gebhart/patrepeval huggingface dataset:
New Insights on the Mechanism of PPAR‐targeted Drugs (2010)

Walk the line! Choi and colleagues recently reported that the protein kinase CDK5 directly phosphorylates PPARγ in response to inflammatory signals, promoting adipose insulin resistance. In light of this, future antidiabetic agents with reduced agonism activity that inhibit PPARγ phosphorylation may have improved efficacy and side-effect profiles.
Synthesis of Chiral Chromium Tricarbonyl Labeled Thymine PNA Monomers via the Ugi Reaction (2002)

[reaction: see text] Ugi condensation was used to synthesize the first examples of chiral racemic Ar.Cr(CO)(3) labeled peptide nucleic acid (PNA) monomers bearing the organometallic moiety linked to the alpha-carbon of the glycine unit.
“Pushing Power Through Walls” - Wireless Power Transfer Through Stainless Steel (2021)

This paper focuses on wireless power transfer (WPT) through an electrically conductive stainless steel (SS) enclosure necessary for high-purity environments such as required for chemical or pharmaceutical industry. The alternating electromagnetic field penetrates the SS and induces eddy currents that are opposing the field of the primary coil and reduce the coupling and efficiency of the WPT system. Considering a WPT system with E-core geometry, we show how to simplify its modeling with an equivalent circuit approach, while including SS enclosure effects. We show that with such WPT system, special care must be taken when designing resonant compensation, because compensating self-inductances, as typically done for WPT systems, results in larger SS losses than if stray inductances are compensated. Additionally, we show that there is an optimal number of turns, for the primary and secondary windings, which depends on the nominal output power and voltage. Finally, the proposed model is verified with measurements on a hardware demonstrator built with two 0.5 mm thick SS walls that emulate the enclosure. The demonstrator is designed for 50 V output voltage, equal numbers of primary and secondary side turns and is operated at 2250 Hz up to 70 W output power.
A Gentle Sedimentation Process for Size-Selecting Porous Silicon Microparticles to Be Used for Drug Delivery Via Fine Gauge Needle Administration (2020)

Abstract Biodegradable porous silicon (pSi) particles are under development for drug delivery applications. The optimum particle size very much depends on medical use, and microparticles can outperform nanoparticles in specific instances. Here we demonstrate the ability of sedimentation to size-select ultrasmall (1–10 μm) nanoporous microparticles in common solvents. Size tunability is quantified for 1–24 h of sedimentation. Experimental values of settling times in ethanol and water are compared to those calculated using Stokes’ Law. Differences can arise due to particle agglomeration, internal gas generation and incomplete wetting. Air-dried and supercritically-dried pSi powders are shown to have, for example, their median diameter d (0.5) particle sizes reduced from 13 to 1 μm and from 20 to 3 μm, using sedimentation times of 6 and 2 h respectively. Such filtered microparticles also have much narrower size distributions and are hence suitable for administration in 27 gauge microneedles, commonly used in intravitreal drug delivery.
Curve Style Analysis in a Set of Shapes (2013)

Abstract The word ‘style’ can be interpreted in so many different ways in so many different contexts. To provide a general analysis and understanding of styles is a highly challenging problem. We pose the open question ‘how to extract styles from geometric shapes?’ and address one instance of the problem. Specifically, we present an unsupervised algorithm for identifying curve styles in a set of shapes. In our setting, a curve style is explicitly represented by a mode of curve features appearing along the 2D silhouettes of the shapes in the set. Unlike previous attempts, we do not rely on any preconceived conceptual characterisations, for example, via specific shape descriptors, to define what is or is not a style. Our definition of styles is data‐dependent; it depends on the input set but we do not require computing a shape correspondence across the set. We provide an operational definition of curve styles which focuses on separating curve features that represent styles from curve features that are content revealing. To this end, we develop a novel formulation and associated algorithm for style‐content separation. The analysis is based on a feature‐shape association matrix (FSM) whose rows correspond to modes of curve features, columns to shapes in the set, and each entry expresses the extent a feature mode is present in a shape. We make several assumptions to drive style‐content separation which only involve properties of, and relations between, rows of the FSM. Computationally, our algorithm only requires row‐wise correlation analysis in the FSM and a heuristic solution of an instance of the set cover problem. Results are demonstrated on several data sets showing the identification of curve styles. We also develop and demonstrate several style‐related applications including style exaggeration, removal, blending, and style transfer for 2D shape synthesis .
Polymer stabilization of cholesteric liquid crystals in the oblique helicoidal state (2018)

Electrical control of the pitch has been reported in a variant of the cholesteric liquid crystal phase composed of chiral dopants and liquid crystal dimers with a bent conformation, such as CB7CB. For a finite range of applied electric field, the dimeric mesogens assume an oblique helicoidal structure, in which the helical axis is aligned along the electric field and the local director is tilted towards the helical axis (rather than being perpendicular to it). An electric field can directly regulate the periodicity (pitch), allowing reconfiguration of the optical response from a scattering or transparent state to a reflective state. Here, we employ po stabilization to retain the oblique helicoidal state absent an applied field. The polymer stabilized oblique helicoidal structures were investigated under various conditions and material compositions. With polymer stabilization, the magnitude of the selective reflection is found to be dependent on the strength of the applied field. Comparison of the electro-optical response of samples with and without a polymer network elucidates the relative role of boundary conditions, anchoring strength, and elastic energy on the stability of the oblique helicoidal state.
Imaging of quantized magnetostatic modes using spatially resolved ferromagnetic resonance (2002)

We present a measurement technique for performing spatially resolved ferromagnetic resonance and directly imaging quantized magnetostatic modes in magnetic samples that undergo high frequency magnetic drive fields (up to 8 GHz). The dynamic response of a 50×50 μm2 permalloy structure (100 nm thick) under a 7.04 GHz highly nonuniform drive field was measured as a function of the dc bias field using this technique. The magnetization variation observed indicates that quantized magnetostatic mode waves appear at certain bias fields, with the number of nodes decreasing with an increase in the bias field. We tentatively assign the indices of each mode using the Damon–Eshbach (DE) model. Similar modes have been observed for a similar sample geometry using an inductive measurement and they showed good agreement with the DE model. However, the result measured using this technique showed some discrepancy with the DE model and the spatial patterns observed are more complicated than simple one-dimensional standing waves. This complexity suggests that analysis beyond that of the DE model is required to explain the observations.
Microsphere based saliva diagnostics (2005)

Saliva presents a minimally invasive alternative medium to blood for performing diagnostics<sup>1</sup>. Microsphere sensors for ions, small organic molecules, and proteins are currently being developed and optical microarrays containing thousands of these sensors will be used for simultaneous multi-analyte analysis. The fiber bundle platform in use is 1mm in diameter and contains approximately 50,000 individually addressable 3.1&#956;m fibers, each with an etched well capable of housing a single 3.1&#956;m microsphere sensor. Micron-sized bead-based chemistries are produced in house, followed by deposition onto a fiber-optic bundle platform, allowing for multiplexed analysis. The ultimate goal is to develop a universal diagnostic system using saliva as the diagnostic medium. This platform will permit multiplexed analysis of a sample by integrating microfluidics with the optical arrays loaded with sensors capable of detecting relevant biomarkers associated with a wide range of disease states. Disease states that are currently under investigation include end stage renal disease (ESRD) and Sjoegrens Syndrome (SS).
Batch-fabricated thin-film magnetic recording heads (1970)

Fabrication of thin-film recording heads with 30-μm wide gaps in 25-μm thick Permalloy have been reported previously. Formation of narrow gaps by chemical etching was limited by undercutting. This paper describes a process for fabricating thin-film recording heads with gaps 2 μm wide in Permalloy film which is 2.5 μm thick. The process makes use of electroplating, photoetching, and electron beam technologies. The narrow gaps with vertical walls are made possible by the use of electron sensitive resist, electron beam exposure of 2-μm wide strips, and electroplating of 2.5-μm thick films of Permalloy on each side of the narrow strip of the electron sensitive resist.
Solvent-Controlled, Site-Selective N-Alkylation Reactions of Azolo-Fused Ring Heterocycles at N1-, N2-, and N3-Positions, Including Pyrazolo[3,4-d]pyrimidines, Purines, [1,2,3]Triazolo[4,5]pyridines, and Related Deaza-Compounds (2018)

Alkylation of 4-methoxy-1 H-pyrazolo[3,4- d]pyrimidine (1b) with iodomethane in THF using NaHMDS as base selectively provided N2-methyl product 4-methoxy-2-methyl-2 H-pyrazolo[3,4- d]pyrimidine (3b) in an 8/1 ratio over N1-methyl product (2b). Interestingly, conducting the reaction in DMSO reversed selectivity to provide a 4/1 ratio of N1/N2 methylated products. Crystal structures of product 3b with N1 and N7 coordinated to sodium indicated a potential role for the latter reinforcing the N2-selectivity. Limits of selectivity were tested with 26 heterocycles which revealed that N7 was a controlling element directing alkylations to favor N2 for pyrazolo- and N3 for imidazo- and triazolo-fused ring heterocycles when conducted in THF. Use of <sup>1</sup>H-detected pulsed field gradient-stimulated echo (PFG-STE) NMR defined the molecular weights of ionic reactive complexes. This data and DFT charge distribution calculations suggest close ion pairs (CIPs) or tight ion pairs (TIPs) control alkylation selectivity in THF and solvent-separated ion pairs (SIPs) are the reactive species in DMSO.
Development of a low-cost hand-held system for optical coherence tomography imaging(Conference Presentation) (2016)

We report the development of a low-cost hand-held optical coherence imaging system. The proposed system is based on the principle of linear optical coherence tomography (Linear OCT), a technique which was proposed in the early 2000s as a simpler alternative to the conventional time-domain and Fourier-domain OCT. In our design, as in the traditional Michaelson interferometer, light from a broadband source is split into sample and reference beams. Unlike in a Michaelson interferometer though, upon return, a tilt is introduced to the reference beam before it is combined with the sample beam to illuminate a detector array. The resulting fringe pattern encodes information about the relative time-of-flight of photons between the sample and reference arms, which can be decoded by standard signal processing techniques to obtain depth resolved reflectivity profiles of the sample. The axial resolution and the SNR of our system was measured to be approximately 5.2 μm and 80 dB, respectively. The performance of the proposed system was compared with a standard state-of-the-art Fourier-domain low coherence interferometry (LCI) system by imaging several biological and non-biological samples. The results of this study indicate that the proposed low-cost system might be a suitable choice for applications where the imaging depth and SNR can be traded for lower cost and simpler optical design. Two potentially useful applications of the proposed imaging system could be for imaging the human tympanic membrane (TM) for diagnosing middle ear pathologies, and to visualize the sub-surface features of materials for non-destructive evaluation and quality inspection.
Genetic design automation for autonomous formation of multicellular shapes from a single cell progenitor (2019)

A bstract Multi-cellular organisms originate from a single cell, ultimately giving rise to mature organisms of heterogeneous cell type composition in complex structures. Recent work in the areas of stem cell biology and tissue engineering have laid major groundwork in the ability to convert certain types of cells into other types, but there has been limited progress in the ability to control the morphology of cellular masses as they grow. Contemporary approaches to this problem have included the use of artificial scaffolds, 3D bioprinting, and complex media formulations, however, there are no existing approaches to controlling this process purely through genetics and from a single-cell starting point. Here we describe a computer-aided design approach for designing recombinase-based genetic circuits for controlling the formation of multi-cellular masses into arbitrary shapes in human cells.
An unwanted guest:Neisseria meningitidis– carriage, risk for invasive disease and the impact of vaccination with insight on Italy incidence (2017)

Invasive Meningococcal Disease (IMD) represents a potentially life-threatening condition caused by Neisseria meningitidis. The disease is characterized by a case fatality rate of 5-10% whereas serious clinical sequelae can develop in survivors within 12-24 h from the first symptoms. However, IMD infection only occurs rarely, in fact, most of the interactions established between N. meningitidis and the host are harmless, and an estimated 10% of the population asymptomatically carries the bacterium in the nasopharynx. Meningococcal carriage represents a critical condition for IMD onset since it represents the first step for disease transmission. Furthermore, high levels of carriage can promote genetic recombination among different N. meningitidis strains potentially leading to the development of new pathogenic variants. Areas covered: The present review discusses N. meningitidis carriage, factors able to influence meningococcal carriage and disease and the effect of vaccinations on both conditions, with a particular focus on Italy. Expert commentary: Data regarding the effect of different meningococcal vaccines on N. meningitidis carriage are available, whereas further studies are needed to investigate the positive impact of the two recently licensed vaccines 4CMenB and rLP2086 on meningococcal carriage.
Science Marries into the Family (2000)

The old Latin word scientia was not much used to designate ordered knowledge until recent times. Galileo would not have called himself a scientist, nor would Newton or Leibniz. Even two hundred years ago Lavoisier still called himself a natural philosopher. Yet each of those people contributed to the radical change that turned natural philosophers into today’s scientists. The change was complex. Roughly speaking, it could be called the evolution of the scientific method. It began during the 1480s, when the new printed books first included accurate illustrations of an observed world. Until then, first Christians and then Moslems had adhered to the Platonist idea that truth is to be reached by deduction far more than by observation. Throughout the sixteenth century the new observational sciences of botany, anatomy, descriptive geometry, geography, and ethnography all took form. In a series of bold steps the new media of print and illustration wrenched a world still shaped around Platonist thinking. Then, in the early sixteen hundreds, Galileo Galilei and Francis Bacon in particular codified the changes that had been afoot. Galileo did more than anyone to establish the methods of the new science, and Francis Bacon framed its philosophical stance. In 1620 Bacon wrote down the new view of nature in unmistakable terms in his Novum Organum. He directly contradicted the Platonists’ belief that truth is to be found in the human mind when he said, “That which nature may produce or bear should be discovered, not imagined or invented.” For over a century, a new breed of scientists had been learning how to take better account of empirical fact than medieval scientists had done. Now Bacon told us flatly that this was the only proper way to practice science. After 1600 Europe gained two new tools of inquiry, both of which led away from medieval thinking. The shift to observational science was certainly strengthened by new kinds of measuring instruments. Clock making was a technology that had led to a new precision in mechanisms. The seventeenth century gave us the telescope, the thermometer, the vacuum pump, and the microscope.
Minimal Potentials with Very Many Minima (2000)

We demonstrate, by construction, that simple renormalizable matrix potentials with S(N), as opposed to O(N), symmetry can exhibit an exponentially large number of inequivalent deep local minima.
Error-free versus mutagenic processing of genomic uracil—Relevance to cancer (2014)

Genomic uracil is normally processed essentially error-free by base excision repair (BER), with mismatch repair (MMR) as an apparent backup for U:G mismatches. Nuclear uracil-DNA glycosylase UNG2 is the major enzyme initiating BER of uracil of U:A pairs as well as U:G mismatches. Deficiency in UNG2 results in several-fold increases in genomic uracil in mammalian cells. Thus, the alternative uracil-removing glycosylases, SMUG1, TDG and MBD4 cannot efficiently complement UNG2-deficiency. A major function of SMUG1 is probably to remove 5-hydroxymethyluracil from DNA with general back-up for UNG2 as a minor function. TDG and MBD4 remove deamination products U or T mismatched to G in CpG/mCpG contexts, but may have equally or more important functions in development, epigenetics and gene regulation. Genomic uracil was previously thought to arise only from spontaneous cytosine deamination and incorporation of dUMP, generating U:G mismatches and U:A pairs, respectively. However, the identification of activation-induced cytidine deaminase (AID) and other APOBEC family members as DNA-cytosine deaminases has spurred renewed interest in the processing of genomic uracil. Importantly, AID triggers the adaptive immune response involving error-prone processing of U:G mismatches, but also contributes to B-cell lymphomagenesis. Furthermore, mutational signatures in a substantial fraction of other human cancers are consistent with APOBEC-induced mutagenesis, with U:G mismatches as prime suspects. Mutations can be caused by replicative polymerases copying uracil in U:G mismatches, or by translesion polymerases that insert incorrect bases opposite abasic sites after uracil-removal. In addition, kataegis, localized hypermutations in one strand in the vicinity of genomic rearrangements, requires APOBEC protein, UNG2 and translesion polymerase REV1. What mechanisms govern error-free versus error prone processing of uracil in DNA remains unclear. In conclusion, genomic uracil is an essential intermediate in adaptive immunity and innate antiviral responses, but may also be a fundamental cause of a wide range of malignancies.
Carotid Artery Wall Segmentation in Multispectral MRI by Coupled Optimal Surface Graph Cuts (2015)

We present a new three-dimensional coupled optimal surface graph-cut algorithm to segment the wall of the carotid artery bifurcation from Magnetic Resonance (MR) images. The method combines the search for both inner and outer borders into a single graph cut and uses cost functions that integrate information from multiple sequences. Our approach requires manual localization of only three seed points indicating the start and end points of the segmentation in the internal, external, and common carotid artery. We performed a quantitative validation using images of 57 carotid arteries. Dice overlap of 0.86 ± 0.06 for the complete vessel and 0.89 ± 0.05 for the lumen compared to manual annotation were obtained. Reproducibility tests were performed in 60 scans acquired with an interval of 15 ± 9 days, showing good agreement between baseline and follow-up segmentations with intraclass correlations of 0.96 and 0.74 for the lumen and complete vessel volumes respectively.
Object Tracking in an Indoor Scenario: Potential for Centimeter Accuracy with LiFi (2022)

Localization in indoor scenarios is difficult based on radio technologies, due to fading and the dominant multipath propagation. Optical wireless technology also denoted as LiFi, propagates mostly via the line-of-sight. Therefore, it has the potential to provide the required centimeter accuracy for indoor Internet-of-Things applications. In this paper, we consider positioning as an extra service offered by the LiFi communication system. Our vision is to detect the required location of automatic guided vehicles, intelligent transport systems, and mobile assembly units in an industrial environment, by using the same hardware also used for wireless communication. Our proposal is based on time-of-flight measurements. We reuse the physical layer from the ITU-T recommendation G.9991 for LiFi for ranging and subsequent trilateration. In this paper, we have further developed this approach towards continuous object tracking and evaluated the accuracy of the 3D position detection in an indoor environment. We observe that the results depend critically on the layout of the LiFi cell. Moreover, we demonstrate that the time-of-flight technique allows object tracking at a speed of 1 measurement / second with an average accuracy of 3 cm in each dimension. The proposed scheme is promising for future real-time implementation and has a high potential for future Internet-of-Things applications.
Schizotypal cognitions as a predictor of psychopathology in adolescents with mild intellectual impairment (2007)

Difficulties experienced by some young people with mild and borderline intellectual disability are associated with enhanced liability to schizophrenia. Clinical methods can both identify those with this extended phenotype and predict those in whom psychosis will occur.
Frequency resolved transverse mode instability in rod fiber amplifiers (2013)

Frequency dynamics of transverse mode instabilities (TMIs) are investigated by testing three 285/100 rod fibers in a single-pass amplifier setup reaching up to ~200W of extracted output power without beam instabilities. The pump power is increased well above the TMI threshold to uncover output dynamics, and allowing a simple method for determining TMI threshold based on standard deviation. The TMI frequency component is seen to appear on top of system noise that may trigger the onset. A decay of TMI threshold with test number is identified, but the threshold is fully recovered between testing to the level of the pristine fiber by thermal annealing the fiber output end to 300°C for 2 h.