gebhart/patrepeval huggingface dataset:
DiSCoVERing Innovative Therapies for Rare Tumors: Combining Genetically Accurate Disease Models with In Silico Analysis to Identify Novel Therapeutic Targets (2016)

We used human stem and progenitor cells to develop a genetically accurate novel model of MYC-driven Group 3 medulloblastoma. We also developed a new informatics method, Disease-model Signature versus Compound-Variety Enriched Response ("DiSCoVER"), to identify novel therapeutics that target this specific disease subtype. Experimental Design: Human neural stem and progenitor cells derived from the cerebellar anlage were transduced with oncogenic elements associated with aggressive medulloblastoma. An in silico analysis method for screening drug sensitivity databases (DiSCoVER) was used in multiple drug sensitivity datasets. We validated the top hits from this analysis in vitro and in vivo. Results: Human neural stem and progenitor cells transformed with c-MYC, dominant-negative p53, constitutively active AKT and hTERT formed tumors in mice that recapitulated Group 3 medulloblastoma in terms of pathology and expression profile. DiSCoVER analysis predicted that aggressive MYC-driven Group 3 medulloblastoma would be sensitive to cyclin-dependent kinase (CDK) inhibitors. The CDK 4/6 inhibitor palbociclib decreased proliferation, increased apoptosis, and significantly extended the survival of mice with orthotopic medulloblastoma xenografts. Conclusions: We present a new method to generate genetically accurate models of rare tumors, and a companion computational methodology to find therapeutic interventions that target them. We validated our human neural stem cell model of MYC-driven Group 3 medulloblastoma and showed that CDK 4/6 inhibitors are active against this subgroup. Our results suggest that palbociclib is a potential effective treatment for poor prognosis MYCdriven Group 3 medulloblastoma tumors in carefully selected patients.
Effect of HPV-Associated p16INK4A Expression on Response to Radiotherapy and Survival in Squamous Cell Carcinoma of the Head and Neck (2009)

Expression of p16(INK4A) has a major impact on treatment response and survival in patients with head and neck cancer treated with conventional radiotherapy.
Initial Rotor Position Estimation of Interior Permanent Magnet Synchronous Motor. (2003)

A new position sensorless control method is proposed for interior permanent magnet (IPM) synchronous motor drives at low speed and standstill. The method utilizes the dependence of inductance on rotor position in IPM. To estimate the position error directly, high frequency waves are injected to the motor voltage. The estimation is achieved by using ripple components of the motor current caused by injected waves. The controller directly estimates the error of rotor position, and adjusts the phase angle to the rotor position. At the initial position estimation, it is possible to estimate the initial rotor position including the direction of the magnetization. The basic idea, computer simulation and experimental results are discussed in this paper.
Synthesis of the Four 3‐Aminotricyclo[2.2.1.0(2,6)] Heptane‐1,3‐dicarboxylic Acid Isomers. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Inhibition of Epidermal Growth Factor Receptor-associated Tyrosine Kinase Blocks Glioblastoma Invasion of the Brain (1997)

OBJECTIVE: Glioblastoma multiforme is a malignant primary brain tumor associated with short patient survival despite aggressive treatment, in part because of its propensity to aggressively infiltrate into brain tissue. Glioblastoma multiforme is also unique because it is the only nonepithelial human tumor for which excessive activation of epidermal growth factor receptor (EGFR) has been consistently linked to tumor growth and patient survival, and EGFR activation promotes glioblastoma multiforme infiltration in vitro. METHODS: Cocultures of human glioblastoma spheroids (derived from three separate patients) and fetal rat brain aggregates were examined for infiltration using confocal microscopy, in the presence of 0 to 100 µmol/L genistein, a tyrosine kinase (TK) inhibitor, and 3 µmol/L tyrphostin A25, a specific EGFR-TK inhibitor. RESULTS: Infiltration (not attachment) was completely inhibited by genistein at 10µmol/L, the IC20 for monolayer growth inhibition in two cell lines. Tyrphostin A25 at 3 µmol/L (the IC20 for monolayers) reduced invasion in a third cell line from 38.8 ± 6.1% invasion-hour per hour (n = 5) to 2.9 ± 1.2% invasion-hour per hour (n = 6)(P = 0.0002, two-tailed t test, 93% inhibition), and from 0.54 ± 0.065% per hour (slope) to 0.028 ± 0.018% per hour(P = 0.00001, 95% inhibition). Maximal percent invasion was reduced from 100 ± 0 to 7.4 ± 5.6% of the fetal rat brain aggregate. No change was detected in EGFR-associated tyrosine phosphorylation at those doses in monolayers by 32P immunolabeling, consistent with the known effects of low concentrations of TK inhibitors. An increase in expression of wild-type and truncated EGFR was demonstrated by Western blotting. Invasion was equally well inhibited by a monoclonal antibody to the high-affinity ligand binding domain of EGFR and not by antibody to an inactive domain. CONCLUSION: Our observations support the role of EGFR activation as a determinant by which glioblastoma invades normal brain tissue, and we show that invasion can be effectively inhibited at much lower concentrations of TK inhibitors than are necessary for growth suppression.
The Antiandrogenic Action of Gonadotropin-Releasing Hormone and Its Agonists on the Mouse Kidney* (1982)

It was recently demonstrated that GnRH and its agonists can inhibit the growth-promoting effects of testosterone on the prostate and seminal vesicle of the rat. In the present study, the kinetics and mechanism of this antiandrogenic response were investigated on the mouse kidney, an organ that has been used extensively to investigate androgen action. GnRH and its agonist, [(imBzl)-D-His6,Pro9-NEt]GnRH (D-His), inhibited the increase in kidney β-glucuronidase activity induced by testosterone propionate (TP) in castrated male mice. D-His also inhibited the action of TP on this enzyme in castrated hypophysectomized male mice. When D-His (10 μgday) was administered with various doses of TP (20–160 μg/day), the dose-dependent increase in β-glucuronidase activity was blunted. Similarly, D-His (0.1–100 μg/day) produced a dose-dependent decrease in the renal β-glucuronidase activity of castrated male mice treated with TP (80 μg/day). Even though GnRH and its agonist inhibited the action of TP in male NCS and Balb/C mice, these peptides slightly potentiated the action of TP on renal β-glucuronidase activity in female mice of these strains. D-His did not compete with [3H]methyltrienolone for binding sites on the androgen receptor as measured in an in vitro assay. In addition, the administration of D-His with TP in vivo did,not affect the total cytosol receptor activity as measured with an exchange assay. It is concluded that the antiandrogenic actions of GnRH and its agonists are not mediated via the androgen receptor in a manner comparable to that of steroid antagonists since 1) no competition between peptide and steroid could be demonstrated for the androgen receptor, and 2) the inhibitory actions of GnRH peptides were not uniform between the kidneys from male and female mice, which are equally sensitive to testosterone. The finding that GnRH has antisteroidal activity on the kidney and other tissues raises the possibility that this, or a similar peptide, could act as a local regulator of hormone action on extragonadal organs.
ChemInform Abstract: OZONOLYTIC CLEAVAGE OF CYCLOALKENES TO TERMINALLY DIFFERENTIATED PRODUCTS (1983)

Abstract Die Ozonolyse der Cycloalkene (I) in Gegenwart von Alkoholen wie Methanol liefert als erste faßbare Zwischenstufe die Verbindung (II), die in Gegenwart von Aminen mit Acetanhydrid zu den Aldehydestern (III) führt.
Reaction patterning of YBa2Cu3O7−δ thin films on Si (1990)

A novel technique exploiting the severe chemical reaction between Si and YBa2Cu3O7−δ (YBCO) has been developed for patterning epitaxial YBCO films in situ. Patterning is achieved by etching features in epitaxial YSZ on Si(100), and then depositing a final layer of YBCO; the material which grows on the exposed Si is insulating. Linewidths down to 3 μm have been demonstrated with a zero resistance critical temperature (Tc) of 86 K and a transport critical current density of 1.6×106 A/cm2 at 77 K. 45° and low-angle twist grain boundaries occur under some circumstances but can be eliminated by regrowing 20 Å of homoepitaxial YSZ on the surface prior to YBCO growth. Si diffusion in insulating portions has been characterized by x-ray photoemission spectroscopy, indicating vertical diffusion through the film.
The elimination of sidelobes in the arrayed waveguide WDM (1996)

Narrow channel wavelength division multiplexing (WDM) is an attractive technique for increasing the capacity of optical fibre transmission systems. An essential component for WDM systems is a wavelength demultiplexer capable of providing high levels of isolation between adjacent channels. Additionally if the components are to be deployed in large volumes then they will be required to be low cost. Silica-on-silicon technology is an attractive technology for producing such components1.
Temporal Tensor Transformation Network for Multivariate Time Series Prediction (2020)

Multivariate time series prediction has applications in a wide variety of domains and is considered to be a very challenging task, especially when the variables have correlations and exhibit complex temporal patterns, such as seasonality and trend. Many existing methods suffer from strong statistical assumptions, numerical issues with high dimensionality, manual feature engineering efforts, and scalability. In this work, we present a novel deep learning architecture, known as Temporal Tensor Transformation Network, which transforms the original multivariate time series into a higher order of tensor through the proposed Temporal-Slicing Stack Transformation. This yields a new representation of the original multivariate time series, which enables the convolution kernel to extract complex and non-linear features as well as variable interactional signals from a relatively large temporal region. Experimental results show that Temporal Tensor Transformation Network outperforms several state-of-the-art methods on window-based predictions across various tasks. The proposed architecture also demonstrates robust prediction performance through an extensive sensitivity analysis.
Approximate absolute rate constants for the reactions of tributyltin radicals with aryl and vinyl halides (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTApproximate absolute rate constants for the reactions of tributyltin radicals with aryl and vinyl halidesDennis P. Curran, Craig P. Jasperse, and Michael J. TotlebenCite this: J. Org. Chem. 1991, 56, 25, 7169–7172Publication Date (Print):December 1, 1991Publication History Published online1 May 2002Published inissue 1 December 1991https://pubs.acs.org/doi/10.1021/jo00025a040https://doi.org/10.1021/jo00025a040research-articleACS PublicationsRequest reuse permissionsArticle Views1021Altmetric-Citations44LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Adhesion to Carbon Nanotube Conductive Scaffolds Forces Action-Potential Appearance in Immature Rat Spinal Neurons (2013)

In the last decade, carbon nanotube growth substrates have been used to investigate neurons and neuronal networks formation in vitro when guided by artificial nano-scaled cues. Besides, nanotube-based interfaces are being developed, such as prosthesis for monitoring brain activity. We recently described how carbon nanotube substrates alter the electrophysiological and synaptic responses of hippocampal neurons in culture. This observation highlighted the exceptional ability of this material in interfering with nerve tissue growth. Here we test the hypothesis that carbon nanotube scaffolds promote the development of immature neurons isolated from the neonatal rat spinal cord, and maintained in vitro. To address this issue we performed electrophysiological studies associated to gene expression analysis. Our results indicate that spinal neurons plated on electro-conductive carbon nanotubes show a facilitated development. Spinal neurons anticipate the expression of functional markers of maturation, such as the generation of voltage dependent currents or action potentials. These changes are accompanied by a selective modulation of gene expression, involving neuronal and non-neuronal components. Our microarray experiments suggest that carbon nanotube platforms trigger reparative activities involving microglia, in the absence of reactive gliosis. Hence, future tissue scaffolds blended with conductive nanotubes may be exploited to promote cell differentiation and reparative pathways in neural regeneration strategies.
Efficient synthesis of the Cu-SSZ-39 catalyst for DeNOx applications (2015)

By using a faujasite zeolite as the sole Si and Al source with simple ammonium cyclic cations, it has been possible to synthesize the SSZ-39 zeolite with high yields, and to prepare a catalyst for potential industrial applications in the SCR of NOx.
Are There Set Theoretic Possible Worlds? (1985)

Journal Article Are there set theoretic possible worlds? Get access Selmer Bringsjord Selmer Bringsjord Brown University, ProvidenceRhode Island 02912, U.S.A. Search for other works by this author on: Oxford Academic Google Scholar Analysis, Volume 45, Issue 1, January 1985, Page 64, https://doi.org/10.1093/analys/45.1.64 Published: 01 January 1985
Tetrahydroisoquinolines as Orexin Receptor Antagonists: Strategies for Lead Optimization by Solution-Phase Chemistry (2003)

Different techniques can be applied for the automated production of small and large compound collections. Large libraries that are often generated and tested during the lead-finding stage of a project are typically produced by solid-phase chemistry. Libraries that are significantly smaller in size are often synthesized in solution. Chemistry in solution is rather versatile, offers numerous advantages and is therefore often the method of choice for generating small libraries during a lead optimization process. Fast and reliable purification procedures are required to yield compounds of high quality that can be immediately used in biological as well as pharmacological assays. Solution-phase chemistry combined with automated purification was applied to optimize initial lead inhibitors for the two human orexin receptors OX1 and OX2. Starting from a submicro-molar OX1 selective lead compound, low nanomolar analogues with improved physico-chemical properties were synthesized that antagonize either one or both orexin receptors.
Immunization with Recombinant Sao Protein Confers Protection against Streptococcus suis Infection (2007)

Sao is a Streptococcus suis surface protein recently identified as a potential vaccine candidate. In this study, recombinant Sao in combination with Quil A provided cross-protection against S. suis serotype 2 disease in mouse and pig vaccination protocols. Subcutaneous immunization of mice elicited strong immunoglobulin G (IgG) antibody responses. All four IgG subclasses were induced, with the IgG2a titer being the highest, followed by those of IgG1, IgG2b, and IgG3. Challenge of the mice with S. suis strain 31533 resulted in a mortality rate of 80% for the control group, which received Quil A only. In contrast, all of the mice immunized with Sao survived. In a pig vaccination protocol, intramuscular immunization with Sao also elicited significant humoral antibody responses, and both the IgG1 and IgG2 subclasses were induced, with a predominance of IgG2 production. In vitro assay showed that Sao-induced antibodies significantly promoted the ability of porcine neutrophils in opsonophagocytic killing of S. suis. An aerosol challenge of the pigs with S. suis strain 166 resulted in clinical signs characteristic of S. suis infection in diseased pigs. The vaccine group showed significantly better survival, lower clinical scores, and less S. suis recovery from postmortem tissue samples than did the control group. Furthermore, this study also revealed that although challenge S. suis strains express Sao size variants, recombinant Sao conferred cross-protection. These data demonstrate that recombinant Sao formulated with Quil A triggers strong opsonizing antibody responses which confer efficient immunity against challenge infection with heterologous S. suis type 2.
Supplementary Methods and Supplementary Figure Legend from Novel Target for Peptide-Based Imaging and Treatment of Brain Tumors (2023)

&lt;p&gt;PDF - 72K, Supplementary Methods and Legend for Supplementary Figures 1 and 2.&lt;/p&gt;
PMD and PDL Tolerances of Transmitter-side Non-linear Mitigation in 112 Gb/s DP-QPSK Transmission (2012)

We experimentally demonstrate that the transmitter-side non-linear mitigation, combination of non-linear pre-distortion with RZ carving is robust against polarization mode dispersion and polarization dependent loss in real-time 112 Gb/s DP-QPSK transmission over 2,000km mixed fiber link.
A 25. 3 <inline-formula> <tex-math notation="LaTeX">$\mu$ </tex-math> </inline-formula>W at 60 fps <inline-formula> <tex-math notation="LaTeX">$240 \times 160$ </tex-math> </inline-formula> Pixel Vision Sensor for Motion Capturing With In-Pixel Nonvolatile Analog Memory Using CAAC-IGZO FET (2016)

Utilizing a c-axis-aligned crystalline oxide semiconductor-based FET, we have fabricated a vision sensor with in-pixel nonvolatile analog memory. The sensor realized normal image data capturing, captured differential data of a given reference frame, and retained the captured data for an extended time in each pixel. Moreover, the sensor realized normal global shutter image capturing and motion capturing by extracting differential images. This is performed using the captured data and depends on the presence or absence of differences between normal images and reference images. The sensor has three operating modes: an imaging mode, a motion capturing mode, and a wait mode. Importantly, power consumption is reduced by powering off circuit blocks that are in a standby state.
Dietary glucoraphanin prevents the onset of psychosis in the adult offspring after maternal immune activation (2018)

Maternal immune activation (MIA) contributes to behavioral abnormalities relevant to schizophrenia in adult offspring, although the molecular mechanisms underlying MIA-induced behavioral changes remain unclear. Here we demonstrated that dietary intake of glucoraphanin (GF), the precursor of a natural antioxidant sulforaphane, during juvenile and adolescent stages prevented cognitive deficits and loss of parvalbumin (PV) immunoreactivity in the medial prefrontal cortex (mPFC) of adult offspring after MIA. Gene set enrichment analysis by RNA sequencing showed that MIA caused abnormal expression of centrosome-related genes in the PFC and hippocampus of adult offspring, and that dietary intake of GF improved these abnormal gene expressions. Particularly, MIA increased the expression of suppressor of fermentation-induced loss of stress resistance protein 1 (Sfi1) mRNA in the PFC and hippocampus of adult offspring, and dietary intake of GF prevented the expression of Sfi1 mRNA in these regions. Interestingly, we found altered expression of SFI1 in the postmortem brains and SFI1 mRNA in hair follicle cells from patients with schizophrenia compared with controls. Overall, these data suggest that centrosome-related genes may play a role in the onset of psychosis in offspring after MIA. Therefore, dietary intake of GF-rich vegetables in high-risk psychosis subjects may prevent the transition to psychosis in young adulthood.
Anomaly Detection in Dynamic Networks (2013)

Anomaly detection in dynamic communication networks has many important security applications. These networks can be extremely large and so detecting any changes in their structure can be computationally challenging; hence, computationally fast, parallelisable methods for monitoring the network are paramount. For this reason the methods presented here use independent node and edge based models to detect locally anomalous substructures within communication networks. As a first stage, the aim is to detect changes in the data streams arising from node or edge communications. Throughout the thesis simple, conjugate Bayesian models for counting processes are used to model these data streams. A second stage of analysis can then be performed on a much reduced subset of the network comprising nodes and edges which have been identified as potentially anomalous in the first stage. The first method assumes communications in a network arise from an inhomogeneous Poisson process with piecewise constant intensity. Anomaly detection is then treated as a changepoint problem on the intensities. The changepoint model is extended to incorporate seasonal behaviour inherent in communication networks. This seasonal behaviour is also viewed as a changepoint problem acting on a piecewise constant Poisson process. In a static time frame, inference is made on this extended model via a Gibbs sampling strategy. In a sequential time frame, where the data arrive as a stream, a novel, fast Sequential Monte Carlo (SMC) algorithm is introduced to sample from the sequence of posterior distributions of the changepoints over time. A second method is considered for monitoring communications in a large scale computer network. The usage patterns in these types of networks are very bursty in nature and don't fit a Poisson process model. For tractable inference, discrete time models are considered, where the data are aggregated into discrete time periods and probability models are fitted to the communication counts. In a sequential analysis, anomalous behaviour is then identified from outlying behaviour with respect to the fitted predictive probability models. Seasonality is again incorporated into the model and is treated as a changepoint model on the transition probabilities of a discrete time Markov process. Second stage analytics are then developed which combine anomalous edges to identify anomalous substructures in the network.
Glucose Fluxes During OGTT in Adolescents Assessed by a Stable Isotope Triple Tracer Method (2008)

The triple tracer method provided accurate assessment of Ra(ogtt), EGP and Rd fluxes during an OGTT in adolescents. Thus, this method might provide novel insight on postprandial glucose fluxes in children/adolescents under various conditions.