gebhart/patrepeval huggingface dataset:
Hybrid analog–digital precoding design for satellite systems (2021)

The work investigates the feasibility of massive multiple-input multiple-output (MIMO) in SatCom. Toward this, the necessary channel models, system parameters, and scenarios are identified and a basic simulator is developed. The work then considers an efficient implementation of the massive MIMO transmission through the use of hybrid analog/digital precoder. Efficient algorithmic solutions are proposed for the partially connected precoder architecture which enables efficiency in power/hardware complexity and its performance evaluated.
Effects of insulin replacement on cardiac apoptotic and survival pathways in streptozotocin‐induced diabetic rats (2009)

Increased myocyte apoptosis in diabetic hearts has been previously reported. Therefore, the purpose of this study was to evaluate the effects of insulin on cardiac apoptotic, hypertrophic, and survival pathways in streptozotocin (STZ)-induced diabetic rats. Forty-eight male Wistar rats at 8 weeks of age were randomly divided into control group (Control), STZ-induced (65 mg/kg STZ i.v.) Type 1-like diabetic rats (DM), and DM rats with 4 IU insulin replacement (DI) for 4 and 8 weeks, respectively. The levels of protein involved in cardiac apoptotic, hypertrophic, and survival pathways were measured by Western blotting. Cardiac mitochondrial-dependent apoptotic pathways, such as Bad, cytosolic cytochrome c, activated caspase 9 and 3, and calcineurin-nuclear factor activation transcription 3 (NFAT3) hypertrophic pathway in DM were increased compared to Control and attenuated in DI group after 8 weeks whereas those were not found after 4 weeks. Cardiac anti-apoptotic Bcl2 and phosphorylated-Bad were significantly decreased in DM group but not in DI group after 8 weeks. Insulin-like growth factor-I receptor (IGFIR), phosphatidylinositol 3'-kinase (PI3K), and the protein kinase B (Akt) were significantly decreased in DM relative to Control and DI after 8 weeks whereas those were not found after 4 weeks. Insulin replacement not only prevents activation of the cardiac mitochondrial-dependent apoptotic pathway and calcineurin-related NFAT3 hypertrophic pathway in diabetes but it also enhances the cardiac insulin/IGFIR-PI3K-Akt survival pathway, all of which are attenuated with insulin therapeutic duration-dependent manners. The findings may provide possible diabetes-related apoptotic, hypertrophic, and survival pathways for potentially preventing cardiac abnormality in diabetes.
Site-Directed Mutagenesis on Putative Macrolactone Ring Size Determinant in the Hybrid Pikromycin-Tylosin Polyketide Synthase (2003)

Streptomyces venezuelae ATCC 15439 is notable in its ability to produce two distinct groups of macrolactones. It has been reported that the generation of two macrolactone structures results from alternative expression of pikromycin (Pik) polyketide synthase (PKS). It was previously reported that the hybrid pikromycin-tylosin PKS can also produce two different macrolactones but its mechanistic basis remains unclear. In order to address this question, a series of site-directed mutagenesis of tentative alternative ribosome binding site and translation start codons in tylGV were performed. The results suggest that macrolactone ring size is not determined by the alternative expression of TylGV but through other mechanism(s) involving direct interaction between the PikAIII and TE domain or skipping of the final chain elongation step. This provides new insight into the mechanism of macrolactone ring size determination in hybrid PKS as well as an opportunity to develop novel termination activities for combinatorial biosynthesis.
Combining Renewable Solar and Open Air Cooling for Greening Internet-Scale Distributed Networks (2019)

The widespread adoption and popularity of Internet-scale Distributed Networks (IDNs) has led to an explosive growth in the infrastructure of these networks. Unfortunately, this growth has also led to a rapid increase in energy consumption with its accompanying environmental impact. Therefore, energy efficiency is a key consideration in operating and designing these power-hungry networks. In this paper, we study the greening potential of combining two contrasting sources of renewable energy, namely solar energy and Open Air Cooling (OAC). OAC involves the use of outside air to cool data centers if the weather outside is cold and dry enough. Therefore OAC is likely to be abundant in colder weather and at night-time. In contrast, solar energy is correlated with sunny weather and day-time. Given their contrasting natures, we study whether synthesizing these two renewable sources of energy can yield complementary benefits. Given the intermittent nature of renewable energy, we use batteries and load shifting to facilitate the use of green energy and study trade-offs in brown energy reduction based on key parameters like battery size, number of solar panels, and radius of load movement. We do a detailed cost analysis, including amortized cost savings as well as a break-even analysis for different energy prices. Our results look encouraging and we find that we can significantly reduce brown energy consumption by about 55% to 59% just by combining the two technologies. We can increase our savings further to between 60% to 65% by adding load movement within a radius of 5000kms, and to between 73% to 89% by adding batteries.
Fine-Tuning Electronic Properties of Luminescent Pt(II) Complexes via Vertex-Differentiated Coordination of Sterically Invariant Carborane-Based Ligands (2018)

We report the synthesis of two isomeric Pt(II) complexes ligated by doubly deprotonated 1,1′-bis(o-carborane) (bc). This work provides a potential route to fine-tune the electronic properties of luminescent metal complexes by virtue of vertex-differentiated coordination chemistry of carborane-based ligands.
Intermittent process analysis with scattering moments (2015)

Scattering moments provide nonparametric models of random processes with stationary increments. They are expected values of random variables computed with a nonexpansive operator, obtained by iteratively applying wavelet transforms and modulus nonlinearities, which preserves the variance. First- and second-order scattering moments are shown to characterize intermittency and self-similarity properties of multiscale processes. Scattering moments of Poisson processes, fractional Brownian motions, Lévy processes and multifractal random walks are shown to have characteristic decay. The Generalized Method of Simulated Moments is applied to scattering moments to estimate data generating models. Numerical applications are shown on financial time-series and on energy dissipation of turbulent flows.
Combining Particle-Based Simulations and Machine Learning to Understand Defect Kinetics in Thin Films of Symmetric Diblock Copolymers (2021)

The self-assembly of soft matter provides a practical and scalable route toward the production of nanostructured materials, with minimal need for direct intervention at nanoscopic length scales. Symmetric diblock copolymers, which can self-assemble into a lamellar phase, are a prototype for this class of materials. In this work, we introduce a machine learning model that is trained by intermediate time-scale simulations of a soft, coarse-grained model. The aim of the model is to simulate defect kinetics in the lamellar morphology, as the material relaxes toward equilibrium. To do so, we exploit the physical characteristics of overdamped dynamics and formulate the problem of time evolution as a Markov chain. The trained artificial neural network (ANN) predicts a time-independent transition probability from one time step to the next. As a result, we arrive at a method that can be repeatedly applied to generate long-time trajectories. Predicting defect kinetics in this manner provides hitherto unavailable insights into the late-time dynamics of block copolymer relaxation. The neural network is purposely designed to be independent of input size, which enables training on small systems, and enabling predictions over large scales. As a demonstration of these capabilities, in this work, we leverage the ANN to obtain information about the statistics of defect motion and lifetimes over a long-range ordering process.
Suppl Fig Table Legends from SMAD4 Loss Is Associated with Cetuximab Resistance and Induction of MAPK/JNK Activation in Head and Neck Cancer Cells (2023)

&lt;p&gt;Supplemental figure and table legends&lt;/p&gt;
Numerical Simulations of the Flow Past Crescent Cylinders – Flow Monitoring (2023)

Abstract The flow characteristics of the vortex shedding system behind two cylinders that have a crescent cross-section, were numerically studied using a lattice Boltzmann approach. Two configurations ate considered, in one the crescent is facing the flow and in the other facing the flow downstream. The system of vortices formed behind the crescent cylinders was compared to the classical case of a circular cylinder for the same geometrical, physical and dynamic conditions at varying Reynolds numbers. The flow properties from all three cases studied have revealed that the crescent shape affects strongly the shedding mechanism. The numerical results showed that the flow past the crescent facing downstream of the flow was very similar to that of the circular cylinder, whereas there were remarkable differences when compared to the crescent cylinder facing the flow upstream.
Characterization of Peptide‐Nanostructure‐Modified Electrodes and Their Application for Ultrasensitive Environmental Monitoring (2010)

Dense arrays of self-assembled nanostructures are highly important for the fabrication of high-performance sensors of large surface area. The organized incorporation of novel biocompatible organic nanostructures into extremely sensitive amperometric biosensors is demonstrated. Peptide nanoforest biosensors for phenol detection were 17-fold more sensitive than uncoated electrode and more sensitive than those modified with carbon nanotubes or combined coating. The high sensitivity reported, together with the biocompatibility and the ability to chemically and biologically modify these elements, may provide a novel platform for biosensors design and fabrication for environmental monitoring, homeland security, and other applications.
Detection of the BRAFV600E protein in human colon carcinomas by a mutation-specific antibody. (2013)

3576 Background: BRAF encodes a serine-threonine kinase that is a downstream effector of activated RAS. A point mutation (V600E) in BRAF occurs in a subset of colorectal cancers (CRCs) and is associated with adverse outcome and may predict non response to anti-EGFR antibodies. Detection of a BRAF V600E mutation in a CRC with microsatellite instability indicates a sporadic origin and excludes Lynch Syndrome. While BRAF V600E mutation status is determined using a DNA-based assay, antibodies against the BRAF V600E protein have recently been developed. We examined mutant BRAF V600E protein expression and its concordance with mutation status. Methods: Primary stage III colon carcinomas (50 BRAF V600E mutation carriers and 25 wild-type cases) were studied from a completed phase III adjuvant trial comparing FOLFOX +/- cetuximab (NCCTG N0147). In archival resection specimens, immunohistochemistry (IHC) was performed using a pan-BRAF antibody and a V600E mutation-specific antibody raised against an immunogenic synthetic peptide derived from the internal region of the BRAF V600E protein. BRAF V600E mutations in codon 15 were analyzed in extracted DNA using a multiplex, allele specific PCR–based assay. BRAF staining was scored independently by two pathologists blinded to mutation status. Results: In primary colon carcinomas stained with a pan-BRAF antibody, diffuse cytoplasmic staining for BRAF proteins was detected in 74 of 75 carcinomas with one case deemed non-evaluable. Using the mutation-specific BRAF V600E antibody, diffuse cytoplasmic staining was detected in 49 of 74 tumors without appreciable heterogeneity of expression. Among these 49 tumors expressing mutant BRAF V600E proteins, all (100%) were found to carry a BRAF V600E mutation according to a DNA-based assay. In contrast, absent BRAF V600E staining was observed in all 25 tumors that were found to have wild-type copies of BRAF V600E detected using a PCR-based assay. Conclusions: For the detection of mutant BRAF V600E , complete concordance was found between IHC and a DNA-based method in colon carcinomas. This finding supports the use of IHC as a simplified strategy to screen CRCs for mutant BRAF V600E proteins in routine clinical practice to inform clinical decision-making.
A Conditional Generative Matching Model for Multi-lingual Reply\n Suggestion (2021)

We study the problem of multilingual automated reply suggestions (RS) model\nserving many languages simultaneously. Multilingual models are often challenged\nby model capacity and severe data distribution skew across languages. While\nprior works largely focus on monolingual models, we propose Conditional\nGenerative Matching models (CGM), optimized within a Variational Autoencoder\nframework to address challenges arising from multi-lingual RS. CGM does so with\nexpressive message conditional priors, mixture densities to enhance\nmulti-lingual data representation, latent alignment for language\ndiscrimination, and effective variational optimization techniques for training\nmulti-lingual RS. The enhancements result in performance that exceed\ncompetitive baselines in relevance (ROUGE score) by more than 10\\% on average,\nand 16\\% for low resource languages. CGM also shows remarkable improvements in\ndiversity (80\\%) illustrating its expressiveness in representation of\nmulti-lingual data.\n
ICONE15-10619 CONDENSATION HEAT TRANSFER ON A VERTICAL TUBE UNDER NON-CONDENSABLE GAS CONDITION (2007)

The Passive Containment Cooling System (PCCS), which remove heat released inside the containment vessel by steam condensation without using active components such as a pump during a postulated design-basis accident, have been investigated extensively. The PCCS is one of the promising safety systems which operates under the design basis accidents and protects the containment vessel by preventing heating and pressurizing. A new type of PCCS with vertical heat transfer tubes has been proposed by us, which is a closed circuit cooling system installed vertically through the containment vessel wall and cools gases inside the containment vessel and is cooled by natural convection outside of it. The objective of this study is to evaluate the mean condensation heat transfer coefficients on the external surface of the perpendicular tube for the new concept of PCCS under a non-condensable gas presence. In this paper, the effects of non-condensable gas concentration and pressure on the heat removal characteristics of the PCCS with vertical heat transfer tubes for a large dry concrete containment to mitigate containment pressure under Loss of Coolant Accident and the mean condensation heat transfer coefficients under a non-condensable gas presence are discussed.
A Systematic Approach to Identify Biased Agonists of the Apelin Receptor through High-Throughput Screening (2017)

Biased agonists are defined by their ability to selectively activate distinct signaling pathways of a receptor, and they hold enormous promise for the development of novel drugs that specifically elicit only the desired therapeutic response and avoid potential adverse effects. Unfortunately, most high-throughput screening (HTS) assays are designed to detect signaling of G protein-coupled receptors (GPCRs) downstream of either G protein or β-arrestin-mediated signaling but not both. A comprehensive drug discovery program seeking biased agonists must employ assays that report on the activity of each compound at multiple discrete pathways, particularly for HTS campaigns. Here, we report a systematic approach to the identification of biased agonists of human apelin receptor (APJ). We synthesized 448 modified versions of apelin and screened them against a cascade of cell-based assays, including intracellular cAMP and β-arrestin recruitment to APJ, simultaneously. The screen yielded potent and highly selective APJ agonists. Representative hits displaying preferential signaling via either G-protein or β-arrestin were subjected to a battery of confirmation assays. These biased agonists will be useful as tools to probe the function and pharmacology of APJ and provide proof of concept of our systematic approach to the discovery of biased ligands. This approach is likely universally applicable to the search for biased agonists of GPCRs.
Surface Activity of an Amphiphilic Association Structure (2005)

Results are presented strongly suggest surface activity of an inverse micelle in an aromatic hydrocarbon/surfactant solution, in which the surfactant itself shows negative adsorption to the surface.
Developmental Characterization of Thymosin β4 and β10 Expression in Enriched Neuronal Cultures from Rat Cerebella (1995)

The beta 4 and beta 10 thymosins are G-actin binding proteins that exhibit complex patterns of expression during rat cerebellar development. Their expression in vivo is initially high in immature granule cells and diminishes as they migrate and differentiate, ceasing altogether by postnatal day 21. Thymosin beta 4 is present in a subset of glia throughout postnatal development, and its synthesis is also induced in maturing Bergmann glia. In contrast, thymosin beta 10 is only present at very low levels in a very small subpopulation of glia in the adult cerebellum. To study the factors differentially regulating expression of the beta-thymosins, we characterized their patterns of expression in primary cultures of rat cerebellum. Both beta-thymosins were initially expressed in granule cells, although expression, especially of thymosin beta 4, was truncated compared with the in vivo time course. As in vivo, thymosin beta 4 was synthesized at much higher levels in astrocytes and microglia in cultures from postnatal cerebellum than was thymosin beta 10. Unlike in vivo, the latter was expressed in glia cultured from fetal cerebellum. The similarities between the in vivo and in vitro expression of the beta-thymosins show that modulation of tissue culture conditions could be used to identify factors regulating beta-thymosin expression in vivo. The differences would identify regulatory mechanisms that are not evident from the in vivo studies alone.
Impact of the Framework Type on the Regeneration of Coked Zeolites by Non-Thermal Plasma in a Fixed Bed Dielectric Barrier Reactor (2019)

The formation of coke as a result of propene transformation at 623 K on zeolites results from a product shape selectivity mechanism of which the products are polyaromatic molecules, such as pyrene on MFI, anthracene on MOR, pyrene and coronene on FAU. Zeolite regeneration can be achieved by using non-thermal plasma (NTP), with decreased energy consumption, employing a fixed bed dielectric barrier reactor. The efficiency of this alternative regeneration process depends on the coke toxicity. On MFI and FAU (featuring three-dimensional 10 and 12 ring channel systems, respectively) coking occurs by poisoning the Brønsted acid sites; on MOR, (presenting a one-dimensional 12 ring channel system) pore blocking takes place, leading to higher coke toxicity. A complete coke removal is achieved on MFI and FAU zeolites using NTP within 3 h, while for MOR coke, removal proceeds slower and is incomplete after 3 h on stream. Hence, the efficiency of regeneration is impacted by the accessibility of active oxygenated species generated under plasma (e.g., O*, O2+) to coke molecules.
Heterojunction double dumb-bell Ag2Te–Te–Ag2Te nanowires (2012)

Growth of isolated axial heterojunction nanowires by a solution phase growth process is reported. The dumb-bell shaped nanowires contain two silver telluride sections at the extremes joined by a tellurium section. Reaction of silver nitrate with tellurium NWs in aqueous solution at a molar ratio of 1 : 1 leads to the formation of amorphous partially silver reacted Te NWs. Low temperature (75 °C) solution phase annealing of these silver deficient NWs results in phase segregation producing crystalline Ag(2)Te and Te phases with clear phase boundaries along the wire axis. Structural characterization of these dumb-bell shaped NWs was performed with different microscopic and spectroscopic tools. Solution phase silver concentration over the course of annealing indicated leaching of silver into the solution during the formation of biphasic NWs. Similar Ag : Te ratios were observed in both partially silver reacted Te NWs and phase segregated Ag(2)Te-Te-Ag(2)Te NWs and this was attributed to redeposition of leached silver on the amorphous NW tips which eventually resulted in complete phase segregation. Successful integration of different chemical components in single NWs is expected to open up new application possibilities as physical and chemical properties of the heterostructure can be exploited.
Aberrant succination of proteins in fumarate hydratase‐deficient mice and HLRCC patients is a robust biomarker of mutation status (2011)

Germline mutations in the FH gene encoding the Krebs cycle enzyme fumarate hydratase predispose to hereditary leiomyomatosis and renal cell cancer (HLRCC) syndrome. FH-deficient cells and tissues accumulate high levels of fumarate, which may act as an oncometabolite and contribute to tumourigenesis. A recently proposed role for fumarate in the covalent modification of cysteine residues to S-(2-succinyl) cysteine (2SC) (termed protein succination) prompted us to assess 2SC levels in our existing models of HLRCC. Herein, using a previously characterized antibody against 2SC, we show that genetic ablation of FH causes high levels of protein succination. We next hypothesized that immunohistochemistry for 2SC would serve as a metabolic biomarker for the in situ detection of FH-deficient tissues. Robust detection of 2SC was observed in Fh1 (murine FH)-deficient renal cysts and in a retrospective series of HLRCC tumours (n = 16) with established FH mutations. Importantly, 2SC was undetectable in normal tissues (n = 200) and tumour types not associated with HLRCC (n = 1342). In a prospective evaluation of cases referred for genetic testing for HLRCC, the presence of 2SC-modified proteins (2SCP) correctly predicted genetic alterations in FH in every case. In two series of unselected type II papillary renal cancer (PRCC), prospectively analysed by 2SCP staining followed by genetic analysis, the biomarker accurately identified previously unsuspected FH mutations (2/33 and 1/36). The investigation of whether metabolites in other tumour types produce protein modification signature(s) that can be assayed using similar strategies will be of interest in future studies of cancer.
The in vivo Response of a C3H Mammary Carcinoma to Treatment with Misonidazole, Cyclophosphamide and Radiation (1990)

The potential chemosensitizing effect of the nitroaromatic radiosensitizer misonidazole (MISO) on the alkylating agent cyclophosphamide (CTX), and the interactions of these agents with radiation, have been investigated in a C3H mammary carcinoma in CDF1 mice. MISO at 1,000 mg/kg caused a small increase in tumour growth time (TGT; time to reach 3 times treatment volume) from 3.6 days to 4.5 days. CTX (100 mg/kg) increased the TGT to 15.7 days. The combined treatment of MISO and CTX given with intervals of either 15 min or 4 h increased the TGT to 23.3 and 23.8 days respectively. The radiation enhancement ratio (ER) was found to be 2.13 and 1.10 for MISO administered before or after x-rays respectively. The corresponding ERs for CTX were 1.16 and 1.22. The two drugs given in combination resulted in significant radiation ERs of 2.68 (both drugs given within 30 min before x-rays), 3.00 (MISO 30 min before and CTX 3 1/2 h after x-rays) and 1.40 (both drugs given after x-rays). In contrast to what has previously been reported, and in contrast to the tumour regrowth delay data, the results of the tumour control experiments were found to reflect no more than an additive action of the two drugs when used together with radiation in vivo.