gebhart/patrepeval huggingface dataset:
Combined determination of sharing and freeness of program variables through abstract interpretation (1991)

In this paper, abstract interpretation algorithms are described for computing the sharmg as well as the freeness information about the run-time instantiations of program variables. An abstract domain is proposed which accurately and concisely represents combined freeness and sharing information for program variables. Abstract unification and all other domain-specific functions for an abstract interpreter working on this domain are presented. These functions are illustrated with an example. The importance of inferring freeness is stressed by showing (1) the central role it plays in non-strict goal independence, and (2) the improved accuracy it brings to the analysis of sharing information when both are computed together. Conversely, it is shown that keeping accurate track of sharing allows more precise inference of freeness, thus resulting in an overall much more powerful abstract interpreter.
Smart Selection of Useful Insights from Wearables (2023)

The popularity of wearable-devices equipped with inertial measurement units (IMUs) and optical sensors has increased in recent years. These sensors provide valuable activity and heart-rate data that, when analysed across multiple users and over time, can offer profound insights into individual lifestyle habits. However, the high dimensionality of such data and user preference dynamics present significant challenges for mining useful insights. This paper proposes a novel approach that employs natural language processing to mine insights from wearable-data, utilising a neural network model that leverages end-to-end feedback from users. Results demonstrate that this approach effectively increased daily step counts among users, showcasing the potential of this method for optimising health and wellness outcomes.
Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range (2002)

Gene expression ratios derived from spotted-glass microarray experiments have become invaluable to researchers by providing sensitive and comprehensive indicators of the molecular underpinnings of cell behaviors and states. However, several drawbacks to this form of data have been noted, including the inability to relate ratios to absolute expression levels or to compare experimental conditions not measured with the same control. In this study we demonstrate a method for overcoming these obstacles. First, instead of cohybridizing labeled experimental and control samples, we hybridize each sample against labeled oligos complementary to every microarray feature. Ratios between sample intensities and intensities of the oligo reference measure sample RNA levels on a scale that relates to their absolute abundance, instead of to the variable and unknown abundances of a cDNA reference. We demonstrate that results from this type of hybridization are accurate and retain absolute abundance information far better than conventional microarray ratios. Next, to ensure the accurate measurement of sample and oligo reference intensities, which may differ by several orders of magnitude, we use a linear regression algorithm, implemented in a freely available PERL script, to combine the linear ranges of multiple scans taken at different scanner sensitivity settings onto an extended linear scale. We discuss future applications of our method to measure RNA expression on the absolute scale of number of transcripts per cell from any organism for which oligo-based spotted-glass microarrays are available.
Golden Gate assembly with a bi-directional promoter (GBid): A simple, scalable method for phage display Fab library creation (2020)

Fabs offer an attractive platform for monoclonal antibody discovery/engineering, but library construction can be cumbersome. We report a simple method - Golden Gate assembly with a bi-directional promoter (GBid) - for constructing phage display Fab libraries. In GBid, the constant domains of the Fabs are located in the backbone of the phagemid vector and the library insert comprises only the variable regions of the antibodies and a central bi-directional promoter. This vector design reduces the process of Fab library construction to "scFv-like" simplicity and the double promoter ensures robust expression of both constituent chains. To maximize the library size, the 3 fragments comprising the insert - two variable chains and one bi-directional promoter - are assembled via a 3-fragment overlap extension PCR and the insert is incorporated into the vector via a high-efficiency one-fragment, one-pot Golden Gate assembly. The reaction setup requires minimal preparatory work and enzyme quantities, making GBid highly scalable. Using GBid, we constructed a chimeric chicken-human Fab phage display library comprising 10<sup>10</sup> variants targeting the multi-transmembrane protein human CD20 (hCD20). Selection/counter-selection on transfected whole cells yielded hCD20-specific antibodies in four rounds of panning. The simplicity and scalability of GBid makes it a powerful tool for the discovery/engineering of Fabs and IgGs.
Visualization and auralization for architectural acoustic simulation (1996)

Numerical simulation of the acoustic field for a large concert hall is normally executed by geometrical acoustics. Although it is a classical method, it needs considerable calculations for practical applications for a large hall. Therefore, some algorithmic technique is needed. As the simulated result contains three-dimensional information, its visualization is useful for intuitive understanding of the field. An auralization of the simulated result is also presented. Because the wave nature of the field should be considered for long wavelength sound, a wave acoustical simulation technique is proposed, which is based on a boundary-element method. A comparison of results from geometrical acoustics and wave acoustics is also presented.
A call to action to evaluate renal functional reserve in patients with COVID-19 (2020)

Coronavirus disease 2019 (COVID-19) poses an unprecedented challenge to world health systems, substantially increasing hospitalization and mortality rates in all affected countries. Being primarily a respiratory disease, COVID-19 is mainly associated with pneumonia or minor upper respiratory tract symptoms; however, different organs can sustain considerable (if not terminal) damage because of coronavirus. Acute kidney injury is the most common complication of COVID-19-related pneumonia, and more than 20% of patients requiring ventilatory support develop renal failure. Additionally, chronic kidney disease is a major risk factor for COVID-19 severity and mortality. All these data demonstrate the relevance of renal function assessment in patients with COVID-19 and the need of early kidney-directed diagnostic and therapeutic approaches. However, the sole assessment of renal function could be not entirely indicative of kidney tissue status. In this viewpoint, we discuss the clinical significance and potential relevance of renal functional reserve evaluation in patients with COVID-19.
Supplementary Tables 1-3 from Multiple Adaptive Mechanisms to Chronic Liver Disease Revealed at Early Stages of Liver Carcinogenesis in the Mdr2-Knockout Mice (2023)

Supplementary Tables 1-3 from Multiple Adaptive Mechanisms to Chronic Liver Disease Revealed at Early Stages of Liver Carcinogenesis in the Mdr2-Knockout Mice
Implementation and Validation of Planar Soft Tissue Structural Constitutive Model (2013)

Constitutive modeling is of fundamental important for numerical simulation and analysis of soft biological tissues. The mechanical behaviors of soft tissues are usually highly nonlinear and anisotropic. The complex behavior is the results from the interaction of tissue microstructure. By incorporating information of fiber orientation and distribution at tissue microscopic scale, the structural model avoids ambiguities in material characterization. Moreover, structural models produce much more information than just simple stress-strain results, but can provide much insight into how soft tissues internally reorganize to external loads by adjusting their internal microstructure. Moreover, it is only through simulation of an entire organ system can such information be derived and provide insight into physiological function. However, accurate implementation and rigorous validation of these models remains very limited. In the present study we implemented a structural constitutive model into a commercial finite element package. The structural model was verified against experiential test data for native bovine pericardium and fetal membrane. In addition to prediction of the mechanical response, we demonstrate how a structural model can provide deeper insights into fiber reorientation and fiber recruitment.
Liver X receptors contribute to the protective immune response against Mycobacterium tuberculosis in mice (2009)

Liver X receptors (LXRs) are key regulators of macrophage function, controlling transcriptional programs involved in lipid homeostasis and inflammation. However, exactly how LXRs modulate inflammation during infection remains unknown. To explore this, we used a mouse model of Mycobacterium tuberculosis infection. Upon intratracheal infection with M. tuberculosis, LXRs and LXR target genes were induced in CD11c+ lung and alveolar cells. Furthermore, mice deficient in both LXR isoforms, LXRalpha and LXRbeta (Lxra-/-Lxrb-/- mice), were more susceptible to infection, developing higher bacterial burdens and an increase in the size and number of granulomatous lesions. Interestingly, mice solely deficient in LXRalpha, but not those lacking only LXRbeta, mirrored the susceptibility of the Lxra-/-Lxrb-/- animals. Lxra-/-Lxrb-/- mice failed to mount an effective early neutrophilic airway response to infection and showed dysregulation of both pro- and antiinflammatory factors in CD11c+ lung cells. T cell responses were strongly affected in Lxra-/-Lxrb-/- mice, showing near-complete abrogation of the infection-induced Th1 function - and even more so Th17 function - in the lungs. Treatment of WT mice with the LXR agonists TO901317 and GW3965 resulted in a 10-fold decrease of the pulmonary bacterial burden and a comparable increase of Th1/Th17 function in the lungs. The dependence of LXR signaling on the neutrophil IL-17 axis represents what we believe to be a novel function for these nuclear receptors in resistance to M. tuberculosis infection and may provide a new target for therapeutics.
Polydopamine Coating as a Scaffold for Ring-Opening Chemistry To Functionalize Gold Nanoparticles (2019)

Gold nanoparticles (GNPs) are promising nanomaterials for various biomedical applications owing to their remarkable optical properties and biocompatibility. However, their interfacial properties require modification for practical use in such applications. Herein, a simple method for modifying the surface of GNPs with polydopamine (PDA) to serve as a scaffold for the subsequent polymerization of hyperbranched polyglycerol (HPG) is reported. GNPs were first coated with PDA (GNP-PDA), and then ring-opening chemistry was used at this interface to modify GNP-PDA with HPG (GNP-PDA-HPG). The produced GNP-PDA-HPG shows not only excellent dispersibility in a salt-containing solution but also strong resistance to aggregation in high- and low-pH solutions, even after 10 days. Moreover, we demonstrate a one-pot method for functionalizing GNP-PDA with HPG and either COOH or trimethylammonium. Finally, we conjugated the trimethylammonium-functionalized GNP-PDA-HPG with fluorescent nanodiamonds to investigate the photothermal ability of the functional GNPs.
On the complexity of join predicates (2001)

We consider the complexity of join problems, focusing on equijoins, spatial-overlap joins, and set-containment joins. We use a graph pebbling model to characterize these joins combinatorially, by the length of their optimal pebbling strategies and computationally, by the complexity of discovering these strategies. Our results show that equijoins are the easiest of all joins, with optimal pebbling strategies that meet the lower bound over all join problems and that can be found in linear time. By contrast, spatial-overlap and set-containment joins are the hardest joins, with instances where optimal pebbling strategies reach the upper bound over all join problems and with the problem of discovering optimal pebbling strategies being NP-complete. For set-containment joins, we show that discovering the optimal pebbling is also MAX-SNP-Complete. As a consequence, we show that unless NP = P, there is a constant ∈o, such that this problem cannot be approximated within a factor of 1 + ∈Ο in polynomial time. Our results shed some light on the difficulty the applied community has had in finding “good” algorithms for spatial-overlap and set-containment joins.
<title>Application of a new matrix formalism to the design of ultrashort pulse lasers</title> (1990)

A Matrix formalism is proposed to treat the propagation of ultrashort light pulses in laser resonators. The existence of "Gaussian temporal eigenmodes" for laser resonators is discussed, with emphasis on the dependence of the time duration of such eigenpulses on various parameters of the resonator. Results of computer simulations based on the formalism are presented.
Occurance ofStaphylococcus nepalensisstrains in different sources including human clinical material (2006)

Five isolates of coagulase-negative staphylococci were obtained from human urine, the gastrointestinal tract of squirrel monkeys, pig skin and from the environment. All key biochemical characteristics of the tested strains corresponded with the description of Staphylococcus xylosus species. However, partial 16S rRNA gene sequences obtained from analysed strains corresponded with those of Staphylococcus nepalensis reference strains, except for two strains which differed in one residue. Ribotyping with EcoRI and HindIII restriction enzymes, whole cell protein profile analysis performed by SDS-PAGE and SmaI macrorestriction analysis were used for more precise characterization and identification of the analysed strains. Obtained results showed that EcoRI and HindIII ribotyping and whole cell protein fingerprinting are suitable and reliable methods for the differentiation of S. nepalensis strains from the other novobiocin resistant staphylococci, whereas macrorestriction analysis was found to be a good tool for strain typing. The isolation of S. nepalensis is sporadic, and according to our best knowledge this study is the first report of the occurrence of this species in human clinical material as well as in other sources.
High spatial uniformity of photoluminescence spectra in semipolar (202¯1) plane InGaN/GaN quantum wells (2015)

Scanning near-field optical spectroscopy was applied to study spatial variations of emission spectra at room temperature in semipolar (202¯1) InxGa1−xN/GaN single quantum wells (QWs) for 0.11≤x≤0.36. Photoluminescence (PL) was found to be highly uniform, with peak wavelength deviations and peak intensity deviations divided by average values in the range of 6–12 meV and 0.03–0.07, respectively. Near-field maps of PL parameters showed large, ∼5 to 10 μm size areas of similar values, as opposed to 100 nm scale variations, often reported for InGaN QWs. The near-field PL spectra were found to broaden with increasing InN molar fraction. In the low In content QWs, the broadening is primarily determined by the random cation distribution, while for larger InN molar fractions 10 nm scale localization sites with increasingly deeper band potentials are suggested as the linewidth broadening cause.
In the Wild Human Pose Estimation Using Explicit 2D Features and Intermediate 3D Representations (2019)

Convolutional Neural Network based approaches for monocular 3D human pose estimation usually require a large amount of training images with 3D pose annotations. While it is feasible to provide 2D joint annotations for large corpora of in-the-wild images with humans, providing accurate 3D annotations to such in-the-wild corpora is hardly feasible in practice. Most existing 3D labelled data sets are either synthetically created or feature in-studio images. 3D pose estimation algorithms trained on such data often have limited ability to generalize to real world scene diversity. We therefore propose a new deep learning based method for monocular 3D human pose estimation that shows high accuracy and generalizes better to in-the-wild scenes. It has a network architecture that comprises a new disentangled hidden space encoding of explicit 2D and 3D features, and uses supervision by a new learned projection model from predicted 3D pose. Our algorithm can be jointly trained on image data with 3D labels and image data with only 2D labels. It achieves state-of-the-art accuracy on challenging in-the-wild data.
Collagen fiber orientation as quantified by small angle light scattering in wounds treated with transforming growth factor‐β2 and its neutalizing antibody (1999)

The purpose of this study was determine quantitative differences in collagen fiber orientation in a wound healing model in the presence of transforming growth factor-beta2 and anti-transforming growth factor-beta2,3 antibody. Full-thickness wounds were made in the paravertebral area of two young pigs. Wounds were treated once, topically, with either transforming growth factor-beta2 or anti-transforming growth factor-beta2 antibody, or with methylcellulose gel. Control wounds were left untreated. Tissue biopsies were obtained from each wound on days 7, 14 and 46 post wounding. Tissue sections were stained with hematoxylin and eosin, and collagen fiber preferred orientation was quantified using small angle light scattering. Our results indicated that wounds treated with transforming growth factor-beta2 and anti-transforming growth factor-beta2,3 antibody had a significantly higher degree of orientation of collagen fibers than normal unwounded skin on days 7, 14 and 46 (p < 0.001). Transforming growth factor-beta2- treated wounds had a higher degree of orientation of collagen fibers than control wounds on days 7 and 14 (p < 0.001), and control wounds displayed a higher degree of orientation than wounds treated with anti-transforming growth factor-beta2,3 and normal unwounded skin at all time points (p < 0.001). These results suggest that differences in the dermal collagen degree of orientation correlate with scarring, and show that small angle light scattering can be used quantitatively to assess differences in the collagen fiber architecture of dermal wounds.
Improved Light Extraction Efficiency of InGaN-Based Multi-Quantum Well Light Emitting Diodes by Using a Single Die Growth (2011)

We have demonstrated that the light extraction efficiency of the InGaN based multi-quantum well light-emitting diodes (LEDs) can be improved by using a single die growth (SDG) method. The SDG was performed by patterning the n-GaN and sapphire substrate with a size of single chip (600 x 250 microm2) by using a laser scriber, followed by the regrowth of the n-GaN and LED structures on the laser patterned n-GaN. We fabricated lateral LED chips having the SDG structures (SDG-LEDs), in which the thickness of the regrown n-GaN was varied from 2 to 6 microm. For comparison, we also fabricated conventional LED chips without the SDG structures. The SDG-LEDs showed lower operating voltage when compared to the conventional LEDs. In addition, the output power of the SDG-LEDs was significantly higher than that of the conventional LEDs. From optical ray tracing simulations, the increase in the thickness and sidewall angle of the regrown n-GaN and LED structures may enhance photon escapes from the tilted facets of the regrown n-GaN, followed by the increase in light output power and extraction efficiency of the SDG-LEDs.
Mechanistic Investigation of Improved Syntheses of Iridium(III)-Based OLED Phosphors (2012)

Treatment of [IrCl3(tht)3] (tht = tetrahydrothiophene) with a stoichiometric amount of PPh3 gave the monosubstitution product [Ir(tht)2(PPh3)Cl3] (5), whose synthesis, particularly that leading to the effective preparation of OLED phosphors, was studied and optimized to achieve the best product yields. Thus, the independent treatment of 5 with 2,4-difluorophenylpyridine (dfppyH) or with variable amounts of benzyldiphenylphosphine (bdpH) gave rise to the formation of the cyclometalation products [Ir(dfppy)(tht)(PPh3)Cl2] (7), [Ir(bdp)(bdpH)(tht)Cl2] (8), and [Ir(bdp)(PPh3)(tht)Cl2] (10), depending on the stoichiometry and conditions employed. Upon further treatment with 5-pyridyl-3-trifluoromethyl-1H-pyrazole (fppzH), these Ir(III) complexes 7, 8, and 10 were capable of yielding the phosphors [Ir(dfppy)(fppz)2] (1), [Ir(bdp)2(fppz)] (4), and [Ir(bdp)(fppz)2] (2), respectively. The general mechanism en route to their formation was studied and discussed.
Electronic conduction in DNA attached to gold electrodes (2004)

Experimental studies of electronic conduction in DNA have produced widely varying electronic properties and the debate is open on DNA electron transfer/transport mechanisms. We have advanced work towards quantifying the electrical conductivity of DNA oligonucleotides by 'studying the conductivity of double stranded DNA that is immobilized in a well defined manner in break junctions. To this end an 18 base pair long (approx. 5 nm) guanine rich double stranded DNA molecule has been designed to be attached to gold electrodes. The oligonucleotides used here have been synthesized using thiol (-SH) end groups that can form strong bonds to gold surfaces, and thus should provide low-resistance coupling to the electrodes. For a number of devices, conductivity between the contact pads increases significantly following exposure to a solution containing the DNA double strands. This increase in conductivity is thought to be due to electronic conduction through DNA double strands which are bonded to the two contacts. This hypothesis is confirmed by the loss in conductivity that is measured upon the denaturation of the double strand in deionized water.
Immune modulation with primed mesenchymal stem cells delivered via biodegradable scaffold to repair an Achilles tendon segmental defect (2016)

Tendon healing is a complex coordinated series of events resulting in protracted recovery, limited regeneration, and scar formation. Mesenchymal stem cell (MSC) therapy has shown promise as a new technology to enhance soft tissue and bone healing. A challenge with MSC therapy involves the ability to consistently control the inflammatory response and subsequent healing. Previous studies suggest that preconditioning MSCs with inflammatory cytokines, such as IFN-γ, TNF-α, and IL-1β may accelerate cutaneous wound closure. The objective of this study was to therefore elucidate these effects in tendon. That is, the in vivo healing effects of TNF-α primed MSCs were studied using a rat Achilles segmental defect model. Rat Achilles tendons were subjected to a unilateral 3 mm segmental defect and repaired with either a PLG scaffold alone, MSC-seeded PLG scaffold, or TNF-α-primed MSC-seeded PLG scaffold. Achilles tendons were analyzed at 2 and 4 weeks post-injury. In vivo, MSCs, regardless of priming, increased IL-10 production and reduced the inflammatory factor, IL-1α. Primed MSCs reduced IL-12 production and the number of M1 macrophages, as well as increased the percent of M2 macrophages, and synthesis of the anti-inflammatory factor IL-4. Primed MSC treatment also increased the concentration of type I procollagen in the healing tissue and increased failure stress of the tendon 4 weeks post-injury. Taken together delivery of TNF-α primed MSCs via 3D PLG scaffold modulated macrophage polarization and cytokine production to further accentuate the more regenerative MSC-induced healing response. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:269-280, 2017.