gebhart/patrepeval huggingface dataset:
The Lagrangian Deformation Structure of Three-Dimensional Steady Flow (2016)

Fluid deformation and strain history are central to wide range of fluid mechanical phenomena ranging from fluid mixing and particle transport to stress development in complex fluids and the formation of Lagrangian coherent structures (LCSs). To understand and model these processes it is necessary to quantify Lagrangian deformation in terms of Eulerian flow properties, currently an open problem. To elucidate this link we develop a Protean (streamline) coordinate transform for steady three-dimensional (3D) flows which renders both the velocity gradient and deformation gradient upper triangular. This frame not only simplifies computation of fluid deformation metrics such as finite-time Lyapunov exponents (FTLEs) and elucidates the deformation structure of the flow, but moreover explicitly recovers kinematic and topological constraints upon deformation such as those related to helicity density and the Poincaré-Bendixson theorem. We apply this transform to several classes of steady 3D flow, including helical and non-helical, compressible and incompressible flows, and find random flows exhibit remarkably simple (Gaussian) deformation structure, and so are fully characterised in terms of a small number of parameters. As such this technique provides the basis for the development of stochastic models of fluid deformation in random flows which adhere to the kinematic constraints inherent to various flow classes.
ChemInform Abstract: Synthesis of Isothiourea Derivatives. (1989)

Abstract Reaction of the thioureas (II) with the chloromethyl‐substituted hydrochlorides (I) of azaarenes yields the isothiourea derivatives (III).
Abstract B38: Developing a functional genomics platform to interrogate rare pediatric cancers (2016)

Abstract Of pediatric solid tumors, as many as 10% of tumors are categorized as rare. Many of these rare tumors lack standard effective known therapy. The ability to identify vulnerabilities for many rare tumors has been significantly limited by the lack of in vitro and in vivo models. Furthermore, current approaches to study such vulnerabilities are usually limited to a specific compound or target. Our objectives were 1) to develop a platform to collect tumor samples and generate in vitro models and 2) to develop systematic and orthogonal approaches focused on currently known druggable cancer targets to identify vulnerabilities in these difficult to treat cancers. We have developed a proof of concept cell line from a patient who succumbed to progressive undifferentiated sarcoma treated on an aggressive multi-therapy regimen. This cell line, in its early passages, has novel gene fusions that match that of the primary tumor. Furthermore, even at early passages, this cell line was amenable to high throughput functional screens. Using a targeted pooled shRNA screen (employing matched seed controls) and an analogous CRISPR screen we identified dependencies to XPO1 and CDK4. In parallel, compounds against these targets were identified in a small molecule compound screen. These targetable dependencies were further validated in vivo with a micro-dosing device. These observations identify new targets in this rare malignancy. Furthermore, this suggests that the interrogation of patient derived cell lines facilitates the identification of testable therapeutic approaches. Citation Format: Andrew L. Hong, Glenn S. Cowley, Yuen-Yi Tseng, Jaime H. Cheah, Oliver Jonas, Mihir B. Doshi, Bryan D. Kynnap, Coyin Oh, Stephanie Meyer, Paul Clemons, Michael Burger, Francisca Vazquez, Barbara Weir, Gregory V. Kryukov, Alanna Church, Alma Imamovic, Aviad Tsherniak, Craig Bielski, Brian Crompton, Elizabeth Mullen, Charles Roberts, Carlos Rodriguez-Galindo, Katherine A. Janeway, Kimberly Stegmaier, Paul van Hummelen, Robert Langer, Levi A. Garraway, Stuart L. Schreiber, David E. Root, Jesse S. Boehm, William C. Hahn. Developing a functional genomics platform to interrogate rare pediatric cancers. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr B38.
Cellobiohydrolase I enzymes (2023)

Provided herein is an isolated Cel7A polypeptide comprising mutations in the catalytic domain of the polypeptide relative to the catalytic domain of a wild type Cel7A polypeptide, wherein the mutations reduce N-linked glycosylation of the isolated polypeptide relative to the wild type polypeptide. Also provided herein is an isolated Cel7A polypeptide comprising increased O-linked glycosylation of the linker domain relative to a linker domain of a wild type Cel7A polypeptide. The increased O-linked glycosylation is a result of the addition of and/or substitution of one or more serine and/or threonine residues to the linker domain relative to the linker domain of the wild type polypeptide. In some embodiments, the isolated Cel7A polypeptide comprising mutations in the catalytic domain of the polypeptide relative to the catalytic domain of a wild type Cel7A polypeptide further comprises increased O-linked glycosylation of the linker domain relative to a linker domain of a wild type Cel7A polypeptide. The mutations in the catalytic domain reduce N-linked glycosylation of the isolated polypeptide relative to the wild type polypeptide. The addition of and/or substitution of one or more serine and/or threonine residues to the linker domain relative to the linker domain of the wild type polypeptide increases O-linked glycosylation of the isolated polypeptide. Further provided are compositions comprising such polypeptides and nucleic acids encoding such polypeptides. Still further provided are methods for making such polypeptides.
Self‐organized neural maps of human protein sequences (1994)

We have recently described a method based on artificial neural networks to cluster protein sequences into families. The network was trained with Kohonen's unsupervised learning algorithm using, as inputs, the matrix patterns derived from the dipeptide composition of the proteins. We present here a large-scale application of that method to classify the 1,758 human protein sequences stored in the SwissProt database (release 19.0), whose lengths are greater than 50 amino acids. In the final 2-dimensional topologically ordered map of 15 x 15 neurons, proteins belonging to known families were associated with the same neuron or with neighboring ones. Also, as an attempt to reduce the time-consuming learning procedure, we compared 2 learning protocols: one of 500 epochs (100 SUN CPU-hours [CPU-h]), and another one of 30 epochs (6.7 CPU-h). A further reduction of learning-computing time, by a factor of about 3.3, with similar protein clustering results, was achieved using a matrix of 11 x 11 components to represent the sequences. Although network training is time consuming, the classification of a new protein in the final ordered map is very fast (14.6 CPU-seconds). We also show a comparison between the artificial neural network approach and conventional methods of biosequence analysis.
Synthesis and Brain Regional Distribution of [11C]NPS 1506 in Mice and Rat: an N-Methyl-D-aspartate (NMDA) Receptor Antagonist (2003)

NPS 1506 [3-fluoro-gamma-(3-fluorophenyl)-N-methylbenzenepropamine] is representative of a non-psychotomimetic class of N-methyl-D-aspartate (NMDA) receptor antagonists. [11C]NPS 1506 was prepared at high radiochemical purity (>98%) with a specific activity of around 50 GBq/micromol at the end of synthesis by methylation of the desmethyl precursor with [11C]methyl iodide in the presence of NaH. Biodistribution of [11C]NPS 1506 in mice and rat demonstrated that uptake into the brain was rapid and occurred at high levels. [11C]NPS 1506 showed no appreciable specific binding in rodent brains under in vivo conditions, possibly because of both a large non-specific bound fraction and low in vitro binding affinity for NMDA receptors.
Experimental Study of Security Architectures for Wireless Mesh Networks (2009)

In this paper we demonstrate the potential of MobiSEC, a complete security architecture for wireless mesh networks (WMNs), that provides both access control for mesh users and routers as well as a key distribution scheme. MobiSEC has been implemented and integrated in MobiMESH, a WMN implementation that provides a complete framework for testing and analyzing the behavior of a mesh network in real-life environments. Our experimental testbed compares MobiSEC both with a static fixed-key approach and with an end-to-end solution that consists in establishing an encrypted IPSec tunnel. Experimental studies show that MobiSEC considerably increases the WMN security, with a negligible impact on the network performance, thus representing an effective solution for wireless mesh networking.
Modulating BET Bromodomain Inhibitor ZEN‐3694 and Enzalutamide Combination Dosing in a Metastatic Prostate Cancer Patient Using CURATE.AI, an Artificial Intelligence Platform (2018)

Abstract Combination chemotherapy is a cornerstone of cancer treatment. Optimizing its effectiveness requires dose‐ and time‐dependent regulation of drug synergy. In this report, CURATE.AI, an artificial intelligence platform, is used to prospectively guide the dosing of a bromodomain inhibitor (ZEN‐3694) and enzalutamide administered in combination to a patient with metastatic castration‐resistant prostate cancer to reduce serum prostate‐specific antigen (PSA) levels. CURATE.AI successfully identifies substantial ZEN‐3694 and enzalutamide dose adjustments, increasing both treatment efficacy and tolerance. CURATE.AI analysis also confirms that the patient's durable response is mediated by ZEN‐3694 inclusion in the regimen. Due to CURATE.AI‐enhanced efficacy and safety, the patient was able to continue with the combination regimen, resulting in a durable response and no disease progression based on CURATE.AI‐sustained control over PSA levels and reduced lesion size.
HAFs having &#x03BB;<inf>0</inf> in a 1.0&#x03BC;m band and high non-linearity (2008)

We designed and fabricated simple-structure HAFs having lambda0 in a 1.0 mum band as well as low confinement loss and single mode operation over wide range of wavelengths. The developed HAFs showed high non-linearity and good connectivity.
A benzoquinone Di-imine from the oxidation of pentafluoroaniline by hypochlorite. X-Ray crystal structure and possible formation via pentafluorophenylnitrene (1989)

Oxidation of pentafluoroaniline by aqueous sodium hypochlorite under phase-transfer conditions gave decafluoroazobenzene (2), octafluorophenazine (3), and the dark red N-chloro-N′-(pentafluorophenyl)-2,3,5,6-tetrafluorobenzo-1,4-quinone di-imine (4) as a mixture of Z- and E-isomers. X-Ray diffraction studies revealed that this chloro imine gives crystals containing both isomers, the structures of which have been solved. Singlet pentafluorophenylnitrene is proposed to be an intermediate in the oxidation reaction whereby compounds (2), (3), and (4) are formed following nucleophilic attack by pentafluoroaniline on the nitrogen atom, and the ortho- and para-positions respectively. A convenient, albeit not high yielding, procedure for the preparation of decafluoroazobenzene is described.
THE HOT PROTOTYPE OF THE PI-MODE STRUCTURE FOR LINAC4 (2010)

The PIMS (Pi-Mode-Structure) cavities for Linac4 are made of 7 coupled cells operating in !-mode at a frequency of 352 MHz. The mechanical concept is derived from the 5-cell cavities used in the LEP machine, whereas cell length and coupling are adapted for proton acceleration in the range from 50 to 160 MeV. Linac4 will be the first machine to employ this type of cavities for low-beta protons. During the first years of operation the PIMS will be used at low duty cycle (0.1%) as part of the consolidated LHC proton injector complex. It is designed, however, to operate eventually in a high duty cycle (10%) proton injector, which could be used as proton front-end for neutrino or RIB applications. To prepare for the series construction of the 12 PIMS units the first cavity (102 MeV beam energy) has been designed and constructed at CERN, to be used as a hot prototype for RF tests and as a pre-series mechanical unit. In this paper we report on some of the design features, the construction experience, and first measurements.
Electrospun, Biofunctionalized Fibers as Tailored in vitro Substrates for Keratinocyte Cell Culture (2010)

Cell adhesion preventing fiber surfaces were tailored differently with bioactive peptides (a fibronectin fragment (GRGDS), a collagen IV fragment (GEFYFDLRLKGDK) and a combination of both) to provide an artificial extracellular matrix as a substrate for HaCaT keratinocyte cell culture. Therefore, a polymer blend containing a six-arm star-shaped statistical copolymer of ethylene oxide and propylene oxide in the ratio 80:20 (NCO-sP[EO-co-PO]) and poly-[D,L-(lactide-co-glycolide)] (PLGA) was electrospun. The resulting fibers were biofunctionalized and investigated as in vitro substrates using the HaCaT kerationcyte cell line. Appropriate surface chemistry on these electrospun fibers proved to prevent adhesion of keratinocytes, while additional immobilization of certain peptide sequences induced cell adhesion. These specific fibers enable investigation of immobilized active molecules and the subsequent cellular response to the scaffold. HaCaT keratinocytes were found to selectively adhere to those fibers modified with either collagen IV segment GEFYFDLRLKGDK or a mixture of the two peptide sequences GEFYFDLRLKGDK and GRGDS (1:1). However, the synergistic effects of both (the fibronectin fragment and the collagen IV fragment) seem to significantly increase the numbers of adherent keratinocytes.
Tuberculosis chemotherapy: current drug delivery approaches (2006)

Tuberculosis is a leading killer of young adults worldwide and the global scourge of multi-drug resistant tuberculosis is reaching epidemic proportions. It is endemic in most developing countries and resurgent in developed and developing countries with high rates of human immunodeficiency virus infection. This article reviews the current situation in terms of drug delivery approaches for tuberculosis chemotherapy. A number of novel implant-, microparticulate-, and various other carrier-based drug delivery systems incorporating the principal anti-tuberculosis agents have been fabricated that either target the site of tuberculosis infection or reduce the dosing frequency with the aim of improving patient outcomes. These developments in drug delivery represent attractive options with significant merit, however, there is a requisite to manufacture an oral system, which directly addresses issues of unacceptable rifampicin bioavailability in fixed-dose combinations. This is fostered by the need to deliver medications to patients more efficiently and with fewer side effects, especially in developing countries. The fabrication of a polymeric once-daily oral multiparticulate fixed-dose combination of the principal anti-tuberculosis drugs, which attains segregated delivery of rifampicin and isoniazid for improved rifampicin bioavailability, could be a step in the right direction in addressing issues of treatment failure due to patient non-compliance.
A learning framework for robust hashing of face images (2010)

Robust image hashing has been actively researched over the last decade with varied applications in image content authentication and identification under distortions. In the existing literature on robust image hashing, hash algorithms are ignorant of the class of images being hashed. There are however significant application domains such as that of face image hashing where apriori knowledge of the image class as well as permissible distortions can benefit hash algorithm design. In this paper, we present a two stage cascade of dimensionality reduction constructs for face image hashing. The first stage aims to project the face image to a space where geometric distortions manifest approximately as additive noise. For this purpose, we use the non-negative matrix approximations based hash vector developed by Monga et al. which is known to possess excellent geometric attack robustness. In the second stage, we employ oriented principal component analysis (OPCA) based on estimating signal as well as noise statistics in a learning phase and deriving a projection that mitigates the effect of noise. We obtain both experimentally based ROC curves as well as analytical ones via a detection theoretic analysis of the proposed framework. The ROC curves reveal clearly that incorporating such a learning phase greatly reduces error probabilities.
A 2.4GHz to 6GHz active balun in GaN technology (2013)

This article presents a S-C band active balun in a GaN integrated technology. Based on a differential pair this circuit realizes the single to differential conversion. Moreover this circuit can be used as preamplifier to drive a power stage. It delivers more than 25dBm in each differential path in the [2,4GHz-6GHz] band with a maximum of 29dBm at 3.8GHz. The chip has been realized in the UMS GH25 process, a GaN HEMT technology with a 0.25μm gate length.
Isoconversional Method for the Modeling of the Curing Kinetics of Epoxy Molding Compounds for Mold Process Simulation (2018)

A characterization and modeling protocol is presented for the measurement and calculus of curing kinetics of epoxy molding compounds to predict the degree of curing under arbitrary thermal conditions. The is conversional approach allows the use of nonisothermal differential scanning calorimetry (DSC) data and obviates the disadvantage of isothermal experiments such as curing and heat generation that is unrecorded during the initial temperature ramp. The described model free kinetics (MFK) method enables the construction of isothermal curing curves without actually performing isothermal measurements, while at the same time verifying the correct value of activation energy. The presented methodology can be applied with the simplest means, without the need for specialized software. Application of the described protocol to epoxy molding compounds provided estimation of the Kamal-Sourour model coefficients having a coefficient of determination of 0.998.
Mitral web--a new concept for mitral valve repair: improved engineering design and in-vitro studies. (2009)

Based on the study results, the mitral web may represent a feasible option to repair different types of mitral valve prolapse. The mitral web may also significantly simplify mitral valve repair for complex lesions.
The Scientific Foundation for Personal Genomics: Recommendations from a National Institutes of Health–Centers for Disease Control and Prevention Multidisciplinary Workshop (2020)

The increasing availability of personal genomic tests has led to discussions about the validity and utility of such tests and the balance of benefits and harms. A multidisciplinary workshop was convened by the National Institutes of Health and the Centers for Disease Control and Prevention to review the scientific foundation for using personal genomics in risk assessment and disease prevention and to develop recommendations for targeted research. The clinical validity and utility of personal genomics is a moving target with rapidly developing discoveries but little translation research to close the gap between discoveries and health impact. Workshop participants made recommendations in five domains: (1) developing and applying scientific standards for assessing personal genomic tests; (2) developing and applying a multidisciplinary research agenda, including observational studies and clinical trials to fill knowledge gaps in clinical validity and utility; (3) enhancing credible knowledge synthesis and information dissemination to clinicians and consumers; (4) linking scientific findings to evidence-based recommendations for use of personal genomics; and (5) assessing how the concept of personal utility can affect health benefits, costs, and risks by developing appropriate metrics for evaluation. To fulfill the promise of personal genomics, a rigorous multidisciplinary research agenda is needed.
Abstract 369: Tumor detection and surgical navigation with fluorescence laparoscopy is enhanced with combinations of differently labeled fluorophore-conjugated antibodies and fluorescent proteins (2012)

Abstract The aim of this study was to improve detection of primary and metastatic lesions of human pancreatic cancer in mouse models with fluorescence laparoscopy by enhancing the fluorescence signal of tumor with different combinations of fluorophores without compromising background illumination. Human pancreatic cancer models were established with combinations of FG-RFP, MiaPaca2-GFP, BxPC-3-RFP, or BxPC-3 cancer cells implanted in 6-week-old female athymic mice. Two weeks post-implantation, diagnostic laparoscopy was performed with a Stryker L9000 LED light source 24 hours after tail vein injection of CEA antibodies conjugated with Alexa 488- and/or Alexa 555. Cancer lesions were detected and localized under the fluorescence light mode. Intravital images were obtained with the Maestro CRI Small Animal Imaging System, serving as a positive control. Tumors were collected for histologic review. Fluorescence laparoscopy with a 495-nm emission filter and an LED light source enabled real-time visualization of differently fluorescence-labeled tumors in the peritoneal cavity simultaneously. The combination of BxPC-3 RFP labeled with anti-CEA-Alexa 488 afforded the brightest signal of all established mouse models. We were able to reproduce this enhanced fluorescence signaling by doubly labeling non-color BxPC-3 tumor with anti-CEA-Alexa 488 and anti-CEA-Alexa 555. The doubly labeled tumor provided a greater signal intensity profile compared to tumors labeled with either anti-CEA-Alexa 488 or -Alexa 555 alone. This enhanced fluorescence signal permitted improved detection of sub-millimeter lesions without compromising background illumination. The ability to visualize tumor deposits expressing fluorescent proteins of different wavelengths simultaneously with an LED light source enabled us to establish the optimal combination of fluorophores that enhanced the signal intensity of fluorescence. With this optimal fluorophore combination, we improved the detection of sub-millimeter tumor lesions without impairing the visualization of surrounding structures necessary for surgical navigation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 369. doi:1538-7445.AM2012-369
Large-Scale Production and Properties of Immunoaffinity- Purified Human Activated Protein C Concentrate (1995)

Activated protein C (APC) is a highly specific serine proteinase which functions as an important naturally occurring antithrombotic enzyme. APC also has antiinflammatory properties. We have developed a large-scale process for the production of APC for therapeutic use starting with cryoprecipitate-poor human plasma. This report describes the process, its performance at the pilot plant scale, and the characteristics of immunoaffmity-purified human APC concentrate referred to as APC (human). The process consists of three chromatographic steps, an enzymatic conversion step, and incorporates a solvent/detergent treatment step for the inactivation of lipid-enveloped viruses. Solvent/detergent was shown to rapidly inactivate spiked HIV-1, as well as three marker viruses to nondetectable levels under process conditions. The immunoaffmity-purified protein C (PC) intermediate was enriched 13,600-fold over plasma and had a specific activity of 231 U/mg. The overall yield of the process following enzymatic conversion of the PC intermediate to APC and its processing by anion exchange chromatography was 36%. APC (human) was shown to be highly purified, functional and stable.