of treatment of human IBD explants with anti-TNF. Our study provides biological evidence that tofacitinib treatment might be beneficial in patients with CD. TheRPA can be used to select patients with IBD more likely to respond to tofacitinib and guide tailored therapies in IBD. Finally, it represents a suitable platform to evaluate newly developed JAK selective inhibitors and uncover their specific mechanisms of actions.
Advance of Seriniquinone Analogues as Melanoma Agents (2019)

Seriniquinone, a marine natural product, displayed potent cytotoxicity and selectivity against melanoma cancer cells. This selectivity, combined with a novel mode of action (MOA), prompted studies to translate a pharmacologically relevant lead. Herein, we report on structure-activity relationships (SARs), and provide a strategy to prepare analogues that retain activity and offer an improved water solubility and isomeric purity. From intermediates made on a gram-scale, derivatives were prepared and evaluated for their antiproliferation activity and melanoma selectivity. Overall these studies provide methods to install side chain motifs that demonstrate a common, and yet unique, biological profile.
Optimal Trajectory Control of LLC Resonant Converters for Soft Start-Up (2013)

In this paper, the soft start-up process for the LLC resonant converter is investigated and optimized based on a graphical state-trajectory analysis. By setting a current limitation band, several optimal switching patterns are proposed to settle the initial condition. After that, by sensing the output voltage, the optimal switching frequency is determined within the current limiting band. This virtually guarantees that there will be no current and voltage stress in the resonant tank during the soft start-up process. Meanwhile, the output voltage is built up quickly and smoothly.
Comparison of Coaxial Holographic Storage Arrangements from the M Number Consumption Point of View (2007)

There are two known competitive arrangements for reflection-type coaxial holographic storage systems: the optical layout developed by optware, which is a so-called collinear or "split-aperture system", and the "common-aperture system" developed by the European consortium named athos. We modeled the reference diffraction noise for both arrangements by the beam propagation method (BPM), and compared the results from the M number (M#) consumption point of view. We suggest the use of reference beam apodization for the split aperture system to reduce the diffraction noise caused by the reference beam at the object area.
Phase-conjugate Fizeau interferometer (1989)

We describe a phase-conjugate interferometer that consists of a partially transmitting conventional mirror placed in front of and in close proximity to a phase-conjugate mirror. The interferometer is self-referencing, compact, and insensitive to environmental disturbances, provides twice the sensitivity of conventional (nonphase-conjugate) interferometers, and produces a direct representation of an incident wave front. We have constructed such a device using internally self-pumped phase conjugation in barium titanate and have used the device to characterize the wave front produced by an aberrated optical system.
An optical technique for detecting fatigue cracks in aerospace structures (2003)

The development of a field-deployable non-intrusive optical-based crack-detection and measurement system based on temperature-sensitive-paint (TSP) technology is described. The TSP developed is based on a platinum porphyrin immobilized in a sol-gel-derived thin film. For this test, the TSP is deposited on top of an aluminum plate that is then subjected to dynamic fatigue through the use of an electrodynamic shaker. Detection of cracks in the aluminum is accomplished by monitoring the changes in the surface temperature of the plate as it was excited at its resonant frequency. Visualization and measurement of the cracks is easily accomplished in near real time using this method. Finally, this method is compared with conventional thermography, and the results indicate that for aluminum, the surface-temperature change was below the resolution of conventional instrumentation.
<title>Complexity reduction on two-dimensional convolutions for image processing</title> (1998)

Presented here is a method for reducing the computational complexity of two-dimensional linear convolutions used in image processing like binary image scaling. This method is a hybrid of convolving at run-time and convolving by table lookup. The convolution step in image processing usually calculates a weighted average of an area of the input image by calculating the entry-by-entry multiplication of the input pixels with a weight table. This method partitions the calculations in the convolution step and stores pre-calculated partial results in lookup tables. When the convolution step takes place, a binary indexing is used to retrieve the partial results and the final result is obtained by summing up the partial results. A line cache and a double buffering scheme are designed to reduce memory access in table lookup. Space and time complexities are analyzed and compared to the conventional two-dimensional linear convolutions. We demonstrate that an order of magnitude reduction in the computational cost can be achieved. Examples, test images and performance data are provided.
Multimodal neonatal procedural and postoperative pain assessment dataset (2021)

This paper presents the first multimodal neonatal pain dataset that contains visual, vocal, and physiological responses following clinically required procedural and postoperative painful procedures. It was collected from 58 neonates (27-41 gestational age) during their hospitalization in the neonatal intensive care unit. The visual and vocal data were recorded using an inexpensive RGB camera while the physiological responses (vital signs and cortical activity) were recorded using portable bedside monitors. The recorded behavioral and physiological responses were scored by expert nurses using two validated pain scales to obtain the ground truth labels. In addition to behavioral and physiological responses, our dataset contains clinical information such as the neonate's age, gender, weight, pharmacological and non-pharmacological interventions, and previous painful procedures. The presented multimodal dataset can be used to develop artificial intelligence systems that monitor, assess, and predict neonatal pain based on the analysis of behavioral and physiological responses. It can also be used to advance the understanding of neonatal pain, which can lead to the development of effective pain prevention and treatment.
Poly(A)-ClickSeq: click-chemistry for next-generation 3´-end sequencing without RNA enrichment or fragmentation (2017)

Abstract The recent emergence of alternative polyadenylation (APA) as an engine driving transcriptomic diversity has stimulated the development of sequencing methodologies designed to assess genome-wide polyadenylation events. The goal of these approaches is to enrich, partition, capture, and ultimately sequence poly(A) site junctions. However, these methods often require poly(A) enrichment, 3´ linker ligation steps, and RNA fragmentation, which can necessitate higher levels of starting RNA, increase experimental error, and potentially introduce bias. We recently reported a click-chemistry based method for generating RNAseq libraries called “ClickSeq”. Here, we adapt this method to direct the cDNA synthesis specifically toward the 3´ UTR/poly(A) tail junction of cellular RNA. With this novel approach, we demonstrate sensitive and specific enrichment for poly(A) site junctions without the need for complex sample preparation, fragmentation or purification. Poly(A)-ClickSeq (PAC-seq) is therefore a simple procedure that generates high-quality RNA-seq poly(A) libraries. As a proof-of-principle, we utilized PAC-seq to explore the poly(A) landscape of both human and Drosophila cells in culture and observed outstanding overlap with existing poly(A) databases and also identified previously unannotated poly(A) sites. Moreover, we utilize PAC-seq to quantify and analyze APA events regulated by CFIm25 illustrating how this technology can be harnessed to identify alternatively polyadenylated RNA.
Lignin oxidation mechanisms under oxygen delignification conditions. Part 1. Results from direct analyses (2011)

Abstract Oxidation of softwood and hardwood kraft lignins was observed under conditions of oxygen delignification (90°C and 110°C; 0.6 and 0.9 MPa) as a function of time by means of a number of analysis techniques and quantitative information was obtained on the degradation and formation of various compounds and structures. The decrease in reactor pressure was monitored during a 4-h reaction period. During the first 60 min, lignin reactivity was high, while a very intense stage took place during the first 20 min. The reactions decelerated after the first 60 min and after 120 min the reactions did not significantly advance. The oxygen consumption after 4-h reaction was 1.3–1.5 mole O 2 per 1 mole lignin depending on the conditions. In the first 20 min, 50%–60% of the oxygen was consumed and the consumption increased only slightly after 60 min. At 90°C, the changes in all observed quantities were smaller throughout the whole 4-h reaction period than at 110°C. Under the studied conditions, increasing the reaction temperature, rather than the pressure, had primary significance in the increasing rate of lignin degradation. Hardwood kraft lignin was more reactive than softwood kraft lignin. The results obtained in this study are the basis for the development of a mechanistic model for the oxygen delignification process of pulps to be published in subsequent papers.
Multi-antenna Cayley differential codes (2002)

Multiple antenna differential modulation using unitary matrices requires no channel knowledge at the receiver, and so is ideal for use on wireless links where channel tracking is undesirable or infeasible, either because of rapid changes in the channel characteristics or because of limited system resources. Although this basic principle is well understood, it is not known how to generate good-performing constellations of unitary matrices, for any number of transmit and receive antennas and especially at high rates. We propose a class of Cayley codes that works with any number of antennas, and allows for polynomial-time near-maximum-likelihood decoding based on either successive nulling/cancelling or sphere decoding. The codes use the Cayley transform, which maps the highly nonlinear Stiefel manifold of unitary matrices to the linear space of skew-Hermitian matrices. This leads to a simple linear constellation structure in the Cayley transform domain and to an information-theoretic design criterion based on emulating a Cauchy random matrix. Simulations show that Cayley codes allow efficient and effective high-rate data transmission in multi-antenna communication systems without knowing the channel.
Sparse orthonormal transforms for image compression (2008)

We propose a block-based transform optimization and associated image compression technique that exploits regularity along directional image singularities. Unlike established work, directionality comes about as a byproduct of the proposed optimization rather than a built in constraint. Our work classifies image blocks and uses transforms that are optimal for each class, thereby decomposing image information into classification and transform coefficient information. The transforms are optimized using a set of training images. Our algebraic framework allows straightforward extension to non-block transforms, allowing us to also design sparse lapped transforms that exploit geometric regularity. We use an EZW/SPIHT like entropy coder to encode the transform coefficients to show that our block and lapped designs have competitive rate-distortion performance. Our work can be seen as nonlinear approximation optimized transform coding of images subject to structural constraints on transform basis functions.
Scientific importance, properties and growing applications of poly(3,4-ethylenedioxythiophene) (2005)

This article summarises the industrial applications of poly-(3,4-ethylenedioxythiophene) (PEDT, PEDOT). The basic chemical and physical properties of PEDT are discussed to outline the fundamentals which lead to PEDT as a highly valuable electric and electronic material. PEDT applications are reviewed depending on the two different ways of preparation: in situ polymerisation of the monomer, usually carried out by the user, and applying the prefabricated polymer in the form of its water-based complex with poly(styrene sulfonic acid). Several applications like antistatic coatings, cathodes in capacitors, through-hole plating, OLED's, OFET's, photovoltaics, and electrochromic applications are discussed in detail.
Efficient and cost-effective photo defect monitoring (1998)

Manufacturing processes for submicron integrated circuits require strict process control for minimizing defects during the fabrication process. Defect densities are monitored on product wafers to determine whether the line maintains an acceptable yield level and to prevent any catastrophic downfall. However, defect detection is difficult for multilayer devices. A short loop defect monitor is often employed in the Photolithography area for inspection on an automated wafer inspection system like the KLA 213x. This monitor usually uses clean bare Silicon wafers which are processed through a Photocluster cell to define a resist pattern for defect inspection. In order to monitor a large set of equipment and resist types, a large quantity of clean Silicon wafers are required. The reuse of these silicon photo monitor wafers becomes difficult due to particles left on wafers after resist clean. Thus, the cost of daily photo defect monitor for equipment/process control becomes considerable. In this paper, we will discuss reusable thermal oxide test wafers as an alternative solution to Si wafers for a cost effective photo defect monitor. The required oxide thickness for I-line and DUV resists was calculated from Prolith/2 simulation. By using a special clean with Sulfuric Acid/Hydrogen Peroxide mixture (SPM) and followed by an Ammonium Hydroxide/Hydrogen Peroxide mixture (APM) for resist strip, very low particle counts were achieved for oxide substrate and better than those of Silicon wafers. Furthermore, due to low oxide thickness loss per clean cycle (1 - 2 A), oxide test wafers retain the optical characteristics for defect metrology tools to work without any recalibration. This makes the oxide photo defect monitor process very robust and production worthy. KLA defect data on unpatterned and patterned oxide test wafers for 20 or more reworks, will be shown. They will be compared to control Silicon test wafers. Some issues with exposure and focus condition and their effect on KLA defect detection will be discussed. Finally, a simple cost analysis model will show the potential saving benefit of oxide test wafer.
Physicochemical Characterization of Zeolites SSZ-26 and SSZ-33 (1994)

Detailed characterization of zeolites SSZ-26 and SSZ-33 is presented and includes data from adsorption experiments, X-ray powder diffraction (XRD), electron diffraction (ED), and high-resolution electron microscopy (HREM). Simulated XRD patterns and HREM images of the proposed structures agree very well with all the experimental data. These zeolites are the first synthetic high-silica molecular sieves to contain a three-dimensional pore system comprised of intersecting 10- and 12-ring pores. The structures of\nSSZ-26 and SSZ-33 are compared to the structures of known zeolites, and the relationships between the geometry of the structure-directing agents used in the synthesis of SSZ-26 and the geometry of the pores are analyzed using energy minimization calculations. Several hypothetical zeolite structures are derived based on the proposed models for SSZ-26 and SSZ-33. SSZ-26 and SSZ-33 are the first examples of molecular sieves whose multidimensional pore systems have been formed by the purposeful design of their structure-directing agents.
A Novel Approach to Structure Alignment (2000)

A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2) Minimization of the error function by an iterative method, where in each iteration a mean field method is employed for the assignment variables and exact rotation/translation of atomic coordinates is performed, weighted with the corresponding assignment variables. The approach allows for extensive search of all possible alignments, including those involving arbitrary permutations. The algorithm is implemented using a C_alpha representation of the backbone and explored on different protein structure categories using the Protein Data Bank (PDB) and is successfully compared with other algorithms. The approach performs very well with modest CPU consumption and is robust with respect to choice of parameters. It is extremely generic and flexible and can handle additional user-prescribed constraints easily. Furthermore, it allows for a probabilistic interpretation of the results.
Elucidation of Fatty Acid Amide Hydrolase Inhibition by Potent α-Ketoheterocycle Derivatives from Monte Carlo Simulations (2005)

Fatty acid amide hydrolase (FAAH) is a serine hydrolase responsible for the degradation of anandamide, an endogenous cannabinoid agonist, and oleamide, a sleep-inducing lipid. Recently, Boger and co-workers reported a potent, selective, and efficacious class of reversible alpha-ketoheterocycle inhibitors of FAAH that produce analgesia in animal models (J. Med. Chem. 2005, 48, 1849-1856; Bioorg. Med. Chem. Lett. 2005, 15, 1423-1428). Key aspects of the structure-activity data are addressed here through computational analysis of FAAH inhibition using Monte Carlo (MC) simulations in conjunction with free energy perturbation (FEP) calculations. The MC/FEP simulations demonstrate that incorporation of pyridine at the C5 position of the 2-keto-oxazole and 2-keto-1,3,4-oxadiazole derivatives significantly enhances binding affinity by formation of a hydrogen-bonded array between the pyridyl nitrogen and Lys142 and Thr236. The results also attribute the activity boost upon substitution of oxazole by oxadiazole to reduced steric interactions in the active site and a lower torsional energy penalty upon binding.