gebhart/patrepeval huggingface dataset:
Metabolic control of primed human pluripotent stem cell fate and function by the miR-200c–SIRT2 axis (2017)

A hallmark of cancer cells is the metabolic switch from oxidative phosphorylation (OXPHOS) to glycolysis, a phenomenon referred to as the 'Warburg effect', which is also observed in primed human pluripotent stem cells (hPSCs). Here, we report that downregulation of SIRT2 and upregulation of SIRT1 is a molecular signature of primed hPSCs and that SIRT2 critically regulates metabolic reprogramming during induced pluripotency by targeting glycolytic enzymes including aldolase, glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase, and enolase. Remarkably, knockdown of SIRT2 in human fibroblasts resulted in significantly decreased OXPHOS and increased glycolysis. In addition, we found that miR-200c-5p specifically targets SIRT2, downregulating its expression. Furthermore, SIRT2 overexpression in hPSCs significantly affected energy metabolism, altering stem cell functions such as pluripotent differentiation properties. Taken together, our results identify the miR-200c-SIRT2 axis as a key regulator of metabolic reprogramming (Warburg-like effect), via regulation of glycolytic enzymes, during human induced pluripotency and pluripotent stem cell function.
Sequence and side-chain specific photofragment (193 nm) ions from protonated substance P by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (1999)

Photodissociation at 193 nm (6. 43 eV) of the protonated substance-P, [M + H]+ ions, in a delayed extraction matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) mass spectrometer, is reported. The photofragment ion spectrum of substance P contains a complete series of a-type fragment ions and abundant side-chain cleavage ions. This article focuses on the utility of MALDI-TOF photodissociation for peptide sequencing.
Endometrial Cancer and Hypermethylation: Regulation of DNA and MicroRNA by Epigenetics (2012)

Endometrial cancer is the seventh most common cancer in women worldwide. Therefore elucidation of the pathogenesis and development of effective treatment for endometrial cancer are important. However, several aspects of the mechanism of carcinogenesis in the endometrium remain unclear. Associations with genetic variation and mutations of cancer-related genes have been shown, but these do not provide a complete explanation. Therefore, in recent years, epigenetic mechanisms that do not involve changes in DNA sequences have been examined. Studies aimed at detection of aberrant DNA hypermethylation in cancer cells present in microscopic amounts in vivo and application of the results to cancer diagnosis have also started. Breakdown of the DNA mismatch repair mechanism is thought to play a large role in the development of endometrial cancer, with changes in the expression of the hMLH1 gene being particularly important. Silencing of genes such as APC and CHFR, Sprouty 2, RASSF1A, GPR54, CDH1, and RSK4 by DNA hypermethylation, onset of Lynch syndrome due to hereditary epimutation of hMLH1 and hMSH2 mismatch repair genes, and regulation of gene expression by microRNAs may also underlie the carcinogenic mechanisms of endometrial cancer. Further understanding of these issues may permit development of new therapies.
A Design Procedure of Dipole Arrangement and Inversion Algorithm for Magnetic Motion Capture Systems (1998)

Magnetic motion capture is an instrument which acquires three dimensional position and orientation of magnetic sensors through several time-shared magnetic field vectors from differently exited transmitter coils. Many small sensors could be attached to pin-points of a moving object including human body to record its motion. Tracking problem in pictorial motion picture will be avoided. Apart from Polhemus's which inherently depends on three orthogonal concentric transmitter coils, various coil arrangements could be devised according to the shape and dimension of required sensing volume. We define design of that instrument as an inversion-based problem and discuss on a solving procedure in which arrangement of coils and excitation pattern could be determined heuristically and almost independently of inversion algorithm since proposed algorithm is rather general to various field distributions. The algorithm starts from selected rotation-invariant quantities derived from sensed field vector components such as vector modulus or pattern-by-pattern angular difference of vector directions, and inverts classical dipole equation by Newton-Raphson's method to obtain xyz position of the magnetic sensor. Then the orientation of the sensor is determined by simple comparison of absolute and sensed vector directions. A simplest but very practical solution named point-scan system is presented in which four to nine solenoids aligned in a plane and excited one by one cover the box-shaped sensing volume below them. Its experimental result with newly designed hardware is also shown which covers 0.75 by 0.75 by 1m volume with resolution and stability of 1 to 3mm.
Abstract 2003: Antibody against TIGIT (T cell immunoreceptor with Ig and ITIM domains) induces anti-tumor immune response and generates long-term immune memory (2017)

Abstract T cell immunoreceptor with Ig and ITIM domains (TIGIT) is a co-inhibitory molecule containing an immunoreceptor tyrosine-based inhibition motif (ITIM) within its cytoplasmic tail, and is highly expressed on regulatory T cells and activated CD4+ T, CD8+ T, and NK cells. TIGIT competes with CD226, which contains an immunoreceptor tyrosine-based activation motif (ITAM) within its cytoplasmic tail for ligands poliovirus receptor (PVR) and poliovirus receptor-related 2 (PVRL2), with higher affinity to PVR. The ligands are expressed on the surface of antigen presenting cells and at high levels on most tumors. Therefore, when TIGIT is present, the ligands preferentially engage TIGIT rather than CD226, leading to cell suppression. We have generated antibodies against TIGIT that blocks ligand binding and inhibits TIGIT signaling. The clinical candidate, OMP-313M32 binds human TIGIT but not rodent and non-human primate TIGIT. Therefore, a surrogate antibody was generated for pre-clinical assessments in mice. Antibody 313R12 is an anti-mouse TIGIT antibody that can block mouse PVR ligand binding and inhibit TIGIT signaling in a manner similar to the clinical candidate OMP-313M32. 313R12 inhibited the growth of syngeneic colon and kidney tumors in immune competent mice. In some cases, anti-TIGIT antibody 313R12 caused complete tumor regression and a potent anti-tumor immune memory response as demonstrated by the lack of tumor growth upon re-challenge of mice that remained tumor-free after prior anti-TIGIT treatment. Mechanistically, anti-TIGIT antibody 313R12 was shown to induce a Th1 response and increase cytotoxic T lymphocyte (CTL) activity. By in vivo depletion of T cell populations, we have shown that CD8 T cell depletion completely abrogated the anti-TIGIT therapeutic effect, whereas CD4 T cell depletion led to partial reversal of efficacy of anti-TIGIT. Therefore, both CD4+ and CD8+ T cells are critical for anti-TIGIT-mediated immune responses. Using mice reconstituted with human hematopoietic stem cells, we also demonstrated that the clinical candidate OMP-313M32 inhibits patient-derived melanoma tumor growth. Taken together, these data demonstrate that anti-TIGIT therapy suppresses tumor growth and generates long-term immunological memory against multiple tumors. Citation Format: Angie Inkyung Park, Minu Srivastava, Erin Mayes, Hyun-Bae Jie, Rui Yun, Christopher Murriel, Ming-hong Xie, Andrew Lam, May Ji, Fumiko Axelrod, Jorge Monteon, John Lewicki, Tim Hoey, Austin Gurney. Antibody against TIGIT (T cell immunoreceptor with Ig and ITIM domains) induces anti-tumor immune response and generates long-term immune memory [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2003. doi:10.1158/1538-7445.AM2017-2003
In vitro analysis of integrin mediated adhesion, migration, and signaling (2019)

Integrins are cellular adhesion receptors whose functions are critical to the progression of solid tissue cancers. The research described here involves four projects aimed at understanding how integrins modulate key elements of carcinogenesis, (adhesion and migration), on laminin basal lamina proteins; In order to carry out these studies, a novel fluorescence based protocol for quantifying cell migration towards a bound substrate was developed (Chapter 2). This method is more reliable, efficient, and informative than currently available protocols. I demonstrate its use as a screen for migration-blocking chemotherapeutic drugs; The small heat shock protein 27 (HSP27) is found to be over-expressed in many mammary carcinomas and can be an effective prognosticator of disease recurrence following treatment. The mechanisms for this action of HSP27 are not fully understood. In chapter 3, I demonstrate that over-expressed and activated HSP27 enhances migration towards laminin-5 in breast carcinoma cells through an intracellular signaling pathway involving mitogen activated protein kinase (MAPK/ERK 1/2). In addition, non-activated HSP27 in the same cells confers resistance to a subset of drugs that would halt migration; In a screen of drugs that block the function of specific intracellular signaling molecules, it was found that an inhibitor of G-protein mediated signaling blocked the integrin induced migration of breast epithelial cells on laminin-5. I demonstrated in chapter 4 that pro-migratory signaling cascades stimulated by the beta1 class of integrins are inhibited specifically by interruption of Galphai and not Galphas heterotrimeric G-protein isoforms. Furthermore, beta1 stimulation caused an increase of an intracellular G-protein effector (cAMP). Artificial manipulation of CAMP mimicked the effects of beta1 stimulation on migration of these cells. These data suggested for the first time that G-proteins function in integrin stimulated signal cascades; Because most cells express several types of integrins simultaneously, in chapter 5 I constructed a model whereby the contribution of individual integrin types to the net effect of integrin engagement could be analyzed. For this I demonstrated that intracellular calcium flux can be used as a reliable downstream marker of integrin stimulated signaling cascades, and that laminin-1 is a good model substrate for stimulating a variety of integrin subtypes. Next I describe the production and testing of six recombinant fragments of laminin-1 for the purpose of producing activating ligands of specific laminin-1 binding integrins.
Evaluating Igusa functions (2014)

The moduli space of principally polarized abelian surfaces is parametrized by three Igusa functions. In this article we investigate a new way to evaluate these functions by using the Siegel Eisenstein series. We explain how to compute the Fourier coefficients of certain Siegel modular forms using classical modular forms of half-integral weight. One of the results in this paper is an explicit algorithm to evaluate the Igusa functions to a prescribed precision.
Discovery of a Potent Chloroacetamide GPX4 Inhibitor with Bioavailability to Enable Target Engagement in Mice, a Potential Tool Compound for Inducing Ferroptosis In Vivo (2023)

Compounds that inhibit glutathione peroxidase 4 (GPX4) hold promise as cancer therapeutics in their ability to induce a form of nonapoptotic cell death called ferroptosis. Our research identified <b>24</b>, a structural analog of the potent GPX4 inhibitor RSL3, that has much better plasma stability (<i>t</i><sub>1/2</sub> > 5 h in mouse plasma). The bioavailability of <b>24</b> provided efficacious plasma drug concentrations with IP dosing, thus enabling <i>in vivo</i> studies to assess tolerability and efficacy. An efficacy study in mouse using a GPX4-sensitive tumor model found that doses of <b>24</b> up to 50 mg/kg were tolerated for 20 days but had no effect on tumor growth, although partial target engagement was observed in tumor homogenate.
Real time volumetric intrasurgical optical coherence tomography with 4D visualization of surgical maneuvers (Conference Presentation) (2020)

Ophthalmic surgery is typically performed through an en-face only surgical microscope that provides limited depth information. This work introduces a high speed (400 kHz) microscope integrated optical coherence tomography (MIOCT) system which provides real time volumetric “4D” visualization via a heads-up stereoscopic display. The MIOCT system provides sub retinal visualization of tools and enables surgeons to perform delicate manipulation of retinal structures during mock surgical procedures. Following these mock surgical procedures in porcine eyes, this system will be readily translated into human ophthalmic microsurgery.
An Improved System for the Aqueous Lipshutz–Negishi Cross‐Coupling of Alkyl Halides with Aryl Electrophiles (2015)

Abstract The development of a palladacyclic precatalyst supported by a new biaryl(dialkyl)phosphine ligand (VPhos) in combination with octanoic acid/sodium octanoate as a simple and effective surfactant system provided an improved catalyst system for the rapid construction of a broad spectrum of alkylated scaffolds from alkyl zinc reagents generated in situ.
Optimal Composite Material for Low Cost Fabrication of Large Composite Aerospace Structures using NASA Resins or POSS Nanoparticle Modifications (2006)

Thermoplastic laminates in situ consolidated via tape or tow placement require full mechanical properties. Realizing full properties requires resin crystallinity to be controlled - partial crystallinity leads to unacceptably low laminate compression properties. There are two approaches: utilize an amorphous matrix resin; or place material made from a semi-crystalline resin featuring kinetics faster than the process. In this paper, a matrix resin evaluation and trade study was completed with commercial and NASA amorphous polyimides on the one hand, and with PEKK mixed with POSS nanoparticles for accelerated crystallinity growth on the other. A new thermoplastic impregnated material, 6 mm wide (0.25-in) AS-4 carbon/LaRC(TradeMark)8515 dry polyimide tow, was fabricated. Since LaRC(TradeMark)8515 is fully amorphous, it attains full properties following in situ consolidation, with no post processing required to build crystallinity. The tow in situ processing was demonstrated via in situ thermoplastic filament winding it into rings.
LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures (2014)

For the Library of Integrated Network-based Cellular Signatures (LINCS) project many gene expression signatures using the L1000 technology have been produced. The L1000 technology is a cost-effective method to profile gene expression in large scale. LINCS Canvas Browser (LCB) is an interactive HTML5 web-based software application that facilitates querying, browsing and interrogating many of the currently available LINCS L1000 data. LCB implements two compacted layered canvases, one to visualize clustered L1000 expression data, and the other to display enrichment analysis results using 30 different gene set libraries. Clicking on an experimental condition highlights gene-sets enriched for the differentially expressed genes from the selected experiment. A search interface allows users to input gene lists and query them against over 100 000 conditions to find the top matching experiments. The tool integrates many resources for an unprecedented potential for new discoveries in systems biology and systems pharmacology. The LCB application is available at http://www.maayanlab.net/LINCS/LCB. Customized versions will be made part of the http://lincscloud.org and http://lincs.hms.harvard.edu websites.
Reduced Mode Sapphire Optical Fiber and Sensing System (2019)

This is the final technical report for the Virginia Tech Center for Photonics Technology (VT-CPT) research project entitled “Reduced Mode Sapphire Optical Fiber and Sensing System”. The objective of the five-year effort was to develop a low modal volume (LMV) single crystal sapphire fiber and demonstrate its advantages in current state-of-the-art sapphire-based temperature sensors and in novel distributed ultra-high temperature sensing systems. The project, sponsored by the Crosscutting Research Program, began in 2014 and had the original goal of developing the next generation of harsh environment sensing systems. After successfully completing the original scope of the award, the project was expanded and extended to allow for the development of harsh environment packaging and testing of a prototype sensor system. These novel fiber optic sensing technologies provide real-time, accurate, and reliable temperature measurements at distributed locations in existing coal-fueled electricity generating units to improve the overall performance, reliability, and flexibility of the nation’s coal-fired power plant fleet. In the final year (2018) of the project, prototype sensing systems were successfully deployed and operated in small commercial coal and natural gas fired boilers at the Virginia Tech Power Plant. The harsh environment quasi-distributed temperature sensing technology was advanced from a (Technology Readiness Level) TRL=1 to a TRL=7 by demonstrating the full validation of the sensing system prototype in a relevant industrial environment. The real-time, accurate and reliable monitoring of temperatures at distributed locations is expected to lower operating costs by allowing more accurate measurement of the harsh conditions inside a boiler system to better control its operation. The technologies developed by Virginia Tech’s Center for Photonics Technology will support the mission of the National Energy Technology Laboratory (NETL) to advance energy options to fuel our economy, strengthen our security, and improve the environment.
Supplementary Figure 1 from Novel Target for Peptide-Based Imaging and Treatment of Brain Tumors (2023)

&lt;p&gt;PDF - 49K, MDGI expression increased binding of the CooP phage.&lt;/p&gt;
Microstructural differences of fibrin and self-assembling peptide hydrogels in dental pulp stem cell behavior: the effect of chlorite-oxidized oxyamylose (2020)

Abstract Tailored hydrogels mimicking the native extracellular environment could aid in overcoming the high variability in regenerative endodontics outcomes. This study aimed to evaluate the effect of the chemokine-binding and antimicrobial polymer, chlorite-oxidized oxyamylose (COAM), on the microstructural properties of fibrin and self-assembling peptide (SAP) hydrogels. Further, to assess the influence of the microstructural differences between the hydrogels on the in vitro behavior of dental pulp stem cells (DPSCs).Structural and mechanical characterization of the hydrogels with and without COAM was performed by atomic force microscopy and scanning electron microscopy to characterize their microstructure (roughness and fiber length, diameter, straightness and alignment) and by nanoindentation to measure their stiffness (elastic modulus). DPSCs were encapsulated in hydrogels with and without COAM. Cell viability and circularity was determined using confocal microscopy imaging, and proliferation was determined using DNA quantification. Inclusion of COAM did not alter the microstructure of the fibrin hydrogels at the fiber level, while affecting the SAP hydrogel microstructure (homogeneity) leading to fiber aggregation. The stiffness of the SAP hydrogels was 7-fold higher than the fibrin hydrogels. The viability and attachment of DPSCs and DNA content was significantly higher in fibrin hydrogels than in SAP hydrogels. The microstructural stability after COAM inclusion and the favorable DPSCs’ response observed in fibrin hydrogels suggest this system as a promising carrier for COAM and for application in endodontic regeneration.
Nanostrukturierte Koordinationspolymere (2011)

Nichtkovalente Nanoröhren: Koordinationspolymere sind eine faszinierende Klasse von Materialien, bei denen sich klassische und moderne Koordinationschemie zur oftmals komplexen Bildung großer supramolekularer Strukturen vereinen (siehe Bild). Ein eindrucksvolles Beispiel ist die Bildung von Nanoröhren aus Koordinationspolymeren, deren Struktur entscheidend von der Art des Azinliganden abhängt.
Development of Mirror Symmetric Type Rehabilitation Support System Using Passive Force Display (2020)

Rehabititation training includes one-handed exercise training and two-handed exercise training. Although many one-handed rehabilitation robots have been developed, the development of two-handed rehabilitation robots is scarce. A two-handed rehabilitation robot is needed to support the paralyzed arm with the non-paralyzed arm. In this paper, we report on the development of mirror symmetric type rehabilitation support system using passive force display as two-handed rehabilitation robot.
Intravascular Coagulation Associated With Pneumococcal Bacteremia and Symmetrical Peripheral Gangrene (1970)

Peripheral gangrene was recently described as an unusual complication of bacteremia caused by staphylococci and streptococci.<sup>1</sup>Results of blood coagulation studies performed on these patients were consistent with a consumption coagulopathy.<sup>1</sup>This communication concerns a patient in whom hypotension, purpura, and peripheral symmetric gangrene developed as consequences of bacteremia by another gram-positive organism, the pneumococcus. Tests of blood-clotting function have not been included in the few previous reports describing patients with pneumococcal bacteremia complicated by peripheral gangrene.<sup>2,3</sup>Coagulation analyses were performed on the patient described here, and a consumption coagulopathy was documented. <h3>Patient Summary</h3> A 32-year-old housewife had undergone a splenectomy in 1957 because of abdominal trauma. She was well until the morning of March 5, 1969, when she had a sudden, shaking chill followed by temperature of 104 F (40 C), faintness, vomiting, and diarrhea. During the following afternoon the patient complained of aching in the
Concave Cubic Gold Nanocrystals with High-Index Facets (2010)

A new class of gold nanostructures, concave nanocubes, enclosed by 24 high-index {720} facets, have been prepared in a monodisperse fashion by a modified seed-mediated synthetic method. The Cl(-) counterion in the surfactant plays an essential role in controlling the concave morphology of the final product. The concave nanocubes exhibit higher chemical activities compared with low-index {111}-faceted octahedra.
The GP’s role in promoting winter wellness (2017)

Every year in the UK there is a seasonal peak in morbidity and mortality during the coldest months. GPs have an important role in promoting winter wellness and we would like to advocate GPs placing more emphasis on a proactive approach designed to reduce risk among vulnerable individuals and families. Although some of the activities we already undertake contribute to this goal, others fall short, and few of us promote winter wellness in a coordinated way across our health and social care community. To maximise our effectiveness, primary care teams should be aware of the modifiable risk factors for excess winter mortality and morbidity; and actively manage these as part of planned as well as opportunistic care.