gebhart/patrepeval huggingface dataset:
Quantitative Zernike phase-contrast microscopy by use of structured birefringent pupil-filters and phase-shift evaluation (2002)

Zernike phase-contrast is a well known and a often used method for the visualization of phase-structures. Because it applies a fixed phase-shift between the zero'th order and the scattered field, quantitative phase-measurements are only possible for small phase-shifts but not for arbitrary ones. The basic idea of the presented generalization of the method is to use polarization-optical pupil-filters for a separation of the zero'th from the higher orders in combination with phase-shifting polarization interferometry: In the simplest version, a drilled half-wave retarder is used in connection with linearly polarized illumination. This pupil-filter rotates the polarization of the scattered field by (pi) /2 while the dc-term is unaffected because it traverses the hole. The transmitted field is analyzed by phase-shifting polarization-interferometry: Using a liquid-crystal phase shifter (LCPS), both components can be phase-shifted relative to each other; they interfere at a subsequent analyzer. By means of a signal-evaluation according to phase-shifting interferometry, the complex amplitude of the scattered field can be determined relative to the dc-term enabling a computation of the complete field's phase. The method works for general complex objects. The applications we consider are in the field of microstructure inspection.
Re-Identification in Differentially Private Incomplete Datasets (2022)

Efforts to counter COVID-19 reaffirmed the importance of rich medical, behavioral, and sociological data. To make data available to many researchers who can conduct statistical analyses and machine learning, personally identifiable information must be excluded to protect individual privacy. It is essential to remove explicit identifiers, sample population data, and apply differential privacy, the de facto standard privacy metric. Despite the general belief that the risk of re-identification is insignificant when these techniques are applied, this study shows that even after applying these techniques, the risk of being re-identified is highly significant for some data. This study proposes in detail an algorithm for estimating the number of people in a population who have certain attribute values based on incomplete, differentially private databases. If the estimated number is one, the probability that only one person with that attribute value is present in the population is high, which means that there is a high probability of re-identification. Therefore, this study concludes that the re-identification risk must be evaluated even after applying state-of-the-art techniques to protect privacy.
Material Analysis of Spontaneously Subluxated Iris-Fixated Phakic Intraocular Lenses (2016)

Deformations of the haptics of iris-fixated phakic IOLs can cause irreversible damage leading to disenclavation and inadequate re-enclavation. In such cases, explantation appears to be the only therapeutic option. It is important to adhere to an appropriate implantation technique to reduce the risk of spontaneous subluxation. [J Refract Surg. 2016;32(9):618-624.].
Framework Policy Information Base (2003)

This document defines a set of PRovisioning Classes (PRCs) and textual conventions that are common to all clients that provision policy using Common Open Policy Service (COPS) protocol for Provisioning.
Abstract 3766: Correlating locus-specific changes in histone trimethylation and gene expression in hypoxia (2022)

Abstract Low oxygen availability (hypoxia) is a common feature of many solid tumors and is associated with poor prognosis and resistance to therapy. The main regulator of cellular responses to hypoxia is the transcription factor HIF (hypoxia-inducible factor). In addition, several histone lysine demethylases (KDMs) are 2-OG dependent dioxygenases and require oxygen for their activity. When oxygen availability is limited, the activity of these KDMs is inhibited leading to global histone hypermethylation, potentially altering gene expression. However, some KDMs are also known to be direct transcriptional targets of HIF, increasing their expression in hypoxia and counteracting this histone hypermethylation. Furthermore, HIF can facilitate recruitment of histone methyltransferase activity to chromatin in cis, leading to local increases in methylation status. Histone methylation can be associated with both gene activation and gene repression, and it remains unclear how the balance of these widespread changes relates to locus-specific regulation of gene expression. Furthermore, previous attempts to analyze regulation of histone methylation by ChIP-seq in hypoxia have not employed normalization methods that take into account global changes in histone modification. We have performed ChIP-seq analysis of histone trimethylation (H3K4me3, H3K9me3, H3K27me3 and H3K36me3) in PC3 prostate cancer cells incubated in normoxia or (16hrs, 1%) hypoxia. We have then examined the effects of the HIF-transcriptional pathway on these marks using the same cell line following deletion of HIF-1b to block the HIF response. We employ an integrated spike-in with drosophila chromatin to provide a normalization control. We then relate our findings to changes in gene expression using RNA-seq analysis, again normalized to a spike-in control. We observe global increases in all 4 histone trimethylations across the genome in hypoxia. In particular, we observe hypoxic increases in histone trimethylation at all gene loci. However, while basal levels of histone trimethylation correlated with basal transcript levels as previously reported, hypoxic increases in promoter-associated histone H3K4me3 trimethylation bore no relation to either the direction or magnitude of gene regulation in hypoxia. Although, more subtle increases were observed across the gene body at gene loci induced by hypoxia. These findings question the currently accepted model that changes in H3K4me3 instruct changes in transcription in hypoxia and suggest that the overall effect of histone trimethylation is a more subtle balance of competing effects. Citation Format: Jessica D. Kindrick, Peter J. Ratcliffe, WIlliam Doug Figg, David R. Mole. Correlating locus-specific changes in histone trimethylation and gene expression in hypoxia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3766.
One-Head Near-Field Writing/Erasing on a Rewritable Dual-Layer Optical Disk Having High-Index Cover and Separation Layers (2011)

Near-field writing and erasing on a rewritable dual-layer optical disk with a single solid immersion lens (SIL) optical head is demonstrated for the first time. A novel beam expander enabled access to both information layers of the disk without exchanging two individual optical heads. A rewritable dual-layer disk having high-index (n=1.8) cover and separation layers was newly developed. By using the SIL optical system and the disk, an effective numerical aperture (NA) of 1.42 is achieved and a recording capacity of 180 Gbyte for the dual-layer rewritable disk is expected.
Nonlinear photoacoustic and ultrasound beamforming through spectral magnitude scaling (2021)

Among clinical photoacoustic and ultrasound beamforming (BF) techniques, a nonlinear p-th root delay and sum (NL-p-DAS) exhibits better contrast and resolution than conventional delay-and-sum. However, despite its advantages, signal loss and grainy speckles often degrade image quality by signal deformation. Thus, we proposed a new nonlinear BF algorithm called nonlinear p-th root spectral magnitude scaling (NL-p-SMS), which scales the signal in the spectral domain instead of the temporal domain. As a result, we achieved the enhanced contrast, contrast noise ratio, spatial resolution, and less grainy texture without significant signal or feature loss in both in vivo photoacoustic and ultrasound images.
Optic axis mapping with catheter-based polarization-sensitive optical coherence tomography (2018)

Birefringence offers an intrinsic contrast mechanism related to the microstructure and arrangement of fibrillary tissue components. Here we present a reconstruction strategy to recover not only the scalar amount of birefringence but also its optic axis orientation as a function of depth in tissue from measurements with catheter-based polarization sensitive optical coherence tomography. A polarization symmetry constraint, intrinsic to imaging in the backscatter direction, facilitates the required compensation for wavelength-dependent transmission through system elements, the rotating catheter, and overlying tissue layers. Applied to intravascular imaging of coronary atherosclerosis in human patients, the optic axis affords refined interpretation of plaque architecture.
Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases (2010)

The Mycobacterium tuberculosis genome encodes 11 serine/threonine protein kinases (STPKs) that are structurally related to eukaryotic kinases. To gain insight into the role of Ser/Thr phosphorylation in this major global pathogen, we used a phosphoproteomic approach to carry out an extensive analysis of protein phosphorylation in M. tuberculosis. We identified more than 500 phosphorylation events in 301 proteins that are involved in a broad range of functions. Bioinformatic analysis of quantitative in vitro kinase assays on peptides containing a subset of these phosphorylation sites revealed a dominant motif shared by six of the M. tuberculosis STPKs. Kinase assays on a second set of peptides incorporating targeted substitutions surrounding the phosphoacceptor validated this motif and identified additional residues preferred by individual kinases. Our data provide insight into processes regulated by STPKs in M. tuberculosis and create a resource for understanding how specific phosphorylation events modulate protein activity. The results further provide the potential to predict likely cognate STPKs for newly identified phosphoproteins.
Coexistence of S. cerevisiae and E. coli in chemostat under substrate competition and product inhibition (1986)

A mixed culture of Saccharomyces cerevisiae and Escherichia coli was established in a stable coexistence steady state in a chemostat under constant operating conditions. The species competed for glucose, the growth-limiting resource, and produced acetate and ethanol. The acetic acid was shown to be very inhibitory to E. coli in pure culture at pH 5 while ethanol inhibition was only marginal. No significant inhibition of S. cerevisiae growth was observed by either acetate or ethanol. Pure culture parameters were measured and used in the analysis. Linearized stability analysis for the case when both organisms produce the inhibitor showed that a transition through three stable outcomes was possible as the feed concentration is lowered. Experimental studies verified these predictions, and successive transitions from a yeast growth steady state, to a coexistence steady state, and to an E. coli growth steady state were obtained by lowering the glucose concentration in the feed from 10 to 5 to 2.5 g/L, respectively. This dynamic behavior is distinct from the outcomes of other competition-inhibition combinations and experimentally demonstrates for the first time that coexistence is possible due to substrate competition and product inhibition.
A Mesoporous Iron−Titanium Oxide Composite Prepared Sonochemically (2003)

Synthesis of a composite mesoporous iron−titanium oxide by ultrasound irradiation is here reported. Iron(III) ethoxide and titanium(IV) isopropoxide were used as precursors, and dodecylamine was used as the templating agent. The synthesis was completed in 6 h in one stage. The product was characterized by XRD, TEM, DSC, TGA, XPS, EDX, and BET methods. Magnetic properties were studied by magnetization and Mössbauer spectroscopy. Short-range ordered structure of the product was demonstrated by low-angle XRD measurements. After heat treatment, this structure collapsed and crystalline phases of γ-Fe2O3 oxide and anatase of TiO2 were observed. The calcinated material showed slight magnetic properties corresponding to the amount of iron oxide. The removal of the surfactant by extraction with diluted nitric acid resulted in the increase of surface area to 650 m2/g and the pore volume to 0.45 mL/g. The catalytic properties of the material were examined in the oxidation of cyclohexane under mild conditions, and a high conversion of the substrate to cyclohexanol and cyclohexanone was obtained.
A ROLE FOR PERSISTING ANTIGEN, ANTIGEN PRESENTATION, AND ICAM-1 IN INCREASED RENAL GRAFT SURVIVAL AFTER ORAL OR PORTAL VEIN DONOR-SPECIFIC IMMUNIZATION1 (1998)

Our data suggest a role for ICAM-1, persistent donor antigen (on host DC), and accessory hepatic monocytes in the induction and maintenance of tolerance after portal vein immunization.
Polyhalogenated heterocyclic compounds.Part 43. Reactions of 4-lithio-2,6-dibromo-3,5 difluoro pyridine (2000)

, readily prepared from 2,4,6-tribromo-3,5 difluoropyridine 1, reacts with a range of electrophiles to give various functionalised pyridine derivatives. A subsequent X-ray crystallographic study of 2,6-dibromo-3,5-difluoro(4-pyridyl) methylphenyl ketone 3e shows an unusual solid state lattice packing arrangement.
On the static failure behaviour of co-cured composite joints with enhanced interlaminar fracture energies via multiscale toughening (2023)

This paper is focused on the multiscale toughened co-cured composite interfaces of carbon/epoxy laminates using vacuum infusion and out-of-autoclave curing—with an emphasis on the role of enhanced interlaminar fracture energies on the static failure of laminate joints. To toughen co-cured interlaminar regions, three toughening routes are used: (i) epoxy matrix toughening with 10 wt% core–shell rubber (CSR) nanoparticles, (ii) 10 g/m2 polyphenylene sulfide (PPS) non-woven micro-fibre veil toughening, and (iii) multiscale toughening by combining epoxy matrix toughening with 10 wt% CSR nanoparticles and 10 g/m2 PPS veils. Double cantilever beam and end-notch flexure tests are conducted with the toughened interfaces for mode-I and mode-II fracture energies. Moreover, three co-cured joint configurations (viz. double-notch single lap, stepped scarf and skin-stiffener joints with the three toughening routes) are tested to characterise the role of enhanced interlaminar fracture energies on the static failure of laminate assemblies. The results show that the three toughening routes have significantly altered the R-curve behaviour and interlaminar fracture energies and that the degree of enhancement in mode-I and mode-II fracture energies is sensitive to the type of toughening route. Based on the material systems tested, the mode-I fracture initiation energy is enhanced by ∼150% with multiscale toughening, ∼65% with particle toughening, and ∼60% with veil toughening; whereas, the mode-II fracture initiation energy is enhanced by ∼85% with veil toughening and ∼35% with multiscale toughening—but reduced by ∼20% with particle toughening. The joint tests show that the toughening routes affect the static failure of the three joint configurations and that the strength and damage evolution of the co-cured joints depend on the interlaminar fracture energies. The strength of the co-cured single lap joints is increased by ∼50% with multiscale toughening and ∼40% with veil toughening; whereas, the strength of the co-cured skin-stiffener joints is enhanced by ∼35% with multiscale toughening and ∼45% with veil toughening. The failure mechanisms observed on the fracture surfaces indicate that the strength/failure behaviour of the co-cured joints depends on the dominant interlaminar fracture mode and the corresponding fracture energies. Overall, it is shown that the multiscale interlaminar toughening routes that are used to address the issue of delamination can also be effectively explored to enhance the static failure of co-cured laminate assemblies by toughening the co-cured interfaces/bondlines.
Supplementary Figure 6 from Impaired IFN-α Production by Plasmacytoid Dendritic Cells Favors Regulatory T-cell Expansion That May Contribute to Breast Cancer Progression (2023)

&lt;p&gt;PDF file, 46K, Purified healthy pDC were cultured with IL-3 either alone or in combination with 25% of TUMSN for 40 h and then incubated for 5 days with allogeneic naive CD4+ T cells.&lt;/p&gt;
Amino Acid Production from Methanol byMethylobacillus glycogenesMutants: Isolation ofL-Glutamic Acid Hyper-producing Mutants fromM. glycogenesStrains, and Derivation ofL-Threonine andL-Lysine-producing Mutants from Them (1993)

L-Glutamic acid (Glu) hyper-producing mutants were isolated from Methylobacillus glycogenes ATCC 21276 and ATCC 21371 during the screening of amino acid auxotrophs. iA111, derived from ATCC 21276, and 1009 (Phe(-)), derived from ATCC 21371, produced about 10 times as much Glu as the wild type strains. The highest producer, RV3, a phenylalanine auxotrophic revertant of 1009, produced 38.8 g/liters of Glu in 84h in a 5-liter jar fermentor. iA111 and 1009 were mutagenized, and L-threonine (Thr) producing mutants were isolated among Thr and L-Iysine (Lys) analog-resistant strains. The highest Thr producer derived from iA111, AL119 (AHV + Lys(R)), produced 11.0g/liters of Thr in 72h in a 5-liter jar fermentor. AL119 was further mutagenized, and a Thr and Lys producer, DHL 122 (DHL(R)), was isolated. DHL 122 co-produced 3.1 g/liters of Lys and 5.6 g/liters of Thr in 72 h in a 5-liter jar fermentor.
The role of oxidative damage in poor scalp health: ramifications to causality and associated hair growth (2015)

The oxidative stress element of unhealthy scalp leads to compromised pre-emergent hair formation and poorly formed hair as it grows. Only cosmetic solutions can minimize the impact of unhealthy hair and to achieve healthy looking and feeling hair, the scalp health must be normalized first. The objectives of this research were to both investigate whether oxidative stress was a relevant aetiological element in scalp dandruff and seborrhoeic dermatitis and whether scalp condition affects the quality of hair that grows from it. Further, this research was designed to determine whether an effective anti-dandruff shampoo would repair and protect the scalp and pre-emergent hair from oxidative stress. This study demonstrated that oxidative stress is an aetiological element relevant to the dandruff condition and that a potentiated ZPT shampoo effectively improves scalp condition, including a reduction in oxidative stress. The compromised hair condition associated with dandruff is concomitantly improved when the scalp condition is improved. It appears that there is a direct link between hair quality and scalp health.
PanoramicData: Data Analysis through Pen & Touch (2014)

Interactively exploring multidimensional datasets requires frequent switching among a range of distinct but inter-related tasks (e.g., producing different visuals based on different column sets, calculating new variables, and observing the interactions between sets of data). Existing approaches either target specific different problem domains (e.g., data-transformation or data-presentation) or expose only limited aspects of the general exploratory process; in either case, users are forced to adopt coping strategies (e.g., arranging windows or using undo as a mechanism for comparison instead of using side-by-side displays) to compensate for the lack of an integrated suite of exploratory tools. PanoramicData (PD) addresses these problems by unifying a comprehensive set of tools for visual data exploration into a hybrid pen and touch system designed to exploit the visualization advantages of large interactive displays. PD goes beyond just familiar visualizations by including direct UI support for data transformation and aggregation, filtering and brushing. Leveraging an unbounded whiteboard metaphor, users can combine these tools like building blocks to create detailed interactive visual display networks in which each visualization can act as a filter for others. Further, by operating directly on relational-databases, PD provides an approachable visual language that exposes a broad set of the expressive power of SQL including functionally complete logic filtering, computation of aggregates and natural table joins. To understand the implications of this novel approach, we conducted a formative user study with both data and visualization experts. The results indicated that the system provided a fluid and natural user experience for probing multi-dimensional data and was able to cover the full range of queries that the users wanted to pose.
The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection (2020)

Identification of the transmitted/founder virus makes possible, for the first time, a genome-wide analysis of host immune responses against the infecting HIV-1 proteome. A complete dissection was made of the primary HIV-1–specific T cell response induced in three acutely infected patients. Cellular assays, together with new algorithms which identify sites of positive selection in the virus genome, showed that primary HIV-1–specific T cells rapidly select escape mutations concurrent with falling virus load in acute infection. Kinetic analysis and mathematical modeling of virus immune escape showed that the contribution of CD8 T cell–mediated killing of productively infected cells was earlier and much greater than previously recognized and that it contributed to the initial decline of plasma virus in acute infection. After virus escape, these first T cell responses often rapidly waned, leaving or being succeeded by T cell responses to epitopes which escaped more slowly or were invariant. These latter responses are likely to be important in maintaining the already established virus set point. In addition to mutations selected by T cells, there were other selected regions that accrued mutations more gradually but were not associated with a T cell response. These included clusters of mutations in envelope that were targeted by NAbs, a few isolated sites that reverted to the consensus sequence, and bystander mutations in linkage with T cell–driven escape.
(Research Papers) Accelerated Screening of Phage-Display Output with Alkaline Phosphatase Fusions (2004)

When using multiple targets and libraries, selection of affinity reagents from phage-displayed libraries is a relatively time-consuming process. Herein, we describe an automation-amenable approach to accelerate the process by using alkaline phosphatase (AP) fusion proteins in place of the phage ELISA screening and subsequent confirmation steps with purified protein. After two or three rounds of affinity selection, the open reading frames that encode the affinity selected molecules (i.e., antibody fragments, engineered scaffold proteins, combinatorial peptides) are amplified from the phage or phagemid DNA molecules by PCR and cloned en masse by a Ligation Independent Cloning (LIC) method into a plasmid encoding a highly active variant of E. coli AP. This time-saving process identifies affinity reagents that work out of context of the phage and that can be used in various downstream enzyme linked binding assays. The utility of this approach was demonstrated by analyzing single-chain antibodies (scFvs), engineered fibronectin type III domains (FN3), and combinatorial peptides that were selected for binding to the Epsin N-terminal Homology (ENTH) domain of epsin 1, the c-Src SH3 domain, and the appendage domain of the gamma subunit of the clathrin adaptor complex, AP-1, respectively.