gebhart/patrepeval huggingface dataset:
Another Use for the Seven-Pinhole Collimator Routine Nontomographic Imaging of the Thyroid (1983)

Relatively few seven-pinhole collimator systems purchased within the last three years are still in routine use. This paper describes a nontomographic use of the collimator for thyroid scanning. One image is obtained which simultaneously shows seven different projections of the thyroid gland. The diagnosis of thyroid abnormalities can frequently be made from this single composite image without the requirement for additional images. Further information can be obtained when needed by computer processing the image into tomographic slices.
Direct observation of the dead-cone effect in quantum chromodynamics (2022)

In particle collider experiments, elementary particle interactions with large momentum transfer produce quarks and gluons (known as partons) whose evolution is governed by the strong force, as described by the theory of quantum chromodynamics (QCD)<sup>1</sup>. These partons subsequently emit further partons in a process that can be described as a parton shower<sup>2</sup>, which culminates in the formation of detectable hadrons. Studying the pattern of the parton shower is one of the key experimental tools for testing QCD. This pattern is expected to depend on the mass of the initiating parton, through a phenomenon known as the dead-cone effect, which predicts a suppression of the gluon spectrum emitted by a heavy quark of mass m<sub>Q</sub> and energy E, within a cone of angular size m<sub>Q</sub>/E around the emitter<sup>3</sup>. Previously, a direct observation of the dead-cone effect in QCD had not been possible, owing to the challenge of reconstructing the cascading quarks and gluons from the experimentally accessible hadrons. We report the direct observation of the QCD dead cone by using new iterative declustering techniques<sup>4,5</sup> to reconstruct the parton shower of charm quarks. This result confirms a fundamental feature of QCD. Furthermore, the measurement of a dead-cone angle constitutes a direct experimental observation of the non-zero mass of the charm quark, which is a fundamental constant in the standard model of particle physics.
Constrained Lagrangian Formulation for Multibody Systems using Bond Graphs. (1991)

A method for deriving the constrained form of Lagrangian equations of motion for an interconnected system of rigid bodies using bond graphs is presented. Intrinsically, this approach allows the formulation of the final form of equations for holonomic systems without recourse to the Lagrangian function. Consequently, the burdens of deriving the expressions for kinetic and potential energies, and performing the necessary differentiations have been eliminated. This method calls only for constructing the Jacobian matrix of constraints, and then employing a bond graph that accounts for the generalized constraint reaction forces.
A chemical bath process for depositing Cu2ZnSnS4 photovoltaic absorbers (2010)

Thin films of Cu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ZnSnS <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> (CZTS) were fabricated through a combination of chemical bath deposition, ion exchange and sulfurization heat treatment. Scanning electron microscopy was used to study the morphology of the thin films, Auger electron spectroscopy for compositional analysis, X-ray diffraction and Raman scattering for structural characterization, and diffuse reflectance UV-Vis measurements for optical properties. With the method described, compositionally uniform microcrystalline CZTS with kesterite structure and a bandgap of 1.45 eV have been produced, and a preliminary solar cell device was fabricated to demonstrate that this material is applicable in earth-abundant, non-toxic thin film photovoltaics.
A technique for measuring the energy resolution of low-Z scintillators (2009)

Scintillator-based Compton cameras for remote localization and identification of radio nuclides require scatter detectors made of low-Z materials. The energy resolution of such detectors in a range dominated by Compton scattering is a crucial parameter. It has to be known for performance estimates, and it must be quantified and optimized for detector designs to be used in real systems, but it is hard to measure. The Compton Coincidence Technique (CCT) appears to be the best method for reliable and direct measurements, but appropriate facilities are expensive. This paper suggests and investigates a modified CCT which provides less expensive means for qualifying of scatter detectors in a reasonable time frame. The assembly consists of a single HPGe detector, the scatter detector to be investigated, and one or more common gamma sources in close geometry. Pulse height and timing information from both detectors is gathered by multi-parameter data acquisition. Coincidences of both detectors are due to a plurality of Compton scattering angles and corresponding energy transfers. A thorough data analysis then allows extracting the detector resolution as well as the non-linearity as a function of energy from data sets measured within hours. Results obtained for NaI and plastic scatter detectors will be presented and discussed.
Abstract 5377: Profiling of aurora kinase signaling in microdissected gastric cancer samples indicates a significant increase in histone deacetylase 4 (HDAC4). (2013)

Abstract Introduction &amp; Methods: Gastric cancer represents one of the leading causes of cancer related death in the world second only to lung cancer resulting in 800,000 deaths per year. Aurora kinases, a family of serine/threonine kinases essential for cytokinesis and chromosome segregation, are frequently over-expressed in various cancer types. Moreover, Aurora kinase has recently been shown to directly regulate epigenetic changes (Guise et al., Mol Cell Proteomics. 2012 Nov;11(11):1220-9). Aurora kinase signaling may also impact E-cadherin function via a GSK3-α/β induced increase in β-catenin. E-cadherin deregulation has been implicated in gastric cancer, especially in diffuse types where it is mutated in many cases. We have profiled Aurora kinase signaling pathway activation and its effects on epigenetic and cytoskeletal changes in gastric cancer. Human gastric cancer tumor samples (n=10; 4 diffuse, 5 intestinal, 1 undifferentiated adenocardinoma) and patient matched normal mucosa were procured by laser capture microdissection. Reverse phase protein microarrays were used to quantify total and post-translationally modified proteins in cell signaling pathways directly and indirectly related to Aurora kinase. Results: We found a significant increase in histone deacetylase 4 levels (HDAC4, p&amp;lt;0.0001) concomitant with increased phosphorylation of Aurora kinase (p&amp;lt;0.1) and a decrease in phosphorylated GSK3-α/β (p&amp;lt;0.05) in gastric tumor epithelia compared to patient matched normal mucosa. Gastric cancer samples of diffuse type showed a significantly reduced expression of E-Cadherin (p&amp;lt;0.05) as compared to intestinal type gastric cancer. In contrast, patient samples with lymph node metastasis (n=6) were associated with an increased level of phospho-GSK3-α/β in both normal mucosa (p&amp;lt;0.05) and matched tumor epithelia (p&amp;lt;0.1). Conclusions: To our knowledge, this is the first time that increased levels of HDAC4 have been reported in gastric cancer. The demonstrated increase in Aurora kinase phosphorylation in gastric tumor epithelia may provide a mechanistic link to the observed HDAC4 upregulation. Citation Format: Lorenzo Colarossi, Lorenzo Memeo, Lance A. Liotta, Virginia Espina, Claudius Mueller. Profiling of aurora kinase signaling in microdissected gastric cancer samples indicates a significant increase in histone deacetylase 4 (HDAC4). [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5377. doi:10.1158/1538-7445.AM2013-5377
Multi-Symmetry Ensembles: Improving Diversity and Generalization via Opposing Symmetries (2023)

Deep ensembles (DE) have been successful in improving model performance by learning diverse members via the stochasticity of random initialization. While recent works have attempted to promote further diversity in DE via hyperparameters or regularizing loss functions, these methods primarily still rely on a stochastic approach to explore the hypothesis space. In this work, we present Multi-Symmetry Ensembles (MSE), a framework for constructing diverse ensembles by capturing the multiplicity of hypotheses along symmetry axes, which explore the hypothesis space beyond stochastic perturbations of model weights and hyperparameters. We leverage recent advances in contrastive representation learning to create models that separately capture opposing hypotheses of invariant and equivariant functional classes and present a simple ensembling approach to efficiently combine appropriate hypotheses for a given task. We show that MSE effectively captures the multiplicity of conflicting hypotheses that is often required in large, diverse datasets like ImageNet. As a result of their inherent diversity, MSE improves classification performance, uncertainty quantification, and generalization across a series of transfer tasks.
Presenilin 1 Mutations Activate γ42-Secretase but Reciprocally Inhibit ε-Secretase Cleavage of Amyloid Precursor Protein (APP) and S3-Cleavage of Notch (2002)

The presenilin 1 (PS1) and presenilin 2 (PS2) proteins are necessary for proteolytic cleavage of the amyloid precursor protein (APP) within its transmembrane domain. One of these cleavage events (termed gamma-secretase) generates the C-terminal end of the Abeta-peptide by proteolysis near residue 710 or 712 of APP(770). Another event (termed gamma-like or epsilon-secretase cleavage) cleaves near residue 721 at approximately 2-5 residues inside the cytoplasmic membrane boundary to generate a series of stable, C-terminal APP fragments. This latter cleavage is analogous to S3-cleavage of Notch. We report here that specific mutations in the N terminus, loop, or C terminus of PS1 all increase the production of Abeta(42) but cause inhibition of both epsilon-secretase cleavage of APP and S3-cleavage of Notch. These data support the hypothesis that epsilon-cleavage of APP and S3-cleavage of Notch are similar events. They also argue that, although both the gamma-site and the epsilon-site cleavage of APP are presenilin-dependent, they are likely to be independent catalytic events.
Mécanismes et contrôles de la recombinaison méiotique chez la levure Saccharomyces cerevisiae (1999)

Les mécanismes moléculaires de la recombinaison méiotique commencent à être mieux compris grâce à une série de travaux récents chez Saccharomyces cerevisiae. Il a été montré que la recombinaison méiotique est initiée par la formation de cassures double-brin de l’ADN qui peuvent être mises en évidence physiquement dans les premières heures de la méiose. Ces cassures double-brin sont localisées préférentiellement dans les régions intergéniques contenant un promoteur de transcription et sont regroupées dans des domaines le long des chromosomes. La protéine Spo11 qui est apparentée à une nouvelle famille de topoisomérases de type II, est très probablement la protéine responsable de la formation de ces cassures doublebrin. Plusieurs intermédiaires du processus de réparation des cassures double-brin ont été détectées physiquement chez la levure et des complexes multiprotéiques qui interviennent à différentes étapes au cours de la réparation ont été identifiés. Ces complexes multiprotéiques sont retrouvés chez les eucaryotes supérieurs, ce qui suggère une conservation des mécanismes de recombinaison méiotique. L’utilisation combinée de la génétique, de la cytologie, de la biochimie et des nouvelles technologies développées pour les études génomiques (puces à ADN) devrait aboutir à une meilleure compréhension des mécanismes de la recombinaison méiotique.
Integrative analysis of functional genomic screening and clinical data identifies a protective role for spironolactone in severe COVID-19 (2023)

We demonstrate that integrative analysis of CRISPR screening datasets enables network-based prioritization of prescription drugs modulating viral entry in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by developing a network-based approach called Rapid proXimity Guidance for Repurposing Investigational Drugs (RxGRID). We use our results to guide a propensity-score-matched, retrospective cohort study of 64,349 COVID-19 patients, showing that a top candidate drug, spironolactone, is associated with improved clinical prognosis, measured by intensive care unit (ICU) admission and mechanical ventilation rates. Finally, we show that spironolactone exerts a dose-dependent inhibitory effect on viral entry in human lung epithelial cells. Our RxGRID method presents a computational framework, implemented as an open-source software package, enabling genomics researchers to identify drugs likely to modulate a molecular phenotype of interest based on high-throughput screening data. Our results, derived from this method and supported by experimental and clinical analysis, add additional supporting evidence for a potential protective role of the potassium-sparing diuretic spironolactone in severe COVID-19.
Time Course of mRNA Induction Elicited by Salt Stress in the Common Ice Plant (Mesembryanthemum crystallinum) (1989)

In the facultative halophyte Mesembryanthemum crystallinum (common ice plant), irrigation with solutions containing NaCl induces an alternate mode of carbon dioxide fixation, Crassulacean acid metabolism (CAM). The salt stress protocol which we have established facilitates the study of CAM induction and the correlation of changes in metabolism and gene expression. We have studied the time course of mRNA induction for phosphoenolpyruvate carboxylase (PEPCase) (gene: ppc) and several other enzymes of carbon metabolism during stress. While CAM is not fully established for at least 10 days after the start of stress, mRNA amounts for PEPCase and for other CAM enzymes, such as Pyruvate orthophosphate dikinase, increase between day 2 and 3 after stress induction. Increases continue for at least 5 days. Concomitant with the increase of CAM transcripts, fluctuations in the mRNA amounts for genes rbcS and cab were observed. Transcript levels for these proteins decreased several-fold during a 3 to 4 day period.
Simulation for the evaluation of energy management algorithms at the district level - Example of use case from the AMBASSADOR project (2015)

In the context of the EU FP7 AMBASSADOR project, a simulation platform has been developed, as a support for the development and the deployment of energy management systems at the district level. Such simulation platform is called District Simulation Platform (DSP), and includes both the models of the physical components from the district, and the models of the energy management algorithms. The DSP is a support for Software In the Loop (SIL) validation: the same algorithm code is first developed and tested on the DSP before being deployed for real-time operation of the district. The DSP can take into account various district configurations through user-defined configuration files. These configurations cover the field tests of the AMBASSADOR project, including the Lavrion experimental site from NTUA close to Athens (Greece), and the INCAS experimental district platform from CEA close to Chambery (France). The last one is detailed in this paper.
Free Radical Formation in Crystals of Guanine Hydrochloride Dihydrate: An ESR and ENDOR Study (1987)

Radiation-induced free radical formation in single crystals of guanine hydrochloride dihydrate has been studied at temperatures between 20 and 300 K using ESR and ENDOR spectroscopy. At low temperatures three radical species are trapped. Two of these are the C8 H-addition radical R1 previously analysed by Alexander and Gordy (1967) and the O6-protonated anion radical R2. The third species (R4) remains unidentified. Upon annealing at 280 K for an extended period the protonated anion R2 transforms into a new radical R3 which exhibit a well-defined hyperfine pattern but still could not be identified unambiguously. Also radical R4 probably transforms into a new radical (R5) upon such treatment. One proton coupling due to R5 was detected. A scheme of radical reactions incorporating these five radicals is proposed. This scheme also suggests that differences in radical formation between the monohydrate and dihydrate crystals of guanine hydrochloride depends upon differences in the hydrogen bonding network.
PerformanceDriven Compaction for Analog Integrated Circuits (2009)

This paper describes a new approach to layout compaction of analog integrated circuits which respects all of the performance and technology constraints necessary to guarantee proper analog circuit functionality. Our approach consists of two stages: a fast constraint graph critical path algorithm followed by a general linear programming algorithm. Circuit performance is guaranteed by mapping high-level performance constraints to low-level bounds on parasitics and then to minimum spacing constraints between adjacent nets.
Chronic opipramol treatment extinguishes cocaine craving through Rac1 in responders: A rat model study (2021)

Ras-related C3 botulinum toxin substrate 1 (Rac1), of the Rho small GTPase family, is a key regulator of actin cytoskeleton rearrangement and plays an important role in dendritic morphogenesis. Cocaine produces neuronal alterations, including structural changes in dendritic number and morphology. Emerging data indicate sigma-1 receptors (σ-1Rs) as a promising candidate for the prevention of cocaine craving. Opipramol is a σ-1R agonist approved in some European countries for depression and anxiety. Here we report that opipramol, mediated by Rac1, attenuates cocaine-seeking behavior in a rat model of self-administration. The opipramol effect was shown in two phases. It decreased cocaine-seeking behavior throughout the withdrawal phase and, interestingly, showed a significant reduction of cocaine-primed reinstatement in 75% of the opipramol-treated group (termed 'responders'). All opipramol-treated rats showed a decrease in σ-1R mRNA expression levels in the nucleus accumbens (NAc) versus controls. Responders also exhibited significantly decreased NAc Rac1 mRNA expression levels, compared with non-responder rats. Hence, Rac1 differentiated responders from non-responders. Rac1 correlated positively with σ-1R mRNA levels in opipramol responders. In another experiment, Rac1 inhibitor injected directly into the NAc core decreased active lever presses on the first day of extinction, indicating the critical role of Rac1 in the opipramol effect on drug seeking. We postulate that chronic activation of σ-1R, through a dynamic interaction with Rac1, may suggest a new approach to treat substance use disorder (SUD). Rac1 inhibition is a prerequisite for decreasing drug seeking and rehabilitation, and this can be achieved by opipramol, a medication that can be given during detoxification.
A Pyrone Strategy for the Synthesis of 3-Acyltetramic Acids (1999)

R. C. F. Jones, G. Bhalay, J. M. Patience and P. Patel, J. Chem. Res. (S), 1999, 250 DOI: 10.1039/A809957J
Development of a microbial high-throughput screening instrument based on elastic light scatter patterns (2012)

A microbial high-throughput screening (HTS) system was developed that enabled high-speed combinatorial studies directly on bacterial colonies. The system consists of a forward scatterometer for elastic light scatter (ELS) detection, a plate transporter for sample handling, and a robotic incubator for automatic incubation. To minimize the ELS pattern-capturing time, a new calibration plate and correction algorithms were both designed, which dramatically reduced correction steps during acquisition of the circularly symmetric ELS patterns. Integration of three different control software programs was implemented, and the performance of the system was demonstrated with single-species detection for library generation and with time-resolved measurement for understanding ELS colony growth correlation, using Escherichia coli and Listeria. An in-house colony-tracking module enabled researchers to easily understand the time-dependent variation of the ELS from identical colony, which enabled further analysis in other biochemical experiments. The microbial HTS system provided an average scan time of 4.9 s per colony and the capability of automatically collecting more than 4000 ELS patterns within a 7-h time span.
Abstract PR07: Phase I/II study of mesothelin-targeted immunotoxin LMB-100 with nab-paclitaxel for patients with advanced pancreatic adenocarcinoma (2019)

Abstract Purpose: LMB-100 recombinant immunotoxin (iTox) consists of a mesothelin-binding Fab for targeting and a modified Pseudomonas exotoxin A payload. Preclinical studies showed that combining taxanes with iTox results in synergistic antitumor activity. The primary objectives of this phase I/II study were to determine the maximum tolerated dose (MTD) of LMB-100 when given with nanoalbumin bound (nab)-paclitaxel to participants with previously treated advanced pancreatic adenocarcinoma and to assess the objective response rate. Patients and Methods: Patients (n = 20) received fixed-dose nab-paclitaxel (125 mg/m2 on Days 1 and 8) with LMB-100 (65 or 100 mcg/kg on Days 1, 3, and 5) in 21-day cycles. Treatment was limited to 2-3 cycles by protocol. Safety and tolerability, pharmacokinetics, immunogenicity, and relationship of activity to tumor mesothelin expression were assessed. Results: Dose-limiting toxicity (DLT) of Grade 3 myalgia was observed in 2 of 5 patients treated with 100 mcg/kg. DLT of Grade 3 edema from capillary leak syndrome (CLS) was observed in 1 of 6 patients at MTD of 65 mcg/kg. Severe toxicities of Grade 4 left ventricular dysfunction and hypotension from CLS were observed in 1 patient in the phase II expansion, resulting in study closure. LMB-100 anti-drug antibody formation limited LMB-100 exposure in 5 of 13 patients during cycle 2. Seven of 17 patients with evaluable CA19-9 experienced &amp;gt;50% decrease of this tumor marker, and one patient developed a partial response. Response was associated with higher tumor mesothelin expression and Cycle 2 LMB-100 exposure. Conclusions: The combination caused serious toxicity. Despite some observed clinical activity, further testing of this combination will not be pursued. This abstract is also being presented as Poster B01. Citation Format: Christine C. Alewine, Mehwish Ahmad, Cody J. Peer, Zishuo Hu, Min-jung Lee, Akiro Yuno, Jessica Kindrick, Anish Thomas, Seth Steinberg, Jane B. Trepel, William D. Figg, Raffit Hassan, Ira Pastan. Phase I/II study of mesothelin-targeted immunotoxin LMB-100 with nab-paclitaxel for patients with advanced pancreatic adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr PR07.