gebhart/patrepeval huggingface dataset:
Genetic and functional characterization of putative Ras/Raf interaction inhibitors in C. elegans and mammalian cells (2019)

Abstract Background Activation of the mammalian Ras-Raf-MEK-ERK MAPK signaling cascade promotes cellular proliferation, and activating Ras mutations are implicated in cancer onset and maintenance. This pathway, a therapeutic target of interest, is highly conserved and required for vulval development in C. elegans. Gain-of-function mutations in the Ras ortholog lead to constitutive pathway signaling and a multivulva (Muv) phenotype. MCP compounds were identified in a yeast two-hybrid screen for their ability to disrupt Ras-Raf interactions. However, this had not been confirmed in another system, and conflicting results were reported regarding selective MCP-mediated blockade of Ras- and Raf-mediated biological activities in mammalian cells. Here we used the easily-scored Muv phenotype as an in vivo readout to characterize the selectivity of MCP110 and its analogs, and performed biochemical studies in mammalian cells to determine whether MCP treatment results in impaired interaction between Ras and its effector Raf. Results Our genetic analyses showed significant dose-dependent MCP-mediated reduction of Muv in C. elegans strains with activating mutations in orthologs of Ras (LET-60) or Raf (LIN-45), but not MAP kinases or an Ets-like transcription factor. Thus, these inhibitors selectively impair pathway function downstream of Ras and upstream of or at the level of Raf, consistent with disruption of the Ras/Raf interaction. Our biochemical analyses of MCP110-mediated disruption of Ras-Raf interactions in mammalian cells showed that MCP110 dose-dependently reduced Raf-RBD pulldown of Ras, displaced a fluorescently-tagged Raf-RBD probe from plasma membrane locations of active Ras to the cytosol and other compartments, and decreased active, phosphorylated ERK1/2. Conclusions We have effectively utilized C. elegans as an in vivo genetic system to evaluate the activity and selectivity of inhibitors intended to target the Ras-Raf-MAPK pathway. We demonstrated the ability of MCP110 to disrupt, at the level of Ras/Raf, the Muv phenotype induced by chronic activation of this pathway in C. elegans. In mammalian cells, we not only demonstrated MCP-mediated blockade of the physical interaction between Ras and Raf, but also narrowed the site of interaction on Raf to the RBD, and showed consequent functional impairment of the Ras-Raf-MEK-ERK pathway in both in vivo and cell-based systems.
Dynamics of photoinduced refractive index changes in As2S3fibers (2012)

We investigate the dynamics of photoinduced index changes in chalcogenide As(2)S(3) fibers. Using a novel phase sensitive technique for measuring the photoinduced index change, we find that the index evolution is a two-stage process: it consists of a fast reduction and a subsequent slow increase in the refractive index. We show that the index change depends strongly on the beam intensity with both positive and negative changes possible. These findings can have application in design and fabrication of photoinduced devices such as Bragg gratings and photonic cavities.
Brief Report: Increased expression of a short splice variant of CTLA‐4 exacerbates lupus in MRL/lpr mice (2012)

Our results indicate that the presence of the alternatively spliced 1/4 CTLA-4 isoform can further promote autoimmunity and autoimmune pathology in lupus-prone mice and suggest that altered splicing of CTLA4 contributes to the expression of autoimmune disease.
Supplementary Table 2 from External Validation of a Multiplex Urinary Protein Panel for the Detection of Bladder Cancer in a Multicenter Cohort (2023)

&lt;p&gt;XLSX file - 8K, Comparison of biomarker concentration data across 3 independent cohort studies (n = 755).&lt;/p&gt;
Supplementary Methods, Figures 1-2, Tables 1-2 from Biochemical, Cellular, and <i>In vivo</i> Activity of Novel ATP-Competitive and Selective Inhibitors of the Mammalian Target of Rapamycin (2023)

Supplementary Methods, Figures 1-2, Tables 1-2 from Biochemical, Cellular, and &lt;i&gt;In vivo&lt;/i&gt; Activity of Novel ATP-Competitive and Selective Inhibitors of the Mammalian Target of Rapamycin
Int-2, an Autocrine and/or Ultra--Short-Range Effector in Transgenic Mammary Tissue Transplants (1992)

Given the limitations of our experimental system and the limited information available to date on the secretion of Int-2 protein, these results suggest that, although the Int-2 protein contains a putative signal peptide, it may act primarily as an autocrine or as an ultra-short-range paracrine growth factor in mammary epithelium.
1331: University of Toronto Clinical Trial of Muscle-Derived Cell Injection in Women with Stress Urinary Incontinence (2007)

You have accessJournal of UrologyModerated Poster 41, Tuesday, May 22, 2007, 10:00 am - 12:00 pm1 Apr 20071331: University of Toronto Clinical Trial of Muscle-Derived Cell Injection in Women with Stress Urinary Incontinence Lesley K. Carr, Deborah Steele, Shannon Steele, David Wagner, Ryan Pruchnic, Ronald J. Jankowski, Janet Erickson, Wendy W. Leng, and Michael B. Chancellor Lesley K. CarrLesley K. Carr More articles by this author , Deborah SteeleDeborah Steele More articles by this author , Shannon SteeleShannon Steele More articles by this author , David WagnerDavid Wagner More articles by this author , Ryan PruchnicRyan Pruchnic More articles by this author , Ronald J. JankowskiRonald J. Jankowski More articles by this author , Janet EricksonJanet Erickson More articles by this author , Wendy W. LengWendy W. Leng More articles by this author , and Michael B. ChancellorMichael B. Chancellor More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)31545-3AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1331: University of Toronto Clinical Trial of Muscle-Derived Cell Injection in Women with Stress Urinary Incontinence." The Journal of Urology, 177(4S), p. 439 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 177Issue 4SApril 2007Page: 439 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Lesley K. Carr More articles by this author Deborah Steele More articles by this author Shannon Steele More articles by this author David Wagner More articles by this author Ryan Pruchnic More articles by this author Ronald J. Jankowski More articles by this author Janet Erickson More articles by this author Wendy W. Leng More articles by this author Michael B. Chancellor More articles by this author Expand All Advertisement PDF DownloadLoading ...
From Research to Proof-of-Concept: Analysis of a Deployment of FPGAs on a Commercial Search Engine (2021)

FPGAs are quickly becoming available in the cloud as a one more heterogeneous processing element complementing CPUs and GPUs. There are many reports in the literature showing the potential for FPGAs to accelerate a wide variety of algorithms, which combined with their growing availability, would seem to also indicate a widespread use in many applications. Unfortunately, there is not much published research exploring what it takes to integrate an FPGA into an existing application in a cost-effective way and keeping the algorithmic performance advantages. Building on recent results exploring how to employ FPGAs to improve the search engines used in the travel industry, this paper analyses the end-to-end performance of the search engine when using FPGAs, as well as the necessary changes to the software and the cost of such deployments. The results provide important insights on current FPGA deployments and what needs to be done to make FPGAs more widely used. For instance, the large potential performance gains provided by an FPGA are greatly diminished in practice if the application cannot submit request in the most optimal way, something that is not always possible and might require significant changes to the application. Similarly, some existing cloud deployments turn out to use a very imbalanced architecture: a powerful FPGA connected to a not so powerful CPU. The result is that the CPU cannot generate enough load for the FPGA, which potentially eliminates all performance gains and might even result in a more expensive system. In this paper, we report on an extensive study and development effort to incorporate FPGAs into a search engine and analyse the issues encountered and their practical impact. We expect that these results will inform the development and deployment of FPGAs in the future by providing important insights on the end-to-end integration of FPGAs within existing systems.
Magnetic Resonance Imaging With Cochlear Implant Magnet in Place (2015)

Objective To evaluate the safety and image quality of 1.5-T MRI in patients with cochlear implants and retained internal magnets. Study Design Retrospective case series from 2012 to 2014. Setting Single tertiary academic referral center. Patients All cochlear implant recipients undergoing 1.5-T MRI without internal magnet removal. Intervention(s) MRI after tight headwrap application. Main Outcome Measures Patient tolerance, complications, and characteristics of imaging artifact. Results Nineteen ears underwent a total of 34 MRI scans. Two patients did not tolerate imaging with the headwrap in place and required magnet removal before rescanning. One subject experienced two separate episodes of polarity reversal in the same device from physical realignment (i.e., flipping) of the internal magnet requiring surgical repositioning. Three patients were discovered to have canting of the internal magnet after imaging. In all three cases, the magnet could be reseated by applying gentle firm pressure to the scalp until the magnet “popped” back into place. These patients continue to use their device without difficulty and have not required surgical replacement. In patients receiving head MRI, the ipsilateral internal auditory canal and cerebellopontine angle could be visualized without difficulty in 94% of cases. There were no episodes of cochlear implant device failure or soft tissue complications. Conclusion Under controlled conditions, 1.5-T MRI can be successfully performed in most patients without the need for cochlear implant magnet removal. In nearly all cases, imaging artifact does not impede evaluation of the ipsilateral skull base. Patients should be counseled regarding the risk of internal magnet movement that may occur in up to 15% of cases, even with tight headwrap application. If internal magnet polarity reversal occurs, a trial of reversing the external magnet can be considered. If canting or mild displacement of the internal magnet occurs, an attempt at reseating can be made by applying gentle firm pressure to the scalp over the internal magnet. If conservative measures fail, the magnet should be surgically repositioned to minimize interruption of device use and to prevent scalp complications.
Inhibitory effects of sodium and other monovalent cations on purified versus membrane-bound kallikrein. (1983)

Glandular kallikrein is a serine proteinase implicated in epithelial ion transport processes. The present studies show that the enzymatic activities (alpha-N-tosyl-L-arginine methyl ester esterase and kininogenase) and the immunoreactivities of rat and human urinary kallikreins are inhibited by monovalent cations. The degree of inhibition, which exceeds 80% with physiological concentrations of cations, is dependent on temperature and preincubation time. The inhibitory effects are reversed when ions are removed via gel filtration. Bovine serum albumin or polyethylene glycol attenuate cationic inhibition, but sucrose or mannitol do not. Detergents, including deoxycholate, 3-[(3-cholamidopropyl)dimethylammonio]-1-propane sulfonate, Triton X-100, and Lubrol PX also attenuate cationic inhibition of enzymatic activity or immunoreactivity. Membrane-bound kallikrein of renal cortical microsomal fractions or detergent-treated purified kallikrein lose less than 30% of their activity, even in the presence of 200 mM cation. These results show that both catalytic activity and immunoreactivity of purified versus membrane-bound kallikreins are affected, but to a different extent, by cations. The data suggest that monovalent cations may play a role in the regulation of soluble versus membrane-bound kallikrein activity.
Inhibition of inflammation and oxidative stress by Angelica dahuricae radix extract decreases apoptotic cell death and improves functional recovery after spinal cord injury (2011)

Inflammation and oxidative stress play major roles in the pathogenesis after spinal cord injury (SCI). Here, we examined the neuroprotective effects of Angelica dahuricae radix (ADR) extract after SCI. ADR extract significantly decreased the levels of proinflammatory factors such as tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), interleukin-6 (IL-6), inducible nitric oxide synthase (iNOS), and cyclooxygenase-2 (COX-2) in a lipopolysaccharide (LPS)-activated microglial cell line, BV2 cells. ADR extract also significantly alleviated the level of reactive oxygen species in LPS-activated BV2 cells. To examine the neuroprotective effect of ADR extract after SCI, spinally injured rats were administered ADR extract orally at a dose of 100 mg/kg for 14 days. ADR extract treatment significantly reduced the levels of TNF-α, IL-1β, IL-6, iNOS, and COX-2. The levels of superoxide anion (O(2·)(-)) and protein nitration were also significantly decreased by ADR extract. In addition, ADR extract inhibited p38 mitogen-activated protein kinase activation and pronerve growth factor expression in microglia after SCI. Furthermore, ADR extract significantly inhibited caspase-3 activation following apoptotic cell death of neurons and oligodendrocytes, thereby improving functional recovery after injury. Thus, our data suggest that ADR extract provides neuroprotection by alleviating inflammation and oxidative stress and can be used as an orally administered therapeutic agent for acute SCI.
Noninvasive characterization of the fission yeast cell cycle by monitoring dry mass with digital holographic microscopy (2009)

Digital holography microscopy (DHM) is an optical technique which provides phase images yielding quantitative information about cell structure and cellular dynamics. Furthermore, the quantitative phase images allow the derivation of other parameters, including dry mass production, density, and spatial distribution. We have applied DHM to study the dry mass production rate and the dry mass surface density in wild-type and mutant fission yeast cells. Our study demonstrates the applicability of DHM as a tool for label-free quantitative analysis of the cell cycle and opens the possibility for its use in high-throughput screening.
Enhancing power and energy systems concepts with laboratory experience (2013)

A new interactive power engineering education laboratory has been recently constructed in the Energy Production and Infrastructure Center (EPIC) at UNC-Charlotte for providing a unique hands-on experience to power students. This facility, named as the AREVA Power Systems Teaching Lab, will be used as an integrated laboratory component for a number of undergraduate power courses in the department. The laboratory equipment can be configured to create exercises which reinforce basic concepts in electric machines and drives, power electronics, protection and power systems. The equipment may be interconnected to form full power system models and microgrids. Contemporary topics, such as smart grid concepts, microgrid management, distributed generation, renewable energy integration, energy storage, etc. form the major emphasis of the lab. New innovative interactive curricula that include class demonstrations and lab experiments are currently being developed for the undergraduate power and energy concentration within the department.
Four products from Escherichia coli pseudogenes increase hydrogen production (2013)

Pseudogenes are considered to be nonfunctional genes that lack a physiological role. By screening 3985 Escherichia coli mutants using chemochromic membranes, we found four pseudogenes involved in hydrogen metabolism. Knockouts of pseudogenes ydfW and ypdJ had a defective hydrogen phenotype on glucose and formate, respectively. Also, the knockout of pseudogene yqiG formed hydrogen from formate but not from glucose. For the yqiG mutant, 100% hydrogen recovery was obtained by the complementation of YqiG via a plasmid. The knockout of pseudogene ylcE showed hydrogen deficiency in minimal media which suggested that the role of YlcE is associated with cell growth. Hence, the products of these four pseudogenes play an important physiological role in hydrogen production in E. coli.
Evolved Sequence Contexts for Highly Efficient Amber Suppression with Noncanonical Amino Acids (2014)

The expansion of the genetic code with noncanonical amino acids (ncAA) enables the function of proteins to be tailored with high molecular precision. In this approach, the ncAA is charged to an orthogonal nonsense suppressor tRNA by an aminoacyl-tRNA-synthetase (aaRS) and incorporated into the target protein in vivo by suppression of nonsense codons in the mRNA during ribosomal translation. Compared to sense codon translation, this process occurs with reduced efficiency. However, it is still poorly understood, how the local sequence context of the nonsense codon affects suppression efficiency. Here, we report sequence contexts for highly efficient suppression of the widely used amber codon in E. coli for the orthogonal Methanocaldococcus jannaschii tRNA(Tyr)/TyrRS and Methanosarcina mazei tRNA(Pyl)/PylRS pairs. In vivo selections of sequence context libraries consisting of each two random codons directly up- and downstream of an amber codon afforded contexts with strong preferences for particular mRNA nucleotides and/or amino acids that markedly differed from preferences of contexts obtained in control selections with sense codons. The contexts provided high amber suppression efficiencies with little ncAA-dependence that were transferrable between proteins and resulted in protein expression levels of 70-110% compared to levels of control proteins without amber codon. These sequence contexts represent stable tags for robust and highly efficient incorporation of ncAA into proteins in standard E. coli strains and provide general design rules for the engineering of amber codons into target genes.
Bayesian semi-supervised audio event transcription based on Markov indian buffet process (2013)

We present a novel generative model for audio event transcription that recognizes “events” on audio signals including multiple kinds of overlapping sounds. In the proposed model, firstly, the overlapping audio events are modeled based on nonnegative matrix factorization into which Bayesian nonparametric approaches: the Markov Indian buffet process and the Chinese restaurant process, are incorporated. This approach allows us to automatically transcribe the events while avoiding the model selection problem by assuming a countably infinite number of possible audio events in the input signal. Then, Bayesian logistic regression annotates the audio frames with the multiple event labels in a semi-supervised learning setup. Experimental results show that our model can better annotate an audio signal in comparison with a baseline method. Additionally, we verify that our infinite generative model is also able to detect unknown audio events that are not included in the training data.
Preferred drug lists: Potential impact on healthcare economics (2008)

The number of concerns raised indicates that further studies are warranted regarding both short-term cost benefits as well as potential long-term effects of Medicaid PDL implementation. Objective analysis of these effects is necessary to ensure cost-effectiveness and quality of care.
Learning to Generate Image Source-Agnostic Universal Adversarial Perturbations (2020)

Adversarial perturbations are critical for certifying the robustness of deep learning models. A universal adversarial perturbation (UAP) can simultaneously attack multiple images, and thus offers a more unified threat model, obviating an image-wise attack algorithm. However, the existing UAP generator is underdeveloped when images are drawn from different image sources (e.g., with different image resolutions). Towards an authentic universality across image sources, we take a novel view of UAP generation as a customized instance of few-shot learning, which leverages bilevel optimization and learning-to-optimize (L2O) techniques for UAP generation with improved attack success rate (ASR). We begin by considering the popular model agnostic meta-learning (MAML) framework to meta-learn a UAP generator. However, we see that the MAML framework does not directly offer the universal attack across image sources, requiring us to integrate it with another meta-learning framework of L2O. The resulting scheme for meta-learning a UAP generator (i) has better performance (50% higher ASR) than baselines such as Projected Gradient Descent, (ii) has better performance (37% faster) than the vanilla L2O and MAML frameworks (when applicable), and (iii) is able to simultaneously handle UAP generation for different victim models and image data sources.
Growth, electrical and optical properties of SnO2: F on ZnO, Si and porous Si structures (2009)

In this work we have analyzed the optical absorption of the ZnO and SnO2:F (FTO) films and applied them in porous silicon light-emitting diodes. The absorption and energy gap were calculated by emp ...
Aorta and Skin Tissues Welded by Near-Infrared Cr 4+ :YAG Laser (2003)

The observation that welding strength as a function of wavelength follows the absorption bands of water suggests that absorption of light by water plays a significant role in laser tissue welding.
Exploiting the DNA Repair Defect in BRCA Mutant Cells in the Design of New Therapeutic Strategies for Cancer (2005)

Individuals harboring germ-line mutations in the BRCA1 or BRCA2 genes are at highly elevated risk of a variety of cancers. Ten years of research has revealed roles for BRCA1 and BRCA2 in a wide variety of cellular processes. However, it seems likely that the function of these proteins in DNA repair is critically important in maintaining genome stability. Despite this increasing knowledge of the defects present in BRCA-deficient cells, BRCA mutation carriers developing cancer are still treated similarly to sporadic cases. Here we describe our efforts, based on understanding the DNA repair defects in BRCAdeficient cells, to define the optimal existing treatment for cancers arising in BRCA mutation carriers and, additionally, the development of novel therapeutic approaches. Finally, we discuss how therapies developed to treat BRCA mutant tumors might be applied to some sporadic cancers sharing similar specific defects in DNA repair.
Progress on Ultra-Dense Quantum Communication Using Integrated Photonic Architecture (2012)

Abstract : We report on the theoretical and experimental progress, including the development of a large-alphabet quantum key distribution protocol that uses measurements in mutually unbiased bases. We also describe recent work for fine-key length analysis of the dispersive-optics QKD protocol, as well as security analysis based on the Franson interferometry measurement.