gebhart/patrepeval huggingface dataset:
ΔNp63α Up-Regulates the Hsp70 Gene in Human Cancer (2005)

Abstract HSP70, a stress response protein, is known to be a determinant of cell death and cell transformation. We show that different isoforms of p63 have different transcriptional activities on hsp70 genes. ΔNp63α, an abundantly expressed isoform of p63, activates (in vitro and in vivo), whereas TAp63γ down-regulates the expression of hsp70. We further show that the transactivation domain at the NH2 terminus of p63 represses, whereas the COOH terminus activates hsp70 transcription. In addition, ΔNp63α regulates transcription of the hsp70 gene through its interaction with the CCAAT binding factor and NF-Y transcription factors which are known to form a complex with the CCAAT box located in the hsp70 promoter. Moreover, ΔNp63α expression correlates with HSP70 expression in all head and neck cancer cell lines. Finally, we show colocalization of ΔNp63α and HSP70 in the epithelium and coexpression of both proteins in 41 primary head and neck cancers. Our study provides strong evidence for the physiologic association between ΔNp63α and hsp70 in human cancer, thus further supporting the oncogenic potential of ΔNp63α.
Packet switch networks: network performance study (1992)

The concept of integrated modular avionics for integrated flight and vehicle management system takes into account system decomposition modularity, function availability and fault tolerance. The system cornprises a number of modules which provide the computing resources and I/O interfaces for all applications. Interconnect architectures provide the intermodule communication and data transfer. The multi-port optoelectronic switch and associated multistage cube network architecture define a possible next step evolution beyond the current interconnect concepts. This paper presents a performance analysis of a serial multistage cube network architecture.
ATPS-28COMBINED DRUG SCREENING AND PHOSPHOPROTEOMICS IDENTIFIES CANDIDATE BRAIN TUMOR THERAPEUTICS IN PRIMARY HUMAN BRAIN TUMOR-INITIATING CELLS (2015)

ATPS-28. COMBINED DRUG SCREENING AND PHOSPHOPROTEOMICS IDENTIFIES CANDIDATE BRAIN TUMOR THERAPEUTICS IN PRIMARY HUMAN BRAIN TUMOR-INITIATING CELLS Natalie Grinshtein1, Constanza Rioseco1, David Uehling2, Ahmed Aman2, Artee Luchman3, Donna Senger3, Steve Robbins3, Greg Cairncross3, Alessandro Datti4, Jeff Wrana4, Steve Jones5, Marco Marra5, Mike Moran6, Rima Al-awar2, Samuel Weiss3, and David Kaplan1,6; Hospital for Sick Children, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Hotchkins Brain Institute, Calgary, AB, Canada; Mount Sinai Hospital, Toronto, ON, Canada; Genome Sciences Center, Vancouver, BC, Canada; University of Toronto, Toronto, ON, Canada multiforme (GBM) is the most common and aggressive brain tumor with a very grim prognosis for the patients. Therapeutic Targeting of Glioblastoma is a new pan-Canadian research team of the Terry Fox Research Institute and the Canadian Stem Cell Network funded to discover efficacious therapeutics for GBM. We use our collection of over 100 primary brain tumor-initiating lines (BTICs) that are subjected to drug screening by over 1500 compounds. Multiple compounds that exhibit nanomolar cytotoxicity towards all of the BTIC lines are prioritized based upon their potency, novelty for GBM, BBB penetration and clinical status. These drugs are currently undergoing efficacy testing in an orthotopic xenograft model as single agents and in combination with TMZ. We also use phosphoproteomics as a complementary strategy to better understand BTIC signaling, identify novel targets and mechanisms of drug resistance. Phosphotyrosine characterization of 14 BTIC lines revealed heterogeneous activation of multiple RTKs in different BTIC lines, whereas non-receptor kinases were found equally phosphorylated in all BTIC lines. Moreover, we have performed phosphoproteomic analysis of 3 matching BTIC lines, tumors and xenograft samples to identify shared phospho-targets. Our results demonstrated that EGFR is the only RTK in common in matched line-tumor-xenograft samples. Other RTKs such as PDGFRA and EPH receptors, were only activated in BTIC lines, suggesting that targeting these proteins may have limited efficacy. In contrast to RTKs, multiple nonreceptor kinases were activated in matched line-tumor-xenograft samples. To validate the biological relevance of the identified shared targets, we are currently using siRNA knockdown of selected candidate proteins to assess the effect on cell viability, migration and invasion in vitro and eventually in vivo. In conclusion, we anticipate that our combined drug screening and phosphoproteomics approach will generate promising clinical candidates as well as shed light on GBM biology. Neuro-Oncology 17:v18–v40, 2015. doi:10.1093/neuonc/nov204.28 Published by Oxford University Press on behalf of the Society for Neuro-Oncology 2015.
Practical Sparse Modeling An Overview and Two Examples from Genetics (2014)

This chapter contains sections titled: 1 Sparse Modeling Road Map, 2 Example 1: Genome-Wide Association Studies (GWAS), 3 Example 2: Gene Microarray Data Analysis, 4 Random Lasso, 5 Summary, Note, References
A Performance-Based Representation for Engineering Design (1999)

Abstract A performance-based representation is presented, which uses the Performance Orientation Chart (POC) to aid the designer throughout an interactive design process. Assuming that all performance attributes can be expressed as functions of the design parameters, three types of graphical matrix are shown in the POC: 1) The design form depicts the performance attributes varying with the correspondent design parameters; 2) The performance dependency addresses the trade-off information among the multiple specifications based on Pareto optimal solutions; 3) The parameter constraint space defines the feasible region of the design, parameters within the, active specification limits. Guided by these graphical matrices, the designer can interactively develop the design solution to satisfy multiple specifications. The methodology was applied to a practical design problem to explicate how the POC can help the designer acquire a satisfying design solution with extensive confidence. Finally, the discussion, indicates that the performance-based representation is significantly compatible with other current engineering design methodologies.
Extraction of Total Phenolic Compounds, Flavonoids, Anthocyanins and Tannins from Grape Byproducts by Response Surface Methodology. Influence of Solid-Liquid Ratio, Particle Size, Time, Temperature and Solvent Mixtures on the Optimization Process (2014)

The current work concerns the optimization process of phenolic compounds solid liquid extraction from grape byproducts at high temperatures and short incubation times. The effect of five experimental parameters (solidliquid ratio, particle size, time, temperature and solvent mixture) mostly believed to affect the extraction process was undertaken. A first response surface methodology experimental design was used to optimize the solid-liquid ratio and milling time parameters. A second design was used for the optimization of the quantitative and qualitative parameters. The quantitative parameters studied are: total phenolic compounds, flavonoid content, total monomeric anthocyanin composition and tannin concentration. The qualitative parameters analyzed are: antiradical activity and antioxidant capacity. The second design was based on the use of time, temperature and solvent mixture as optimization parameters. The assays were first conducted separately revealing the best experimental conditions for the maximization of each response variable alone. A simultaneous response surface methodology of all the responses taken together was then conducted, showing the optimal extraction conditions to be: 93 minutes at 94?C and in 66% ethanol/water solvent. The maximal response values obtained for each parameter are: Total Phenolic Compounds yield (5.5 g GAE/100g DM), Flavonoid Content (5.4 g GAE/100g DM), Total Monomeric Anthocyanin yield (70.3 mg/100g DM), Tannin Concentration (12.3 g/L), Antiradical Activity (67.3%) and Total Antioxidant Capacity (393 mgAAE/L). All of the optimal values were acquired at 3 mL/g solid-liquid ratio and 6.8 min milling time. The obtained extracts could be used as natural bioactive compounds in several industrial applications.
Cheminformatics Tools for Analyzing and Designing Optimized Small-Molecule Collections and Libraries (2019)

Libraries of well-annotated small molecules have many uses in chemical genetics, drug discovery, and therapeutic repurposing. Multiple libraries are available, but few data-driven approaches exist to compare them and design new libraries. We describe an approach to scoring and creating libraries based on binding selectivity, target coverage, and induced cellular phenotypes as well as chemical structure, stage of clinical development, and user preference. The approach, available via the online tool http://www.smallmoleculesuite.org, assembles sets of compounds with the lowest possible off-target overlap. Analysis of six kinase inhibitor libraries using our approach reveals dramatic differences among them and led us to design a new LSP-OptimalKinase library that outperforms existing collections in target coverage and compact size. We also describe a mechanism of action library that optimally covers 1,852 targets in the liganded genome. Our tools facilitate creation, analysis, and updates of both private and public compound collections.
Understanding the Impact of Schottky Barriers on the Performance of Narrow Bandgap Nanowire Field Effect Transistors (2012)

Semiconductor nanowires have been explored as alternative electronic materials for high performance device applications exhibiting low power consumption specs. Electrical transport in III-V nanowire (NW) field-effect transistors (FETs) is frequently governed by Schottky barriers between the source/drain and the NW channel. Consequently the device performance is greatly impacted by the contacts. Here we present a simple model that explains how ambipolar device characteristics of NW-FETs and in particular the achievable on/off current ratio can be analyzed to gain a detailed idea of (a) the bandgap of the synthesized NWs and (b) the potential performance of various NW materials. In particular, we compare the model with our own transport measurements on InSb and InAs NW-FETs as well as results published by other groups. The analysis confirms excellent agreement with the predictions of the model, highlighting the potential of our approach to understand novel NW based materials and devices and to bridge material development and device applications.
Plasma Doped (PLAD) Deep Sub-Half Micron Buried Channel PMOSFETS and its Application to Next Generation ULSI Circuits (1996)

Results are presented from work aimed at demonstrating the feasibility of Plasma Doping (PLAD) to fabricate P+ source/drain regions for 0.25-0.3?m buried channel PMOSFETS for the first time. Device characteristics are compared between PLAD and conventionally-formed source/drain junctions using ion implantation of Boron and BF 2 at energies of 2,5, and 10 keV Superior threshold voltage roll-off, off-current leakage, and high punch-through resistance are obtained for PLAD MOSFETs processed at pulsed negative voltage of 3.5 kV applied to the wafer with a BF 3 source gas used to implant boron ions. The process capability of PLAD is examined by looking at sheet resistance uniformity and junction leakage. Plasma Doping is shown to be a viable alternative to ion implantation for the fabrication of next generation deep sub-half micron devices with the potential for significantly reduced cost.
Analysis of angiogenesis related factors in glioblastoma, peritumoral tissue and their derived cancer stem cells (2016)

The formation of new blood vessels represents a crucial event under both physiological and pathological circumstances. In this study, we evaluated by immunohistochemistry, and/or Western blotting and/or quantitative real time-PCR the expression of HIF1α, HIF2α, VEGF, VEGFR1 and VEGFR2 in surgical glioblastoma multiforme (GBM) and peritumoral tissue samples obtained from 50 patients as well as in cancer stem cells (CSCs) isolated from GBM (GCSCs) and peritumoral tissue (PCSCs) of 5 patients. We also investigated the contribution of both GCSCs and PCSCs on the behavior of endothelial cells (ECs) in vitro. Immunohistochemistry demonstrated the expression of angiogenesis markers in both GBM and peritumoral tissue. In addition, in vitro tube formation assay indicated that both GCSCs and PCSCs stimulate EC proliferation as well as tube-like vessel formation. An increased migration aptitude was mainly observed when ECs were cultured in the presence of GCSCs rather than in the presence of PCSCs. These findings suggest that relevant neoangiogenetic events may occur in GBM. In particular, VEGF/VEGFR co-expression in PCSCs leads to hypothesize the involvement of an autocrine signaling. Moreover, our results suggest that both GCSCs and PCSCs own the skill of activating the "angiogenic switch" and the capability of modulating EC behavior, indicating that both cell types are either responsive to angiogenic stimuli or able to trigger angiogenic response. Together with our previous findings, this study adds a further piece to the challenging puzzle of the characterization of peritumoral tissue and of the definition of its real role in GBM pathophysiology.
Current Issues Involving the Treatment of Small Rectal Carcinoid Tumors (2012)

submucosal dissection, and local surgical excision, including transanal excision and transanal endoscopic microsurgery (TEM). In a study by Kim et al. [6], the complete resection rate for TEM was over 97%. Although TEM is superior to other endoscopic procedures, TEM must be considered to be more invasive because of the risk associated with the use of anesthesia.
Phrase Based Decoding using a Discriminative Model (2010)

In this paper, we present an approach to statistical machine translation that combines the power of a discriminative model (for training a model for Machine Translation), and the standard beam-search based decoding technique (for the translation of an input sentence). A discriminative approach for learning lexical selection and reordering utilizes a large set of feature functions (thereby providing the power to incorporate greater contextual and linguistic information), which leads to an effective training of these models. This model is then used by the standard state-of-art Moses decoder (Koehn et al., 2007) for the translation of an input sentence. We conducted our experiments on Spanish-English language pair. We used maximum entropy model in our experiments. We show that the performance of our approach (using simple lexical features) is comparable to that of the state-of-art statistical MT system (Koehn et al., 2007). When additional syntactic features (POS tags in this paper) are used, there is a boost in the performance which is likely to improve when richer syntactic features are incorporated in the model. 1
How neutral red modified carbon and electron flow inClostridium acetobutylicumgrown in chemostat culture at neutral pH (1995)

The metabolism of Clostridium acetobutylicum was manipulated, at neutral pH and in chemostat culture, by the addition of Neutral red, a molecule that can replace ferredoxin in the oxido-reduction reactions catalysed by the enzymes involved in the distribution of the electron flow. Cultures grown on glucose alone produced mainly acids while cultures grown on glucose plus Neutral red produced mainly alcohols and butyrate and low levels of hydrogen. We demonstrated that just after addition of Neutral red to an acidogenic culture, the simultaneous utilizations of ferredoxin and dye deviate electron flow from hydrogen to NADH production initially by the enzymatic regulation of in vivo hydrogenase and ferredoxin NAD reductase activities. The higher NAD(P)H pool generated might, thereafter, be the signal for the setting up of a new metabolism. In the resulting steady-state, the NAD(P)H ‘pressure’ is maintained by high ferredoxin NAD and NADP reductases level associated to a low NADH ferredoxin reductase level. The regeneration of NAD is mainly achieved via the induced or increased NADH-dependent aldehyde and alcohol dehydrogenase activities.
Author Correction: A phase 1 trial of lipid-encapsulated mRNA encoding a monoclonal antibody with neutralizing activity against Chikungunya virus (2022)

In the version of this article initially published, there were errors in the inset graph to Fig. The labels and plots have been corrected in the HTML and PDF versions of the article. The original and corrected Fig 2a graphs are shown below.
Cache as point of coherence in multiprocessor system (2023)

In a multiprocessor system, a conflict checking mechanism is implemented in the L2 cache memory. Different versions of speculative writes are maintained in different ways of the cache. A record of speculative writes is maintained in the cache directory. Conflict checking occurs as part of directory lookup. Speculative versions that do not conflict are aggregated into an aggregated version in a different way of the cache. Speculative memory access requests do not go to main memory.
Characterisation of electron beams at different focus settings and work distances in multiple welders using the enhanced modified Faraday cup (2007)

Using the enhanced modified Faraday cup (EMFC), the differences in the beams produced by two electron beam welders are characterised at different focus settings and work distances. For example, EMFC measurements show that sharply focused beams display different shapes and peak power densities which vary by nearly 20% for the same welding parameters on these two welders. Increases in work distance on each machine were shown to result in decreases in both the peak power density and the resulting weld size and shape. Because of the differences in machine performance, additional differences also arise when comparing the welds produced by each machine. These different weld dimensions are attributed to differences in the beam shape and a 70 mm difference in the theoretical beam crossover location in the upper column of the two welders. The crossover location, which can not be physically measured, is determined using the EMFC by analysing the beam distribution parameters of sharply focused beams over a range of work distances. By combining these results with simplified optics calculations, the magnification of the beam optics can be determined and the machine performance of each welder characterised. The work distance on each machine at which beams with similar peak power density values will be produced can then be determined. With this knowledge, changes in either the beam focus or work distance can be made to attain similar beams from different welders, thus providing a baseline for developing modern weld transfer procedures.
A Case Study of On-Orbit System Identification Experiments on Engineering Test Satellite-VIII (2002)

This paper studies on-orbit system identification experiment using ETS-VIII, which will be launched in 2003 by H-II A rocket. In the proposed method herein, the state-space model of the closed loop system is firstly realized by sigular value decomposion of Hankel matrices. The effect of controller is then eliminated by iterative least square curve fitting process using time response signal. Numerinal simulation of ETS-VIII shows the validity of the algorithm.
Hybrid Analog-Digital Transceiver Designs for Cognitive Large-Scale Antenna Array Systems (2016)

Milimeter wave (mmWave) band mobile communications can be a solution to the continuously increasing traffic demand in modern wireless systems. Even though mmWave bands are scarcely occupied, the design of a prospect transceiver should guarantee the efficient coexistence with the incumbent services in these bands. To that end, in this paper, two underlay cognitive transceiver designs are proposed that enable the mmWave spectrum access while controlling the interference to the incumbent users. MmWave systems usually require large antenna arrays to achieve satisfactory performance and thus, they cannot support fully digital transceiver designs due to high demands in hardware complexity and power consumption. Thus, in order to develop efficient solutions, the proposed approaches are based on a hybrid analog-digital pre-coding architecture. In such hybrid designs, the overall beamformer can be factorized in a low dimensional digital counterpart applied in the baseband and in an analog one applied in the RF domain. The first cognitive solution developed in this paper designs the cognitive hybrid pre-coder by maximizing the mutual information between its two ends subject to interference, power and hardware constraints related to the analog counterpart. The second solution aims at reduced complexity requirements and thus derives the hybrid pre-coder by minimizing the Frobenious norm of its difference to the optimal digital only one. A novel solution for the post-coder at the cognitive receiver part is further proposed here based on a hardware constrained Minimum Mean Square Error criterion. Simulations show that the performance of both the proposed hybrid approaches is very close to the one of the fully digital solution for typical wireless environments.
Coexistent Multiple Myeloma or Increased Bone Marrow Plasma Cells Define Equally High-Risk Populations in Patients With Immunoglobulin Light Chain Amyloidosis (2013)

Patients with AL amyloidosis who have more than 10% BMPCs have a poor prognosis, similar to that of patients with AL-CRAB, and should therefore be considered together as AL amyloidosis with MM.