gebhart/patrepeval huggingface dataset:
Thin films and instrumental polarization (1986)

A general method for calculating the polarization effects of thin films on the instrumental polarization of symmetrical optical systems is presented. This method treats the coated optical surfaces as weak spatially varying polarizers and sums the surface contributions to determine the overall instrumental polarization. The Fresnel and thin-film equations for the interfaces are expanded in a Taylor series which describe the amplitude, phase, dichroism, and birefringence as functions of the angle of incidence. Using paraxial optics, these low-order surface polarization contributions may be readily summed to determine the variation of instrumental polarization for arbitrary paraxial ray paths. The resulting polarization behavior displays a close correspondence to the wavefront aberrations of geometrical optics and are thus called polarization aberrations. Suggestions for thin-film designs which compensate for instrumental polarization follow naturally.
In vivo OCT imaging of the airways (Conference Presentation) (2017)

Chronic dysregulated influx of neutrophil into the airway increases neutrophil burden and augments the inflammatory processes often observed in diseases such as cystic fibrosis. The quantification of neutrophil influx is often accomplished with the use of destructive tests such as imaging cytometry and myeloperoxidase assay. However, those methods are unable to capture information about the cascade of events that precede trans-epithelium migration. In this work, we employed a high resolution micro-optical coherence tomography (µOCT) technology to perform real time imaging of neutrophil activity across airway epithelial cells grown on the underside of Transwell permeable supports. This inverted configuration allows the creation of an air-liquid interface at the apical side of the cells. The µOCT imaging technology, based on the principles of spectral-domain OCT, has a lateral and axial resolution of 2 and 1.3µm, respectively. In addition, it has an axial range of approximately 300µm and is capable of recording cross-sectional images at 40 fps. By raster scanning the illumination beam, the behavior of the neutrophils across a 3D volume can be recorded over time. Thus, this imaging modality is capable of resolving individual neutrophils and, potentially, capturing the cascading events involving neutrophil tethering, subsequent adhesion to activated epithelial cells and the ultimate passage through the epithelial cells to the air space on the apical side. As a result, not only can the amount of neutrophil migration be quantified, how neutrophils behave, organize and interact with the epithelial cells and each other can also be more closely analyzed by µOCT imaging.
Self‐Assembled Microactuators Using Chiral Liquid Crystal Elastomers (2023)

Materials that undergo reversible changes in form typically require top-down processing to program the microstructure of the material. As a result, it is difficult to program microscale, 3D shape-morphing materials that undergo non-uniaxial deformations. Here, a simple bottom-up fabrication approach to prepare bending microactuators is described. Spontaneous self-assembly of liquid crystal (LC) monomers with controlled chirality within 3D micromold results in a change in molecular orientation across thickness of the microstructure. As a result, heating induces bending in these microactuators. The concentration of chiral dopant is varied to adjust the chirality of the monomer mixture. Liquid crystal elastomer (LCE) microactuators doped with 0.05 wt% of chiral dopant produce needle-shaped actuators that bend from flat to an angle of 27.2 ± 11.3° at 180 °C. Higher concentrations of chiral dopant lead to actuators with reduced bending, and lower concentrations of chiral dopant lead to actuators with poorly controlled bending. Asymmetric molecular alignment inside 3D structure is confirmed by sectioning actuators. Arrays of microactuators that all bend in the same direction can be fabricated if symmetry of geometry of the microstructure is broken. It is envisioned that the new platform to synthesize microstructures can further be applied in soft robotics and biomedical devices.
Pulse-Width Optical Modulation for CRAN Front-Hauling (2015)

Future (5G) mobile networks aim to pervasivity (cell size <; 1 km) and high data-rate (>20-50 Mb/s), centralized radio access network (CRAN) is the most promising paradigm that aggregates the baseband processing to comply with dense antennas deployment. Even if optical networks are the most promising solution for CRAN front-hauling, there is the need to investigate alternative and/or complementary solutions to digital front-hauling (e.g., CPRI protocol) that can make a parsimonious usage of the optical bandwidth and related electronics. In this framework, here we propose a new waveform coding for the transport of analog RAN signals by employing the pulse width modulation (PWM) for optical front-hauling. At the transmitter, the radio-signal is sampled and mapped onto the duration of an on/off optical signal, at the fiber receiving-end each PW optical modulated sample is digitized so that the overall communication is transparent. Conceptually, the front- hauling PW waveform is equivalent to split sampling (at transmitter) and quantization (at receiver) so as to avoid the bandwidth expansion of CPRI digitalization. Pros and cons of PW waveforms for CRAN front-hauling are evaluated by investigating the outcomes of an in-lab experiment transmitting 100-MHz RF signals with 16QAM modulation up to 20-km standard single mode fiber. Experimental results provide some room for discussion on this novel front-hauling technique.
Improving the measurement robustness of active stereo 3D sensors by optimization of shifted aperiodic fringe patterns (2020)

Pattern projection-based 3D sensors are widely used for contactless, non-destructive optical 3D shape measurements. In previous works, we have shown 3D measurement systems based on stereo matching between two cameras with GOBO-projected aperiodic fringe patterns. In this contribution, we demonstrate a method to optimize the projection patterns for high measurement robustness, i.e., high completeness of the resulting point cloud with low probability of outliers. To calculate the 3D coordinates of an object point by triangulation, a pixel correspondence between the two cameras must be found. The search for such pixel correspondences can be broken into two parts: a coarse correspondence search and a sub-pixel-accurate refinement. The former is responsible for the completeness and correctness of the 3D result, while the quality of the latter determines the accuracy. The correctness of the correspondence search depends on the property of the projection pattern to uniquely encode each point on the measurement object. If the pattern is very self-similar, the points are not well distinguishable from each other and there is a high probability of mismatches during correspondence search. We introduce a mathematical measure to evaluate the self-similarity of a GOBO-projected fringe pattern. This measure operates on patterns, which we simulate with a simplified 1D model. Based on this measure and its derivatives, we developed an algorithm to optimize the fringe patterns. We compare results achieved with unoptimized and optimized fringe patterns.
Following musical sources by example (2012)

In this paper we present a system that is capable of tracking the pitch and volume of a musical source by making use of training data. We show how we can use pitch-tagged training example sounds to construct a model of a target source, and then use that model to track such a source in unseen mixtures. We do so using a regularized decomposition approach that is designed to strive for semantic continuity in its estimates.
Design and Production in Aspergillus niger of a Chimeric Protein Associating a Fungal Feruloyl Esterase and a Clostridial Dockerin Domain (2004)

A chimeric enzyme associating feruloyl esterase A (FAEA) from Aspergillus niger and dockerin from Clostridium thermocellum was produced in A. niger. A completely truncated form was produced when the dockerin domain was located downstream of the FAEA (FAEA-Doc), whereas no chimeric protein was produced when the bacterial dockerin domain was located upstream of the FAEA (Doc-FAEA). Northern blot analysis showed similar transcript levels for the two constructs, indicating a posttranscriptional bottleneck for Doc-FAEA production. The sequence encoding the first 514 amino acids from A. niger glucoamylase and a dibasic proteolytic processing site (kex-2) were fused upstream of the Doc-FAEA sequence. By using this fusion strategy, the esterase activity found in the extracellular medium was 20-fold-higher than that of the wild-type reference strain, and the production yield was estimated to be about 100 mg of chimeric protein/liter. Intracellular and extracellular production was analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, dockerin-cohesin interaction assays, and Western blotting. Labeled cohesins detected an intact extracellular Doc-FAEA of about 43 kDa and a cleaved-off dockerin domain of about 8 kDa. In addition, an intracellular 120-kDa protein was recognized by using labeled cohesins and antibodies raised against FAEA. This protein corresponded to the unprocessed Doc-FAEA form fused to glucoamylase. In conclusion, these results indicated that translational fusion to glucoamylase improved the secretion efficiency of a chimeric Doc-FAEA protein and allowed production of the first functional fungal enzyme joined to a bacterial dockerin.
On Providing OS Support to Allow Transparent Use of Traditional Programming Models for Persistent Memory (2020)

The advent of persistent memory (PM) into our everyday computing environment is now imminent. New programming models and algorithms based on these models are being developed for such systems. However, current models require programs to be rewritten with persistence related primitives such as clflush and clwb or at least recompiled so that persistent mechanisms can be automatically inserted. This is a burden to program developers. Furthermore, executing legacy programs as-is can lead to application and system inconsistencies as unexpected faults occur. In this article, we propose µSnap, an operating system support that is based on checkpointing that allows legacy applications to be executed as-is without compromising consistency in systems that deploy PM. We implement a prototype of µSnap in the Linux kernel version 4.3.3, and measure and quantify the effect of µSnap for a wide range of applications. We find that µSnap incurs overhead for application execution compared to applications run without any notion of persistency, but that the overhead can be controlled to be minimal by appropriately setting the checkpointing interval. We argue that the benefit for paying this small cost can be tremendous in the sense that one can transparently guarantee the consistency of all legacy software written under the traditional programming model.
Uniform Sampling over Episode Difficulty (2021)

Episodic training is a core ingredient of few-shot learning to train models on tasks with limited labelled data. Despite its success, episodic training remains largely understudied, prompting us to ask the question: what is the best way to sample episodes? In this paper, we first propose a method to approximate episode sampling distributions based on their difficulty. Building on this method, we perform an extensive analysis and find that sampling uniformly over episode difficulty outperforms other sampling schemes, including curriculum and easy-/hard-mining. As the proposed sampling method is algorithm agnostic, we can leverage these insights to improve few-shot learning accuracies across many episodic training algorithms. We demonstrate the efficacy of our method across popular few-shot learning datasets, algorithms, network architectures, and protocols.
Formation of a Digital Image: The Imaging Chain Simplified (2012)

Creating a digital picture is so simple today that when we pick up our camera and push the button, we don't put any thought into the process that we just set into motion. The chain of events that occurs to create the photograph is called the imaging chain. The scientists and engineers who design digital cameras love to dive deep into the physics and the mathematics of the imaging chain, but discussing the imaging chain with people not well versed in this language will usually produce a blank stare or a yawn. This book discusses the concepts used to design digital cameras for people who don't want to be blinded with equations and bored with geek speak. It will help the individuals who work with camera designers and want to know, but are sometimes afraid to ask, why they keep babbling about an "MTF" or some other mysterious acronym. If you ever wondered why pinstripe suits turn psychedelic on TV or why crosses appear on pictures of stars, the imaging chain will give you the answers, and this book is for you
MHC class II super-enhancer increases surface expression of HLA-DR and HLA-DQ and affects cytokine production in autoimmune vitiligo (2016)

Genetic risk for autoimmunity in HLA genes is most often attributed to structural specificity resulting in presentation of self-antigens. Autoimmune vitiligo is strongly associated with the MHC class II region. Here, we fine-map vitiligo MHC class II genetic risk to three SNPs only 47 bp apart, located within a predicted super-enhancer in an intergenic region between HLA-DRB1 and HLA-DQA1, localized by a genome-wide association study of 2,853 Caucasian vitiligo patients. The super-enhancer corresponds to an expression quantitative trait locus for expression of HLA-DR and HLA-DQ RNA; we observed elevated surface expression of HLA-DR (P = 0.008) and HLA-DQ (P = 0.02) on monocytes from healthy subjects homozygous for the high-risk SNP haplotype. Unexpectedly, pathogen-stimulated peripheral blood mononuclear cells from subjects homozygous for the high-risk super-enhancer haplotype exhibited greater increase in production of IFN-γ and IL-1β than cells from subjects homozygous for the low-risk haplotype. Specifically, production of IFN-γ on stimulation of dectin-1, mannose, and Toll-like receptors with Candida albicans and Staphylococcus epidermidis was 2.5- and 2.9-fold higher in high-risk subjects than in low-risk subjects, respectively (P = 0.007 and P = 0.01). Similarly, production of IL-1β was fivefold higher in high-risk subjects than in low-risk subjects (P = 0.02). Increased production of immunostimulatory cytokines in subjects carrying the high-risk haplotype may act as an "adjuvant" during the presentation of autoantigens, tying together genetic variation in the MHC with the development of autoimmunity. This study demonstrates that for risk of autoimmune vitiligo, expression level of HLA class II molecules is as or more important than antigen specificity.
Molecular Targeting Chemistry in Rational Drug Design (2020)

The effector moieties under investigation include a broad range: radiation, drugs, enzymatic toxins, and immune-active peptides and proteins. The chemistries associated with attachment of these radionuclides to targeting moieties, primarily antibodies. A peptide derivative of methotrexate was also conjugated to IgG antibody with a thioether linker by reaction of IgG thiols with its iodoacetyl derivative. The utility of disulfide linkers for drug conjugation is illustrated by the preparation of an antibody neocarzinostatin disulfide conjugate. Oligopeptide spacers such as poly(l-lysine) and poly(l-aspartic acid) provide an additional mechanism to carry larger quantities of drug on a protein. However, they still hold tremendous promise as conjugates, providing both specific binding and carrying capacity for a variety and number of effector agents, such as small-molecule drugs, protein toxins, and radioisotopes. Drugs can act in a direct manner in which a molecule results in a desired cytocidal, cytostatic, or stimulatory effect on target cells.
Synthesis and Structure Characterization of Copper Terephthalate Metal–Organic Frameworks (2009)

Abstract In this paper, we report on a high‐throughput (gram quantities) solvothermal method for the synthesis of copper terephthalate metal–organic frameworks in dmf. While the structure of MOF‐2 and some of the associated polymorphs are well known, we know of no equivalent structural studies for the isostructural copper terephthalate (Cu–tpa). The material we have made crystallizes in the C 2/ m space group. Cu–tpa also exhibits reversible solvent‐exchange properties. These properties make this material useful for potential applications in gas storage and catalysis applications. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2009)
Complexity of Shapes and Quantitative Reasoning in Geometry (2008)

ABSTRACT— We explored the effects of task‐related factors on reasoning processes in geometry focusing on a comparison‐of‐perimeters task in which the irrelevant feature area interferes with the reasoning process. We studied the effects of congruity, salience, and complexity on participants’ accuracy of responses and reaction times. The study shows that incongruent trials yield lower accuracy and longer reaction times than congruent ones. In addition, increasing the salience of the irrelevant feature results in a lower rate of success. Previous research suggested that a high cognitive load leads to higher interference in the incongruent condition. The current study shows that, in this condition, increasing the level of complexity of shapes associated with a higher cognitive load decreases the accuracy of responses and increases reaction times. Our findings can aid educators to select appropriate tasks and examples in their classrooms, taking into account how the level of difficulty is affected by complexity, salience, and congruity.
Random scalar fields and hyperuniformity (2017)

Disordered many-particle hyperuniform systems are exotic amorphous states of matter that lie between crystals and liquids. Hyperuniform systems have attracted recent attention because they are endowed with novel transport and optical properties. Recently, the hyperuniformity concept has been generalized to characterize two-phase media, scalar fields, and random vector fields. In this paper, we devise methods to explicitly construct hyperuniform scalar fields. Specifically, we analyze spatial patterns generated from Gaussian random fields, which have been used to model the microwave background radiation and heterogeneous materials, the Cahn-Hilliard equation for spinodal decomposition, and Swift-Hohenberg equations that have been used to model emergent pattern formation, including Rayleigh-Bénard convection. We show that the Gaussian random scalar fields can be constructed to be hyperuniform. We also numerically study the time evolution of spinodal decomposition patterns and demonstrate that they are hyperuniform in the scaling regime. Moreover, we find that labyrinth-like patterns generated by the Swift-Hohenberg equation are effectively hyperuniform. We show that thresholding (level-cutting) a hyperuniform Gaussian random field to produce a two-phase random medium tends to destroy the hyperuniformity of the progenitor scalar field. We then propose guidelines to achieve effectively hyperuniform two-phase media derived from thresholded non-Gaussian fields. Our investigation paves the way for new research directions to characterize the large-structure spatial patterns that arise in physics, chemistry, biology, and ecology. Moreover, our theoretical results are expected to guide experimentalists to synthesize new classes of hyperuniform materials with novel physical properties via coarsening processes and using state-of-the-art techniques, such as stereolithography and 3D printing.
Human Neural Stem Cell-Based Drug Product: Clinical and Nonclinical Characterization (2022)

Translation of cell therapies into clinical practice requires the adoption of robust production protocols in order to optimize and standardize the manufacture and cryopreservation of cells, in compliance with good manufacturing practice regulations. Between 2012 and 2020, we conducted two phase I clinical trials (EudraCT 2009-014484-39, EudraCT 2015-004855-37) on amyotrophic lateral sclerosis secondary progressive multiple sclerosis patients, respectively, treating them with human neural stem cells. Our production process of a hNSC-based medicinal product is the first to use brain tissue samples extracted from fetuses that died in spontaneous abortion or miscarriage. It consists of selection, isolation and expansion of hNSCs and ends with the final pharmaceutical formulation tailored to a specific patient, in compliance with the approved clinical protocol. The cells used in these clinical trials were analyzed in order to confirm their microbiological safety; each batch was also tested to assess identity, potency and safety through morphological and functional assays. Preclinical, clinical and in vitro nonclinical data have proved that our cells are safe and stable, and that the production process can provide a high level of reproducibility of the cultures. Here, we describe the quality control strategy for the characterization of the hNSCs used in the above-mentioned clinical trials.
Organization of the Nuclear Genome in Tomato and Related Diploid Species (1987)

Genetically, tomato is one of the best-studied higher plants. Both morphological markers (genes detected by visible effects on the plant phenotype) and molecular markers (isozymes and DNA clones) have been characterized and compiled into an extensive linkage map of the chromosomes. This paper summarizes what is known about the organization of genes in tomato chromosomes. Even though this plant is a classic diploid species (2n = 24), it harbors numerous gene duplications, many of which are unlinked. The preponderance of such duplications raises questions about the mechanism(s) by which plant genes duplicate. Pepper has the same chromosome number and belongs to the same family as tomato (Solanaceae); yet, when one compares the genetic map of tomato with that of pepper, it is obvious that the linkage groups have been extensively rearranged since these species diverged.
Impact of Erb-B Signaling on Myelin Repair in the CNS Following Virus-Induced Damage (2008)

Abstract : The objective of these studies is to examine the impact of erbB-mediated signaling on myelin destruction and repair in a novel model of central nervous system (CNS) demyelination. In these studies, we utilize a model of demyelination triggered by direct injection of Theiler s murine encephalomyelitis virus (TMEV) into the spinal cord. This method of lesioning permits us to precisely identify the age and site of the lesion. We hypothesize that increased erbB-mediated signaling will protect animals from disease. Conversely, reduced signaling will worsen demyelination. Our studies have shown that animals that have been exogenously treated with glial growth factor (GGF; a member of the neuregulin family that binds to erbB receptors) have improved clinical function compared to animals receiving glial growth factor 2 or sensory motor derived factor (other members of the neuregulin family). Data to date suggest that the affect of GGF is likely indirect and does not directly affect myelination. Results to date support a role for microRNAs as mediators of this observation. In addition, EGFR levels are low and do not appear to modulate over the course of infection. Myelinating cells do not appear to undergo proliferation, but rather appear to migrate to the site of damage in mice with conditional erbB2 deletions. It is likely that these cells are Schwann cells.