gebhart/patrepeval huggingface dataset:
Algorithms, Protocols and Cloud-RAN Implementation Aspects of 5G Networks (2018)

The future fifth generation (5G) mobile networks will support a number of use cases such as extreme Mobile BroadBand (eMBB), Ultra Reliable and Low Latency Communication (URLLC) and Machine Type Communications (MTC) with massive number of connected devices. The thesis studies implementation constraints of 5G requirements and proposes practical physical layer algorithms together with protocol and architectural designs that could support the 5G use cases. &#13;\n&#13;\nNetwork densification and centralized/co-ordinated processing are important elements that enable reliable and high-speed Internet access. Towards this end, Distributed Antenna Systems (DAS) and Massive MIMO with centralized processing will be used to serve high data rate applications and provide uniform coverage. Massive MIMO offers huge capacity gain by exploiting spatial diversity of the radio environment and minimizing interference among users. The main limiting factor is channel estimation error due to pilot-contamination which requires novel but practically realizable algorithms. MTC is characterized by huge number of low-data-rate users per cell. In many cases, MTC applications require transmission of only small number of packets per day. The classical cellular technologies are built on complex signaling protocols which can cause excessive overhead to MTC traffic. Another major concern in current cellular networks is deployment and maintenance costs which come from growing number of radio access technologies and deployment scenarios. This calls for a new architecture that enables flexible and low-cost deployments of various use cases. &#13;\n&#13;\nThe thesis tackles these problems both from theoretical and from practical implementation perspectives. First, multi-user access schemes for efficient use the radio resources are proposed and evaluated through analytical tools and simulations. The proposed techniques include signal processing techniques for DAS systems, and efficient but less complex data-aided channel estimation algorithm to combat pilot-contamination in Massive MIMO systems. Moreover, a new MAC protocols for MTC is proposed. The protocol significantly reduces the overhead and is able to support large number of simultaneous transmissions. Finally, the thesis addresses practical implementation aspects of 5G systems in a Cloud RAN infrastructure that allows coordinated/centralized processing of data across multiple cells. Virtualization of baseband processing also offers deployment flexibility and low maintenance cost.
FSMP-10. CYSTEINE INDUCES CYTOTOXICITY IN GLIOBLASTOMA THROUGH MITOCHONDRIAL HYDROGEN PEROXIDE PRODUCTION (2021)

Abstract Glioblastoma (GBM) is a poorly treatable disease with high mortality. Tumor metabolism in GBM is a critical mechanism responsible for growth because of upregulation of glucose, amino acid, and fatty acid utilization. However, little is known about the specific metabolic alterations in GBM that are targetable with FDA-approved compounds. To investigate metabolic signatures unique to GBM, we interrogated the TCGA and a cancer metabolite database for alterations in glucose and amino acid signatures in GBM relative to other human cancers and relative to low-grade glioma. From these analyses, we found that GBM exhibits the highest levels of cysteine and methionine pathway gene expression of 32 human cancers and that GBM exhibits high levels of cysteine metabolites compared to low-grade gliomas. To study the role of cysteine in GBM pathogenesis, we treated patient-derived GBM cells with FDA-approved cyst(e)ine-promoting compounds in vitro, including N-acetylcysteine (NAC) and the cephalosporin antibiotic, Ceftriaxone (CTX), which induces cystine import through system Xc transporter upregulation. Cysteine-promoting compounds, including NAC and CTX, inhibit growth of GBM cells, which is exacerbated by glucose deprivation. This growth inhibition is associated with reduced mitochondrial metabolism, manifest by reduction in ATP, NADPH/NADP+ ratio, mitochondrial membrane potential, and oxygen consumption rate. Mechanistic experiments revealed that cysteine compounds induce a rapid increase in the rate of H2O2 production in isolated GBM mitochondria, an effect blocked by the H2O2 scavenger, catalase. Such findings are consistent with reductive stress, a ROS-producing process whereby excess mitochondrial reducing equivalents prevent electron transfer to oxidized electron acceptors, inducing O2 reduction to H2O2. We show that cysteine-promoting compounds reduce cell growth and induce rapid mitochondrial toxicity in GBM, which may be due to reductive stress. This pathway is targetable with FDA-approved cysteine-promoting compounds and could synergize with glucose-lowering treatments, including the ketogenic diet, for GBM.
Throughput Maximization in Cooperation Based Symbiotic Cognitive Radio Networks (2010)

In the symbiotic cognitive radio (CR) networks, the CR users (CUs) may assist the primary transmission in a cooperation time, and obtain an incentive time for their own data transmission. In this letter, we study the throughput maximization problem in the symbiotic CR networks. Under the symbiosis and transmit power constraints, we aim to find the optimal cooperation time to assist the primary transmission and power allocations among the CUs. Given the cooperation time, the optimal power allocations can be solved by multi-level water-filling (MWF) with individual volume limits. A theoretical analysis is presented on the cooperation time and a modified bisection algorithm with low complexity is proposed to find the sub-optimal cooperation time. Simulation results show that the spectrum usage efficiency can be significantly improved as the number of CUs increases.
Maladies héréditaires du métabolisme en réanimation: explorations, stratégies diagnostiques et principes thérapeutiques (2012)

Les maladies héréditaires du métabolisme (MHM) sont dues à des mutations de gènes codant pour des enzymes ou des protéines du métabolisme. De nombreuses maladies métaboliques répondent à des traitements spécifiques, d’où l’importance d’en faire le diagnostic avant la survenue de lésions neurologiques irréversibles. Une maladie métabolique héréditaire doit être évoquée devant tout épisode neurologique aigu inexpliqué à n’importe quel âge, ce d’autant plus qu’il existe un facteur déclenchant (effort, infection, jeûne prolongé, chirurgie...). Les maladies par « intoxication endogène » et les troubles du métabolisme énergétique sont à évoquer en priorité en urgence. En plus de l’imagerie par résonance magnétique cérébrale qui permet souvent de guider le diagnostic et le type d’investigations, les dosages à demander devant une suspicion d’encéphalopathie métabolique sont l’ammoniémie, la lactatémie, la pyruvatémie, l’homocystéinémie, la recherche de porphyrines et de porphobilinogène, ainsi que les chromatographies des acides aminés plasmatiques et des acides organiques urinaires. L’interprétation des résultats et les modalités des traitements à mettre en oeuvre demandent une expertise particulière; d’où la nécessité d’avoir recours à un centre de référence ou de compétence.
Blind Watermarking of Three-Dimensional Meshes (2012)

Digital watermarking of three-dimensional (3-D) meshes has numerous potential applications and has received more and more attention from both academic researchers and industrial practitioners. This chapter focuses on the study of blind mesh watermarking techniques, which do not need the original cover mesh for watermark extraction and thus have a much larger application range than the non-blind techniques. The authors first review the existing methods proposed so far, by classifying them into three groups: fragile schemes, high-capacity schemes and robust schemes. They then present their recent work on quantization-based blind watermarking of semi-regular meshes. Finally, some future working directions are suggested.
Highly Enantioselective Hydrosilylation of Simple Ketones Catalyzed by Rhodium Complexes of P‐Chiral Diphosphine Ligands Bearing tert‐Butylmethylphosphino Groups. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
SuFEx Activation with Ca(NTf2)2: A Unified Strategy to Access Sulfamides, Sulfamates and Sulfonamides from S(VI) Fluorides (2020)

A method to activate sulfamoyl fluorides, fluorosulfates, and sulfonyl fluorides with calcium triflimide, and DABCO for SuFEx with amines is described. The reaction was applied to a diverse set of sulfamides, sulfamates, and sulfonamides at room temperature under mild conditions. Additionally, we highlight the application of this transformation to parallel medicinal chemistry to generate a broad array of nitrogen-based S(VI) compounds.
Monochromated Low-Voltage Aberration-Corrected TEM for Imaging the Soft/Hard Materials Interface (2012)

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.
Abstract 2560: MicroRNA target site polymorphisms and colorectal cancer risk in the Ashkenazi Jewish population. (2013)

Abstract MicroRNAs (miRNAs) act as key post-transcriptional regulators of gene expression via binding to the 3’ untranslated regions (UTRs) of mRNAs. Single nucleotide polymorphisms (SNPs) found in the miRNA sequence and/or corresponding binding sites can affect the fidelity of this interaction, and evidence from candidate miRNA studies suggests that such SNPs may increase or decrease risk of tumor development. This study was designed to expand the search for miRNA-related polymorphisms important in cancer etiology across the genome and to investigate the association between thousands of genetic variants in miRNA target sites and colorectal cancer (CRC) risk using a novel genotyping platform, the Axiom® miRNA Target Site Genotyping Array (237,858 markers). The final study sample after quality control filtering included 605 cases and 615 controls from the Molecular Epidemiology of Colorectal Cancer (MECC) study, a population-based case-control study of incident CRC cases in a geographically-defined area of northern Israel. The marginal association between each marker with minor allele frequency &amp;gt;=1% and CRC risk was examined assuming a log-additive genetic model using logistic regression adjusted for sex, age, and the first two principal components (PC) to capture fine-scale population structure. There were 11 markers with p-values less than 3E-4, and the most statistically significant association involved rs12130051 (chr1:19545053; 3’-UTR of KIAA0090) with an OR of 2.24 (1.52,3.31) and p=4.48E-5. In addition, rs1051690 (chr5:142605172; 3’-UTR of ARHGAP26), was statistically significantly associated with decreased CRC risk (OR (95% CI): 0.71 (0.59, 0.85); p = 2.03E-4). Further, this study provided evidence for replication of a previously published locus, rs1051690 in the 3’UTR region of the insulin receptor gene, INSR (OR (95% CI): 1.27 (0.96,1.67); p = 0.09). A fixed-effects meta-analysis of sample-size weighted p-values from a recent publication in Carcinogenesis describing the INSR variant (Landi et al., 2012) and from the current MECC study yielded a combined p-value of 0.01. To our knowledge, this is the first study to examine the association between genetic variation in miRNA target sites and cancer risk using a genome-wide approach. Work is ongoing to replicate findings from this study and to characterize the functional impact of prioritized polymorphisms. Citation Format: Stephanie L. Stenzel, Jeremy Gollub, Michael Shapero, Andrea Finn, Gad Rennert, Stephen B. Gruber. MicroRNA target site polymorphisms and colorectal cancer risk in the Ashkenazi Jewish population. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2560. doi:10.1158/1538-7445.AM2013-2560
Blood volume based dialysis patient-identification (2003)

In this paper a method for identifying and classifying hemodialysis patients based on the relative blood volume (RBV) is presented. A group of 42 hemodialysis patients were treated with a special ultrafiltration pattern. The response in RBV to this pattern was recorded and analysed. Using the steady state and time constant of a fitted and estimated function, the patients can clearly be separated into 4 different groups. The analysed parameters give information about the fluid-status, the hemodynamic stability and the physiologic and pathologic patient conditions.
Fabrication of Controllable Pore and Particle Size of Mesoporous Silica Nanoparticles via a Liquid-phase Synthesis Method and Its Absorption Characteristics (2011)

Monodisperse spherical mesoporous silica nanoparticles were successfully synthesized using a liquid‐phase synthesis method. The result showed particles with controllable pore size from several to tens nanometers with outer diameter of several tens nanometers. The ability in the control of pore size and outer diameter was altered by adjusting the precursor solution ratios. In addition, we have conducted the adsorption ability of the prepared particles. The result showed that large organic molecules were well‐absorbed to the prepared silica porous particles, in which this result was not obtained when using commercial dense silica particle and/or hollow silica particle. With this result, the prepared mesoporous silica particles may be used efficiently in various applications, such as sensors, pharmaceuticals, environmentally sensitive pursuits, etc.
The effect of fibers on coagulation of casein-based enteral nutrition in an artificial gastric digestion model (2014)

A serious complication seen in critically ill patients is the solidification of enteral nutrition causing gastrointestinal obstruction. It has been suggested that enteral nutrition enriched with insoluble fibers may increase the risk of this complication. Therefore, we investigate the effect of soluble and insoluble dietary fibers on the coagulation of a casein-based enteral nutrition in an artificial gastric digestion model. A 100% casein-based enteral nutrition was enriched with increasing concentrations of soluble fibers (acacia fiber, oligofructose and inulin) and insoluble fibers (soy polysaccharide, resistant starch and alpha cellulose). After digestion in an artificial gastric model, the chyme was poured over sequentially placed sieves, separating the coagulate into size fractions of larger than 2 mm, between 1 and 2 mm, and between 0.25 and 1 mm. Of these fractions we measured wet weight, dry weight and protein content. A significant effect on the fraction larger than 2 mm was considered to be clinically relevant. Addition of high concentrations soy polysaccharide and resistant starch to a casein-based enteral nutrition, did not alter the wet weight, whereas dry weight and protein content of the coagulate was significantly reduced. When high concentrations of soy polysaccharide and resistant starch are added to a 100% casein-based enteral nutrition, the coagulate consist of more water and less proteins, which may lead to an increased protein digestion and absorption in a clinical setting. The suggestion that insoluble fibers increase the risk of gastrointestinal obstruction in critically ill patients is not supported by these data.
Force Field for Tricalcium Silicate and Insight into Nanoscale Properties: Cleavage, Initial Hydration, and Adsorption of Organic Molecules (2013)

Improvements in the sustainability and durability of building materials depend on understanding interfacial properties of various mineral phases at the nanometer scale. Tricalcium silicate (C3S) is the major constituent of cement clinker and we present and validate a force field for atomistic simulations that provides excellent agreement with available experimental data, including X-ray structures, cleavage energies, elastic moduli, and IR spectra. Using this model and available measurements, we quantify key surface and interface properties of the dry and superficially hydrated mineral. An extensive set of possible cleavage planes shows cleavage energies in a range of 1300 to 1600 mJ/m2 that are consistent with the observation of faceted crystallites with an aspect ratio near one. Using pure and hydroxylated surface models that represent the first step in the hydration reaction, we examined the adsorption mechanism of several organic amines and alcohols at different temperatures. Strong attraction between −20 and −50 kcal/mol is found as a result of complexation of superficial calcium ions, electrostatic interactions, and hydrogen bonds on the ionic surface. Agglomeration of cleaved C3S surfaces in the absence of organic molecules was found to recover less than half the original cleavage energy (∼450 mJ/m2) associated with reduced Coulomb interactions between reconstructed surfaces. Additional adsorption of organic compounds below monolayer coverage reduced the attraction between even surfaces to less than 5% of the original cleavage energy (∼50 mJ/m2) related to their action as spacers between cleaved surfaces and mitigation of local electric fields. Computed agglomeration energies for a series of adsorbed organic compounds correlate with the reduction in surface forces in the form of measured grinding efficiencies. The force field is extensible to other cement phases and compatible with many platforms for molecular simulations (PCFF, COMPASS, CHARMM, AMBER, OPLS-AA, CVFF).
A non-functional neoepitope specific CD8+ T-cell response induced by tumor derived antigen exposure in vivo (2018)

Cancer-associated mutations, mostly single nucleotide variations, can act as neoepitopes and prime targets for effective anti-cancer T-cell immunity. T cells recognizing cancer mutations are critical for the clinical activity of immune checkpoint blockade (ICB) and they are potent vaccine antigens. High frequencies of mutation-specific T cells are rarely spontaneously induced. Hence, therapies that broaden the tumor specific T-cell response are of interest. Here, we analyzed neoepitope-specific CD8<sup>+</sup> T-cell responses mounted either spontaneously or after immunotherapy regimens, which induce local tumor inflammation and cell death, in mice bearing tumors of the widely used colon carcinoma cell line CT26. A comprehensive immune reactivity screening of 2474 peptides covering 628 transcribed CT26 point mutations was conducted. All tested treatment regimens were found to induce a single significant CD8<sup>+</sup> T-cell response against a non-synonymous D733A point mutation in the Smc3 gene. Surprisingly, even though Smc3 D733A turned out to be the immune-dominant neoepitope in CT26 tumor bearing mice, neither T cells specific for this neoepitope nor their T cell receptors (TCRs) were able to recognize or lyse tumor cells. Moreover, vaccination with the D733A neoepitope did not result in anti-tumoral activity despite induction of specific T cells. This is to our knowledge the first report that neoepitope specific CD8<sup>+</sup> T cells primed by tumor-released antigen exposure <i>in vivo</i> can be functionally irrelevant.
Free energy landscapes of the encapsulation mechanism of DNA nucleobases onto carbon nanotubes (2013)

The confinement mechanism of DNA nucleobases onto single-walled carbon nanotubes is probed at physiological temperature (310 K) using classical molecular dynamics and fully atomistic molecular potentials. The corresponding free energy landscapes are constructed in terms of two order parameters, ξ1 and ξ2, for both purine (adenine) and pyrimidine (thymine) moieties, by a metadynamics scheme. Two zig-zag topologies, (16, 0) and (23, 0), are employed as solid models with limiting skeletal diameters, D = 1.25 nm and D = 1.8 nm, respectively, considering hydrophobic and electrically charged nanopores, q = +0.05 e−/C. The uncharged nanotubes always exhibit a single free energy minimum located close to the pore center, regardless of individual diameter, whereas the charged nanotubes either inhibit encapsulation or exhibit two energetically distinct confining regions, at the center and close to the pore termini. Very interestingly, the purely hydrophobic solids exhibit a quasi-isotropic free-energy landscape around the nanopore center, F (ξ1, ξ2). Independent umbrella sampling calculations show that for the (23, 0) electrically charged nanotubes, the probability maximum at a distance of Ω = 0.54 nm from the pore center is the global one for adenine. These subtle differences are quantified by decomposing the interaction energy between a nucleobase and the solid into its dispersive and electrostatic contributions, and a critical comparison with DFT and experimental data for graphite is discussed. Purine and pyrimidine show similar interaction energies within the hydrophobic nanopores, however, adenine confinement results in slightly more stable hybrids by 0.9–1.4 kJ mol−1; binding affinity increases with the nanotube curvature as a result of enhanced dispersive energy. The detailed thermodynamical analysis reported herein is of paramount importance to study the sequence specific properties of DNA/carbon nanotube hybrids.
Faculty Opinions recommendation of Mutations in LCA5, encoding the ciliary protein lebercilin, cause Leber congenital amaurosis. (2007)

Leber congenital amaurosis (LCA) causes blindness or severe visual impairment at or within a few months of birth. Here we show, using homozygosity mapping, that the LCA5 gene on chromosome 6q14, which encodes the previously unknown ciliary protein lebercilin, is associated with this disease. We detected homozygous nonsense and frameshift mutations in LCA5 in five families affected with LCA. In a sixth family, the LCA5 transcript was completely absent. LCA5 is expressed widely throughout development, although the phenotype in affected individuals is limited to the eye. Lebercilin localizes to the connecting cilia of photoreceptors and to the microtubules, centrioles and primary cilia of cultured mammalian cells. Using tandem affinity purification, we identified 24 proteins that link lebercilin to centrosomal and ciliary functions. Members of this interactome represent candidate genes for LCA and other ciliopathies. Our findings emphasize the emerging role of disrupted ciliary processes in the molecular pathogenesis of LCA. PMID: 17546029 Funding information This work was supported by: Wellcome Trust, United Kingdom Grant ID: 068579 Wellcome Trust, United Kingdom Grant ID: 061682 Wellcome Trust, United Kingdom Grant ID: 073477
In vitro and in vivo pharmacological characterization of nociceptin/orphanin FQ tetrabranched derivatives (2014)

The results showed that the PWT can be successfully applied to the peptide sequence of N/OFQ to generate tetrabranched derivatives characterized by a pharmacological profile similar to the native peptide and associated with a higher potency and marked prolongation of action in vivo.
Digital Consciousness: The Business of Sensing, Modeling, Analyzing, Predicting, and Taking Action (2022)

Recent advances in genomics, neuroscience, and the general theory of information herald a new understanding of how information processing structures in nature operate. Living organisms use autopoietic and cognitive behaviors to manage the business of sensing, modeling, analyzing, predicting, and taking action to maintain stability in the face of non-deterministic and rapid fluctuations while dealing with finite resources. Autopoiesis provides self-management of the organism with an identity, and the ability to reconfigure its structure to maintain stability. Cognition allows sensing, analyzing, predicting, and acting to mitigate risk. This paper examines the key ingredients required to infuse autopoietic and cognitive behaviors into digital automata and make them self-managing to maintain stability in the face of fluctuations and mitigate risk in dealing with the external world.