gebhart/patrepeval huggingface dataset:
Viscous effects and complex local flow behaviors dominate hemolymph circulation in the living wings of locusts (2021)

ABSTRACT An insects’ living systems – circulation, respiration, and a branching nervous system – extend from the body into the wing. 1,2 . Hemolypmh circulation in the wing is critical for hydrating tissues, such as the highly elastic resilin 3 that enhances wing flexibility, and for supplying nutrients to living systems, including sensory organs such as scent-producing patches, sound-receiving tympana, and wind-sensing sensilla distributed across the wing. 4–7 During flight, the presence of hemolymph in the wings reduces aerodynamic instabilities like flutter 8,9 , and faster hemolymph flows are induced by flapping. 10 Despite the critical role of hemolymph circulation in maintaining healthy wing function, wings are often considered “lifeless” cuticle, and most measurements remain qualitative or employ coarse, bulk-flow techniques. While pioneering work in the 1960s mapped hemolymph flow direction in 100 insect species, 11 half a century later we still only have quantitative measurements of flow within the wings of a few insects. Here, we focused on the North American locust Schistocerca americana , a well-studied agricultural pest species, and performed a detailed, quantitative study of global and local hemolymph flows in the densely venated fore and hind wings, along with key regions in the body and pumping organs. Through high-speed fluorescent microscopy, we measured 800 individual trajectories of neutrally buoyant fluorescent particles that move in sync with hemolymph, in the wings and body of 8 live, resting locusts. Our data show that overall flow within the wings is circuitous, but local flow behavior is highly complex, with three distinct types of flow (pulsatile, continuous, and “leaky”) occurring in various combinations in different areas of the wing. We provide the first quantitative measurements of “leaky” flow into wing regions that act as sinuses, where hemolymph flows out of tubular veins and pools within thin membranous regions. We also calculate Péclet, Reynolds, and Womersley numbers, and find that viscous effects dominate flow regimes throughout the wing. Pumping organs and wing regions closest to the body display significantly faster flows and higher Reynolds numbers, but remain within the viscous flow regime. Given the central role of wings in sustaining ecologically important insect behaviors such as pollination, migration, and mating, along with the vast diversity of insect wings seen in nature, this first detailed, quantitative map of hemolymph flows across a wing provides a template for future studies investigating the dynamics of hemolymph flows critical to sustaining wing health among insects.
Characterization of small-core diameter Er-doped fibers from far-field radiation measurements and analysis (1992)

Erbium-doped fibers used in optical fiber amplifiers are designed to guide high intensity pump and signal light beams. They typically have approximately step-index profile shapes with large core-cladding index differences and small core diameters in the range of 2–4 μm. Such small diameter profiles are difficult to resolve with available fiber refractive-index profilers or vidicon cameras. This paper describes a simple technique for resolving small core diameters of step-index fibers by scaling transmission measurements of far-field radiation patterns so that they overlay previously calculated mode-field profiles.
Introduction (2006)

Ever since the invention of the transistor in the late 50’s, its fabrication technology has been evolving, allowing the device integration in a continuously shrinking area. High-performance integrated analog systems have always been difficult to design. Sometimes, calibration is used to gather the extra performance that the analog devices cannot provide intrinsically. But the evolution of the manufacturing technology renders even basic analog systems difficult to design today. With the size reduction, the intrinsic precision of the components degrades. In parallel, the supply voltage decreases, limiting the topologies which can be used. Many modern technologies are specifically suited for pure digital circuits, and some analog devices, like capacitors, are not available. In these conditions, analog design is a challenge even for experienced designers.
In a Transgenic Model of Spontaneous Autoimmune Diabetes, Expression of a Protective Class II MHC Molecule Results in Thymic Deletion of Diabetogenic CD8+ T Cells (2004)

H-2(d) mice expressing both the influenza virus hemagglutinin (HA) as a transgene-encoded protein on pancreatic islet beta cells (InsHA), as well as the Clone 4 TCR specific for the dominant H-2K(d)-restricted HA epitope, can be protected from the development of spontaneous autoimmune diabetes by expression of the H-2(b) haplotype. Protection occurs due to the deletion of K(d)HA-specific CD8+ T cells. This was unexpected as neither the presence of the InsHA transgene nor H-2(b), individually, resulted in thymic deletion. Further analyses revealed that thymic deletion required both a hybrid MHC class II molecule, Ebeta(b) Ealpha(d), and the K(d) molecule presenting the HA epitope, which together synergize to effect deletion of CD4+CD8+ thymocytes. This surprising example of protection from autoimmunity that maps to a class II MHC molecule, yet effects an alteration in the CD8+ T cell repertoire, suggests that selective events in the thymus represent the integrated strength of signal delivered to each cell through recognition of a variety of different MHC-peptide ligands.
Proteins specifically hyperexpressed in a coeliac disease patient with aberrant T cells (2007)

An aberrant T cell population is the basis for diagnosis of refractory coeliac disease and determines the risk of enteropathy-associated T cell lymphoma. This disease is serious with a poor survival. Pathogenetic mechanisms sustaining aberrant T cell proliferation remain unknown. Recently, alemtuzumab has been proposed as a promising new approach to treat these patients. Only few single cases have been tested at present; nevertheless, in all the cases a clinical improvement was observed. However, whether intraepithelial lymphocytes have been targeted effectively by alemtuzumab is still debated. This study reports, using two-dimensional difference gel electrophoresis (2D DIGE), hyperexpressed proteins associated specifically with aberrant T cells found in a patient with coeliac disease by comparison of the protein expression of this sample with that of patients with coeliac disease and polyclonal T cells or with control subjects. The data demonstrated a significantly higher expression of IgM, apolipoprotein C-III and Charcot-Leyden crystal proteins in a duodenal biopsy specimen of the patient with clonal T cells compared with that of other patients. These preliminary results allow hypothesizing different clinical effects of alemtuzumab in patients with coeliac disease and aberrant T cell proliferation, because as well as the probable effect on T cells, alemtuzumab could exert its effect by acting on inflammatory associated CD52(+) IgM(+) B cells and eosinophil cells, known to produce IgM and Charcot-Leyden crystal proteins, that we demonstrated to be altered in this patient. The results also emphasize the possible association of apolipoprotein with aberrant T cell proliferation.
Identification of biomarkers of chronic kidney disease among kidney-derived proteins (2022)

Overall, our results indicate that our approach of focusing on kidney-derived proteins is useful for identifying new CKD biomarkers and that C1q has potential as a biomarker of renal function.
Evidence for normal formation of positronium in gaseous Xe (1988)

Angular correlation of photons from positrons annihilating in the rare gases have been measured in order to investigate positronium formation in these gases at low pressures. A piece of silica aerogel was used to stop positrons in such a thin region that high-resolution angular correlation measurements could be performed with high statistics regardless of the density of the gases. Formation of parapositronium in xenon has been found to be higher than in the other gases under the present experimental conditions. The results, apparently contradictory to the low orthopositronium fraction observed in lifetime experiments, is consistent with the Ore model (1949) of the positronium formation and the measured positronium formation cross sections for the gases. By applying a static magnetic field, the fraction of orthopositronium in xenon has been also measured. It has been confirmed that xenon has a strong quenching effect on orthopositronium. This is consistent with the reported dearth of long-lived components in the positron lifetime spectra in xenon.
Ultrafast dynamics of hole self-localization in β -Ga2O3 (2020)

Hole self-localization into polaron states is a phenomenon characteristic of many wide bandgap compounds including transparent semiconducting oxide β-Ga2O3. While this effect has been recognized for some time, its dynamics remained elusive, and self-localization has often been considered instantaneous. In this work, using the two-color ultrafast pump–probe technique, we have measured the hole self-localization time in β-Ga2O3. At room temperature, this time has been found to be 0.5 ps increasing to 1.1 ps at 10 K. In terms of the configuration coordinate diagram, at room temperature, tunneling and thermal activation contribute to the process with similar weights. The hole self-trapping coefficient is estimated to be 6.4 × 10−8 cm3/s.
Structural and Kinetic Basis for Substrate Selectivity in Populus tremuloides Sinapyl Alcohol Dehydrogenase (2005)

We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities.
A new functional test program generation methodology (2002)

This paper introduces a new method for manually generating test programs to validate a processor design. Current manual methods do not utilize high level of abstraction for describing test programs and lack many important features like reusability, incremental validation, and test program compaction; they also work on a formal model specifically developed for validation purposes. To solve the above problems, we use test specification expressions to describe test programs and generate test sequences based on an instruction-set description of a processor written for synthesis purposes. We provide experimental results of generating test programs for several processors to show the effectiveness of our method.
Supplementary Table S5 from MMP16 Mediates a Proteolytic Switch to Promote Cell–Cell Adhesion, Collagen Alignment, and Lymphatic Invasion in Melanoma (2023)

&lt;p&gt;Supplementary Table S5. Proteins which shedding/release to conditioned media was changed more than 20% after MMP16 knockdown in Proteome Profiler Array.&lt;/p&gt;
Regulation of class I genes by interferons (1988)

The Wnt signaling pathway is deregulated in over 90% of human colorectal cancers. β-Catenin, the central signal transducer of the Wnt pathway, can directly modulate gene expression by interacting with transcription factors of the TCF/LEF family. In the present study we investigate the role of Wnt signaling in the homeostasis of intestinal epithelium by using tissue-specific, inducible β-catenin gene ablation in adult mice. Block of Wnt/β-catenin signaling resulted in rapid loss of transient-amplifying cells and crypt structures. Importantly, intestinal stem cells were induced to terminally differentiate upon deletion of β-catenin, resulting in a complete block of intestinal homeostasis and fatal loss of intestinal function. Transcriptional profiling of mutant crypt mRNA isolated by laser capture microdissection confirmed those observations and allowed us to identify genes potentially responsible for the functional preservation of intestinal stem cells. Our data demonstrate an essential requirement of Wnt/β-catenin signaling for the maintenance of the intestinal epithelium in the adult organism. This challenges attempts to target aberrant Wnt signaling as a new therapeutic strategy to treat colorectal cancer.
ScaDL 2022 Invited Talk 2: AI/ML Pipelines using CodeFlare (2022)

Pipelines have become a ubiquitous construct in machine learning spanning tasks ranging from data cleaning and preprocessing, training foundational models, model optimization and transfer learning and low latency inferencing. While the many pipeline construct has existed for many years (e.g., SciKit learn pipelines, Spark pipelines), this talk will focus on a process calculus style definition of pipeline - called CodeFlare pipelines - that makes it readily amenable to scaling complex AI/ML workflows on a commodity cluster. CodeFlare pipelines not only enable data scientists to introduce compute, data and multi-stage parallelism using simple annotations on the pipeline graph, but also operationalize them on a hybrid cloud platform (Red Hat OpenShift), thereby making the solution deployable just about anywhere and leverage the benefits of serverless computing. This talk will cover a basic realization of CodeFlare pipelines on the Ray platform (1.7.0 release) that has shown near linear scalability for transfer learning and inferencing on foundational models.
HDR and WCG Image Quality Assessment Using Color Difference Metrics (2019)

High Dynamic Range (HDR) and Wide Color Gamut (WCG) imagery is now mainstream across content creation. Thus, having a reliable way of evaluating HDR systems is essential. One common way of measuring the quality of an HDR system is measuring the color errors introduced along the imaging pipeline. Unfortunately, development of color difference metrics has been based on test patches, as opposed to natural imagery, with evaluation mostly limited to Standard Dynamic Range (SDR) databases. In this paper, we evaluate several color difference metrics on five publicly available HDR distortion databases consisting of natural images and subjective scores. Distortion types include lower frequency distortions such as those from tone-mapping as well as higher frequency distortions resulting from compression artifacts by the various compression schemes such as JPEG. We analyze these databases with the well-established CIE L*a*b* metrics (ΔE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">00</inf> , ΔE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">94</inf> ) as well as two HDR specific metrics: ΔE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">z</inf> (J <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">z</inf> a <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">z</inf> b <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">z</inf> ) and ΔE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ITP</inf> (IC <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</inf> C <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">P</inf> ). To quantify the performance, we use four standard performance evaluation procedures. We observe that ΔE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ITP</inf> outperforms the other color difference metrics on four out of five databases. We also perform statistical analysis which demonstrates the effectiveness of using ΔE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ITP</inf> to assess overall image quality of HDR/WCG content. Weaknesses of all metrics for one database suggests more advanced spatio-chromatic visual models are worth pursuing.
New low temperature preparation of ferroelectric Bi4Ti3O12 thin films by MOCVD method (1999)

Abstract Pt/Bi4Ti3O12(001)/Bi2SiO5(100)/Si(100) structures have been fabricated by the metal-organic chemical vapor deposition (MOCVD) at 500°C. Bi2SiO5 film is used as a buffer layer to grow ferroelectric Bi4Ti3O12 films because of its relatively high dielectric constant (∊r=30). The memory window has a C-V characteristic of about 0.8 V, and the retention time estimated by the zero-bias capacitance for the Pt/100-nm-Bi4Ti3O12/30-nm-Bi2SiO5/Si/Al structure is more than 11 days.
Triboelectric Nanogenerator for Sustainable Wastewater Treatment via a Self‐Powered Electrochemical Process (2016)

By harvesting the flowing kinetic energy of water using a rotating triboelectric nanogenerator (R‐TENG), this study demonstrates a self‐powered wastewater treatment system that simultaneously removes rhodamine B (RhB) and copper ions through an advanced electrochemical unit. With the electricity generated by R‐TENG, the removal efficiency (RE) of RhB can reach the vicinity of 100% within just 15 min when the initial concentration of RhB is around 100 ppm at optimized conditions. The removal efficiency of copper ions can reach 97.3% after 3 h within an initial concentration of 150 ppm at an optimized condition. Importantly, a better performance and higher treating efficiency are found by using the pulsed output of R‐TENG than those using direct current (DC) supply for pollutant removal when consuming equal amount of energy. The recovered copper layer on the cathode through R‐TENG is much denser, more uniform, and with smaller grain size ( d = 20 nm) than those produced by DC process, which also hints at very promising applications of the R‐TENG in electroplating industry. In light of the merits such as easy portability, low cost, and effectiveness, this R‐TENG‐based self‐powered electrochemical system holds great potential in wastewater treatment and electroplating industry.
The priority ceiling protocol: A method for minimizing the blocking of high priority Ada tasks (1988)

article Free Access Share on The priority ceiling protocol: A method for minimizing the blocking of high priority Ada tasks Authors: J. B. Goodenough Carnegie Mellon Univ., Pittsburgh, PA Carnegie Mellon Univ., Pittsburgh, PAView Profile , L. Sha Carnegie Mellin Univ., Pittsburgh, PA Carnegie Mellin Univ., Pittsburgh, PAView Profile Authors Info & Claims ACM SIGAda Ada LettersVolume VIIIIssue 7June 1-3, 1988 pp 20–31https://doi.org/10.1145/59368.59371Online:01 June 1988Publication History 96citation726DownloadsMetricsTotal Citations96Total Downloads726Last 12 Months41Last 6 weeks11 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Reconfigurable Intelligent Surfaces Relying on Non-Diagonal Phase Shift Matrices (2022)

Reconfigurable intelligent surfaces (RIS) have been actively researched as a potential technique for future wireless communications, which intelligently ameliorate the signal propagation environment. In the conventional design, each RIS element configures and reflects its received signal independently of all other RIS elements, which results in a diagonal phase shift matrix. By contrast, we propose a novel RIS architecture, where the incident signal impinging on one element can be reflected from another element after an appropriate phase shift adjustment, which increases the flexibility in the design of RIS phase shifts, hence, potentially improving the system performance. The resultant RIS phase shift matrix also has off-diagonal elements, as opposed to the pure diagonal structure of the conventional design. Compared to the state-of-art fully-connected/group-connected RIS structures, our proposed RIS architecture has lower complexity, while attaining a higher channel gain than the group-connected RIS structure, and approaching that of the fully-connected RIS structure. We formulate and solve the problem of maximizing the achievable rate of our proposed RIS architecture by jointly optimizing the transmit beamforming and the non-diagonal phase shift matrix based on alternating optimization and semi-define relaxation (SDR) methods. Moreover, the closed-form expressions of the channel gain, the outage probability and bit error ratio (BER) are derived. Simulation results demonstrate that our proposed RIS architecture results in an improved performance in terms of the achievable rate compared to the conventional architecture, both in single-user as well as in multi-user scenarios.
Bisphenol A derivatives act as novel coactivator binding inhibitors for estrogen receptor β (2021)

Abstract Bisphenol A and its derivatives are recognized endocrine disruptors based on their complex effects on estrogen receptor (ER) signaling. While the effects of bisphenol derivatives on ERα have been thoroughly evaluated, how these chemicals affect ERβ signaling is not well understood. Herein, we identified novel ERβ ligands by screening a chemical library of bisphenol derivatives. Many of the compounds identified showed intriguing dual activities as ERα agonists and ERβ antagonists. Docking simulations suggested that these compounds act as coactivator binding inhibitors (CBIs). Direct binding experiments using wild-type and mutated ERβ demonstrated the presence of a second ligand interaction position at the coactivator binding site in ERβ. Our study is the first to propose that bisphenol derivatives act as CBIs, presenting a critical view point for future ER signaling-based drug development.