gebhart/patrepeval huggingface dataset:
High-density, targeted monitoring of tyrosine phosphorylation reveals activated signaling networks in human tumors (2020)

Abstract Tyrosine phosphorylation (pTyr) plays a pivotal role in signal transduction and is commonly dysregulated in cancer. As a result, profiling tumor pTyr levels may reveal therapeutic insights critical to combating disease. Existing discovery and targeted mass spectrometry-based methods used to monitor pTyr networks involve a tradeoff between broad coverage of the pTyr network, reproducibility in target identification across analyses, and accurate quantification. To address these limitations, we developed a targeted approach, termed “SureQuant pTyr,” coupling low input pTyr enrichment with a panel of isotopically labeled, tyrosine phosphorylated internal standard (IS) peptides. Using internal standard guided acquisition, the real-time detection of IS peptides during the analysis initiates the sensitive and selective quantitation of endogenous pTyr targets. This framework allows for reliable quantification of several hundred commonly dysregulated pTyr targets with high quantitative accuracy, enhances target detection success rates, and improves the robustness and usability of targeted acquisition. We establish the clinical applicability of SureQuant pTyr by profiling pTyr signaling levels in human colorectal tumors using minimal sample input, characterizing patient specific oncogenic driving mechanisms. While in some cases pTyr profiles align with previously reported proteomic, genomic, and transcriptomic molecular characterizations, we highlight instances of new insights gained using pTyr characterization and emphasize the complementary nature of pTyr measurements with traditional biomarkers for improving patient stratification and identifying therapeutic targets. The turn-key nature of this approach opens the door to rapid and reproducible pTyr profiling in research and clinical settings alike and enable pTyr-based measurements for applications in precision medicine. Summary A targeted, mass spectrometry-based method, termed “SureQuant pTyr,” enables highly sensitive and reproducible profiling of tyrosine phosphorylation levels in human colorectal tumors and reveals dysregulated signaling networks for enhanced tumor characterization and biomarker identification.
Oral mucositis (2010)

Chapter 15 discusses mucositis, one of the most common, debilitating, and disruptive toxicities of chemotherapy and radiation therapy (radiotherapy) used for the treatment of malignant disease. Whilst mucositis may occur in virtually any segment of the gastrointestinal tract, it has been best documented and studied in its oral manifestation.
An integrated functional genomics approach identifies the regulatory network directed by brachyury (<i>T</i>) in chordoma (2012)

Chordoma is a rare malignant tumour of bone, the molecular marker of which is the expression of the transcription factor, brachyury. Having recently demonstrated that silencing brachyury induces growth arrest in a chordoma cell line, we now seek to identify its downstream target genes. Here we use an integrated functional genomics approach involving shRNA-mediated brachyury knockdown, gene expression microarray, ChIP-seq experiments, and bioinformatics analysis to achieve this goal. We confirm that the T-box binding motif of human brachyury is identical to that found in mouse, Xenopus, and zebrafish development, and that brachyury acts primarily as an activator of transcription. Using human chordoma samples for validation purposes, we show that brachyury binds 99 direct targets and indirectly influences the expression of 64 other genes, thereby acting as a master regulator of an elaborate oncogenic transcriptional network encompassing diverse signalling pathways including components of the cell cycle, and extracellular matrix components. Given the wide repertoire of its active binding and the relative specific localization of brachyury to the tumour cells, we propose that an RNA interference-based gene therapy approach is a plausible therapeutic avenue worthy of investigation.
Initial performance evaluation of spatial modulation OFDM in LTE-based systems (2011)

In this paper, we explore the spatial modulation (SM) orthogonal frequency division multiplexing (SM-OFDM) transmission to achieve good performance in Long Term Evolution (LTE) based systems. For assessment purposes, the performance results of SM-OFDM systems are compared with the popular Alamouti-coded OFDM systems and vertical Bell Labs layered space-time (V-BLAST) OFDM systems. Simulation results show that SM-OFDM systems achieve better performance than other systems at low spectral efficiencies. However, at high spectral efficiencies, the performance of SM depends on a trade-off between the spatial constellation size and signal constellation size. Furthermore, the results also show that SM provides a flexible transceiver configuration, especially for an unbalanced multiple-input multiple-output (MIMO) channel.
Quantification of Methylmalonic Acid in Human Plasma with Hydrophilic Interaction Liquid Chromatography Separation and Mass Spectrometric Detection (2008)

This robust assay allows analysis of MMA in human plasma without derivatization. Sample preparation is simple and suitable for automation.
The Effect of Primary Graft Dysfunction on Survival after Lung Transplantation (2005)

Primary graft dysfunction contributes to nearly half of the short-term mortality after lung transplantation. Survivors of primary graft dysfunction have increased risk of death extending beyond the first post-transplant year.
Contrast-enhancement techniques for particle-image velocimetry (2000)

In video-based particle-image velocimetry (PIV) systems for fluid mechanics research, it is sometimes desirable to image seed particles to be smaller than a camera pixel. However, imaging to this size can lead to marginal image contrast such that significant numbers of erroneous velocity vectors can be computed, even for simple flow fields. A variety of image-enhancement techniques suitable for a low-cost PIV system that uses video cameras are examined and tested on three representative flows. Techniques such as linear contrast enhancement and histogram hyperbolization are shown to have good potential for improving the image contrast and hence the accuracy of the data-reduction process with only a 15% increase in the computational time. Some other schemes that were examined appear to be of little practical value in PIV applications. An automated shifting algorithm based on mass conservation is shown to be useful for displacing the second interrogation region in the direction of flow, which minimizes the number of uncorrelated particle images that contribute noise to the data-reduction process.
5-Fluorocytosine in DNA is a mechanism-based inhibitor of HhaI methylase (1988)

5-Fluorodeoxycytidine (FdCyd) was incorporated into a synthetic DNA polymer containing the GCGC recognition sequence of HhaI methylase to give a polymer with about 80% FdCyd. In the absence of AdoMet, poly(FdC-dG) bound competitively with respect to poly(dG-dC) (Ki = 3 nM). In the presence of AdoMet, the analogue caused a time-dependent, first-order (k = 0.05 min-1) inactivation of the enzyme. There is an ordered mechanism of binding in which enzyme first binds to poly(FdC-dG), then binds to AdoMet, and subsequently forms stable, inactive complexes. The complexes did not dissociate over the course of 3 days and were stable to heat (95 degrees C) in the presence of 1% SDS. Gel filtration of a complex formed with HhaI methylase, poly(FdC-dG), and [methyl-3H] AdoMet gave a peak of radioactivity eluting near the void volume. Digestion of the DNA in the complex resulted in a reduction of the molecular weight to the size of the methylase, and the radioactivity in this peak was shown to be associated with protein. These data indicate that the complexes contain covalently bound HhaI methylase, poly(FdC-dG), and methyl groups and that 5-fluorodeoxycytidine is a mechanism-based inactivator of the methylase. By analogy with other pyrimidine-modifying enzymes and recent studies on the mechanism of HhaI methylase (Wu & Santi, 1987), these results suggest that an enzyme nucleophile attacks FdCyd residues at C-6, activating the 5-position for one-carbon transfer.(ABSTRACT TRUNCATED AT 250 WORDS)
Real‐time cardiac MRI at 3 tesla (2004)

Real-time cardiac and coronary MRI at 1.5T is relatively "signal starved" and the 3T platform is attractive for its immediate factor of two increase in magnetization. Cardiac imaging at 3T, however, is both subtly and significantly different from imaging at 1.5T because of increased susceptibility artifacts, differences in tissue relaxation, and RF homogeneity issues. New RF excitation and pulse sequence designs are presented which deal with the fat-suppression requirements and off-resonance issues at 3T. Real-time cardiac imaging at 3T is demonstrated with high blood SNR, blood-myocardium CNR, resolution, and image quality, using new spectral-spatial RF pulses and fast spiral gradient echo pulse sequences. The proposed sequence achieves 1.5 mm in-plane resolution over a 20 cm FOV, with a 5.52 mm measured slice thickness and 32 dB of lipid suppression. Complete images are acquired every 120 ms and are reconstructed and displayed at 24 frames/sec using a sliding window. Results from healthy volunteers show improved image quality, a 53% improvement in blood SNR efficiency, and a 232% improvement in blood-myocardium CNR efficiency compared to 1.5T.
Dynamic resource allocation for quality of service on a PON with home networks (2000)

Earlier efforts on optical access concentrated on the design of PONs for the collection and distribution portion of the access network. A possible evolution scenario for these types of access networks could be the SuperPON system. The SuperPON system exploits all possible upgrades of an FSAN APON system. In these networks the optical hardware is very simple, but a media access control protocol is needed for upstream traffic control. Even so, the role of communications is already well established in the office environment, thanks to networking innovations such as the Ethernet LAN. With the development of cheap, affordable broadband communications and the increasing complexity of consumer goods, it seems natural to extend the network into homes. As home area network application ever increases, we consider connectivity between the access network and the home network, which generates multiple traffic, in order to design a MAC protocol over the SuperPON access network with home networks. Global FIFO is quite simple, and allows dynamic upstream bandwidth allocation on the basis of a request-and-permit mechanism on the APON architecture. It has good bandwidth efficiency; however, being cell-based, it does not consider multiple traffic types from home networks. In this article we describe and analyze a new dynamic MAC resource allocation algorithm called multiple queue-FIFO that can achieve good performance under the SuperPON access network in the home network environment.
Monoclonal Antibody against CXCL1 (HL2401) as a Novel Agent in Suppressing IL6 Expression and Tumoral Growth (2019)

<b>Rationale</b>: The expression of the chemokine (C-X-C motif) ligand 1 (CXCL1), an inflammatory protein, has been reported to be up-regulated in many human cancers. The mechanisms through which aberrant cellular CXCL1 levels promote specific steps in tumor growth and progression are unknown. <b>Methods</b>: We described the anticancer effects and mechanism of action of HL2401, a monoclonal antibody directed at CXCL1 with <i>in vitro</i> and <i>in vivo</i> data on bladder and prostate cancers. <b>Results</b>: HL2401 inhibited proliferation and invasion of bladder and prostate cells along with disrupting endothelial sprouting <i>in vitro</i>. Furthermore, novel mechanistic investigations revealed that CXCL1 expression stimulated interleukin 6 (IL6) expression and repressed tissue inhibitor of metalloproteinase 4 (TIMP4). Systemic administration of HL2401 in mice bearing bladder and prostate xenograft tumors retarded tumor growth through the inhibition of cellular proliferation and angiogenesis along with an induction of apoptosis. Our findings reveal a previously undocumented relationship between CXCL1, IL6 and TIMP4 in solid tumor biology. <b>Principal conclusions</b>: Taken together, our results argue that CXCL1 plays an important role in sustaining the growth of bladder and prostate tumors via up-regulation of IL6 and down-regulation of TIMP4. Targeting these critical interactions with a CXCL1 monoclonal antibody offers a novel strategy to therapeutically manage bladder and prostate cancers.
Dialogue Natural Language Inference (2019)

Consistency is a long standing issue faced by dialogue models. In this paper, we frame the consistency of dialogue agents as natural language inference (NLI) and create a new natural language inference dataset called Dialogue NLI. We propose a method which demonstrates that a model trained on Dialogue NLI can be used to improve the consistency of a dialogue model, and evaluate the method with human evaluation and with automatic metrics on a suite of evaluation sets designed to measure a dialogue model’s consistency.
Inhalation injury: epidemiology, pathology, treatment strategies (2013)

Lung injury resulting from inhalation of smoke or chemical products of combustion continues to be associated with significant morbidity and mortality. Combined with cutaneous burns, inhalation injury increases fluid resuscitation requirements, incidence of pulmonary complications and overall mortality of thermal injury. While many products and techniques have been developed to manage cutaneous thermal trauma, relatively few diagnosis-specific therapeutic options have been identified for patients with inhalation injury. Several factors explain slower progress for improvement in management of patients with inhalation injury. Inhalation injury is a more complex clinical problem. Burned cutaneous tissue may be excised and replaced with skin grafts. Injured pulmonary tissue must be protected from secondary injury due to resuscitation, mechanical ventilation and infection while host repair mechanisms receive appropriate support. Many of the consequences of smoke inhalation result from an inflammatory response involving mediators whose number and role remain incompletely understood despite improved tools for processing of clinical material. Improvements in mortality from inhalation injury are mostly due to widespread improvements in critical care rather than focused interventions for smoke inhalation.Morbidity associated with inhalation injury is produced by heat exposure and inhaled toxins. Management of toxin exposure in smoke inhalation remains controversial, particularly as related to carbon monoxide and cyanide. Hyperbaric oxygen treatment has been evaluated in multiple trials to manage neurologic sequelae of carbon monoxide exposure. Unfortunately, data to date do not support application of hyperbaric oxygen in this population outside the context of clinical trials. Cyanide is another toxin produced by combustion of natural or synthetic materials. A number of antidote strategies have been evaluated to address tissue hypoxia associated with cyanide exposure. Data from European centers supports application of specific antidotes for cyanide toxicity. Consistent international support for this therapy is lacking. Even diagnostic criteria are not consistently applied though bronchoscopy is one diagnostic and therapeutic tool. Medical strategies under investigation for specific treatment of smoke inhalation include beta-agonists, pulmonary blood flow modifiers, anticoagulants and antiinflammatory strategies. Until the value of these and other approaches is confirmed, however, the clinical approach to inhalation injury is supportive.
Proton beam therapy for hepatocellular carcinoma with portal vein tumor thrombus (2005)

Proton beam therapy for patients with HCC who had PVTT was feasible and effective. It appeared to improve survival and local control significantly for these patients.
Space Mouse - Hand movement and gesture recognition using Leap Motion Controller (2017)

A code based analysis of the user’s performance in selection tasks using a space mouse in comparison with a standard device is presented in this paper. A new contact free gesture based human interaction with declared point to point accuracy has been used in space mouse. Systematic evaluation of this new system as not been done prior to this point. Accurate tacking of hand fingers, and the track movement was proved testing, accuracy is last when the hand moves in to a position obstructing the controller’s ability to view.
Increasing Appearance of Reassortant Influenza B Virus in Taiwan from 2002 to 2005 (2006)

Genetic and antigenic analyses of influenza B virus field strains isolated in Taiwan from 1998 to 2005 were performed. To investigate the molecular evolution of influenza B viruses, sequence analysis of the hemagglutinin (HA1 subunit) and neuraminidase genes was performed. All influenza B viruses isolated between 1998 and 2000 belonged to the B/Yamagata/16/88 lineage. The B/Victoria/2/87 lineage, which was cocirculating with the Yamagata lineage, was identified in Taiwan in March 2001. Concurrently, there was an increasing prevalence of this lineage in many parts of the world, including North America and Europe, during the 2001-2002 season. Since 2002, genetic reassortants of influenza B virus with the Victoria lineage of hemagglutinin and the Yamagata lineage of neuraminidase have been found at a rate of 46%. Therefore, in 2002, at least three sublineages of influenza B virus strains, the B/Shanghai/361/2002-like strain (Yamagata lineage), the B/Hong Kong/330/01-like strain (Victoria lineage), and the B/Hong Kong/1351/02-like strain (B reassortant lineage), were identified in Taiwan. The results showed that genetically distinct lineages can cocirculate in the population and that the reassortment among these strains plays a role in generating the genetic diversity of influenza B viruses. Interestingly, from January to April 2005, B reassortant viruses became dominant (73%) in Taiwan, which indicated that a mismatch had occurred between the influenza B vaccine strain recommended for the 2004-2005 season in the Northern hemisphere by the World Health Organization and the epidemic strain.
WWW server load balancing technique based on passive performance measurement (2009)

Server load balancing is indispensable in World Wide Web for providing high-quality service. In server load balancing, since the server loads and capacities are not always identical, traffic should be distributed by measuring server performance to improve the service quality. This paper proposes a load balancing technique conducted by passive measurement, which estimates the server performance through user traffic passing the load balancer. Since this method evaluates server performance without executing any programs on the server, no additional server or network load is generated. The effectiveness of the proposed measurement method and load balancing technique is confirmed experimentally.
Simulation building blocks for airport terminal modeling (2003)

Airports are an ideal application area for simulation. The processes are in a continuous state of change, are complex and stochastic, involve many moving objects, and require a good performance that can be measured in several different performance indicators. Within airports, but also between airports, the same kind of questions are answered over and over again. Often, however, new simulation models are built for each question, if possible copying some parts of previous models. Structured reuse of simulation components is rarely seen. This paper shows an approach for airport terminal modeling that departs from the assumption that reusable simulation building blocks can form the core of a powerful airport modeling tool, which is able to answer different questions at airports better and faster than traditional models. The building blocks have been implemented in the commercially available simulation language eM-Plant. Several studies carried out with this library were very successful.
Recursive Bayesian Human Intent Recognition in Shared-Control Robotics (2018)

Effective human-robot collaboration in shared control requires reasoning about the intentions of the human user. In this work, we present a mathematical formulation for human intent recognition during assistive teleoperation under shared autonomy. Our recursive Bayesian filtering approach models and fuses multiple non-verbal observations to probabilistically reason about the intended goal of the user. In addition to contextual observations, we model and incorporate the human agent's behavior as goal-directed actions with adjustable rationality to inform the underlying intent. We examine human inference on robot motion and furthermore validate our approach with a human subjects study that evaluates autonomy intent inference performance under a variety of goal scenarios and tasks, by novice subjects. Results show that our approach outperforms existing solutions and demonstrates that the probabilistic fusion of multiple observations improves intent inference and performance for shared-control operation.
A comparison of SLAM implementations for indoor mobile robots (2007)

This paper compares the performances of four different Simultaneous Localization and Mapping (SLAM) implementations: Teambotica1,5, ICP 6D-SLAM2,5, SGI-J DP SLAM3, and ERSP vSLAM4,5. All the tested implementations used odometry for dead-reckoning as a base position measurement, and all but vSLAM use lasers as a main sensor (ERSP vSLAM uses a video camera). The comparison was taken using two different types of robots in three different environments: an office corridor, an office entry area, and an indoor robot driving course. The comparison uses a novel approach for map accuracy evaluation, one of the key factors in evaluating the performance of a SLAM implementation. The results show that even for similar setups, the outcomes can vary significantly for the different implementations, suggesting that the underlying implementations likely play a significant role in the SLAM performance.
Staphylococcal Protein A as a Pharmacological Treatment for Autoimmune Disorders (2017)

International audience
The isolation by ligand affinity chromatography of a novel form of alpha-L-fucosidase from almond. (1990)

An alpha-fucosidase has been extracted from almond meal and purified 163,000-fold to apparent homogeneity using a novel affinity ligand, N-(5-carboxy-1-pentyl)-1,5-dideoxy-1,5-imino-L-fucitol, coupled to Affi-Gel 102. Substrate specificity studies demonstrate that the enzyme hydrolyzes the alpha-fucosidic linkages in Gal(beta 1----3)(Fuc(alpha 1----4]GlcNAc(beta 1----3)Gal(beta 1----4)Glc and Gal(beta 1----4)(Fuc(alpha 1----3]GlcNAc(beta 1----3)Gal(beta 1----4)Glc at similar rates but is unable to hydrolyze Fuc(alpha 1----2)Gal, Fuc(alpha 1----6)GlcNAc, or the synthetic substrate, p-nitrophenyl alpha-L-fucopyranoside. Hence, the enzyme closely resembles an alpha-fucosidase I isolated previously from a commercial preparation of partially purified almond beta-glucosidase (Ogata-Arakawa, M., Muramatsu, T., and Kobata, A. (1977) Arch. Biochem. Biophys. 181, 353-358). However, native and subunit relative molecular masses of 106,000 and 54,000 respectively, different charge and hydrophobicity properties, and the absence of stimulation by NaCl clearly distinguish this enzyme, designated alpha-fucosidase III, from other almond alpha-fucosidases reported previously.