gebhart/patrepeval huggingface dataset:
Turbo-like Decoding Algorithm for Structured LDPC codes (2006)

This paper presents a high-speed "turbo-like" decoding algorithm for certain structured LDPC codes such as those adopted in IEEE 802.16e and in the draft 802.11n standards. It is shown that after a key modification, such LDPC codes may be processed as generalized repeat accumulate codes, codes which are known to support "turbo-like" decoding. A GRA-like encoder of structured LDPC codes is derived, which in turn leads to the decoding algorithm. It is also shown that the "structured" properties result in an inherent parallelism, leading to an efficient high speed decoder implementation
Encapsulation of Hydrophobic Porphyrins into Biocompatible Nanoparticles: An Easy Way to Benefit of Their Two-Photon Phototherapeutic Effect without Hydrophilic Functionalization (2022)

Star-shaped hydrophobic porphyrins, acting as powerful fluorescent two-photon photosensitizers for oxygen in organic solvents, can easily be loaded into PMLABe polymeric nanoparticles at various concentrations. In this contribution, the performance of these porphyrin-containing nanoparticles in terms of photodynamic therapy (PDT) is compared to those of the corresponding water-soluble porphyrin analogues when irradiated in MCF-7 cancer cells. While quite promising results are obtained for performing PDT with these nanoparticles, validating this approach as a mean for using more easily accessible and less expensive photosensitizers, from a synthetic perspective, we also show that their luminescence can still be used for bioimaging purposes in spite of their confinement in the nanoparticles, validating also the use of these nano-objects for theranostic purposes.
Tuning the electrochemiluminescent properties of iridium complexes of N-heterocyclic carbene ligands (2018)

A series of five heteroleptic Ir(iii) complexes of the general form Ir(dfppy)2(C^C) have been prepared (where dfppy represents 2-(2,4-difluorophenyl)pyridine and C^C represents a bidentate cyclometalated phenyl substituted imidazolylidene ligand). The cyclometalated phenyl ring of the imidazolylidene ligand was either unsubstituted or substituted with electron donating (OMe and Me) or electron withdrawing (Cl and F) groups in the 2 and 4 positions. The synthesised Ir(iii) complexes have been characterised by elemental analysis, NMR spectroscopy, cyclic voltammetry and electronic absorption and emission spectroscopy. The molecular structures for four Ir(iii) complexes were determined by single crystal X-ray diffraction. Each of the Ir(iii) complexes exhibited intense photoluminescence in acetonitrile solution at room temperature with quantum yields (ΦPL) ranging from 58% to 86%. Cyclic voltammetry experiments revealed one oxidation process (formally ascribed to the metal centre), and two ligand-based reductions for each complex. Complexes 1-5 gave moderate to intense annihilation and co-reactant electrochemiluminescence (ECL). Consideration of the electrochemical, spectroscopic and theoretical investigations provide insights into the electrochemiluminescence behaviour.
Comparison of tissue segmentation algorithms in neuroimage analysis software tools (2008)

Accurate segmentation of different brain tissues is of much importance in magnetic resonance imaging. This paper presents a comparison of the existing segmentation algorithms that are deployed in the neuroimaging community as part of two widely used software packages. The results obtained in this comparison can be used to select the appropriate segmentation algorithm for the neuroimaging application of interest. In addition to the entire brain area, a comparison is carried out for the subcortical region of the brain in terms of its gray matter composition.
Testing specificity and sensitivity of wastewater-based epidemiology for detecting SARS-CoV-2 in four communities on Vancouver Island, Canada (2022)

We report wastewater surveillance of the spread of SARS-CoV-2 based upon 24-h composite influent samples taken weekly from four wastewater treatment plants (WWTP) on Vancouver Island, BC, Canada between January 3, 2021 and July 10, 2021. Samples were analyzed by reverse transcription quantitative polymerase chain reaction targeting the N1 and N2 gene fragments of SARS-CoV-2 and a region of the replication associate protein of the pepper mottle mosaic virus (PMMoV) serving as endemic control. Only a small proportion of samples had quantifiable levels of N1 or N2. Overall case rates are weakly correlated with the concentration (gene copies/L) and with the flux of viral material influent to the WWTP (gene copies/day); the latter accounts for influent flow variations. Poisson multimodal rank correlation accounts for differences between the four WWTP and shows a significant correlation with a significant positive intercept. Receiver operator characteristics (ROC) analysis confirms a cut-off of cases based on amplified/not-amplified experimental data. At the optimal cut point of 19 (N1) or 17 (N2) cases/week/100,000 the sensitivity and specificity is about 75% for N1 and 67% for N2.
Silicon Photonics-Based All-Optical Image Compression (2023)

We demonstrate an all-optical image compression technique using on-chip nanophotonic disordered media to perform local random transformations. Our compression technique is fast, scalable, and may consume about 50 times less energy than electronic compression.
1079 Effect of milk yield genotype on hepatic metabolic gene expression and repeated lipopolysaccharide (LPS) administration (2016)

Objectives were to determine effects of milk yield genotype on hepatic expression of genes related to the somatotropic axis and glucose and lipid metabolism during an LPS challenge. Multiparous cows (n = 12/genotype) from unselected (stable milk yield since 1964, UH) and contemporary (CH) Holsteins that differed by more than 4500 kg milk/305-d were housed together and fed the same diet ad libitum for more than 4 mo before being blocked (2/genotype) by DIM and randomly assigned within genotype to receive saline or 0.25 μg/kg BW of LPS (Escherichia coli 055:B5). Cows were synchronized to be at Day 8 of their estrous cycle for the first challenge (C1) at 70–84 DIM. Liver biopsies were collected at 0, 4, and 24 h relative to treatment. A second identical challenge (C2) and sampling was conducted 4 d later. RNA was extracted and expression of 23 genes associated with metabolism were determined by digital multiplexed analysis (nanoString nCounter). Expression was normalized to the positive control and the geometric mean of 4 internal control genes. Data were transformed (square root) and analyzed by repeated measures using PROC MIXED (SAS) with time as the repeated effect. Means differed when P < 0.05. Sixteen genes presented a time by treatment interaction due to changes in expression after LPS. Expression of INSR, INSR-b, and IGFBP2 was greater and GHR-1A was less in CH than UH, expression of these genes decreased in response to LPS in both challenges, but the response did not differ between genotypes. There was a time by challenge interaction for IGFBP2 as it was decreased at 24 h in C1 but not in C2. There were challenge effects for IGF1 and GHR-1A due to greater expression in C1 than in C2 but the response did not differ between genotypes. There were time by treatment interactions for PC1, PCK1, PPARa, and PPARd. In response to LPS expression of PC1 and PPARd increased, and PCK1 and PPARa decreased at 4 h in both challenges, but the response did not differ between genotypes. Results indicate that LPS administration altered hepatic expression of genes related to the somatotropic axis, glucose, and lipid metabolism and that these responses were similar for the low and high milk yield genotypes.
Search for supersymmetry at $\sqrt{s}$ = 8 TeV in final states with jets and two same-sign leptons or three leptons with the ATLAS detector (2014)

A bstract A search for strongly produced supersymmetric particles is conducted using signatures involving multiple energetic jets and either two isolated leptons ( e or μ) with the same electric charge, or at least three isolated leptons. The search also utilises jets originating from b -quarks, missing transverse momentum and other observables to extend its sensitivity. The analysis uses a data sample corresponding to a total integrated luminosity of 20.3 fb −1 of $ \sqrt{s} $ = 8 TeV proton-proton collisions recorded with the ATLAS detector at the Large Hadron Collider in 2012. No deviation from the Standard Model expectation is observed. New or significantly improved exclusion limits are set on a wide variety of supersymmetric models in which the lightest squark can be of the first, second or third generations, and in which R-parity can be conserved or violated.
Comparative study of the photochemistry of the cutting (etching) of a synthetic polymer and bovine cornea by excimer laser radiation (1985)

Earlier work1–3 on the etching of an organic polymer by UV laser radiation has emphasized the depth of the etching/pulse If as a function of fluence F. In this work, the If vs InF curves for polymethyl methacrylate (PMMA) have been ex- tended over a larger range of fluences at 193 and 24B nm (Fig. 1). At the same time, the quantum yields for methyl methacrylate (MMA), the principal polyatomic product from PMMA, were also determined (Fig. 2). The quantum yields of MMA at 248 nm were tenfold smaller than at 193 nm and are, therefore, not inclued in Fig. 2. Etch curves for bovine cornea1 which were determined from laser exposure in vitro are shown in Fig. 3.
Ribonuclease A as a substrate of the protease from human immunodeficiency virus-1. (1990)

Bovine pancreatic ribonuclease A (RNase) contains two bonds, Met29-Met30 and Tyr92-Pro93 which are representative of sites in the human immunodeficiency virus-1 (HIV-1) gag polyprotein precursors that are cleaved by the HIV-1 protease during viral maturation. Nevertheless, neither native nor performic acid-oxidized RNase is a substrate for the protease. However, RNase derivatives obtained by reduction and S-alkylation with iodoacetate or iodoacetamide undergo cleavage by the HIV-1 protease at a single site, Ala109-alkyl-Cys110, that is distinct from either of the two predicted bonds mentioned above. The neutral carboxyamido-methylcysteinyl derivative is cleaved 8 times faster than that containing the negatively charged carboxy-methyl substituent at P1'. Succinylation of these S-alkylated RNase derivatives creates a second site of cleavage by the protease between succinyl-Lys7 and Phe8. Thus, the pattern of cleavage of denatured RNase by the HIV-1 protease can be manipulated by chemical derivatization of the substrate, and the new sites of hydrolysis revealed by these studies add to our understanding of the specificity of this important enzyme.
Supplementary Figure 6C from Aberrant Silencing of Cancer-Related Genes by CpG Hypermethylation Occurs Independently of Their Spatial Organization in the Nucleus (2023)

Supplementary Figure 6C from Aberrant Silencing of Cancer-Related Genes by CpG Hypermethylation Occurs Independently of Their Spatial Organization in the Nucleus
High-Yield Transfer Printing of Metal–Insulator–Metal Nanodiodes (2012)

Nanoscale metal-insulator-metal (MIM) diodes represent important devices in the fields of electronic circuits, detectors, communication, and energy, as their cutoff frequencies may extend into the "gap" between the electronic microwave range and the optical long-wave infrared regime. In this paper, we present a nanotransfer printing method, which allows the efficient and simultaneous fabrication of large-scale arrays of MIM nanodiode stacks, thus offering the possibility of low-cost mass production. In previous work, we have demonstrated the successful transfer and electrical characterization of macroscopic structures. Here, we demonstrate for the first time the fabrication of several millions of nanoscale diodes with a single transfer-printing step using a temperature-enhanced process. The electrical characterization of individual MIM nanodiodes was performed using a conductive atomic force microscope (AFM) setup. Our analysis shows that the tunneling current is the dominant conduction mechanism, and the electrical measurement data agree well with experimental data on previously fabricated microscale diodes and numerical simulations.
Optimization of the fourth self-imaging spectral response in magnetic fluid cladded-MMI fiber optic sensor for magnetometry (2023)

Optical fiber based electro-magnetic field sensors is a diverse and expanding field in fiber sensor technology with applications spanning from geomagnetism, biomagnetism, nuclear magnetism to safety and operational monitoring of power grid systems. Particularly, because of the dielectric silica material of the fiber that provides high electric insulation and immunity to the electromagnetic interference (EMI), a major reason contributing to the limitations in conventional sensors, the efforts have been focused on developing the fiber-optic sensors with increased sensitivity, bandwidth, and detection range specific to an application but all benefit from the advantages of the platform. Various fiber structures, interrogation schemes and sensing materials have been investigated. One major interest is on the fiber-optic sensor based on multi-mode interference (MMI) where a multimode mode fiber is fusion spliced between two single mode fibers also known as SMS (single-mode/multimode/single mode) fiber sensor. Ease of fabrication, compactness, higher sensitivity, and low cost are some of the driving factors in addition to the potential for direct integration of the platform with functional sensor materials to tailor for specific applications. For the purpose of magnetic field sensing, the magnetic fluid is the most widely used functional material as the sensing/cladding layer on the fiber-structure. Here we present efforts to enhance and optimize the sensitivity of such SMS structure with magnetic fluid as the sensing material exploiting the unique “self-imaging” property of the SMS sensor where the sensor produces a filterlike spectral response and is highly sensitive to the change in magneto-optical property of surrounding medium. The performance metrics of the sensor are analyzed against DC magnetic field range keeping an eye in detecting typical current induced magnetic field in power grid systems.
Robust position servo system based on vibration suppression control for industrial robotics (2010)

This paper proposes two vibration suppression control systems for industrial robots. Industrial robots often occur vibration phenomenon which is caused by the resonant frequency and nonlinear interference force from various joints of the robot. The compact high-gear reduction without backlash, such as the harmonic gear is frequently used in the driving system for the sake of high load-to-weight performance. Generally, the industrial robots have used the sensors mounted to actuator-side because hardware setting using load-side sensor is very difficult to mount signal lines. At first, this paper proposes a new vibration suppression control system uses the estimated load information due to repress the effect of external disturbance force and nonlinear inertia variation due to posture change of robot. The robust position servo system is designed based on the state, disturbance observer and robust speed control system using coprime factorization controller. Next, a zero-phase notch filter is very useful for suppressing the resonant phenomenon. However, as the design method of zero-phase notch filter is more difficult than that of the zero-phase low-pass filter, the high-performance zero-phase notch filter cannot be realized in motion control field. In order to overcome this problem, this paper proposes a new design method of the zero-phase notch filter which has no phase delay for fast robot motion control reference. The effectiveness of both proposed systems is confirmed by experimental results and numerical simulation results.
Experimental studies of surface plasmon polariton band gap effect (2003)

Surface plasmon polaritons (SPPs) propagation at a gold film surface covered by periodic arrays of approximately 40-nm-high scatterers arranged in a triangular lattice of different periods containing straight line defects is studied using collection scanning near-field optical microscopy. The results reveal the dependence of the SPP band gap (SPPBG) effect manifested via the SPP reflection and guiding (along line defects) on the parameters of the surface structures (period, filling factor and lattice orientation). We find that the SPPBG effect is stronger along GammaK direction for all investigated periodic structures. Our results demonstrate that the SPPBG effect becomes less pronounced with a decrease of the filling factor and disappears for a filling factor close to 0.2. We also observe that the centre of the SPPBG shifts towards longer wavelengths with an increase of the lattice period.
Evaluation of virtualization models for optical connectivity service providers (2014)

Network virtualization technologies combined with Software-Defined Networking (SDN) principles provide a number of benefits to optical networks in terms of agility and ease of management. However, the multi-layer nature of optical systems poses challenges to system design. In this paper, we present topology virtualization models for optical connectivity service providers using an SDN-enabled flexible optical network. The virtual optical network topology will be advertised to clients of the service provider. Scheduled as well as on-demand lightpath services can be provisioned via Application Programming Interfaces (API), either based on the prominent OpenFlow [1] protocol, or via IETF-based protocols centered on an active stateful PCE (Path Computation Element) [2][3]. We discuss and compare different topology virtualization models along with their benefits and challenges. In addition, first evaluation results, based on an Optical Network Hypervisor at the service provider and OpenDaylight [4], an open-source SDN controller, as the client controller, are discussed.
Data from Global Phosphoproteomics Reveal CDK Suppression as a Vulnerability to KRas Addiction in Pancreatic Cancer (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Among human cancers that harbor mutant (mt) KRas, some, but not all, are dependent on mt KRas. However, little is known about what drives KRas dependency.&lt;/p&gt;Experimental Design:&lt;p&gt;Global phosphoproteomics, screening of a chemical library of FDA drugs, and genome-wide CRISPR/Cas9 viability database analysis were used to identify vulnerabilities of KRas dependency.&lt;/p&gt;Results:&lt;p&gt;Global phosphoproteomics revealed that KRas dependency is driven by a cyclin-dependent kinase (CDK) network. CRISPR/Cas9 viability database analysis revealed that, in mt KRas-driven pancreatic cancer cells, knocking out the cell-cycle regulators CDK1 or CDK2 or the transcriptional regulators CDK7 or CDK9 was as effective as knocking out KRas. Furthermore, screening of a library of FDA drugs identified AT7519, a CDK1, 2, 7, and 9 inhibitor, as a potent inducer of apoptosis in mt KRas-dependent, but not in mt KRas-independent, human cancer cells. &lt;i&gt;In vivo&lt;/i&gt; AT7519 inhibited the phosphorylation of CDK1, 2, 7, and 9 substrates and suppressed growth of xenografts from 5 patients with pancreatic cancer. AT7519 also abrogated mt KRas and mt p53 primary and metastatic pancreatic cancer in three-dimensional (3D) organoids from 2 patients, 3D cocultures from 8 patients, and mouse 3D organoids from pancreatic intraepithelial neoplasia, primary, and metastatic tumors.&lt;/p&gt;Conclusions:&lt;p&gt;A link between CDK hyperactivation and mt KRas dependency was uncovered and pharmacologically exploited to abrogate mt KRas-driven pancreatic cancer in highly relevant models, warranting clinical investigations of AT7519 in patients with pancreatic cancer.&lt;/p&gt;&lt;/div&gt;
Nickel Metal Alloy’s As PGM-Free Catalysts for Hydrogen Oxidation Reaction in Anion Exchange Membrane Fuel Cells (2017)

Anion exchange membrane fuel cells (AEMFCs) offer considerable advantages over proton exchange membrane fuel cells (PEMFCs) in that the kinetics for oxygen reduction reaction (ORR) are greatly improved in alkaline media [1]. The improved kinetics of ORR in alkaline media thus allows for the use of PGM-Free catalysts in AEMFCs. Though there have been many efforts to develop PGM-Free cathode catalysts for AEMFCs, PGM-Free anode catalysts, with catalytic activity for HOR comparable to Pt, are still in the early stages of development [2]. The slow development of these AEMFC anode catalysts is largely due to the lack of compatible ionomers for anion exchange. However, recent development of anion exchange ionomers show great improvements over PEMFC ionomers, such as NAFION, in AEMFCs [3]. Carbon supported nickel has been shown to have high activity for HOR in AEMFCs, however the susceptibility of Ni to electrochemical oxidation, as well as the less than optimal hydrogen binding energy to the Ni active site, suggest there is further room for optimization of the Ni/C system [1]. Here, we have proposed to address these issues through alloying Ni with transition metals to tune the electronic environment of Ni, as well as to improve the corrosion resistance of Ni in alkaline media. For this project, catalysts are prepared by an incipient wetness method using the metal nitrates as catalyst precursors and KetjenblackÒ, DENKA BLACKÒ, graphene oxide (GO) and reduced graphene oxide (rGO) as support materials. GO and rGO have been prepared from Hummers’ method. In some cases, a sacrificial support method is also used to control the primary particle size of the NiM materials. Figure 1 shows the open circuit and close circuit polarization curves for NiMo/C with peak power density observed for HOR of ~ 120 mW/cm 2 , which is an encouraging result though not competitive with Pt or Pd. Therefore, our aim is to explore the role of the alloying metal (M = Mo, W, Cr, Co, Cu) as well as to investigate the role of the carbon support (ex: GO, rGO, N-doped rGO) on the kinetics of HOR in alkaline media on these NiM/C catalysts. References: [1] Zhuang, Z.; Giles, S. A.; Zheng, J.; Jenness, G. R.; Caratzoulas, S.; Vlachos, D. G.; Yan, Y. Nature Communications 2016, 7, 10141. [2] Serov, A.; Kwak, C. Applied Catalysis B: Environmental 2009, 90 (3-4), 313–320. [3] Kreuer, K.-D. Fuel cells: selected entries from the Encyclopedia of Sustainability Science and Technology; Springer: New York, 2013. Figure 1