gebhart/patrepeval huggingface dataset:
Properties of 3-D imaging systems (1988)

We discuss the problem of specifying and reconstructing 3-D objects using electromagnetic fields. This problem is of interest in volume holographic optical information processing and in 3-D imaging systems such as synthetic aperture radars. In systems, such as optical neural computers, which make efficient use of large scale holographic transformations, volume holographic optical elements offer the potential for information storage at very high spatial densities. To realize this potential it is necessary to overcome the bottleneck on the recording and reconstruction of volume holograms created by the limited space–bandwidth product of the entrance aperture of a volume medium. Only N 2 of the N 3 degrees of freedom of the volume may be recorded or read out by a single monochromatic exposure. In general, at least N monochromatic exposures are necessary to specify or reconstruct fully a volume hologram. Under polychromatic illumination, a volume hologram may be recorded in a single exposure if the recording beam contains at least N independently controllable frequency components. By decomposing the 3-D field into the eigenfunctions of an imaging system we demonstrate specific limitations on the recording and reconstruction of 3-D information using optical fields. We present a method for writing volume holograms based on eigenmode decomposition of the desired field. Finally, we discuss the amount of information needed to reconstruct targets with fractal dimension between 2 and 3.
Spatially aware expectation maximization (SpAEM): application to prostate TRUS segmentation (2014)

In this paper we introduce Spatially Aware Expectation Maximization (SpAEM), a new parameter estimation method which incorporates information pertaining to spatial prior probability into the traditional expectation- maximization framework. For estimating the parameters of a given class, the spatial prior probability allows us to weight the contribution of any pixel based on the probability of that pixel belonging to the class of interest. In this paper we evaluate SpAEM for the problem of prostate capsule segmentation in transrectal ultrasound (TRUS) images. In cohort of 6 patients, SpAEM qualitatively and quantitatively outperforms traditional EM in distinguishing the foreground (prostate) from background (non-prostate) regions by around 45% in terms of the Sorensen Dice overlap measure, when compared against expert annotations. The variance of the estimated parameters measured via Cramer-Rao Lower Bound suggests that SpAEM yields unbiased estimates. Finally, on a synthetic TRUS image, the Cramer-Von Mises (CVM) criteria shows that SpAEM improves the estimation accuracy by around 51% and 88% for prostate and background, respectively, as compared to traditional EM.
131 MODIFICATION OF AMINO ACID CONCENTRATIONS IN MEDIUM BY PIG EMBRYOS FROM THE ZYGOTE TO THE BLASTOCYST STAGE (2004)

Pre-implantation embryos can produce and consume amino acids in a manner dependent upon stage of embryonic development (Partridge and Leese 1996 Reprod. Fert. Dev. 8, 945) that may also be predictive of subsequent viability (Houghton et al. 2002 Hum. Reprod. 17, 999). To examine these relationships in the pig, the appearance or depletion of 18 amino acids from a presumptive near-physiological mixture was determined by HPLC in porcine in vitro-produced embryos from the zygote to the blastocyst stage. Cumulus oocyte complexes derived from slaughterhouse prepubertal pig ovaries were matured for 40 h in modified TCM-199 before being fertilized (Day 0) with frozen thawed semen in tris-based medium. After 6 h, presumptive zygotes were denuded and cultured in groups of 20 in NCSU medium modified to contain a physiological mixture of 18 amino acids including 0.1 mM glutamine (NCSUaa). Groups of 2–10 embryos (dependent on stage) were removed on Day 0 (1 cell), Day 1 (2- and 4-cell), Day 4 (compact morula), and Day 6 (blastocyst) and placed in 4 µL NCSUaa for 24 h. After incubation, the embryos were removed and the medium analyzed by HPLC. Each stage was replicated 3–9 times. Since amino acid profiles of 2- and 4-cell embryos were not different, data were combined. Overall, arginine (1.19 ± 0.33), glutamine (0.78 ± 0.34) and threonine (0.05 ± 0.04) were significantly (P &amp;lt; 0.01) depleted from the medium whereas alanine (0.21 ± 0.1), glycine (0.20 ± 0.06), asparagine (0.13 ± 0.5), lysine (0.1 ± 0.03), isoleucine (0.08 ± 0.01), valine (0.05 ± 0.01), leucine (0.04 ± 0.02), phenylalanine (0.03 ± 0.01), and histidine (0.02 ± 0.04) significantly (P &amp;lt; 0.05) accumulated (mean of the 4 sampling timepoints; all values pmol/embryo/h ± SEM). The difference between amino acid accumulation and depletion (balance) was approximately equivalent between Day 0 and the morula stage although turnover (sum of depletion and accumulation) steadily decreased during this period from 3.1 on Day 0 to 1.35 pmol/embryo/h at the morula stage. However, at the blastocyst stage, turnover and balance increased to 6.32 and 2.42 pmol/embryo/h, respectively, i.e. net appearance occurred. Notable changes in amino acid profile during development included decreases in accumulation of asparagine, glutamate, and glycine in the medium and the depletion of glutamine over Days 0, 1, and 4, followed by reversal of these trends by Day 6. These data suggest that pig embryos can alter the accumulation and depletion rates of amino acids in a manner that is dependent on the specific amino acid and the stage of embryonic development. This work was supported by BBSRC.
Induction of Airway Allergic Inflammation by Hypothiocyanite via Epithelial Cells (2016)

Hypothiocyanite (OSCN<sup>-</sup>) serves as a potent innate defense system against microbes in the lungs. OSCN<sup>-</sup> is generated by the catalysis of peroxidases using thiocyanate transported via several anion transporters, including pendrin/SLC26A4 and hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) generated by Duox1 and Duox2. We previously demonstrated that expression of pendrin, peroxidases, and Duox1/Duox2 is up-regulated in bronchial asthma patients and/or asthma model mice and that these molecules are important in accelerating airway inflammation. However, it remained unclear how activating these molecules would lead to airway inflammation. In this study, we examined whether OSCN<sup>-</sup> produced via the pendrin/peroxidase/Duox pathway causes inflammation via airway epithelial cells. In an in vitro OSCN<sup>-</sup> production system, OSCN<sup>-</sup>, but not H<sub>2</sub>O<sub>2</sub>, activated NF-κB, a transcription factor critical for inflammatory responses, in the airway epithelial cells. OSCN<sup>-</sup> was sensed by protein kinase A (PKA) followed by formation of the dimerization of PKA. The dimerized PKA, the active form, was critical in activating NF-κB. Detoxifying H<sub>2</sub>O<sub>2</sub>, mainly by catalase, enabled the dominant abilities of OSCN<sup>-</sup> to dimerize PKA and activate NF-κB, compared with untreated H<sub>2</sub>O<sub>2</sub> Furthermore, OSCN<sup>-</sup> in high doses caused necrosis of the cells, inducing release of IL-33, a trigger to initiate type 2 inflammation. These results demonstrate that OSCN<sup>-</sup> in low doses activates NF-κB via PKA in airway epithelial cells, whereas OSCN<sup>-</sup> in high doses causes necrosis, suggesting an important role in airway allergic inflammation for the production of OSCN<sup>-</sup> via the pendrin/peroxidase/Duox pathway.
Advances in directed assembly: a themed collection (2017)

Guest Editors Paul F. Nealey and Mark Stoykovich introduce this themed collection of papers.
Overproduction of DnaJ inEscherichia coliImprovesin VivoSolubility of the Recombinant Fish-derived Transglutaminase (1998)

The overexpression of red sea bream (Pagrus major) transglutaminase (TGase, E.C. 2.3.2.13) in Escherichia coli mostly leads to the accumulation of biologically inactive enzyme. Although the solubility of the gene products could be improved by cultivation at a lower temperature (26-28 degrees C), most of the synthesized TGase was still in the form of insoluble aggregates. The effects of overproduction of molecular chaperones on the intracellular solubility of newly produced recombinant TGase were examined. The overexpression of dnaK or groES/EL did not improve solubility. However, DnaJ greatly increased the solubility of the recombinant TGase, resulting in active enzyme in the presence of calcium ions. Co-expression of dnaK along with dnaJ further increased the content of soluble TGase. Under our experimental conditions, supplementation with both DnaJ and DnaK elevated the TGase activity in the producer cells by roughly 4-fold, compared with the control strain cultured at 30 degrees C. Thus, we found that DnaJ is important in controlling the solubility of protein overproduced in E. coli.
Report on the International Conference on Design of Experimental Search & Information Retrieval Systems (DESIRES 2018) (2019)

This is a report on the first edition of the International Conference on Design of Experimental Search &amp; Information REtrieval Systems ( DESIRES 2018) held in Bertinoro, Italy, from August 28 to August 31, 2018.
Parkin Mutation Affects Clock Gene-Dependent Energy Metabolism (2019)

Growing evidence highlights a tight connection between circadian rhythms, molecular clockworks, and mitochondrial function. In particular, mitochondrial quality control and bioenergetics have been proven to undergo circadian oscillations driven by core clock genes. Parkinson's disease (PD) is a chronic neurodegenerative disease characterized by a selective loss of dopaminergic neurons. Almost half of the autosomal recessive forms of juvenile parkinsonism have been associated with mutations in the <i>PARK2</i> gene coding for parkin, shown to be involved in mitophagy-mediated mitochondrial quality control. The aim of this study was to investigate, in fibroblasts from genetic PD patients carrying parkin mutations, the interplay between mitochondrial bioenergetics and the cell autonomous circadian clock. Using two different in vitro synchronization protocols, we demonstrated that normal fibroblasts displayed rhythmic oscillations of both mitochondrial respiration and glycolytic activity. Conversely, in fibroblasts obtained from PD patients, a severe damping of the bioenergetic oscillatory patterns was observed. Analysis of the core clock genes showed deregulation of their expression patterns in PD fibroblasts, which was confirmed in induced pluripotent stem cells (iPSCs) and induced neural stem cells (iNSCs) derived thereof. The results from this study support a reciprocal interplay between the clockwork machinery and mitochondrial energy metabolism, point to a parkin-dependent mechanism of regulation, and unveil a hitherto unappreciated level of complexity in the pathophysiology of PD and eventually other neurodegenerative diseases.
New Paradigms for Organic Catalysts: The First Organocatalytic Living Polymerization (2001)

Ohne Metallionen kommt die lebende Ringöffnungs-Polymerisation (ROP, schematisch dargestellt) von Lactid aus, wenn stark basische Amine wie 4-(Dimethylamino)pyridin als Umesterungskatalysatoren verwendet werden. Die Zugabe des Katalysators allein genügt aber noch nicht, es muss noch ein Nucleophil (z. B. ein Alkohol) zugegeben werden, das die eigentlich initiierende Spezies darstellt.
Long-term thermal stability tests at 1000 °C of silica fibre Bragg gratings made with ultrafast laser radiation (2006)

Using an ultrafast Ti:sapphire 800 nm laser and a phase mask, fibre Bragg gratings (FBGs) with high thermal stability were fabricated in Ge-doped SMF-28 fibre for sensor applications and were subjected to long annealing tests at 1000 °C. FBGs that maintained more than 99.95% reflectivity after several hundred hours at this temperature are demonstrated. The gratings perform well in cycling experiments up to 1000 °C, and hysteresis in the wavelength response was not detected. At a temperature of 1050 °C, a permanent drift of the central wavelength is observed which is associated with a reduction of the grating strength. The capability of this new type of FBG to be used for high temperature sensors is discussed.
Protocol for Microfluidic System to Automate the Preparation and Fractionation of the Nucleic Acids in the Cytoplasm Versus Nuclei of Single Cells (2016)

This protocol describes the extraction, fractionation, and recovery of cytoplasmic nucleic acids (e.g., cytoplasmic RNA) versus nucleic acids in the cell nucleus (including genomic DNA, gDNA) from single cells with a microfluidic system. The method enables independent, sequence-specific analyses of these critical markers (Kuriyama et al., 2015). The system uses a microfluidic chip with a simple geometry and four end-channel electrodes, and completes the entire process in less than 5 min, including lysis, purification, fractionation, and delivery to two output reservoirs: One for the nucleus (including gDNA and nuclear RNA) and one for cytoplasmic RNA. Each reservoir then contains high quality and purity aliquots with no measurable cross-contamination of cytoplasmic RNA versus nucleic acids in nucleus. As described here, our protocol focuses on the analysis of cytoplasmic RNA versus gDNA from the nucleus. We have tested this protocol with mouse and human cells but not with walled cells such as plant cells.
The Perceptual Basis of Some Rules of Thumb in Photography (2011)

We communicate increasingly with visual imagery such as realistic pictures (e.g., photographs, computer graphic images, perspective drawings and paintings). People are readily able to interpret pictures, but the means by which they do so is poorly understood. Photographers utilize many guidelines for creating natural-looking pictures. One guideline concerns the lens focal length required to produce pictures that are not spatially distorted. Photography texts recommend choosing a focal length of 50mm. There are two phenomena related to this guideline. One is perceived spatial distortions in wide-angle (short focal length) pictures. I will argue that the perceived distortions are caused by the perceptual mechanisms people employ to take into account oblique viewing positions. The second phenomenon is perceived depth in pictures taken with different focal lengths. The textbooks argue that pictures taken with short focal lengths expand perceived depth and those taken with long focal lengths compress it. I will argue that these effects are due to a combination of the viewing geometry and peoples' viewing. Another guideline concerns the camera aperture and depth-of-field blur. Photography textbooks do not describe a quantitative rule and treat the magnitude of depth-of-field blur as arbitrary. I examine apertures, lenses, and image formation. From that examination, I argue that there is a natural relationship between depth-of-field blur and the 3D layout of the photographed scene. Human viewers are sensitive to this relationship. In particular, depicted scenes are perceived differently depending on the relationship between blur and 3D layout. Understanding the perceptual basis of these guidelines provides insight into how to construct photographs, perspective paintings, and computer graphic images for more effective visual communication.
Control method for Inductive Power Transfer with high partial-load efficiency and resonance tracking (2014)

Frequency controlled Inductive Power Transfer (IPT) systems for Electric Vehicle (EV) battery charging applications often suffer from high power losses in partial-load, because the transmitter coil current is not significantly reduced at low output power. Therefore, in this paper a novel control method is presented that exhibits a substantially higher partial-load efficiency, while it also enables full control of the power semiconductor switching conditions. The power flow control is based on the dynamic regulation of the dc-link voltages on both sides of the resonant system with dc-dc-converters. Additionally, a tracking of the resonance with a current zero crossing detection circuit and a PLL makes the switched current an additional degree of freedom, that can be used, e.g., for the minimization of IGBT soft-switching losses due to stored-charge. All calculated results are supported by experimental measurements on an existing 5 kW/52mm air gap/210mm coil diameter prototype system with an efficiency of more than 96.5% at maximum power and above 96% down to 20% rated power.
Distance protection in distribution systems: How it assists with integrating distributed resources (2012)

The integration of distributed generation (DG) or distributed resources in the distribution system poses technical constraints for the electrical power system owner or manager. The addition of relatively large amounts of generation to the distribution system can potentially challenge the historical settings principles and design assumptions made in developing protection and control strategies based on overcurrent protection. The necessity and complexity of additional protection and control measures increase as the aggregate DG capacity within a potential island approaches or offsets the load within that island. In addition, the varying nature of DG availability and fault current capability must also be considered. The key issues discussed and associated with DG on the distribution feeder include anti-islanding, temporary overvoltages during fault conditions, and loss of sensitivity of feeder overcurrent protection for long feeders. As the distribution system evolves to accommodate more DG, the design and implementation of the feeder protection must also evolve. This paper presents the use of distance relays for distribution protection to solve some of the DG integration problems. This paper provides real-world event report data to further demonstrate the performance of distance protection on the distribution system. A relative cost comparison between various feeder protection solutions is presented along with a discussion on options for education of distribution companies challenged with implementing distance protection for the first time.
In Vivo, In Vitro, and In Silico Characterization of Peptoids as Antimicrobial Agents (2016)

Bacterial resistance to conventional antibiotics is a global threat that has spurred the development of antimicrobial peptides (AMPs) and their mimetics as novel anti-infective agents. While the bioavailability of AMPs is often reduced due to protease activity, the non-natural structure of AMP mimetics renders them robust to proteolytic degradation, thus offering a distinct advantage for their clinical application. We explore the therapeutic potential of N-substituted glycines, or peptoids, as AMP mimics using a multi-faceted approach that includes in silico, in vitro, and in vivo techniques. We report a new QSAR model that we developed based on 27 diverse peptoid sequences, which accurately correlates antimicrobial peptoid structure with antimicrobial activity. We have identified a number of peptoids that have potent, broad-spectrum in vitro activity against multi-drug resistant bacterial strains. Lastly, using a murine model of invasive S. aureus infection, we demonstrate that one of the best candidate peptoids at 4 mg/kg significantly reduces with a two-log order the bacterial counts compared with saline-treated controls. Taken together, our results demonstrate the promising therapeutic potential of peptoids as antimicrobial agents.
Perlecan/HSPG2 and matrilysin/MMP-7 as indices of tissue invasion: tissue localization and circulating perlecan fragments in a cohort of 288 radical prostatectomy patients (2016)

Prostate cancer (PCa) cells use matrix metalloproteinases (MMPs) to degrade tissue during invasion. Perlecan/HSPG2 is degraded at basement membranes, in reactive stroma and in bone marrow during metastasis. We previously showed MMP-7 efficiently degrades perlecan. We now analyzed PCa tissue and serum from 288 prostatectomy patients of various Gleason grades to decipher the relationship between perlecan and MMP-7 in invasive PCa. In 157 prostatectomy specimens examined by tissue microarray, perlecan levels were 18% higher than their normal counterparts. In Gleason grade 4 tissues, MMP-7 and perlecan immunostaining levels were highly correlated with each other (average correlation coefficient of 0.52) in PCa tissue, regardless of grade. Serial sections showed intense, but non-overlapping, immunostaining for MMP-7 and perlecan at adjacent borders, reflecting the protease-substrate relationship. Using a capture assay, analysis of 288 PCa sera collected at prostatectomy showed elevated levels of perlecan fragments, with most derived from domain IV. Perlecan fragments in PCa sera were associated with overall MMP-7 staining levels in PCa tissues. Domain IV perlecan fragments were present in stage IV, but absent in normal, sera, suggesting perlecan degradation during metastasis. Together, perlecan fragments in sera and MMP-7 in tissues of PCa patients are measures of invasive PCa.
Supplementary Table 1 from Host-Dependent Phenotypic Resistance to EGFR Tyrosine Kinase Inhibitors (2023)

&lt;p&gt;Supplementary Excel File 1&lt;/p&gt;
Reduction of artifacts by digital filtering in Fourier image reconstruction (2003)

The use of digital filtering is explored as a means of minimizing artifacts in a general class of image reconstruction approaches commonly referred to as direct Fourier reconstruction methods. In the polar-to-Cartesian conversion, applications of windowing operations for the two-dimensional interpolation-type methods are seen to reduce artifacts according to a number of error measures. For the one-dimensional case, the use of a high-resolution spline interpolation gives the lowest error measures. The use of the chip-Z transform is proposed as a way to generate transformed projection data in a concentric square grid to eliminate part of the one-dimensional interpolation currently needed for the processing.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>