gebhart/patrepeval huggingface dataset:
Simultaneous gastrointestinal stromal tumor (GIST) and desmoid fibromatosis (DF) (2009)

10568 Background: Desmoid Fibromatosis (DF) is one of a group of rare fibrous tissue proliferations (2–4 cases per year per million) which tend to be locally aggressive but have no propensity for metastasis. Gastrointestinal Stromal Tumor (GIST) is the most common mesenchymal tumors of the gastrointestinal tract and also rare (15–20 cases per year per million). Anecdotal reports of individuals with both diseases led us to investigate the number of patients at our institute with both types of cancer and their clinical, and histopathologic features. Methods: We identified four cases of GIST associated with DF at the M. D. Anderson Cancer Center between 1995 and 2008 using an IRB-approved protocol. Two more cases were identified from the patient database at the University of Helsinki. Results: Our patients were three men and three women aged from 39 to 66. Two patients were African Americans and 3 were Caucasians. In 5 cases, the GIST was diagnosed prior to the DF while one case had both tumors synchronous at presentation. The primary site of the GIST was gastric in 4 cases and the others were jejunal and mesenteric. Three patients had their DF occur in the surgical incision site mimicking a recurrence of GIST. The 3 others were intra-abdominal DF. There were no cases of DF occurring outside of the GI tract. One GIST patient was metastatic at presentation and one developed metastasis before DF was diagnosed. In 5 cases, imatinib mesylate was administered to the patients with partial response. In all cases KIT expression was observed immunohistochemically for GIST and but not for DF. Additionally, all cases of DF but no cases of GIST were found to have beta-catenin expression by immunohistochemistry. Conclusions: Our findings suggest that concurrent DF may occur in patients with GIST. Additionally, DF may mimic the recurrence of GIST or imatinib resistance. The association of these two sarcomas should be further explored. No significant financial relationships to disclose.
ChemInform Abstract: Intramolecular sp3 Functionalization of Cyclopropyl α‐Amino Acid‐Derived Benzamides. (2016)

ChemInformVolume 47, Issue 20 Heterocyclic Compounds ChemInform Abstract: Intramolecular sp3 Functionalization of Cyclopropyl α-Amino Acid-Derived Benzamides. Carolyn L. Ladd, Carolyn L. Ladd Dep. Chem., Univ. Montreal, Montreal, Que. H3C 3J7, Can.Search for more papers by this authorAudrey V. Belouin, Audrey V. Belouin Dep. Chem., Univ. Montreal, Montreal, Que. H3C 3J7, Can.Search for more papers by this authorAndre B. Charette, Andre B. Charette Dep. Chem., Univ. Montreal, Montreal, Que. H3C 3J7, Can.Search for more papers by this author Carolyn L. Ladd, Carolyn L. Ladd Dep. Chem., Univ. Montreal, Montreal, Que. H3C 3J7, Can.Search for more papers by this authorAudrey V. Belouin, Audrey V. Belouin Dep. Chem., Univ. Montreal, Montreal, Que. H3C 3J7, Can.Search for more papers by this authorAndre B. Charette, Andre B. Charette Dep. Chem., Univ. Montreal, Montreal, Que. H3C 3J7, Can.Search for more papers by this author First published: 27 April 2016 https://doi.org/10.1002/chin.201620160Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume47, Issue20April, 2016 RelatedInformation
Algorithmes géométriques, théorie et pratique (2004)

Ce cours traite de la geometrie algorithmique par la triangulation de Delaunay et les diagrammes de Voronoi. 
Ce cours est accompagne d'une demonstration des fonctionnalites de CGAL.
Le but de ce module est de presenter les grandes tendances de la geometrie algorithmique actuelle, et en particulier son evolution vers ce que nous appellerons le calcul geometrique. Apres plusieurs annees ou la geometrie algorithmique a connu des developpements plutot theoriques, une des grandes questions actuelles est : Comment passer a des algorithmes effectivement programmes ? On explorera les principaux problemes de la geometrie et leurs solutions. On regardera les algorithmes classiques (theoriques) mais aussi les problemes plus pratiques poses par les incertitudes numeriques ou la complication excessive de ces algorithmes classiques. On utilisera la bibliotheque CGAL (www.cgal.org) pour passer a la pratique.
Les domaines d'applications sont extremement varies allant de la modelisation des sites archeologiques au placement d'antennes dans un reseau de telephonie mobile en passant par la simulation d'ecoulement de fluides.
System Design Issues for Wireless Communication in a Multi-Processor Computer: Carrier Acquisition Phase Noise and Modulation Constellation (2003)

Abstract : The purpose of this study is to investigate system-level design issues for a wireless communication system that links the central processing units (CPUs) in an advanced multi-processor computer system. The three primary requirements for the wireless communication system are that it must (1) support dynamic reconfigurability of the CPUs, (2) achieve very high data rates (on the order of 100 Gbps system capacity), and (3) achieve extremely low latencies (on the order of 10 nanoseconds). These requirements differ significantly from commercial wireless communication networks for voice and data. The objective of this effort is to identify and quantify the critical communication system design issues and trade-xoffs that will enable the successful achievement of the stringent requirements on dynamic reconfigurability, data rate, and latency.
Phase Segregation of Polymethylsilsesquioxane in Antireflection Coatings (2011)

We herein describe the preparation and characterization of a phase-separated fluorinated polymethylsilsesquioxane (PMSQ), which may be used as an antireflective coating. The results of FTIR analysis showed that when PMSQ is synthesized from methyltrimethoxysilane (MTMS), it exists mostly in the form of a cage structure. Its reflectivity of normally incident light (R) may be reduced from 3.9 to 0.9% by grafting 1H,1H,2H,2H-perfluorooctyltriethoxysilane (FTES) by means of a sol–gel process. In the study described herein, the minimum reflectivity of PMSQ was lowered to less than 1% by coating it with a single layer of fluorinated polymethylsilsesquioxane, through phase segregation of PMSQ and FTES that took place during film formation. The RI of PMSQ at 550 nm was also reduced from 1.51 to 1.42 by heating at 80 °C for 30 min, a temperature suitable for substrates, such as plastics, that have low heat resistance. Wetting and adhesion to substrates were both improved by the additional grafting of tetraethoxysilane (TEOS), again by means of a sol–gel process. Results of solid-state 29Si NMR and GPC showed increases in T3, Q3, Q4, and the molecular weight, which signal the effective grafting of both the TEOS and the FTES on the PMSQ. Results from energy-dispersive X-ray spectroscopy (EDX) show that the quantity of fluorine atoms at the surface of the PMSQ film increased from 0 to 22%, providing the evidence of the phase segregation within the PMSQ film. When FTES is used, we found an increase in the water contact angle from 92° to 108°, which indicated that the hydrophobicity at the PMSQ film surface increased by increasing the FTES content from 0 to 100 wt %, using the weight of MTMS as 100%.
EUS-Guided Fine-Needle Aspiration of Suspected Hilar Cholangiocarcinoma in Potentially Operable Patients with Negative Brush Cytology (2004)

These results suggest that EUS-FNA is of value as a new, less-invasive approach for tissue diagnosis of hilar strictures of unknown cause. It was technically feasible without significant risks, when other diagnostic tests were inconclusive and was able to change preplanned management in about half of the patients.
Compartmentalization of Total and Virus-Specific Tissue-Resident Memory CD8+ T Cells in Human Lymphoid Organs (2016)

Disruption of T cell memory during severe immune suppression results in reactivation of chronic viral infections, such as Epstein Barr virus (EBV) and Cytomegalovirus (CMV). How different subsets of memory T cells contribute to the protective immunity against these viruses remains poorly defined. In this study we examined the compartmentalization of virus-specific, tissue resident memory CD8+ T cells in human lymphoid organs. This revealed two distinct populations of memory CD8+ T cells, that were CD69+CD103+ and CD69+CD103-, and were retained within the spleen and tonsils in the absence of recent T cell stimulation. These two types of memory cells were distinct not only in their phenotype and transcriptional profile, but also in their anatomical localization within tonsils and spleen. The EBV-specific, but not CMV-specific, CD8+ memory T cells preferentially accumulated in the tonsils and acquired a phenotype that ensured their retention at the epithelial sites where EBV replicates. In vitro studies revealed that the cytokine IL-15 can potentiate the retention of circulating effector memory CD8+ T cells by down-regulating the expression of sphingosine-1-phosphate receptor, required for T cell exit from tissues, and its transcriptional activator, Kruppel-like factor 2 (KLF2). Within the tonsils the expression of IL-15 was detected in regions where CD8+ T cells localized, further supporting a role for this cytokine in T cell retention. Together this study provides evidence for the compartmentalization of distinct types of resident memory T cells that could contribute to the long-term protection against persisting viral infections.
Analysis of design alternatives for reverse proxy cache providers (2004)

Reverse proxy caches are used to provide scalability and improved latency to popular sites on the Web. In this paper we provide analytical performance models for distributed reverse proxy cache architectures, and study the trade-offs between various design alternatives. Specifically, we consider static and dynamic assignment of proxy cache nodes to Web sites, with different levels of sharing of proxy caches among Web sites. Innovative modeling contributions have been introduced to handle real design constraints, such as bounded cache size and bounded processing power, and different characteristics related to the hosted objects, including reference rates, popularity distributions and update rates. In the analysis we have modeled both system steady state as well as transient interaction between proxy sites and Web sites. We have found different trade-offs between various design alternatives depending on characteristics of the Web site workloads.
2P1-K08 Vibration Suppression of Power-Amplifying Master-Slave Systems Using Nonlinear Filtering and Phase-Lead Compensation(New Control Theory and Motion Control) (2013)

It has been known that the power-amplifying master-slave control architecture, which has been proposed by Kanaoka (2009), produces undesirable vibration especially when the force sensor is firmly grasped. This vibration is presumably caused by the phase lag and the dead time in the closed loop. This paper presents some techniques for vibration suppression by using nonlinear filters and phase lead compensators.
Therapeutic Vaccination against Murine Lymphoma by Intratumoral Injection of Naive Dendritic Cells (2005)

Dendritic cells are potent antigen-presenting cells that can induce both immune responses and tolerance depending on their state of activation. Immunologic tolerance to established tumors is a major impediment for the development of effective cancer immunotherapy. Dendritic cells may be deficient in number or in function at the tumor site. To address this problem, we evaluated the ability of immature naïve dendritic cells to induce an antitumor immune response when injected directly into a murine B-cell lymphoma. Mice with advanced transplanted syngeneic tumor were given intratumoral injections of bone marrow-derived dendritic cells. Intratumoral dendritic cell injection alone had no antitumor effect. Systemic chemotherapy alone resulted in only transient tumor regression. However, the intratumoral injection of dendritic cells after chemotherapy led to complete, long-term tumor regression in the majority of treated mice. This dendritic cell-mediated antitumor effect was systemic, resulting in simultaneous elimination of the tumor at second uninjected sites. In addition, it resulted in long-term memory with resistance to tumor rechallenge. Both CD4+ and CD8+ T cells are necessary for the antitumor effect. Furthermore, tumors that occasionally recurred in mice with initial complete tumor regression could be retreated by the same combined chemoimmunotherapy approach. These results show that immunotherapy can succeed in the setting of advanced lymphoma if dendritic cells are restored and loaded with tumor antigens in situ at a single tumor site.
Enhanced nerve cell proliferation and differentiation on electrically conductive scaffolds embedded with graphene and carbon nanotubes (2020)

Conduits that promote nerve regeneration are currently of great medical concern, particularly when gaps exist between nerve endings. To address this issue, our laboratory previously developed a nerve conduit from biodegradable poly(caprolactone fumarate) (PCLF) that supports peripheral nerve regeneration. The present study improves upon this work by further developing an electrically conductive, positively charged PCLF scaffold through the incorporation of graphene, carbon nanotubes (CNTs), and [2-(methacryloyloxy)ethyl]trimethylammonium chloride (MTAC) (PCLF-Graphene-CNT-MTAC) using ultraviolet (UV) induced photocrosslinking. Scanning electron microscopy, transmission electron microscopy, and atomic force microscopy were used to assess the incorporation of CNTs and graphene into PCLF-Graphene-CNT-MTAC scaffolds, which displayed enhanced surface roughness and reduced electrochemical impedance when compared to neat PCLF. Scaffolds with these surface modifications also showed improved growth and differentiation of rat pheochromocytoma 12 cells in vitro, with enhanced cell growth, neurite extension, and cellular migration. Furthermore, an increased number of neurite protrusions were observed when the conduit was electrically stimulated. These results show that the electrically conductive PCLF-Graphene-CNT-MTAC nerve scaffolds presented here support the cellular behaviors that are critical for nerve regeneration, ultimately making this material an attractive candidate for regenerative medicine applications.
Expression of a Major Plant Allergen as Membrane-Anchored and Secreted Protein in Human Cells with Preserved T Cell and B Cell Epitopes (2011)

Secreted and membrane-anchored Phl p 5 expressed in human cells preserved B cell as well as T cell epitopes and may be used to develop and test various cell-based strategies for allergen-specific immunomodulation and to delineate the tolerance mechanisms involved therein.
Chemotherapy of cancer of the head and neck (1973)

Single agent chemotherapy employing either hydroxyurea, cyclophosphamide, bleomycin, or methotrexate has been reported to produce objective remissions in 30–40% of patients with advanced epidermoid carcinoma of the head and neck region. Responses are usually incomplete with remission durations of a few months. Methotrexate, the most extensively studied agent, appears to be most effective when used in an intermittent (every 4–7 day) dosage schedule or when used in high dosage followed by leucovorin “rescue.” In some reports, the intra-arterial administration of these drugs achieved better response rates, but the value of this approach is diminished by the high frequency of lesions that extend beyond the infused arterial supply and the high complication rate of catheterization procedures. Initial studies with dichlo-romethotrexate, an equipotent analog of methotrexate which is hydroxylated to an inactive form by the liver, suggest that intra-arterial use of this unique compound may be of value. Several studies indicate that the use of drugs in combination with radiotherapy may achieve greater tumor regression and longer response durations than radiotherapy alone; however, more controlled studies will be needed to establish this. The availability of effective agents with diverse mechanisms of action strongly suggests that major gains in chemotherapy of these tumors will be made in the next decade using combinations of drugs.
The Johns Hopkins-Nanjing Center for Synthetic Genomics (2012)

Johns Hopkins has pioneered a very ambitious synthetic biology project over the last few years, namely to design and synthesize the first re-coded eukaryotic genome (Sc2.0 project). Arguably, engineering a synthetic genome is the most complicated engineering project a human being has ever undertaken, but it is clear that we will have a unique opportunity to explore many profound questions in the process of designing, building and analyzing this synthetic genome. Additionally, this Center will build on our educational success with the Build A Genome course, which uses undergraduate power to produce the starting materials, called building blocks, for the project. The educational and scientific value of this project has attracted the attention of several top Chinese universities, and in particular we have been in discussions with four of them to launch an international initiative around the Sc2.0 project in 2011. The collaboration will lead to new interdisciplinary undergraduate courses, student/scholar exchanges between Hopkins and China, and to create a new research institute in Nanjing, which fits very well with the Yeung Center’s scope and mission. Altogether, our Chinese partners have secured over 8 million US dollars and other valuable assets from the Chinese government and funding agencies. However due to the source of the funding, these funds cannot be spent outside China. Therefore, we are requesting critically needed support for the home initiative from the Johns Hopkins Yeung Center to keep the Sc2.0 project running and innovating at Johns Hopkins, and specifically to support a rich collaboration between Hopkins and top Chinese Universities.
Reverse Phase Thin Layer Chromatography of Some Aroclors, Halowaxes, and Pesticides (1973)

Abstract The components of Aroclors® 1232, 1248, 1254, and 1260; Halowaxes® 1099, 1013, and 1014; and several chlorinated pesticides are resolved by reverse phase thin layer chromatography (RPTLC), which permits component separation by partition between a nonpolar stationary phase and a polar mobile phase. Rf values of resulting spots were calculated for 2 of 4 new solvent systems (mobile phases). RPTLC patterns were reproducible and characteristic of each material examined. The spots were recovered from the plates and characterized by gas-liquid chromatography (GLC) and/or GLC-mass spectrometry. In some cases, single GLC peaks of Aroclor standards were resolved into more than one component by RPTLC, whereas some RPTLC spots of Halowaxes were resolved into as many as 4 GLC peaks. The analysis of environmental residues of chlorinated compounds was facilitated by this technique.
Quantitative Profiling of Endogenous Fat-Soluble Vitamins and Carotenoids in Human Plasma Using an Improved UHPSFC-ESI-MS Interface (2017)

Analytical solutions enabling the quantification of circulating levels of liposoluble micronutrients such as vitamins and carotenoids are currently limited to either single or a reduced panel of analytes. The requirement to use multiple approaches hampers the investigation of the biological variability on a large number of samples in a time and cost efficient manner. With the goal to develop high-throughput and robust quantitative methods for the profiling of micronutrients in human plasma, we introduce a novel, validated workflow for the determination of 14 fat-soluble vitamins and carotenoids in a single run. Automated supported liquid extraction was optimized and implemented to simultaneously parallelize 48 samples in 1 h, and the analytes were measured using ultrahigh-performance supercritical fluid chromatography coupled to tandem mass spectrometry in less than 8 min. An improved mass spectrometry interface hardware was built up to minimize the post-decompression volume and to allow better control of the chromatographic effluent density on its route toward and into the ion source. In addition, a specific make-up solvent condition was developed to ensure both analytes and matrix constituents solubility after mobile phase decompression. The optimized interface resulted in improved spray plume stability and conserved matrix compounds solubility leading to enhanced hyphenation robustness while ensuring both suitable analytical repeatability and improved the detection sensitivity. The overall developed methodology gives recoveries within 85-115%, as well as within and between-day coefficient of variation of 2 and 14%, respectively.
Complement Activation by Neutrophil Granulocytes (2008)

Complement plays a vital role in the body's defence systems. Cardiopulmonary bypass induces a detrimental inflammatory reaction in which the complement system is known to participate through direct effects as well as through activation of neutrophils, platelets and endothelial cells. On the other hand, it has been suggested that in the setting of cardiopulmonary bypass, complement may be activated by neutrophils, perhaps due to fragmentation caused by the heart-lung machine. We therefore investigated whether intact or fragmented neutrophils were able to activate the complement system, and whether neutrophil-platelet interaction could influence such complement activation. Lepirudin-anticoagulated plasma was incubated at 37 degrees C with resting or activated intact neutrophils or neutrophils combined with platelets, or increasing amounts of fragmented neutrophils. Complement activation was evaluated by measurement of C1rs-C1 inhibitor complexes, C4bc, C3bBbP, C3bc, C5a and sC5b-9. We found significant activation of complement only by unphysiological doses of fragmented neutrophils or supernatant from fragmented neutrophils, consistent with a limited clinical significance related to neutrophil destruction during cardiopulmonary bypass. Unstimulated neutrophils induced C3bPBb formation but little formation of other activation products, indicating an increased C3 hydrolysis which was kept under control by regulatory mechanisms. Neutrophils and platelets combined increased classical activation and decreased alternative activation, similar to the findings with platelets alone. Our data confirm that in the setting of acute neutrophil fragmentation or activation, complement activation is much more important in the inflammatory network as an event upstream to neutrophil activation than vice versa.
Alloimmunization Against Well Defined Polymorphic Major Histocompatibility or Class I MHC Transfected L Cells Antigens Can Prevent Poly IC Induced Fetal Death in Mice (1995)

These results indicate that defined MHC antigens can mediate fetal protection from induced fetal resorption, and suggest that one driving force in promoting MHC antigen polymorphism in mammals is their capacity to confer protection from NK mediated fetal demise.