gebhart/patrepeval huggingface dataset:
A collaborative annotation system for data visualization (2004)

We present Collaborative Annotations on Visualizations (CAV), a system for annotating visual data in remote and collocated environments. Our system consists of a network framework, and a client application built for tablet PC's. CAV is designed to support the collection and sharing of annotations, through the use of mobile devices connected to visualization servers. We have developed a working system prototype based on tablet PC's that supports digital ink, voice and text annotation, and illustrates our approach in a variety of application domains, including biology, chemistry, and telemedicine. We have created an XML based open standard that supports access to a variety of client devices by publishing visualizations (data and annotations) as streams of images. CAV's primary goal is to enhance scientific discovery by supporting collaboration in the context of data visualizations.
Emergence of Colloidal Patterns in ac Electric Fields (2022)

Suspended microparticles subjected to ac electrical fields collectively organize into band patterns perpendicular to the field direction. The bands further develop into zigzag shaped patterns, in which the particles are observed to circulate. We demonstrate that this phenomenon can be observed quite generically by generating such patterns with a wide range of particles: silica spheres, fatty acid, oil, and coacervate droplets, bacteria, and ground coffee. We show that the phenomenon can be well understood in terms of second order electrokinetic flow, which correctly predicts the hydrodynamic interactions required for the pattern formation process. Brownian particle simulations based on these interactions accurately recapitulate all of the observed pattern formation and symmetry-breaking events, starting from a homogeneous particle suspension. The emergence of the formed patterns can be predicted quantitatively within a parameter-free theory.
Comparison of the fiber optic dosimeter and semiconductor dosimeter for use in diagnostic radiology (2014)

A fiber-optic dosimeter (FOD) was fabricated using a plstic scintillating fiber, a plastic optical fiber, and a multi-pixel photon counter to measure entrance surface dose (ESD) in diagnostic radiology. Under changing tube current and irradition time of the digital radiography (DR) system, we measured the scintillating light and the ESD simultaneously. As experiemtnal results, the total counts of the FOD were changed in a manner similar to the ESDs of the semiconductor dosimeter (SCD). In conclusion, we demonstrated that the proposed FOD minimally affected the diagnostic information of DR image while the SCD caused serious image artifacts.
Component Model for Macroscopic Tumour Biomechanics (2016)

The CHIC (Computational Horizons in Cancer) [1] project develops computational models for the cancer domain, as well as a secure infrastructure for data and model access, and reuse. It addresses challenges related to the development, validation and maintenance of multi-scale models by proposing the creation of complex disease models as composition of reusable component models. We present a versatile component model for the simulation of bio-mechanical aspects of macroscopic tumor growth. The model computes mechanical stresses and strains, resulting from tumor growth or shrinkage in a patient-specific anatomy, from a map of cancer cell concentration. In iterative coupled execution with other component models, its output can be used, for example, to guide the directionality of tumour expansion [2], or to simulate the effect of increased pressure on blood perfusion. Simulation of the bio-mechanic interaction relies on the finite element method (FEM); it is based on a hyper-elastic material model, as well as organ-specific boundary conditions and material properties. A pre-processing pipeline has been developed to automate the configuration process. In combination with automatic segmentation tools, this pipeline permits rapid generation of patient-specific FEM models for personalized simulations, including the assignment of suitable material parameters and boundary conditions from simple configuration options. Model and pre-processing pipeline are implemented using Open Source libraries and software packages (CGAL, VTK, FEBio). The model can be parametrised easily for different organs and body sites of interests; it has been applied to the simulation of kidney, lung and brain cancers in the context of CHIC.
Involvement of Phosphatidate Phosphohydrolase in Arachidonic Acid Mobilization in Human Amnionic WISH Cells (1998)

Prostaglandins are known to play a central role in the initiation of labor in humans, and amnionic cells constitute a major source of these compounds. Prostaglandin synthesis and release by amnion cells in response to hormones and ligands takes place after a characteristic 4-5 h lag. However, we report herein that free arachidonic acid (AA), the metabolic precursor of prostaglandins, can be induced at much shorter times (1 h) in human amnionic WISH cells by phorbol 12-myristate 13-acetate (PMA) through activation of protein kinase Calpha (PKCalpha). WISH cells were found to possess both cytosolic group IV phospholipase A2 (cPLA2) and Group VI Ca2+-independent phospholipase A2 (iPLA2). Of these, the cPLA2 was found to be the likely mediator of AA mobilization in PMA-activated WISH cells. PMA also activates phospholipase D (PLD) in these cells and ethanol, a compound that inhibits PLD-mediated phosphatidic acid (PA) formation, blocked AA release. Moreover, prevention of PA dephosphorylation by the PA phosphohydrolase inhibitors propranolol and bromoenol lactone, resulted in inhibition of AA release by PMA-treated WISH cells. Collectively, these data suggest that activation of cPLA2 and attendant AA release by phorbol esters in WISH cells requires prior generation of DAG by phosphatidate phosphohydrolase.
Corrosion of 316H Stainless Steel in Flowing FLiBe (LiF-BeF<sub>2</sub>) (2022)

This milestone was originally envisioned for completion in FY21 and was delayed due to the COVID-19 response and difficulties in fabricating/obtaining fluoride salts. A monometallic type 316H stainless steel thermal convection loop (TCL) was operated for 1000 h with flowing LiFBeF<sub>2</sub> (i.e. FLiBe) salt and a peak temperature of 650°C. In general, the attack was minimal. However, classic mass transfer was not clearly observed with mass losses in both the hot and cold legs. There was an issue with cleaning the loop with water and specimens may have oxidized, which was not an issue with the previous FLiNaK TCL.
Trade-Offs in Sensor Systems Design: A Tutorial (2022)

In this tutorial, we discuss trade-offs in sensor system design. With examples from engineered systems in our laboratories, we address design considerations at the different system levels, from the choice of a particular sensor to the signal conditioning circuits, the choice of data converter, and data communication physical interfaces. Fundamental concepts from communication and information theory, as well as practical considerations applied to specific case studies, are presented for sensor readout systems. In particular, we address both fundamental trade-offs such as choice of signal representation for signal conditioning and conversion, as well as practical and technological trade-offs such as place of quantization (signal data conversion) application demands and integration technologies. The tutorial deals with what is commonly referred to as the Analog Front End (AFE) up to the point where the physical signal is represented in digital symbols. Although the discussion focuses on all the processing steps of the AFE, a more system-level approach is further explored, including stand-alone system approaches and system communication. Major system trade-offs during system design are discussed, providing important methodology insights towards the design of sensory systems operating within demanding constraints.
Active grounded inductor circuit (2011)

In this article, a novel active grounded inductor is proposed. The circuit utilises two optical amplifiers in a simple configuration that has a buffered output capable of delivering relatively high currents. The circuit possesses good characteristics with inductance error and quality factor that with compensation are better than the corresponding parameters for the Antoniou GIC. Experimental results confirm the theoretical analysis.
NMR studies of structure, hydrogen exchange, and main‐chain dynamics in a disrupted‐core mutant of thioredoxin (1996)

Core-packing mutants of proteins often approach molten globule states, and hence may have attributes of folding intermediates. We have studied a core-packing mutant of thioredoxin, L78K, in which a leucine residue is substituted by lysine, using 15N heteronuclear two- and three-dimensional NMR. Chemical shift differences between the mutant and wild-type main-chain resonances reveal that structural changes caused by the mutation are localized within 12 A of the altered side chain. The majority of resonances are unchanged, as are many 1H-1H NOEs indicative of the main-chain fold, suggesting that the structure of L78K is largely similar to wild type. Hydrogen exchange studies reveal that residues comprising the central beta-sheet of both mutant and wild-type proteins constitute a local unfolding unit, but with the unfolding/folding equilibrium approximately 12 times larger in L78K. The dynamics of main-chain NH bonds in L78K were studied by 15N spin relaxation and compared with a previous study of wild type. Order parameters for angular motion of NH bonds in the mutant are on average lower than in wild type, suggesting greater spatial freedom on a rapid time scale, but may also be related to different rotational correlation times in the two proteins. There is also evidence of greater conformational exchange in the mutant. Differences between mutant and wild type in hydrogen exchange and main-chain dynamics are not confined to the vicinity of the mutation. We infer that mispacking of the protein core in one location affects local dynamics and stability throughout.
Disease Severity in Patients with Simultaneous Influenza and Bacterial Pneumonia (2007)

The severity of pneumonia in patients co-infected with influenza virus and bacteria was significantly higher than in those infected with bacteria alone. These data suggested that the influenza virus infection enhanced the bacterial pneumonia. Further study of the pathogenesis of the synergic interaction between influenza virus and bacteria is warranted.
A New Method for Completely Force Balancing Simple Linkages (1969)

A new method, herein referred to as the “Method of Linearly Independent Vectors,” is shown to permit the complete force balancing of certain planar linkages. This method consists of writing the equation describing the position of the total mechanism center of mass in such a way that the coefficients of the time-dependent terms may be set equal to zero. In this way, the total center of mass can be made stationary, and the shaking force vanishes. Derivations as well as practical applications are shown for four-bar and six-bar linkages with arbitrary link mass distributions.
Interferon-alpha and hydroxyurea in early chronic myeloid leukemia: a comparative analysis of the Italian and German chronic myeloid leukemia trials with interferon-alpha [letter] (1996)

In 1994, the Italian and the German Chronic myeloid leukemia (CML) trials comparing interferon-alpha (IFN-alpha) with conventional chemotherapy were published. The survival advantage in favor of IFN-alpha compared with hydroxyurea (HU; 72 v 52 months) was significant in the Italian (P < .002), but not in the German trial (66 v 56 months, P < .44). We set up a collaborative study to identify the reasons for the different outcomes. There are major differences in the trial protocols concerning admission criteria, treatment strategy, and definitions. The German patients were older and more seriously sick. Fifty-two of the 327 patients in the German IFN and HU arms did not fulfil Italian admission criteria, and 41 of the 322 Italian patients did not fulfil German admission criteria. Using mutually uniform admission criteria, the median survival times of the IFN patients are 76 (Italian) and 72 (German) months (P = .56). The Italian group administered IFN combined with HU as needed, whereas the German group strictly used IFN as monotherapy with rerandomization to busulfan (BU) or HU after IFN resistance or intolerability. The differences seen between the Italian and the German trial results can be accounted for by objective differences in study design, especially the admission criteria, treatment strategy, and bias due to intention to treat analysis. The detailed analysis of the data suggests that the combination of IFN with HU as needed is more effective than either agent alone.
Generation Scavenging (1984)

Many interactive computing environments provide automatic storage reclamation and virtual memory to ease the burden of managing storage. Unfortunately, many storage reclamation algorithms impede interaction with distracting pauses. Generation Scavenging is a reclamation algorithm that has no noticeable pauses, eliminates page faults for transient objects, compacts objects without resorting to indirection, and reclaims circular structures, in one third the time of traditional approaches. We have incorporated Generation Scavenging in Berkeley Smalltalk(BS), our Smalltalk-80 implementation, and instrumented it to obtain performance data. We are also designing a microprocessor with hardware support for Generation Scavenging .
CBP/EP300 acetylates and stabilizes the stress-responsive Heat Shock Factor 2, a process compromised in Rubinstein-Taybi syndrome (2019)

SUMMARY Cells respond to protein-damaging insults by activating heat shock factors (HSFs), key transcription factors of proteostasis. Abnormal levels of HSFs occur in cancer and neurodegenerative disorders, highlighting the strict control of their expression. HSF2 is a short-lived protein, which is abundant in the prenatal brain cortex and required for brain development. Here, we report that HSF2 is acetylated and co-localized with the lysine-acetyl transferases CBP and EP300 in human brain organoids. CBP/EP300 mediates the acetylation of HSF2 on specific lysine residues, through critical interaction between the CBP-KIX domain and the HSF2 oligomerisation domain, and promotes HSF2 stabilization. The functional importance of acetylated HSF2 is evidenced in Rubinstein-Taybi syndrome (RSTS), characterized by mutated CBP or EP300. We show that cells derived from RSTS patients exhibit decreased HSF2 levels and impaired heat shock response. The dysregulated HSF pathway in RSTS opens new avenues for understanding the molecular basis of this multifaceted pathology.
Composite Block Polymer−Microfabricated Silicon Nanoporous Membrane (2009)

Block polymers offer an attractive route to densely packed, monodisperse nanoscale pores. However, their fragility as thin films complicates their use as membranes. By integrating a block polymer film with a thin (100 microm) silicon substrate, we have developed a composite membrane providing both nanoscale size exclusion and fast transport of small molecules. Here we describe the fabrication of this membrane, evaluate its mechanical integrity, and demonstrate its transport properties for model solutes of large and small molecular weight. The ability to block large molecules without hindering smaller ones, coupled with the potential for surface modification of the polymer and the microelectromechanical system style of support, makes this composite membrane an attractive candidate for interfacing implantable sensing and drug-delivery devices with biological hosts.
Co-expressed subunits of dual genetic origin define a conserved supercomplex mediating essential protein import into chloroplasts (2020)

Abstract In photosynthetic eukaryotes, thousands of proteins are translated in the cytosol and imported into the chloroplast through the concerted action of two translocons — termed TOC and TIC — located in the outer and inner membranes of the chloroplast envelope, respectively. The degree to which the molecular composition of the TOC and TIC complexes is conserved over phylogenetic distances has remained controversial. Here, we combine transcriptomic, biochemical, and genetic tools in the green alga Chlamydomonas ( Chlamydomonas reinhardtii ) to demonstrate that, despite a lack of evident sequence conservation for some of its components, the algal TIC complex mirrors the molecular composition of a TIC complex from Arabidopsis thaliana. The Chlamydomonas TIC complex contains three nuclear-encoded subunits, Tic20, Tic56 and Tic100, and one chloroplast-encoded subunit, Tic214, and interacts with the TOC complex, as well as with several uncharacterized proteins to form a stable supercomplex (TicToc), indicating that protein import across both envelope membranes is mechanistically coupled. Expression of the nuclear and chloroplast genes encoding both known and the here newly identified TicToc components is highly coordinated, suggesting that a mechanism for regulating its biogenesis across compartmental boundaries must exist. Conditional repression of Tic214, the only chloroplast-encoded subunit in the TicToc complex, impairs the import of chloroplast proteins with essential roles in chloroplast ribosome biogenesis and protein folding and induces a pleiotropic stress response, including several proteins involved in the chloroplast unfolded protein response. These findings underscore the functional importance of the TicToc supercomplex in maintaining chloroplast proteostasis.
Calcium‐dependent inhibition of polo‐like kinase 3 activity by CIB1 in breast cancer cells (2010)

Members of the polo-like kinases (Plk1, Plk2, Plk3 and Plk4) are involved in the regulation of various stages of the cell cycle and have been implicated in cancer progression. Unlike its other family members, the expression of Plk3 remains steady during cell cycle progression, suggesting that its activity may be spatiotemporally regulated. However, the mechanism of regulation of Plk3 activity is not well understood. Here, we show that calcium- and integrin-binding protein 1 (CIB1), a Plk3 interacting protein, is widely expressed in various cancer cell lines. Expression of CIB1 mRNA as well as protein is increased in breast cancer tissue as compared to normal tissue. CIB1 constitutively interacts with Plk3 as determined by both in vitro and in vivo assays. This interaction of CIB1 with Plk3 is independent of intracellular Ca(2+). Furthermore, binding of CIB1 results in inhibition of Plk3 kinase activity both in vitro and in vivo. Interestingly, this inhibition of the Plk3 activity by CIB1 is Ca(2+)-dependent. Taken together, our results suggest that CIB1 is a regulatory subunit of Plk3 and it regulates Plk3 activity in a Ca(2+)-dependent manner. Furthermore, upregulation of CIB1 in cancer cells could thus inhibit Plk3 activity leading to abnormal cell cycle regulation in breast cancer cells. Thus, in addition to Plk3, CIB1 may be a potential biomarker and target for therapeutic intervention of breast cancer.
Uncovering inherent cellular plasticity of multiciliated ependyma leading to ventricular wall transformation and hydrocephalus (2018)

Specialized, differentiated cells often perform unique tasks that require them to maintain a stable phenotype. Multiciliated ependymal cells (ECs) are unique glial cells lining the brain ventricles, important for cerebral spinal fluid circulation. While functional ECs are needed to prevent hydrocephalus, they have also been reported to generate new neurons: whether ECs represent a stable cellular population remains unclear. Via a chemical screen we found that mature ECs are inherently plastic, with their multiciliated state needing constant maintenance by the Foxj1 transcription factor, which paradoxically is rapidly turned over by the ubiquitin-proteasome system leading to cellular de-differentiation. Mechanistic analyses revealed a novel NF-κB-independent IKK2 activity stabilizing Foxj1 in mature ECs, and we found that known IKK2 inhibitors including viruses and growth factors robustly induced Foxj1 degradation, EC de-differentiation, and hydrocephalus. Although mature ECs upon de-differentiation can divide and regenerate multiciliated ECs, we did not detect evidence supporting EC's neurogenic potential.
Brake Design and Safety (1999)

This book was written to help engineers to design safer brakes that can be operated and maintained easily. All the necessary analytical tools to study and determine the involvement of brakes in accident causation are included as well as all essential concepts, guidelines, and design checks.
Epidermal phospholipase Cδ1 regulates granulocyte counts and systemic interleukin-17 levels in mice (2012)

Phospholipase C is a key enzyme in phosphoinositide turnover. Although its functions have been extensively studied at the cellular level, many questions remain concerning its functions at the organ and individual animal levels. Here we demonstrate that mice lacking phospholipase Cδ1 develop granulocytosis associated with elevated serum levels of the granulopoietic cytokine interleukin-17. Re-introduction of phospholipase Cδ1 into keratinocytes of phospholipase Cδ1-deficient mice reverses this phenotype, whereas conditional ablation of phospholipase Cδ1 in keratinocytes recreates it. Interleukin-17 and its key upstream regulator interleukin-23 are also upregulated in epidermis. Loss of phospholipase Cδ1 from keratinocytes causes features of interleukin-17-associated inflammatory skin diseases. Phospholipase Cδ1 protein is downregulated in the epidermis of human psoriatic skin and in a mouse model of psoriasis. These results demonstrate that phosphoinositide turnover in keratinocytes regulates not only local inflammatory responses but also serum cytokine levels and systemic leukocyte counts, and affects distant haematopoietic organs.
Faltung und Impulsantwort (1997)

In Kapitel 6 hatten wir mit (6.5) die grundlegende Beziehung zwischen Ein- und Ausgangssignal eines LTI-Systems angegeben. Hier stehen die Systemfunktion H(s) und die Transformierte des Eingangssignals X(s) als Laplace-Transformierte gleichberechtigt nebeneinander. Nach den Rechenregeln der Multiplikation sind sie sogar vertauschbar. Andererseits scheint es sich nach unserem momentanen Kenntnisstand um zwei völlig verschiedene Funktionen zu handeln. X(s) ist die Laplace-Transformierte einer Zeitfunktion und kann nach (4.1) aus dem Eingangssignal x(t) berechnet werden: X(s) = ℒ{x(t)}.
Estrogenic Triarylethylene Acetic Acids:  Effect of Structural Variation on Estrogen Receptor Affinity and Estrogenic Potency and Efficacy in MCF-7 Cells (1996)

Triarylethylenecarboxylic acids exemplified by (E,Z)-2-{4-[1-(p-hydroxyphenyl)-2-phenyl]-1-butenyl}phenoxyacetic acid (8) are a new class of estrogen receptor (ER) ligands capable of tissue selective estrogen agonist and antagonist effects. We report the syntheses of 8 and of analogues incorporating structural features known or anticipated to facilitate ER affinity in triarylethylenes. These studies revealed that the p-hydroxyphenyl moiety, ethylenic bond, and ether oxygen of 8 were all critical for high ER affinity. Although a 1,1-bisphenolic analogue bearing the p-(oxyacetic acid) moiety on its 2-phenyl ring, 12, had low ER affinity, it exhibited estrogenic potency approaching that of 8 in MCF-7 cells. Unlike 8 which was a partial agonist with weak antagonist potency, 12 was a full agonist. A similar profile of potency/efficacy in MCF-7 cells was seen in 9, an ethylenic bond saturated analogue of 8. Growth-promoting effects of 8, 9, and 12 were fully antagonized by the antiestrogen tamoxifen, suggesting that such effects were mediated solely via ER. Thus, our studies in MCF-7 cells have confirmed the estrogenicity of 8 and have enabled identification of two analogues with favorable estrogenic potency and full estrogen efficacy. On this basis, these three (triarylethylene)acetic acids have been selected for more intensive animal studies of their extrareproductive tract estrogenic effects.