gebhart/patrepeval huggingface dataset:
Supplementary Figure 3 from The Association of PI3 Kinase Signaling and Chemoresistance in Advanced Ovarian Cancer (2023)

&lt;p&gt;PDF file, 44KB, Probes for PIK3CA, AKT2 and PTEN.&lt;/p&gt;
GaN-based electronics (2012)

An overview of III-nitride heterojunction FET technologies is given in this paper. Structural parameter designs of HEMTs, including various field-plate parameters, are described for high-voltage applications. For low-leakage operation, future HEMT technology on a free-standing GaN substrate is presented. Some of the theoretical design issues will be also addressed.
Permeability prediction based on induced polarization: Insights from measurements on sandstone and unconsolidated samples spanning a wide permeability range (2015)

ABSTRACT We have compared various induced polarization (IP) models for permeability prediction of the same general form that were all based on two parameters, the first being an electric substitute of effective porosity (the formation factor) and the second being an electric proxy of pore-normalized surface area (the imaginary part of electric conductivity). These models (empirically derived and based on mechanistic formulations) were applied to an extensive database acquired on sandstones and unconsolidated sandy materials. Whereas previous studies on permeability prediction mainly concentrated on either sandstone or unconsolidated sediments, we investigated a database composed of 94 samples including sandstones and unconsolidated material. Most of the samples in the database were saturated with a NaCl solution with an electric conductivity close to 100 mS/m. Samples with a saturating fluid that deviated from this composition were corrected using recently published relationships describing the IP dependence on the pore fluid composition. In the case of the sandstone samples, the electric formation factor exerts the primary control on permeability, and the imaginary conductivity was found to be of little importance in permeability prediction. The opposite was observed for the unconsolidated samples, in which the imaginary conductivity was the most important term for permeability and the formation factor was found to be of little importance. The findings suggest that only one property (formation factor in the case of sandstone, imaginary conductivity in the case of unconsolidated samples) might be needed for the order of magnitude estimates of permeability from the popular form of the model based on the IP observations examined here. Whereas the formation factor was challenging to reliably estimate in situ, the imaginary conductivity was directly obtainable from an IP measurement. This suggests that field scale, single-frequency, IP-based estimation of permeability would be challenging, and possibly ineffective, in sandstones.
[Transient increased retinal hemorrhage and the retinal venous blood flow change in the course of non-ischemic central retinal vein occlusion treated with an anticoagulant]. (2007)

We can judge whether an increase in retinal hemorrhage is transient or the clinical condition is getting worse in an early stage by measuring the retinal vein blood flow quantitatively by laser Doppler flowmetry.
Synthesis and Kinase Inhibitory Activity of 3′‐(S)‐epi‐K‐252a. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Associations of Serum Neurofilament Light Chain with Outcomes in Children with Autoimmune Encephalitis (P4-5.009) (2023)

To examine associations between serum neurofilament light chain (sNfL) levels at disease onset with markers of clinical severity in children with autoimmune encephalitis (AE).
Binding site residues control inhibitor selectivity in the human norepinephrine transporter but not in the human dopamine transporter (2015)

The transporters for norepinephrine and dopamine (NET and DAT, respectively) constitute the molecular targets for recreational drugs and therapeutics used in the treatment of psychiatric disorders. Despite a strikingly similar amino acid sequence and predicted topology between these transporters, some inhibitors display a high degree of selectivity between NET and DAT. Here, a systematic mutational analysis of non-conserved residues within the extracellular entry pathway and the high affinity binding site in NET and DAT was performed to examine their role for selective inhibitor recognition. Changing the six diverging residues in the central binding site of NET to the complementary residues in DAT transferred a DAT-like pharmacology to NET, showing that non-conserved binding site residues in NET are critical determinants for inhibitor selectivity. In contrast, changing the equivalent residues in the central site of DAT to the corresponding residues in NET had modest effects on the same inhibitors, suggesting that non-conserved binding site residues in DAT play a minor role for selective inhibitor recognition. Our data points towards distinct structural determinants governing inhibitor selectivity in NET and DAT, and provide important new insight into the molecular basis for NET/DAT selectivity of therapeutic and recreational drugs.
Improving anti-tumor immunity by engineering T cell receptors to prevent mispairing (VAC7P.1033) (2015)

Abstract T cells transduced with the genes encoding the α and β chains of a tumor-specific T cell receptor (TCR) can mediate anti-tumor immunity in patients. Such TCR-transduced T cells co-express both the therapeutic and an endogenous TCR. As each receptor is an αβ heterodimer, the endogenous α chain can mispair with the therapeutic β chain and vice versa. Such mispairing - which is observed in transduced human T cells - reduces export of the therapeutic TCR and produces potentially self-reactive TCRs. The latter can precipitate graft-vs-host disease, a lethal complication reported in mice following TCR gene transfer. We have developed a general strategy for preventing TCR mispairing. Select constant domains are swapped between the α and β chains of a tumor-specific T cell receptor, creating a domain-swapped (ds)TCR. When correctly paired, these dsTCR chains retain all domains necessary to recruit CD3 proteins, to express on the T cell surface, and to mediate functional T cell responses upon engaging a target antigen. By contrast, mispaired TCRs containing one dsTCR chain and one wild-type TCR chain lack key domains necessary for CD3 recruitment, export, and signaling, and thus are unable to mediate deleterious autoimmunity. We validate the potential of this approach in cell-based assays, as well as in a mouse model of TCR gene transfer-induced graft-vs-host disease. Thus, this work will enable the design of safer, more effective TCR gene therapy candidates for cancer immunotherapy.
Synergism between Hedgehog-GLI and EGFR Signaling in Hedgehog-Responsive Human Medulloblastoma Cells Induces Downregulation of Canonical Hedgehog-Target Genes and Stabilized Expression of GLI1 (2013)

Aberrant activation of Hedgehog (HH) signaling has been identified as a key etiologic factor in many human malignancies. Signal strength, target gene specificity, and oncogenic activity of HH signaling depend profoundly on interactions with other pathways, such as epidermal growth factor receptor-mediated signaling, which has been shown to cooperate with HH/GLI in basal cell carcinoma and pancreatic cancer. Our experimental data demonstrated that the Daoy human medulloblastoma cell line possesses a fully inducible endogenous HH pathway. Treatment of Daoy cells with Sonic HH or Smoothened agonist induced expression of GLI1 protein and simultaneously prevented the processing of GLI3 to its repressor form. To study interactions between HH- and EGF-induced signaling in greater detail, time-resolved measurements were carried out and analyzed at the transcriptomic and proteomic levels. The Daoy cells responded to the HH/EGF co-treatment by downregulating GLI1, PTCH, and HHIP at the transcript level; this was also observed when Amphiregulin (AREG) was used instead of EGF. We identified a novel crosstalk mechanism whereby EGFR signaling silences proteins acting as negative regulators of HH signaling, as AKT- and ERK-signaling independent process. EGFR/HH signaling maintained high GLI1 protein levels which contrasted the GLI1 downregulation on the transcript level. Conversely, a high-level synergism was also observed, due to a strong and significant upregulation of numerous canonical EGF-targets with putative tumor-promoting properties such as MMP7, VEGFA, and IL-8. In conclusion, synergistic effects between EGFR and HH signaling can selectively induce a switch from a canonical HH/GLI profile to a modulated specific target gene profile. This suggests that there are more wide-spread, yet context-dependent interactions, between HH/GLI and growth factor receptor signaling in human malignancies.
Vom Labortisch zur Feldforschung: zwei Fallstudien kostengünstiger Diagnostik (2015)

Abstract Die universitäre Forschung an Point‐of‐Care‐Diagnostik für die globale Gesundheit verzeichnet ein stetes Wachstum, allerdings verlassen viele Testsysteme niemals das Labor. Prozesse, die die diagnostische Technologie vom Labor ins Feld überführen – Prozesse, mit deren Hilfe Betrieb und Leistungsvermögen unter realistischen Bedingungen evaluiert werden sollen –, sind komplizierter, als sie scheinen mögen. Zwei Fallstudien illustrieren diesen Prozess: die Entwicklung eines papierbasierten Testsystems zur Messung der Leberfunktion sowie die eines Testsystems zur Identifikation von Sichelzellanämie, das auf wässrigen, mehrphasigen Systemen sowie Unterschieden in der Dichte normaler und sichelförmiger Zellen beruht. Aus den Details der Entwicklung dieser beiden Testsysteme lassen sich allgemeingültige Strategien zum Aufbau von Kooperationen, zum Herstellen von Prototypen, zur Validierung, zum Design von Studien und zur Evaluation von Point‐of‐Care‐Diagnostik ableiten. Die aus diesen Erfahrungen gezogenen (verfahrens)technischen Lehren können Wissenschaftlern nutzen, die diagnostische Tests für Entwicklungsländer und – allgemeiner – Technologien für den Einsatz bei begrenzten Ressourcen entwerfen.
Implementation of a Pipelined Optoelectronic Processor: OCULAR-II (1999)

Recent advances in technologies such as modulators, vertical cavity surface-emitting laser (VCSEL) arrays, optoelectronic VLSI, and micro-optics has allowed the construction of parallel optoelectronic computing systems utilising the high bandwidth, high density and global nature of optical communication paths to overcome some of the limitations of conventional electronic connections interconnections.
D-SPTF: Decentralized Request Distribution in Brick-based Storage (CMU-CS-03-202) (2018)

Distributed Shortest-Positioning Time First (D-SPTF) is a request distribution protocol for decentralized systems of storage servers. D-SPTF exploits high-speed interconnects to dynamically select which server, among those with a replica, should service each read request. In doing so, it simultaneously balances load, exploits the aggregate cache capacity, and reduces positioning times for cache misses. For network latencies of up to 0.5ms, D-SPTF performs as well as would a hypothetical centralized system with the same collection of CPU, cache, and disk resources. Compared to existing decentralized approaches, such as hash-based request distribution, D-SPTF achieves up to 65% higher throughput and adapts more cleanly to heterogenous server capabilities.
Applications Driving IDAES Process Systems Engineering Framework Capabilities. (2021)

Abstract not provided.
Four New Steroidal Saponins from the Seeds of Allium tuberosum (2001)

Four new steroidal saponins, 26-O-beta-D-glucopyranosyl-(25S,20R)-20-O-methyl-5alpha-furost-22(23)-en-2alpha,3beta,20,26-tetraol 3-O-alpha-L-rhamnopyranosyl-(1-->2)-[alpha-L-rhamnopyranosyl-(1-->4)]-beta-D-glucopyranoside (1); 26-O-beta-D-glucopyranosyl-(25S,20R)-5alpha-furost-22(23)-en-2alpha,3beta,20,26-tetraol 3-O-alpha-L-rhamnopyranosyl-(1-->2)-[alpha-L- rhamnopyranosyl-(1-->4)]-beta-D-glucopyranoside (2); 26-O-beta-D-glucopyranosyl-(25S,20S)-5alpha-furost-22(23)-en-2alpha,3beta,20,26-tetraol 3-O-alpha-L-rhamnopyranosyl-(1-->2)-[alpha-L- rhamnopyranosyl-(1-->4)]-beta-D-glucopyranoside (3); and 26-O-beta-D-glucopyranosyl-(25S,20S)-5alpha-furost-22(23)-en-3beta,20,26-triol 3-O-alpha-L-rhamnopyranosyl-(1-->2)-[alpha-L-rhamnopyranosyl-(1-->4)]-beta-D-glucopyranoside (4), have been isolated from the seeds of Allium tuberosum. Their structures were established by spectroscopic studies such as MS, IR, NMR, and 2D-NMR and the results of acid hydrolysis and named tuberosides F, G, H, and I, respectively.
A high performance switch for OC-12 SONET self-healing ring networks (1996)

The progress of ITU-T and ANSI standards on SDH/SONET is accelerating the evolution of transmission systems all over the world. The advanced operation administration and maintenance (OAM) functions it provides makes it possible to create a self healing ring network which protects against failure. This self-healing ring consists of add/drop multiplexers (ADM's). The switch in the ADM plays an important role in achieving self-healing operation. In this paper, self-healing ring architecture and operations are analyzed in order to determine the requirements for the ADM switch. On the basis of this result, new space division switching methods, which significantly reduce the amount of hardware needed, are proposed. A parallel processing architecture which makes it possible to develop a low-cost large-scale switch is also devised. Finally, a developed switch LSI chip is presented. Combining two identical chips with the proposed parallel processing architecture, a 32/spl times/32 STS-3 switch (5 Gb/s throughput) with an STS-1 time slot interchange (TSI) function is realized.
Hepatotoxicity of Tolbutamide in Dogs (1970)

SUMMARY Three normal dogs were given sodium tolbutamide in daily oral doses of 30, 65, or 130 mg./kg.; a fourth served as the control. By day 37, the 2 that were given the larger doses became debilitated and had to be killed. They had developed hypoglycemia, degranulation of pancreatic beta cells, reduction in extractable pancreatic insulin, and increased prothrombin time. Glutamic oxalacetic transaminase ( got ) and alkaline phosphatase ( alp ) activities were elevated in serum. Clinical and biochemical measures were within normal limits in the dog that was given 30 mg./kg. for 100 days, and then 60 mg./kg. for an additional 60 days, but structural changes in the liver were prominent. Profound changes occurred only after the dog was given the drug at 120 mg./kg. for 90 subsequent days. The hypothesis that this dog developed tolerance to the drug was supported by the finding of a dilated hepatocystic smooth endoplasmic reticulum ( ser ). Light microscopic changes in the liver of dogs that were given tolbutamide included cloudy swelling, increased amounts of fat and glycogen in parenchymal cells, and foci of coagulation necrosis. Electron microscopic changes in addition to dilatation of the ser included decreased density of the cytoplasmic ground substance, increased numbers of lysosomes, microbodies, glycogen granules, and fat droplets. The hepatotoxic effect of tolbutamide, along with certain pharmacologic and pathologic considerations, precludes its usefulness in the treatment of spontaneously diabetic dogs.
Reconfigurable 2D optical tapped-delay-line to perform correlation on images (2014)

We demonstrate a reconfigurable 2D optical tapped-delay-line (OTDL) to correlate quadrature-phase-shift-keying (QPSK) 20 Gbaud data. By implementing two independent tapped-delay-lines which performs correlation over rows (inner sum), along with a coherent multiplexing of the correlated rows which performs correlation over columns (outer sum), a 2D correlator is achieved with average error vector magnitude (EVM) of ∼7.8%. Here we also search different 2×2 patterns in a 31×31 image and successfully recognize the target patterns in the image.
Fluorescent Retinoic Acid Analogues as Probes for Biochemical and Intracellular Characterization of Retinoid Signaling Pathways (2019)

Retinoids, such as all- trans-retinoic acid (ATRA), are endogenous signaling molecules derived from vitamin A that influence a variety of cellular processes through mediation of transcription events in the cell nucleus. Because of these wide-ranging and powerful biological activities, retinoids have emerged as therapeutic candidates of enormous potential. However, their use has been limited, to date, due to a lack of understanding of the complex and intricate signaling pathways that they control. We have designed and synthesized a family of synthetic retinoids that exhibit strong, intrinsic, solvatochromatic fluorescence as multifunctional tools to interrogate these important biological activities. We utilized the unique photophysical characteristics of these fluorescent retinoids to develop a novel in vitro fluorometric binding assay to characterize and quantify their binding to their cellular targets, including cellular retinoid binding protein II (CRABPII). The dihydroquinoline retinoid, DC360, exhibited particularly strong binding ( K<sub>d</sub> = 34.0 ± 2.5 nM), and we further used X-ray crystallography to determine the structure of the DC360-CRABPII complex to 1.8 Å, which showed that DC360 occupies the known hydrophobic retinoid binding pocket. Finally, we used confocal fluorescence microscopy to image the cellular behavior of the compounds in cultured human epithelial cells, highlighting a fascinating nuclear localization, and used RNA sequencing to confirm that the compounds regulate cellular processes similar to those of ATRA. We anticipate that the unique properties of these fluorescent retinoids can now be used to cast new light on the vital and highly complex retinoid signaling pathway.
Benefits of object-oriented models and ModeliChart: modern tools and methods for the interdisciplinary research on smart biomedical technology (2017)

Computational models of biophysical systems generally constitute an essential component in the realization of smart biomedical technological applications. Typically, the development process of such models is characterized by a great extent of collaboration between different interdisciplinary parties. Furthermore, due to the fact that many underlying mechanisms and the necessary degree of abstraction of biophysical system models are unknown beforehand, the steps of the development process of the application are iteratively repeated when the model is refined. This paper presents some methods and tools to facilitate the development process. First, the principle of object-oriented (OO) modeling is presented and the advantages over classical signal-oriented modeling are emphasized. Second, our self-developed simulation tool ModeliChart is presented. ModeliChart was designed specifically for clinical users and allows independently performing in silico studies in real time including intuitive interaction with the model. Furthermore, ModeliChart is capable of interacting with hardware such as sensors and actuators. Finally, it is presented how optimal control methods in combination with OO models can be used to realize clinically motivated control applications. All methods presented are illustrated on an exemplary clinically oriented use case of the artificial perfusion of the systemic circulation.
Learning Intuitive Physics with Multimodal Generative Models (2021)

Predicting the future interaction of objects when they come into contact with their environment is key for autonomous agents to take intelligent and anticipatory actions. This paper presents a perception framework that fuses visual and tactile feedback to make predictions about the expected motion of objects in dynamic scenes. Visual information captures object properties such as 3D shape and location, while tactile information provides critical cues about interaction forces and resulting object motion when it makes contact with the environment. Utilizing a novel See-Through-your-Skin (STS) sensor that provides high resolution multimodal sensing of contact surfaces, our system captures both the visual appearance and the tactile properties of objects. We interpret the dual stream signals from the sensor using a Multimodal Variational Autoencoder (MVAE), allowing us to capture both modalities of contacting objects and to develop a mapping from visual to tactile interaction and vice-versa. Additionally, the perceptual system can be used to infer the outcome of future physical interactions, which we validate through simulated and real-world experiments in which the resting state of an object is predicted from given initial conditions.
Something from Nothing: Enhancing Electrochemical Charge Storage with Cation Vacancies (2012)

The performance of electrochemical energy storage devices (e.g., batteries and electrochemical capacitors) is largely determined by the physicochemical properties of the active electrode materials, such as the thermodynamic potential associated with the charge-storage reaction, ion-storage capacity, and long-term electrochemical stability. In the case of mixed ion/electron-conducting metal oxides that undergo cation-insertion reactions, the presence of cation vacancies in the lattice structure can enhance one or more of these technical parameters without resorting to a drastic change in material composition. Examples of this enhancement include the charge-storage properties of certain cation-deficient oxides such as γ-MnO2 and γ-Fe2O3 relative to their defect-free analogues. The optimal cation-vacancy fraction is both material- and application-dependent because cation vacancies enhance some materials properties at the expense of others, potentially affecting electronic conductivity or thermal stability. Although the advantages of structural cation vacancies have been known since at least the mid-1980s, only a handful of research groups have purposefully integrated cation vacancies into active electrode materials to enhance device performance. Three protocols are available for the incorporation of cation vacancies into transition metal oxides to improve performance in both aqueous and nonaqueous energy storage. Through a processing approach, researchers induce point defects in conventional oxides using traditional solid-state-ionics techniques that treat the oxide under appropriate atmospheric conditions with a driving force such as temperature. In a synthetic approach, substitutional doping of a highly oxidized cation into a metal-oxide framework can significantly increase cation-vacancy content and corresponding charge-storage capacity. In a scaling approach, electrode materials that are expressed in morphologies with high surface areas, such as aerogels, contain more defects because the increased fraction of surface sites favors the formation of cation vacancies. In this Account, we review studies of cation-deficient electrode materials from the literature and our laboratory, focusing on transition metal oxides and the impact cation vacancies have on electrochemical performance. We also discuss the challenges and limitations of these defective structures and their promise as battery materials.
Graphene Growth Using a Solid Carbon Feedstock and Hydrogen (2011)

Graphene has been grown on Cu at elevated temperatures with different carbon sources (gaseous hydrocarbons and solids such as polymers); however the detailed chemistry occurring at the Cu surface is not yet known. Here, we explored the possibility of obtaining graphene using amorphous-carbon thin films, without and with hydrogen gas added. Graphene is formed only in the presence of H(2)(g), which strongly suggests that gaseous hydrocarbons and/or their intermediates are what yield graphene on Cu through the reaction of H(2)(g) and the amorphous carbon. The large area, uniform monolayer graphene obtained had electron and hole mobilities of 2520 and 2050 cm(2) V(-1) s(-1), respectively.