gebhart/patrepeval huggingface dataset:
Abstract B25: SMARCA4/BRG1 and AP-1 co-regulate an epithelial-like signature in small-cell carcinoma of ovary, hypercalcemic type (SCCOHT) (2020)

Abstract Mutations in SMARCA4 (BRG1), one of the two mutually exclusive ATPases of the SWI/SNF chromatin remodeling complex, occur in &amp;gt;95% of small cell carcinomas of the ovary, hypercalcemic type (SCCOHT), a rare and aggressive form of ovarian cancer. Because of its apparent role as a driver for SCCOHT, we performed integrative multi-omic analyses in a SCCOHT cell line +/- BRG1 re-expression to identify its role in SCCOHT tumorigenesis. After re-expression, BRG1 was recruited to both distal and promoter regions. We also observed increased chromatin accessibility at distal sites enriched for transcription factor binding motifs for AP-1 family members. Of interest, BRG1 re-expression induced an epithelial-like gene and protein expression concomitant with enrichment of AP-1 motifs at the TSS of highly upregulated epithelial genes. To determine the biologic relevance of these changes at AP-1 binding sites, we used a dominant negative AP-1 cell line to demonstrate that the necessity of AP-1 DNA binding activity and BRG1 re-expression for the protein expression of epithelial genes. Our study demonstrates that BRG1 loss may drive SCCOHT tumorigenesis by diminishing an epithelial-like gene and protein signature of its cell of origin driven by altered AP-1 binding. Citation Format: Krystal A. Orlando, Jesse R. Raab, Amber K. Douglas, Aierken Abudu, Yemin Wang, Gian Luca Negri, Shane Colborne, Gregg B. Morin, Jessica D. Lang, William P.D. Hendricks, Elizabeth A. Raupach, Patrick Pirrotte, David G. Huntsman, Jeffrey M. Trent, Joel S. Parker, Bernard E. Weissman. SMARCA4/BRG1 and AP-1 co-regulate an epithelial-like signature in small-cell carcinoma of ovary, hypercalcemic type (SCCOHT) [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr B25.
Slot-antenna for autonomous sensor systems mounted on overhead power lines (2011)

A slot antenna for mounting on overhead power lines is presented. The antenna enables autonomous sensor systems to communicate in the 2.4 GHz band. Using two radiating slots the simulated antenna gain is 7.9 dBi. The usable bandwidth is more than 300 MHz. The general concept of the sensor system is outlined. It contains a DC-isolating bandpass filter with 1.5 dB insertion loss and more than 60 dB attenuation at frequencies below 1.0 GHz. Experiments performed on a deactivated power line confirm that the conductors and the power poles do not influence the radiation characteristic significantly. The transmission follows the Friis transmission equation. Using only 7.5 dBm of transmitted power yields -79.9 dBm at the receiver side at a distance of 1420 m. The immunity to interference of the communication system was tested by exposing it to strong artificially generated partial discharges.
Synergistic activation of functional estrogen receptor (ER)-alpha by DNA methyltransferase and histone deacetylase inhibition in human ER-alpha-negative breast cancer cells. (2001)

Formation of transcriptional repression complexes such as DNA methyltransferase (DNMT) 1/histone deacetylase (HDAC) or methyl-CpG binding protein/HDAC is emerging as an important mechanism in silencing a variety of methylated tissue-specific and imprinted genes. Our previous studies showed that treatment of estrogen receptor (ER)-alpha-negative human breast cancer cells with the DNMT inhibitor 5-aza-2'-deoxycytidine (5-aza-dC) led to ER mRNA and protein re-expression. Also, the HDAC inhibitor trichostatin A (TSA) could induce ER transcript about 5-fold. Here we show that 5-aza-dC alone induced ER transcript about 30-40-fold, and the addition of TSA elevated ER mRNA expression about 10-fold more in the human ER-negative breast cancer cell lines MDA-MB-231 and MDA-MB-435. Overall, the combination of 5-aza-dC and TSA induced a 300-400-fold increase in ER transcript. Restoration of estrogen responsiveness was demonstrated by the ability of the induced ER protein to elicit estrogen response element-regulated reporter activity from an exogenous plasmid as well as induce expression of the ER target gene, progesterone receptor. The synergistic activation of ER occurs concomitantly with markedly reduced soluble DNMT1 expression and activity, partial demethylation of the ER CpG island, and increased acetylation of histones H(3) and H(4). These data suggest that the activities of both DNMT1 and HDAC are key regulators of methylation-mediated ER gene silencing.
Electrochemical Cyclization of Dipeptides To Form Novel Bicyclic, Reverse-Turn Peptidomimetics. 2. Synthesis and Conformational Analysis of 6,5-Bicyclic Systems (1996)

Novel, highly constrained, 6,5-bicyclic dipeptides (1-aza-5-oxa-2-oxobicyclo[4.3.0]nonane ring skeletons, 2) have been synthesized by a one-step electrochemical cyclization from the dipeptides Boc-(S)-serine-(S)-proline-OMe (Boc-(S)-Ser-(S)-Pro-OMe, 3) and Boc-(R,S)-α-methylserine-(S)-proline-OMe (Boc-(R,S)-α-MeS-(S)-Pro-OMe, 12) in yields of 10−25% and 41%, respectively. The one-pot reaction uses selective anodic amide oxidation to generate an N-acyliminium cation which is trapped by an intramolecular hydroxyl group. The cyclization of Boc-(S)-Ser-(S)-Pro-OMe (3) to the 6,5-bicyclic skeleton 4 was highly diastereoselective, generating a new chiral center with an S configuration. This bicyclic compound was sufficiently stable to trifluoroacetic acid and anhydrous hydrofluoric acid for use in standard solid phase peptide synthesis methodologies. Oxidation of Boc-(R,S)-MeS-(S)-Pro-OMe (12) gave different results for each diastereoisomer. Cyclization only occurred for the S,S-diastereoisomer with very low stereoselectivity (6:4 ratio of diastereomers) at the newly-formed ring fusion. In terms of conformation, the 6,5-bicyclic system restricts two (ψ2 and φ3) of the four torsion angles that characterize a reverse turn. Conformational analyses of tetrapeptides containing the 6,5-bicyclic system were performed using Monte Carlo conformational searches and molecular dynamics simulations. All of the eight possible diastereomers arising from the three stereogenic centers (Ser Cα, Pro Cα, and newly formed bridgehead) were considered. These studies revealed that the 3S,7S,10S and 3R,7R,10R configurations are effective turn inducers although the torsion angles of the backbone do not exactly mimic those of classical β-turns. Other diastereomers were found to stabilize the peptide backbone in an extended conformation.
Fast restoration of real-time communication service from component failures in multi-hop networks (1997)

For many applications it is important to provide communication services with guaranteed timeliness and fault-tolerance at an acceptable level of overhead. In this paper, we present a scheme for restoring real-time channels, each with guaranteed timeliness, from component failures in multi-hop networks. To ensure fast/guaranteed recovery, backup channels are set up a priori in addition to each primary channel. That is, a dependable real-time connection consists of a primary channel and one or more backup channels. If a primary channel fails, one of its backup channels is activated to become a new primary channel. We describe a protocol which provides an integrated solution to the failure-recovery problem (i.e., channel switching, resource re-allocation, ...). We also present a resource sharing method that significantly reduces the overhead of backup channels. The simulation results show that good coverage (in recovering from failures) can be achieved with about 30% degradation in network utilization under a reasonable failure condition. Moreover, the fault-tolerance level of each dependable connection can be controlled, independently of other connections, to reflect its criticality.
Recent advances in cluster analysis (2008)

Purpose The purpose of this paper is to provide a review of the issues related to cluster analysis, one of the most important and primitive activities of human beings, and of the advances made in recent years. Design/methodology/approach The paper investigates the clustering algorithms rooted in machine learning, computer science, statistics, and computational intelligence. Findings The paper reviews the basic issues of cluster analysis and discusses the recent advances of clustering algorithms in scalability, robustness, visualization, irregular cluster shape detection, and so on. Originality/value The paper presents a comprehensive and systematic survey of cluster analysis and emphasizes its recent efforts in order to meet the challenges caused by the glut of complicated data from a wide variety of communities.
Opportunities for RTL and gate level simulation using GPUs (2020)

This paper summarizes the opportunities in accelerating simulation on parallel processing hardware platforms such as GPUs. First, we give a summary of prior art. Then, we propose the idea that coding frameworks usually used for popular machine learning (ML) topics, such as PyTorch/DGL.ai, can also be used for exploring simulation purposes. We demo a crude oblivious two-value cycle gate-level simulator using the higher level ML framework APIs that exhibits >20X speedup, despite its simplistic construction. Next, we summarize recent advances in GPU features that may provide additional opportunities to further state-of-the-art results. Finally, we conclude and touch upon some potential areas for furthering research into the topic of GPU accelerated simulation.
Age-Related Macular Degeneration and Cancer Mortality in the Atherosclerosis Risk in Communities Study (2007)

Middle-aged African American individuals with early AMD may be at increased risk of dying of cancer, particularly lung cancer. This association was not present in white individuals and needs confirmation in other studies.
Organocatalytic selective coupling of episulfides with carbon disulfide for the synthesis of poly(trithiocarbonate)s and cyclic trithiocarbonates (2022)

Selective coupling of CS 2 with episulfides affords perfectly alternating poly(trithiocarbonate)s or cyclic trithiocarbonates upon the onium salts used.
Constructions of fractional repetition codes from combinatorial designs (2013)

We consider the design of regenerating codes for distributed storage systems at the minimum bandwidth regeneration (MBR) point. Our codes consist of an outer MDS code followed by an inner fractional repetition (FR) code (introduced in prior work). In these systems a failed node can be repaired by simply downloading packets from surviving nodes. We present constructions that use the Kronecker product to construct new fractional repetition codes from existing codes. We demonstrate that an infinite family of codes can be generated by considering the Kronecker product of two Steiner systems that have the same storage capacity. The resultant code inherits its normalized repair bandwidth from the storage capacity of the original Steiner systems and has the maximum level of failure resilience possible. We also present some properties of the Kronecker product of resolvable designs and the corresponding file sizes.
Synaptic vesicle proteins under conditions of rest and activation: Analysis by 2‐D difference gel electrophoresis (2006)

Synaptic vesicles are organelles of the nerve terminal that secrete neurotransmitters by fusion with the presynaptic plasma membrane. Vesicle fusion is tightly controlled by depolarization of the plasma membrane and a set of proteins that may undergo post-translational modifications such as phosphorylation. In order to identify proteins that undergo modifications as a result of synaptic activation, we induced massive exocytosis and analysed the synaptic vesicle compartment by benzyldimethyl-n-hexadecylammonium chloride (BAC)/SDS-PAGE and difference gel electrophoresis (DIGE) followed by MALDI-TOF-MS. We identified eight proteins that revealed significant changes in abundance following nerve terminal depolarization. Of these, six were increased and two were decreased in abundance. Three of these proteins were phosphorylated as detected by Western blot analysis. In addition, we identified an unknown synaptic vesicle protein whose abundance increased on synaptic activation. Our results demonstrate that depolarization of the presynaptic compartment induces changes in the abundance of synaptic vesicle proteins and post-translational protein modification.
Blind CFO estimation in OFDM systems (2005)

We rely on a kurtosis-type criterion to derive blind carrier frequency offset (CFO) estimation algorithms for various orthogonal frequency-division multiplexing (OFDM) systems. Identifiability and performance of the resulting blind CFO estimators depend on the channel's frequency selectivity and the input distribution. We also apply this approach to blind CFO estimation in multiinput multioutput (MIMO) OFDM systems. The effects of multiple antennas are addressed analytically and tested via simulations.
Cobalt Phthalocyanine Catalyzed Aerobic Oxidation of Secondary Alcohols: An Efficient and Simple Synthesis of Ketones. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Applications of liquid biopsies for cancer (2019)

Liquid biopsies have the potential to detect, characterize, and monitor cancers earlier than is possible with conventional approaches.
Soluble manganese(iv); a new chemiluminescence reagent (2001)

The oxidations of twenty five organic and inorganic species, with solublised manganese(IV), were found to elicit analytically useful chemiluminescence with detection limits (3 × S/N) for Mn(II), Fe(II), morphine and codeine of 5 × 10−8 M, 2.5 × 10−7 M, 7.5 × 10−8 M and 5 × 10−8 M, respectively. Additionally, the corrected spectra from four different analytes gave wavelengths of maximum emission in the range from 733 nm up to 740 nm suggesting that all these chemiluminescence reactions shared a common emitting species.
Expression Cloning of a Na+-independent Aromatic Amino Acid Transporter with Structural Similarity to H+/Monocarboxylate Transporters (2001)

A cDNA was isolated from rat small intestine by expression cloning which encodes a novel Na+-independent transporter for aromatic amino acids. When expressed in Xenopus oocytes, the encoded protein designated as TAT1 (T-type amino acid transporter 1) exhibited Na+-independent and low-affinity transport of aromatic amino acids such as tryptophan, tyrosine, and phenylalanine (Km values: approximately 5 mm), consistent with the properties of classical amino acid transport system T. TAT1 accepted some variations of aromatic side chains because it interacted with amino acid-related compounds such as l-DOPA and 3-O-methyl-DOPA. Because TAT1 accepted N-methyl- and N-acetyl-derivatives of aromatic amino acids but did not accept their methylesters, it is proposed that TAT1 recognizes amino acid substrates as anions. Consistent with this, TAT1 exhibited sequence similarity (approximately 30% identity at the amino acid level) to H+/monocarboxylate transporters. Distinct from H+/monocarboxylate transporters, however, TAT1 was not coupled with the H+ transport but it mediated an electroneutral facilitated diffusion. TAT1 mRNA was strongly expressed in intestine, placenta, and liver. In rat small intestine TAT1 immunoreactivity was detected in the basolateral membrane of the epithelial cells suggesting its role in the transepithelial transport of aromatic amino acids. The identification of the amino acid transporter with distinct structural and functional characteristics will not only facilitate the expansion of amino acid transporter families but also provide new insights into the mechanisms of substrate recognition of organic solute transporters.
Oxidative Stress Is Associated with Greater Mortality in Older Women Living in the Community (2007)

Greater oxidative stress, as indicated by elevated serum protein carbonyl concentrations, was associated with greater risk of death in older women living in the community who were moderately to severely disabled. Prevention of oxidative stress may reduce the risk of mortality.
Field emission study of decomposition of ammonia on individual tungsten planes (1976)

The decomposition of ammonia adsorbed on the 211, 100 and 110 tungsten planes was studied by means of a probe-hole field emission microscope, at low pressures and over a wide range of temperatures. The experimental system consisted of a field emission tube combined with a molecular beam apparatus. The results obtained indicate that when ammonia interacts with a clean surface decomposition begins below 300 K and is completed above 400 K on all planes, the only products being hydrogen and nitrogen. On the 211 and 111 planes both nitrogen are initially adsorbed. On the 100 plane only nitrogen remains above 400 K. At about 600 K nitrogen leaves the 211 plane by surface diffusion. This causes an increase of nitrogen coverage on the 111 plane. When NH3 is adsorbed onto the 100 plane, precovered with nitrogen, the decomposition process terminates at higher temperatures compared with the clean surface. Species containing hydrogen are formed and are most probably bound to the surface via N—N bonds. These species decompose above 600 K to give nitrogen in the β1 state in addition to the existing β2 layer. On the 110 plane incomplete results were obtained owing to difficulties caused by field desorption.
Different Domains of Pseudomonas aeruginosa Exoenzyme S Activate Distinct TLRs (2004)

Some bacterial products possess multiple immunomodulatory effects and thereby complex mechanisms of action. Exogenous administration of an important Pseudomonas aeruginosa virulence factor, exoenzyme S (ExoS) induces potent monocyte activation leading to the production of numerous proinflammatory cytokines and chemokines. However, ExoS is also injected directly into target cells, inducing cell death through its multiple effects on signaling pathways. This study addresses the mechanisms used by ExoS to induce monocyte activation. Exogenous administration resulted in specific internalization of ExoS via an actin-dependent mechanism. However, ExoS-mediated cellular activation was not inhibited if internalization was blocked, suggesting an alternate mechanism of activation. ExoS bound a saturable and specific receptor on the surface of monocytic cells. ExoS, LPS, and peptidoglycan were all able to induce tolerance and cross-tolerance to each other suggesting the involvement of a TLR in ExoS-recognition. ExoS activated monocytic cells via a myeloid differentiation Ag-88 pathway, using both TLR2 and the TLR4/MD-2/CD14 complex for cellular activation. Interestingly, the TLR2 activity was localized to the C-terminal domain of ExoS while the TLR4 activity was localized to the N-terminal domain. This study provides the first example of how different domains of the same molecule activate two TLRs, and also highlights the possible overlapping pathophysiological processes possessed by microbial toxins.
Thalamic functional connectivity predicts seizure laterality in individual TLE patients: Application of a biomarker development strategy (2014)

Noninvasive markers of brain function could yield biomarkers in many neurological disorders. Disease models constrained by coordinate-based meta-analysis are likely to increase this yield. Here, we evaluate a thalamic model of temporal lobe epilepsy that we proposed in a coordinate-based meta-analysis and extended in a diffusion tractography study of an independent patient population. Specifically, we evaluated whether thalamic functional connectivity (resting-state fMRI-BOLD) with temporal lobe areas can predict seizure onset laterality, as established with intracranial EEG. Twenty-four lesional and non-lesional temporal lobe epilepsy patients were studied. No significant differences in functional connection strength in patient and control groups were observed with Mann-Whitney Tests (corrected for multiple comparisons). Notwithstanding the lack of group differences, individual patient difference scores (from control mean connection strength) successfully predicted seizure onset zone as shown in ROC curves: discriminant analysis (two-dimensional) predicted seizure onset zone with 85% sensitivity and 91% specificity; logistic regression (four-dimensional) achieved 86% sensitivity and 100% specificity. The strongest markers in both analyses were left thalamo-hippocampal and right thalamo-entorhinal cortex functional connection strength. Thus, this study shows that thalamic functional connections are sensitive and specific markers of seizure onset laterality in individual temporal lobe epilepsy patients. This study also advances an overall strategy for the programmatic development of neuroimaging biomarkers in clinical and genetic populations: a disease model informed by coordinate-based meta-analysis was used to anatomically constrain individual patient analyses.
Optimization of sawtooth surface-relief gratings: effects of substrate refractive index and polarization (2006)

The effect of the refractive index of the substrate together with the incident polarization on the optimization of sawtooth surface-relief gratings (SRGs) is investigated. The global optimum diffraction efficiencies of the -1st forward-diffracted order of sawtooth SRGs are 63.3% occurring at n2=1.47 for TE polarization and 73.8% occurring at n2=2.88 for TM polarization. Incident TE polarization has higher optimum diffraction efficiency than TM polarization for all n2<1.85. In contrast, TM polarization has higher optimum diffraction efficiency than TE polarization for all n2>1.85. A polymer (n2=1.5) optimum sawtooth SRG exhibits 62.6% efficiency for TE polarization. A silicon (n2=3.475) optimum sawtooth SRG exhibits 68.6% efficiency for TM polarization. These sawtooth SRGs are compared to right-angle-face trapezoidal SRGs. It is found that the optimum profiles of right-angle-face trapezoidal SRGs have only very slightly increased efficiencies over sawtooth SRGs (0.04% for TE and 0.55% for TM).
Investigation of Phase Transitional Behavior of Poly(l-lactide)/Poly(d-lactide) Blend Used to Prepare the Highly-Oriented Stereocomplex (2007)

By using the highly oriented 1:1 stoichiometric blend of high-molecular-weight PLLA and middle-molecular-weight PDLA species and by choosing a suitable annealing condition, we have succeeded for the first time to observe the phase transition phenomenon in the heating and cooling processes by measuring the temperature dependence of the X-ray fiber diagram and polarized IR spectra. The as-drawn sample was found to consist of the two crystalline phases; disordered α form (α‘) and stereocomplex (βc). In the heating process, the α‘ form was found to be reorganized into the oriented α phase above 120 °C, which melted around 180 °C. However, by heating this sample some more, some parts of the molten chains are found to crystallize on the surface of the βc crystallites with high degree of chain orientation. In the subsequent cooling process from the βc phase, the unoriented α crystal appeared at around 120 °C and coexisted with the highly oriented βc crystals.