gebhart/patrepeval huggingface dataset:
Fast metabolite mapping in the pig heart after injection of hyperpolarized 13C‐pyruvate with low‐flip angle balanced steady‐state free precession imaging (2012)

The conversion of hyperpolarized (13)C pyruvate to metabolic products in the Krebs cycle provides valuable information about the metabolic status and the viability of the myocardium. Therefore, imaging methods must be able to spectrally discriminate different (13)C metabolites. However, the requirement for spectral selectivity conflicts with the demands for rapid image acquisition and high spatial resolution in cardiac imaging. In this work, the feasibility of a balanced steady state free precession sequence with low flip angles was investigated in the pig heart after injection of hyperpolarized (13)C(1)-pyruvate. Using cardiac gating, it was possible to acquire (13)C-bicarbonate images within a single heartbeat (acquisition time 150 ms) without destroying the substrate signal from the hyperpolarized pyruvate. Therefore, the technique may be useful in dynamic studies of cardiac metabolism.
Miniature eye-safe laser system for high-resolution three-dimensional lidar (2007)

A microchip-laser-pumped optical parametric amplifier produces 35-microJ, 1.537-microm pulses of 190-ps duration at 8 kHz, in a near-diffraction-limited output beam with a Fourier-transform-limited spectrum. The flight-ready laser head is pumped by 20 W of optical power from two fiber-coupled laser-diode arrays, occupies a volume of 0.14 liters, and has a mass of 0.34 kg.
50GBd 64APSK Coded Modulation Transmission over Long Haul Submarine Distance with Nonlinearity Compensation and Subcarrier Multiplexing (2017)

We achieve transoceanic distance transmission with 350-390 Gb/s 64APSK coded modulation channels and explore the benefit of nonlinearity compensation with subcarrier multiplexing. Estimated total capacity with variable spectral efficiency is 66.8 Tb/s.
Monocyte Cell Surface Glycosaminoglycans Positively Modulate IL-4-Induced Differentiation toward Dendritic Cells (2008)

IL-4 induces the differentiation of monocytes toward dendritic cells (DCs). The activity of many cytokines is modulated by glycosaminoglycans (GAGs). In this study, we explored the effect of GAGs on the IL-4-induced differentiation of monocytes toward DCs. IL-4 dose-dependently up-regulated the expression of DC-specific ICAM-3-grabbing nonintegrin (DC-SIGN), CD80, CD206, and CD1a. Monocytes stained positive with Abs against heparan sulfate (HS) and chondroitin sulfate (CS) B (CSB; dermatan sulfate), but not with Abs that recognize CSA, CSC, and CSE. Inhibition of sulfation of monocyte/DC cell surface GAGs by sodium chlorate reduced the reactivity of sulfate-recognizing single-chain Abs. This correlated with hampered IL-4-induced DC differentiation as evidenced by lower expression of DC-SIGN and CD1a and a decreased DC-induced PBL proliferation, suggesting that sulfated monocyte cell surface GAGs support IL-4 activity. Furthermore, removal of cell surface chondroitin sulfates by chondroitinase ABC strongly impaired IL-4-induced STAT6 phosphorylation, whereas removal of HS by heparinase III had only a weak inhibitory effect. IL-4 bound to heparin and CSB, but not to HS, CSA, CSC, CSD, and CSE. Binding of IL-4 required iduronic acid, an N-sulfate group (heparin) and specific O sulfates (CSB and heparin). Together, these data demonstrate that monocyte cell surface chondroitin sulfates play an important role in the IL-4-driven differentiation of monocytes into DCs.
Towards a Vaccine Against Escherichia Coli -Associated Urinary Tract Infections (2010)

Evaluation of: Alteri CJ, Hagan EC, Sivick KE, Smith SN, Mobley HLT: Mucosal immunization with iron receptor antigens protects against urinary tract infections. PLoS Pathog. 5(9), E1000586 (2009). Urinary tract infection is one of the most common infections in humans. The eradication of uropathogenic Escherichia coli-mediated urinary tract infections has still not been achieved and no effective licensed vaccines are currently available. To overcome the limitations of previous approaches in developing an efficacious vaccine, Alteri et al., through a functional genomic approach, identified six novel vaccine candidates shown to be protective against urinary tract infection in a mouse model. The six proteins all belong to the class of outer membrane iron receptors, are upregulated in iron-restricted conditions and were demonstrated to induce, upon mucosal vaccination, antigen-specific antibodies and cytokine responses, which correlated with protection in a mouse model of urinary tract infection. Therefore, for the first time, antigens that were previously recognized as necessary for bacterial pathogenesis, being involved in iron acquisition in an iron-limited environment such as the urinary tract, are now proposed as potential candidates for the development of a vaccine against uropathogenic strain-associated urinary tract infections.
Herpes Simplex Virus-1 infection in human primary corneal epithelial cells is blocked by a stapled peptide that targets processive DNA synthesis (2020)

Hydrocarbon stapled peptides that simulate the α-helix from the C-terminus of HSV-1 DNA polymerase can specifically block DNA synthesis and infection of HSV-1 in human primary corneal epithelial cells. These stapled peptides provide a foundation for developing a topical therapeutic for treating human ocular Herpes Keratitis.
Systems-wide analyses of mucosal immune responses toHelicobacter pyloriat the interface between pathogenicity and symbiosis (2016)

Helicobacter pylori is the dominant member of the gastric microbiota in over half of the human population of which 5-15% develop gastritis or gastric malignancies. Immune responses to H. pylori are characterized by mixed T helper cell, cytotoxic T cell and NK cell responses. The presence of Tregs is essential for the control of gastritis and together with regulatory CX3CR1+ mononuclear phagocytes and immune-evasion strategies they enable life-long persistence of H. pylori. This H. pylori-induced regulatory environment might contribute to its cross-protective effect in inflammatory bowel disease and obesity. Here we review host-microbe interactions, the development of pro- and anti-inflammatory immune responses and how the latter contribute to H. pylori's role as beneficial member of the gut microbiota. Furthermore, we present the integration of existing and new data into a computational/mathematical model and its use for the investigation of immunological mechanisms underlying initiation, progression and outcomes of H. pylori infection.
Ultrasonic analyses algorithm on an EX VIVO produced oral mucosal equivalent (2011)

This study examines the use of high-resolution ultrasound with an analyses algorithm to accurately monitor development of an ex vivo produced oral mucosal equivalent (EVPOME). We used ultrasonic profilometry to examine EVPOME development as seeded cells on its surface proliferate. As these engineered structures develop, seeded cells stratify from their differentiation and produce a keratinized protective upper layer. Some of these transformations could alter backscatter of ultrasonic signals and produce scattering of the signal similar to an unseeded scaffold. Developing non-invasive in vitro ultrasonic monitoring allows adjusting tissue cultivation in-process, accounting for biological variations in the development of the EVPOME.

	Key words: Acoustic microscopy, oral mucosa, non-invasive assessment, tissue engineering, ultrasound.
P‐212: Late‐News Poster: Influence of Index Matching Epoxy Filler at the Encapsulation Part for the Performance of TEOLED with Internal Wrinkle Structure (2019)

In this work, we applied random wrinkle structure to top emitting organic light emitting diodes (TEOLEDs) inside. Also, by introducing index matching epoxy filler into the encapsulation part, we could dramatically improve the current efficiency with maintaining the suppression effect of viewing angle dependence as well as color shift.
ChemInform Abstract: Inorganic Carbonates as Nucleophiles for the Asymmetric Synthesis of Vinylglycidols. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Techno-Economic Analysis of Biocatalytic Processes for Production of Alkene Epoxides (2007)

A techno-economic analysis of two different bioprocesses was conducted, one for the conversion of propylene to propylene oxide (PO) and other for conversion of styrene to styrene epoxide (SO). The first process was a lipasemediated chemo-enzymatic reaction, whereas the second one was a one-step enzymatic process using chloroperoxidase. The PO produced through the chemo-enzymatic process is a racemic product, whereas the latter process (based on chloroperoxidase) produces an enantio-pure product. The former process thus falls under the category of high-volume commodity chemical (PO); whereas the latter is a low-volume, high-value product (SO). A simulation of the process was conducted using the bioprocess engineering software SuperPro Designer v6.0 (Intelligen, Inc., Scotch Plains, NJ) to determine the economic feasibility of the process. The purpose of the exercise was to compare biocatalytic processes with existing chemical processes for production of alkene expoxides. The results show that further improvements are needed in improving biocatalyst stability to make these bioprocesses competitive with chemical processes.
Type-Driven Automated Learning with Lale (2019)

Machine-learning automation tools, ranging from humble grid-search to hyperopt, auto-sklearn, and TPOT, help explore large search spaces of possible pipelines. Unfortunately, each of these tools has a different syntax for specifying its search space, leading to lack of portability, missed relevant points, and spurious points that are inconsistent with error checks and documentation of the searchable base components. This paper proposes using types (such as enum, float, or dictionary) both for checking the correctness of, and for automatically searching over, hyperparameters and pipeline configurations. Using types for both of these purposes guarantees consistency. We present Lale, an embedded language that resembles scikit learn but provides better automation, correctness checks, and portability. Lale extends the reach of existing automation tools across data modalities (tables, text, images, time-series) and programming languages (Python, Java, R). Thus, data scientists can leverage automation while remaining in control of their work.
Non-Intrusive Cloud Application Transaction Pattern Discovery (2019)

Cloud application performance profiling is a complex task in view of multiple distributed micro-services running over varied physical and virtual machines, each implemented by different developers using diverse software components. Existing methods, usually as part of an cloud based Application Performance Management (APM) employ intrusive instrumentation techniques in order to map the calls between services depending on specific programming languages and affecting performance. We present Fibratus, an automatic non-intrusive solution for application service call pattern discovery of cloud applications. Fibratus is capable of discerning patterns of inter-service messages per transaction by employing modified Machine Learning clustering algorithms on live network traces. Fibratus can correlate service-specific protocol data patterns with transactional flow patterns to provide additional insights for performance profiling. Over an extensive set of experiments in the cloud, with various applications, utilizing different technologies and usage patterns, Fibratus demonstrated high accuracy and performance on interleaved traffic. In addition, Fibratus allows pluggable descriptive pattern discovery as demonstrated in our tests for example in SQL query, HTTP url and Redis REST calls.
Effects of Steric Bulkiness of Substituents on Quantum Yields of Photochromic Reactions of Furylfulgides (1994)

Abstract Furylfulgides with different sizes of alkyl substituents were synthesized and their photochromic properties were examined. While the quantum yield of coloring reaction increased and the quantum yield of the E-to-Z isomerization decreased as the steric bulkiness of the alkyl substitutent on the 2,5-dimethyl-3-furylmethylidene moiety increased, the bleaching quantum yield increased as the isopropylidene group was replaced by an adamantylidene group. Both effects worked independently, and a furylfulgide with an isopropyl group on the furylmethylidene moiety and an adamantylidene group in one molecule showed the coloring quantum yield of 0.51 (366 nm) and the bleaching quantum yield of 0.26 (492 nm) in toluene.
The Role of Water Molecules in the Structure-Based Design of (5-Hydroxynorvaline)-2-cyclosporin: Synthesis, Biological Activity, and Crystallographic Analysis with Cyclophilin A (1995)

Analysis of the contact surface of the cyclophilin A (CypA)/cyclosporin A (CsA, 1) crystal structure delineates a unique cavity between both molecules in the vicinity of the Abu-2 side chain atoms of 1 (Abu pocket). Therefore, (5-hydroxynorvaline)-2-cyclosporin (2) was designed and prepared as a CsA derivative which could mediate additional interactions within the pocket. The X-ray crystal structure of the CypA/2 complex at 1.76 A resolution shows that 1 and 2 have identical backbone conformations and that the introduced hydroxypropyl chain makes indeed the expected supplemental interactions with CypA. However, 2 has 8-9-fold lower binding affinity than 1 for CypA. This results from a presumed unfavorable free energy change associated with the displacement of one of the tightly bound water molecules within the pocket and a change in prebinding equilibria. The role of the later was assessed by comparing the conformation distribution of 1 and 2 to that of norvaline-2-cyclosporin (3) and norvaline-2-(D-MeSer)-3-cyclosporin (4).
SE_MC sequence improves image quality of carotid arteries and atherosclerotic plaques (2010)

Purpose FSE images suffer from blurring because of non-uniform T2-weighting of k-space [Constable, Gore.MRM.1992.28(1):9-24], which is stronger on small structures with short T2 times, such as carotid arteries. To avoid this, we propose to generate T1-PD-T2-weighted images using Spin-Echo Multi-Contrast (SE_MC) sequence. FSE and SE_MC are both CPMG multi-echo sequences; however FSE acquires different lines of the same k-space at different TEs, whereas SE_MC samples multiple k-spaces (with constant TE) at different TEs.
Introductory Commentary on The Role of Stromal Integrin Interactions in Pro-B-Cell Proliferation Hahn et al (2000)

"Introductory Commentary on The Role of Stromal Integrin Interactions in Pro-B-Cell Proliferation Hahn et al." Hematology, 5(2), p. 151
<title>Adaptive wavefront correction using a VLSI implementation of the parallel gradient descent algorithm</title> (1999)

An adaptive laser beam focusing system using a 127 channel liquid crystal phase modulator is presented. The controller for the system is a circuit built with prototype VLSI chips that implement the stochastic parallel gradient descent algorithm. The controller is driven by a scalar laser beam quality metric and can run at the rate of 150 kHz. The system performance is characterized and a secondary control loop manipulating one of the algorithm parameters is experimentally investigated. The performance of the system is reported and performance improvements obtained by using the recent history of the beam quality metric to control an algorithm parameter is demonstrated.
Detection of the outer membrane lipoprotein I and its gene in fluorescent and non-fluorescent pseudomonads: implications for taxonomy and diagnosis (1993)

The open reading frame of the OprI lipoprotein gene from Pseudomonas aeruginosa was amplified by polymerase chain reaction (PCR) starting from purified DNA or colony lysates. A fragment of the expected size (249 bp) was detected in all P. aeruginosa strains from various clinical and geographical origins. The gene could only be amplified in pseudomonads of rRNA group I which are considered to be the authentic genus Pseudomonas. Digestions with HaeIII, PvuII and SphI of the amplified fragments demonstrated a sequence variation in the oprI gene. Colony, dot and Western blots with two monoclonal antibodies (mAbs) against the lipoprotein I confirmed our PCR results. These findings open interesting perspectives for the molecular taxonomy of the genus Pseudomonas and the development of diagnostic tools.
Upper electronic excited states of quadruply bonded M2X4(PMe3)4 complexes (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTUpper electronic excited states of quadruply bonded M2X4(PMe3)4 complexesMichael D. Hopkins, Vincent M. Miskowski, and Harry B. GrayCite this: J. Am. Chem. Soc. 1988, 110, 6, 1787–1793Publication Date (Print):March 1, 1988Publication History Published online1 May 2002Published inissue 1 March 1988https://pubs.acs.org/doi/10.1021/ja00214a021https://doi.org/10.1021/ja00214a021research-articleACS PublicationsRequest reuse permissionsArticle Views83Altmetric-Citations12LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Defining the human kidney N‐glycome in normal and cancer tissues using MALDI imaging mass spectrometry (2019)

Clear-cell renal cell carcinoma (ccRCC) presents challenges to clinical management because of late-stage detection, treatment resistance, and frequent disease recurrence. Metabolically, ccRCC has a well-described Warburg effect utilization of glucose, but how this affects complex carbohydrate synthesis and alterations to protein and cell surface glycosylation is poorly defined. Using an imaging mass spectrometry approach, N-glycosylation patterns and compositional differences were assessed between tumor and nontumor regions of formalin-fixed clinical ccRCC specimens and tissue microarrays. Regions of normal kidney tissue samples were also evaluated for N-linked glycan-based distinctions between cortex, medullar, glomeruli, and proximal tubule features. Most notable was the proximal tubule localized detection of abundant multiantennary N-glycans with bisecting N-acetylglucosamine and multziple fucose residues. These glycans are absent in ccRCC tissues, while multiple tumor-specific N-glycans were detected with tri- and tetra-antennary structures and varying levels of fucosylation and sialylation. A polycystic kidney disease tissue was also characterized for N-glycan composition, with specific nonfucosylated glycans detected in the cyst fluid regions. Complementary to the imaging mass spectrometry analyses was an assessment of transcriptomic gene array data focused on the fucosyltransferase gene family and other glycosyltransferase genes. The transcript levels of the FUT3 and FUT6 genes responsible for the enzymes that add fucose to N-glycan antennae were significantly decreased in all ccRCC tissues relative to matching nontumor tissues. These striking differences in glycosylation associated with ccRCC could lead to new mechanistic insight into the glycobiology underpinning kidney malignancies and suggest the potential for new therapeutic interventions and diagnostic markers.
Natural Human Interferon‐γ Derived from Lipopolysaccharide‐stimulated Human Myelomonocytic HBL‐38 Cells (1988)

A human myelomonocytic cell line, HBL-38 cells, propagated in vivo, spontaneously produced interferon (IFN)-gamma and IFN-alpha. Whereas hemmagglutinating virus of Japan (HVJ) enhanced the production of IFN-alpha, bacterial lipopolysaccharide (LPS) markedly enhanced the production of IFN-gamma. LPS could be replaced with lipid A. Furthermore, the enhancement of production of IFN-gamma by LPS was completely abolished by polymixin B. IFN-gamma derived from LPS-stimulated HBL-38 cells was purified to homogeneity and characterized. The apparent molecular weight, subspecies composition, amino acid sequence and glycosylated sites were in agreement with those of the product of normal human peripheral blood lymphocytes (PBL). These results indicate that the myelomonocytic HBL-38 cells, not a T-cell line, can also produce IFN-gamma identical to the product of normal human PBL.
Abstract LB-334: Imaging caspase dependent cell death as a surrogate for efficacy of cancer therapeutics (2011)

Abstract Induction of cell death in malignant lesions still represents the major goal in the treatment of cancer patients. Imaging of apoptosis would enhance the development of optimal dosing, schedule and combination therapies. Here we used a luciferase biosensor (Promega) and developed a bioluminescent assay system with optimized signal to noise for the detection of cell death in vitro and in living animals. Using D54-MG cells stably expressing the reporter, we demonstrate that TRAIL treatment resulted in a 100–200 fold induction of bioluminescence activity which correlated with cell death as demonstrated by increased cleavage of Caspase-3. Furthermore inhibition of apoptosis using the pan caspase inhibitor Z-VAD-FMK resulted in inhibition of reporter activity. The utility of this cell death reporter was further demonstrated in human glioma xenografted tumors wherein induction of apoptosis was correlated with reporter activation. The high signal to noise and dynamic range of reporter activity provides for a sensitive and quantitative surrogate for evaluation of experimental therapeutics. In addition, the ability to image repeatedly provides a unique opportunity to understand the dynamics of cell death in response to specific drugs or combination therapies. We are also investigating the application of this technology in a high throughput screening of compound and targeted siRNA libraries in diverse cells and in pre-clinical cancer mouse models. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-334. doi:10.1158/1538-7445.AM2011-LB-334