gebhart/patrepeval huggingface dataset:
Regional lymph node metastasis in colon adenocarcinoma (2019)

Whole slide pathology images from regional lymph node metastasis in colon adenocarcinoma produced at Region Gävleborg Clinical Pathology and Cytology department and Region Östergötland Clinical Pathology department. Annotations for AI training produced as part of AIDA clinical fellowship project investigating AI decision support in metastasis detection. This dataset has been extended with a second collection series in the LNCO2 dataset using different collection and annotation parameters.
Water Clustering in Glassy Polymers (2013)

In this study, water solubility and water clustering in several glassy polymers, including poly(methyl methacrylate) (PMMA), poly(styrene) (PS), and poly(vinylpyrrolidone) (PVP), were measured using both quartz spring microbalance (QSM) and Fourier transform infrared-attenuated total reflectance (FTIR-ATR) spectroscopy. Specifically, QSM was used to determine water solubility, while FTIR-ATR spectroscopy provided a direct, molecular-level measurement of water clustering. The Flory-Huggins theory was employed to obtain a measure of water-polymer interaction and water solubility, through both prediction and regression, where the theory failed to predict water solubility in both PMMA and PVP. Furthermore, a comparison of water clustering between direct FTIR-ATR spectroscopy measurements and predictions from the Zimm-Lundberg clustering analysis produced contradictory results. The failure of the Flory-Huggins theory and Zimm-Lundberg clustering analysis to describe water solubility and water clustering, respectively, in these glassy polymers is in part due to the equilibrium constraints under which these models are derived in contrast to the nonequilibrium state of glassy polymers. Additionally, FTIR-ATR spectroscopy results were compared to temperature-dependent diffusivity data, where a correlation between the activation energy for diffusion and the measured water clustering was observed.
Flow injection system for the scanning tunneling microscope (1995)

A flow injection scanning tunneling microscopy (FISTM) system is described and characterized which permits observation of surface chemical processes. This modification to a standard scanning tunneling microscope consists of a peristaltic pump attached via a manual HPLC-type flow injector to a constant-volume sample cell. Images recorded as fluids continuously exchange in the cell are reported. Evidence supports that analytes are transported into the tip region through a stagnant fluid domain by diffusion from the adjacent, circulating bulk solution. Electrochemical measurements of the exposed tip surface area and rates of diffusion of analytes are presented and interpreted. Erosion of contaminants on a gold surface exposed to hydrogen peroxide was observed using FISTM, and these results are presented.
Distributed simulation using a real-time shared memory network (1993)

The Advanced Control Technology Branch of the NASA Lewis Research Center performs research in the area of advanced digital controls for aeronautic and space propulsion systems. This work requires the real-time implementation of both control software and complex dynamical models of the propulsion systems. We are implementing these systems in a distributed, multi-vendor computer environment. Therefore, a need exists for real-time communication and synchronization between the distributed multi-vendor computers. A shared memory network is a potential solution which offers several advantages over other real- time communication approaches. In this effort, a candidate shared memory network was tested for basic performance. The shared memory network was then used to implement a distributed simulation of a ramjet engine. The accuracy and execution time of the distributed simulation was measured and compared to the performance of the non-partitioned simulation. The ease of partitioning the simulation, the minimal time required to develop software for communication between the processors and the resulting execution time all indicate that the shared memory network is a real-time communication technique worthy of serious consideration.
Antennas for the detection of radio emission pulses from cosmic-ray induced air showers at the Pierre Auger Observatory (2012)

The Pierre Auger Observatory is exploring the potential of the radio detection technique to study extensive air showers induced by ultra-high energy cosmic rays. The Auger Engineering Radio Array (AERA) addresses both technological and scientific aspects of the radio technique. A first phase of AERA has been operating since September 2010 with detector stations observing radio signals at frequencies between 30 and 80 MHz. In this paper we present comparative studies to identify and optimize the antenna design for the final configuration of AERA consisting of 160 individual radio detector stations. The transient nature of the air shower signal requires a detailed description of the antenna sensor. As the ultra-wideband reception of pulses is not widely discussed in antenna literature, we review the relevant antenna characteristics and enhance theoretical considerations towards the impulse response of antennas including polarization effects and multiple signal reflections. On the basis of the vector effective length we study the transient response characteristics of three candidate antennas in the time domain. Observing the variation of the continuous galactic background intensity we rank the antennas with respect to the noise level added to the galactic signal.
Novel Pure αVβ3 Integrin Antagonists That Do Not Induce Receptor Extension, Prime the Receptor, or Enhance Angiogenesis at Low Concentrations (2019)

The integrin αVβ3 receptor has been implicated in several important diseases, but no antagonists are approved for human therapy. One possible limitation of current small-molecule antagonists is their ability to induce a major conformational change in the receptor that induces it to adopt a high-affinity ligand-binding state. In response, we used structural inferences from a pure peptide antagonist to design the small-molecule pure antagonists TDI-4161 and TDI-3761. Both compounds inhibit αVβ3-mediated cell adhesion to αVβ3 ligands, but do not induce the conformational change as judged by antibody binding, electron microscopy, X-ray crystallography, and receptor priming studies. Both compounds demonstrated the favorable property of inhibiting bone resorption <i>in vitro</i>, supporting potential value in treating osteoporosis. Neither, however, had the unfavorable property of the αVβ3 antagonist cilengitide of paradoxically enhancing aortic sprout angiogenesis at concentrations below its IC<sub>50</sub>, which correlates with cilengitide's enhancement of tumor growth <i>in vivo</i>.
Recurrent Half‐Sib Selection with Testcross Evaluation for Increased Oil Content in Soybean (2004)

Protein meal and oil are the two commodities produced from soybean [ Glycine max (L.) Merr.] that give the crop its value. Increasing seed concentrations of either or both may add value. Objectives of this study were to investigate the effectiveness of recurrent half‐sib selection for increased seed oil, to evaluate the effect of tester oil content on selection response, and to investigate testcross heterosis and inbreeding depression for seed oil content. A recurrent half–sib selection system was devised for soybean and selection for increased oil content was conducted in a population for seven and three cycles using a high and a low‐oil tester, respectively. The base population was a high‐oil composite with gray pubescence ( tt ) that was segregating for nuclear genetic ms 1 male sterility. In summer, the base population was planted in single plant hills and bordered with the tester ( Ms 1 Ms 1 TT ) in a random mating block in North Carolina. About 100 to 200 random male‐sterile plants with hybrid seeds were harvested. Half‐sib families derived from each male‐sterile plant were then grown in Puerto Rico in winter. At maturity, seeds from tawny plants (tester hybrid) were used to identify half‐sib families with high‐oil content. Corresponding gray plant hybrids from sib matings within the population were bulked to start the next cycle of selection. Random progenies from the base populations and selected progenies from each cycle of selection were evaluated in a replicated field experiment at three locations in North Carolina. Cycle × tester hybrids and cycle × cycle sib hybrids were also included in the tests. The results showed that oil content was significantly increased at a rate of 1.1 ± 0.2 g kg −1 cycle −1 in the high‐oil tester populations but not in the low‐oil tester populations. The realized heritability estimate for the high‐oil tester population was 0.12 ± 0.03. Evidence of heterosis indicated that some dominance effects on oil content existed. Dominance effects may affect the evaluation accuracy of the genotypes being tested. A high‐oil tester and high‐oil populations may have many common alleles resulting in less dominance and more additive effects in their hybrids. Consequently, a high‐oil tester can lead to better evaluation and selection precision, compared with a low‐oil tester which could mask additive effects and reduce selection precision.
Detection of a Biomarker for Alzheimer's Disease from Synthetic and Clinical Samples Using a Nanoscale Optical Biosensor (2005)

A nanoscale optical biosensor based on localized surface plasmon resonance (LSPR) spectroscopy has been developed to monitor the interaction between the antigen, amyloid-beta derived diffusible ligands (ADDLs), and specific anti-ADDL antibodies. Using the sandwich assay format, this nanosensor provides quantitative binding information for both antigen and second antibody detection that permits the determination of ADDL concentration and offers the unique analysis of the aggregation mechanisms of this putative Alzheimer's disease pathogen at physiologically relevant monomer concentrations. Monitoring the LSPR-induced shifts from both ADDLs and a second polyclonal anti-ADDL antibody as a function of ADDL concentration reveals two ADDL epitopes that have binding constants to the specific anti-ADDL antibodies of 7.3 x 10(12) M(-1) and 9.5 x 10(8) M(-1). The analysis of human brain extract and cerebrospinal fluid samples from control and Alzheimer's disease patients reveals that the LSPR nanosensor provides new information relevant to the understanding and possible diagnosis of Alzheimer's disease.
Microtubule assembly in meiotic extract requires glycogen (2011)

The assembly of microtubules during mitosis requires many identified components, such as γ-tubulin ring complex (γ-TuRC), components of the Ran pathway (e.g., TPX2, HuRP, and Rae1), and XMAP215/chTOG. However, it is far from clear how these factors function together or whether more factors exist. In this study, we used biochemistry to attempt to identify active microtubule nucleation protein complexes from Xenopus meiotic egg extracts. Unexpectedly, we found both microtubule assembly and bipolar spindle assembly required glycogen, which acted both as a crowding agent and as metabolic source glucose. By also reconstituting microtubule assembly in clarified extracts, we showed microtubule assembly does not require ribosomes, mitochondria, or membranes. Our clarified extracts will provide a powerful tool for activity-based biochemical fractionations for microtubule assembly.
A novel point-based nonrigid image registration scheme based on learning optimal landmark configurations (2013)

Image registration plays an increasingly important role in the field of medical image processing given the plurality of images often acquired from different sensors, time points, or viewpoints. Landmark-based registration schemes represent the most popular class of registration methods due to their simplicity and high accuracy. Previous studies have shown that these registration schemes are sensitive to the number and location of landmarks. Identifying important landmarks to perform an accurate registration remains a very challenging task. Current landmark selection methods, such as feature-based approaches, focus on optimization of global transformation and may have poor performance in recovering local deformation, e.g. subtle tissue changes caused by tumor resection, making them inappropriate for registering pre- and post-surgery images as a small cancerous region will be deformed after removing a tumor. In this work, a novel method is introduced to estimate optimal landmark configurations. An important landmark configuration that will be used as a training landmark set was learned for an image pair with a known deformation. This landmark configuration can be considered as a collection of discrete points. A generic transformation matrix between a pair of training landmark sets with different deformation locations was computed via an iterative close point (ICP) alignment technique. A new landmark configuration was determined by simply transforming the training landmarks to the current displacement location while preserving the topological structure of the configuration of landmarks. Two assumptions are made: 1) In a new pair of images the deformation is approximately the same size and has only been spatially relocated in the image, and that by a simple affine transformation one can identify the optimal configuration on this new pair of images; and 2) The deformation is of similar size and shape on the original pair of images. These are reasonable assumptions in many cases where one seeks to register tumor images at multiple time points following application of therapy and to evaluate changes in tumor size. The experiments were conducted on 286 pairs of synthetic MRI brain images. The training landmark configurations were obtained through 2000 iterations of registration where the points with consistently best registration performance were selected. The estimated landmarks greatly improved the quality metrics compared to a uniform grid placement scheme and a speeded-up robust features (SURF) based method as well as a generic free-form deformation (FFD) approach. The quantitative results showed that the new landmark configuration achieved 95% improvement in recovering the local deformation compared to 89% for the uniform grid placement, 79% for the SURF-based approach, and 10% for the generic FFD approach.
The impact of GPCR structures on pharmacology and structure‐based drug design (2009)

After many years of effort, recent technical breakthroughs have enabled the X-ray crystal structures of three G-protein-coupled receptors (GPCRs) (beta1 and beta2 adrenergic and adenosine A(2a)) to be solved in addition to rhodopsin. GPCRs, like other membrane proteins, have lagged behind soluble drug targets such as kinases and proteases in the number of structures available and the level of understanding of these targets and their interaction with drugs. The availability of increasing numbers of structures of GPCRs is set to greatly increase our understanding of some of the key issues in GPCR biology. In particular, what constitutes the different receptor conformations that are involved in signalling and the molecular changes which occur upon receptor activation. How future GPCR structures might alter our views on areas such as agonist-directed signalling and allosteric regulation as well as dimerization is discussed. Knowledge of crystal structures in complex with small molecules will enable techniques in drug discovery and design, which have previously only been applied to soluble targets, to now be used for GPCR targets. These methods include structure-based drug design, virtual screening and fragment screening. This review considers how these methods have been used to address problems in drug discovery for kinase and protease targets and therefore how such methods are likely to impact GPCR drug discovery in the future.
A hybrid cascaded multilevel inverter with supercapacitor direct integration for wind power systems (2011)

This paper presents a grid-side inverter based supercapacitor direct integration scheme for wind power systems. The inverter used in this study consists of a conventional two-level inverter and three H-bridge modules. Three supercapacitor banks are directly connected to the dc-links of H-bridge modules. This approach eliminates the need for interfacing dc-dc converters and thus considerably improves the overall efficiency. However, for the maximum utilization of super capacitors their voltages should be allowed to vary. As a result of this variable voltage space vectors of the hybrid inverter get distributed unevenly. To handle this issue, a modified PWM method and a space vector modulation method are proposed and they can generate undistorted current even in the presence of unevenly distributed space vectors. A supercapacitor voltage balancing method is also presented in this paper. Simulation results are presented to validate the efficacy of the proposed scheme, modulation methods and control techniques.
Mucoadhesive nanomedicines: characterization and modulation of mucoadhesion at the nanoscale (2011)

The mucoadhesion behavior of materials in bulk and at the nanoscale can significantly differ. Advances in the methodology used for studying the mucoadhesion phenomenon have contributed to its better understanding and, more importantly, the development of strategies to increase/decrease mucoadhesion. However, development of new methodologies for studying mucoadhesion at the nanoscale and the refinement of existing methodologies are still required. Also, a substantial amount of information is still lacking, particularly related to formulation issues, on how to translate lessons learnt at the bench top to the bed side.
Dissimilar cavitation dynamics and damage patterns produced by parallel fiber alignment to the stone surface in holmium:yttrium aluminum garnet laser lithotripsy (2023)

Recent studies indicate that cavitation may play a vital role in laser lithotripsy. However, the underlying bubble dynamics and associated damage mechanisms are largely unknown. In this study, we use ultra-high-speed shadowgraph imaging, hydrophone measurements, three-dimensional passive cavitation mapping (3D-PCM), and phantom test to investigate the transient dynamics of vapor bubbles induced by a holmium:yttrium aluminum garnet laser and their correlation with solid damage. We vary the standoff distance (<i>SD</i>) between the fiber tip and solid boundary under parallel fiber alignment and observe several distinctive features in bubble dynamics. First, long pulsed laser irradiation and solid boundary interaction create an elongated "pear-shaped" bubble that collapses asymmetrically and forms multiple jets in sequence. Second, unlike nanosecond laser-induced cavitation bubbles, jet impact on solid boundary generates negligible pressure transients and causes no direct damage. A non-circular toroidal bubble forms, particularly following the primary and secondary bubble collapses at <i>SD</i> = 1.0 and 3.0 mm, respectively. We observe three intensified bubble collapses with strong shock wave emissions: the intensified bubble collapse by shock wave, the ensuing reflected shock wave from the solid boundary, and self-intensified collapse of an inverted "triangle-shaped" or "horseshoe-shaped" bubble. Third, high-speed shadowgraph imaging and 3D-PCM confirm that the shock origins from the distinctive bubble collapse form either two discrete spots or a "smiling-face" shape. The spatial collapse pattern is consistent with the similar BegoStone surface damage, suggesting that the shockwave emissions during the intensified asymmetric collapse of the pear-shaped bubble are decisive for the solid damage.
Soluble iron nanoparticles as cheap and environmentally benign alkene and alkyne hydrogenation catalysts (2009)

Iron nanoparticles prepared by reducing FeCl3 with three equivalents of EtMgCl in THF are effective catalysts for the hydrogenation of alkenes and alkynes under moderate conditions.
Measures of Deprivation and their Meaning in Terms of Social Satisfaction (1998)

This paper proposes relative and absolute measures of deprivation using social satisfaction functions. The relative (absolute) measure gives us the amount by which social satisfaction can be increased in proportional (absolute) terms by redistributing incomes equally. We also demonstrate the existence of a relationship between summary indices of deprivation (including the Gini coefficient, the maximin index, the coefficient of variation and their absolute counterparts) and social satisfaction.
Extraction of Vitamin E Isomers from Palm Oil: Methodology, Characterization, and in Vitro Anti‐Tumor Activity (2017)

Vitamin E refers to a family of eight tocopherols (T) and tocotrienol (T3) isomers. Due to the unique pharmacological and anticancer activity of the individual isomers, there is a need to extract and separate the individual T3 isomers from T/T3 rich fractions of palm oil. The objective of the present study was to present a detailed protocol for the extraction of gram quantities of vitamin E isomers from a T3 rich fraction (Tocotrol™) that was obtained from palm oil, by column chromatography using a binary hexane:EtOAc (1-12%) phase system. The chemical integrity and identity of the extracted isomers was confirmed by TLC, HPLC, <sup>1</sup>H-NMR, and Raman analysis. To evaluate their anticancer activity, vitamin E isomers were first entrapped into nanoemulsions and then tested against a panel of breast and pancreatic cancer cell lines. Nanoemulsions were prepared by the solvent evaporation technique. They had an average droplet size between 156-200 nm. In confirmation to what has been reported in the literature, γ-T3 and δ-T3 isomers were found to be significantly more active against tumor cells than the α-T and α-T3 isomers. The current study has demonstrated the feasibility of extracting the individual vitamin E isomers at high yields from natural sources while maintaining their chemical integrity and pharmacological activity.
Inducible Resistance to Macrolides, Lincosamides, and Streptogramin Type-B Antibiotics: The Resistance Phenotype, Its Biological Diversity, and Structural Elements That Regulate Expression (1983)

INTRODUCTION Reports of erythromycin-resistant strains of Staphylococcus aureus began to appear in the clinical literature in the mid-1950s, shortly after the introduction of this drug into clinical practice (Chabbert 1956; Jones et al. 1956; Garrod 1957). The mechanism of resistance in these clinical isolates can be ascribed to reduced affinity between erythromycin and its binding site on the 50S subunit of the ribosome (Saito et al. 1969; Weisblum et al. 1971), which in turn results from a specific structural modification of the ribosome (Lai and Weisblum 1971; Lai et al. 1973a,b; Saito and Mitsuhashi 1980). The structural modification, methylation of adenine in 23S ribosomal RNA (rRNA), confers resistance to three chemically distinct groups of antibiotics that inhibit 50S ribosome subunit function: the macrolides, lincosamides, and Streptogramin type-B (MLS) antibiotics. The material presented in this paper has been organized under the headings of three genera (namely Stapphylococcus, Streptococcus, and Streptomyces ), which illustrate the biological diversity of MLS resistance, the more general form of clinical erythromycin resistance, with emphasis on the variations of inducer and induced phenotype that occur in these organisms, followed by a discussion of the structure and function of genetic control elements, studied in model systems, which regulate expression of this interesting resistance mechanism at the molecular level. MLS RESISTANCE IN Staphylococcus SPECIES Historical Background Early reports of erythromycin-resistant S. aureus noted that such strains were either coresistant to other macrolides or that they could rapidly become so (Chabbert 1956; Jones et al. 1956; Garrod 1957). It was also...