gebhart/patrepeval huggingface dataset:
Supplementary Materials and Methods from Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks (2023)

&lt;p&gt;Description of Supplemental Materials and Methods&lt;/p&gt;
Resolving the memory bottleneck for single supply near-threshold computing (2014)

This paper focuses on a review of state-of-the-art memory designs and new design methods for near-threshold computing (NTC). In particular, it presents new ways to design reliable low-voltage NTC memories cost-effectively by reusing available cell libraries, or by adding a digital wrapper around existing commercially available memories. The approach is based on modeling at system level supported by silicon measurement on a test chip in a 40nm low-power processing technology. Advanced monitoring, control and run-time error mitigation schemes enable the operation of these memories at the same optimal near-V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sub> voltage level as the digital logic. Reliability degradation is thus overcome and this opens the way to solve the memory bottleneck in NTC systems. Starting from the available 40 nm silicon measurements, the analysis is extended to future 14 and 10 nm technology nodes.
Sterilizing Immunity against SARS‐CoV‐2 Infection in Mice by a Single‐Shot and Lipid Amphiphile Imidazoquinoline TLR7/8 Agonist‐Adjuvanted Recombinant Spike Protein Vaccine** (2021)

The search for vaccines that protect from severe morbidity and mortality because of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19) is a race against the clock and the virus. Here we describe an amphiphilic imidazoquinoline (IMDQ-PEG-CHOL) TLR7/8 adjuvant, consisting of an imidazoquinoline conjugated to the chain end of a cholesterol-poly(ethylene glycol) macromolecular amphiphile. It is water-soluble and exhibits massive translocation to lymph nodes upon local administration through binding to albumin, affording localized innate immune activation and reduction in systemic inflammation. The adjuvanticity of IMDQ-PEG-CHOL was validated in a licensed vaccine setting (quadrivalent influenza vaccine) and an experimental trimeric recombinant SARS-CoV-2 spike protein vaccine, showing robust IgG2a and IgG1 antibody titers in mice that could neutralize viral infection in vitro and in vivo in a mouse model.
Denticity Changes of Hydrotris(pyrazolyl)borate Ligands in RhI and RhIII Compounds: From κ3- to Ionic “κ0”-Tp′ (2000)

Isolierte Hydrotris(pyrazolyl)borat-Anionen (Tp′) wurden in Form von Salzen mit Übergangsmetallkomplex-Kationen (siehe Bild) durch Austausch von Rh-koordinierten κ3-N,N′,N″-Tp′-Liganden gegen PMe3 erhalten (Tp′=Tp und TpMe2). Ausgehend von [(κ3-TpMe2)Rh(C2H4)2] ermöglichte die schrittweise Verdrängung von TpMe2 die Isolierung von Komplexen, in denen dieser Ligand κ2- und κ1-Koordination aufweist.
Parton energy loss in heavy-ion collisions via direct-photon and charged-particle azimuthal correlations (2010)

Charged-particle spectra associated with direct photon (${\ensuremath{\gamma}}_{\mathrm{dir}}$) and ${\ensuremath{\pi}}^{0}$ are measured in $p+p$ and $\mathrm{Au}+\mathrm{Au}$ collisions at center-of-mass energy $\sqrt{{s}_{{}_{\mathit{NN}}}}=200$ GeV with the STAR detector at the Relativistic Heavy Ion Collider. A shower-shape analysis is used to partially discriminate between ${\ensuremath{\gamma}}_{\mathrm{dir}}$ and ${\ensuremath{\pi}}^{0}$. Assuming no associated charged particles in the ${\ensuremath{\gamma}}_{\mathrm{dir}}$ direction (near side) and small contribution from fragmentation photons (${\ensuremath{\gamma}}_{\mathrm{frag}}$), the associated charged-particle yields opposite to ${\ensuremath{\gamma}}_{\mathrm{dir}}$ (away side) are extracted. In central $\mathrm{Au}+\mathrm{Au}$ collisions, the charged-particle yields at midrapidity ($|\ensuremath{\eta}|&lt;1$) and high transverse momentum ($3&lt;{p}_{T}^{\mathrm{assoc}}&lt;16$ GeV/$c$) associated with ${\ensuremath{\gamma}}_{\mathrm{dir}}$ and ${\ensuremath{\pi}}^{0}$ ($|\ensuremath{\eta}|&lt;0.9$, $8&lt;{p}_{T}^{\mathrm{trig}}&lt;16$ GeV/$c$) are suppressed by a factor of 3--5 compared with $p+p$ collisions. The observed suppression of the associated charged particles is similar for ${\ensuremath{\gamma}}_{\mathrm{dir}}$ and ${\ensuremath{\pi}}^{0}$ and independent of the ${\ensuremath{\gamma}}_{\mathrm{dir}}$ energy within uncertainties. These measurements indicate that, in the kinematic range covered and within our current experimental uncertainties, the parton energy loss shows no sensitivity to the parton initial energy, path length, or color charge.
Mass spectrometry of stanozolol and its analogues using electrospray ionization and collision‐induced dissociation with quadrupole‐linear ion trap and linear ion trap‐orbitrap hybrid mass analyzers (2005)

Mass spectrometric identification and characterization of growth-promoting anabolic-androgenic steroids in biological matrices has been a major task for doping control as well as food safety laboratories. The fragmentation behavior of stanozolol, its metabolites 17-epistanozolol, 3'-OH-stanozolol, 4alpha-OH-stanozolol, 4beta-OH-stanozolol, 17-epi-16alpha-OH-stanozolol, 16alpha-OH-stanozolol, 16beta-OH-stanozolol, as well as the synthetic analogues 4-dehydrostanozolol, 17-ketostanozolol, and N-methyl-3'-OH-stanozolol, was investigated after positive electrospray ionization and subsequent collision-induced dissociation utilizing a quadrupole-linear ion trap and a novel linear ion trap-orbitrap hybrid mass spectrometer. Stable isotope labeling, H/D-exchange experiments, MS3 analyses and high-resolution/high mass accuracy measurements of fragment ions were employed to allow proposals for charge-driven as well as charge-remote fragmentation pathways generating characteristic product ions of stanozolol at m/z 81, 91, 95, 105, 119, 135 and 297 and 4-hydroxylated stanozolol at m/z 145. Fragment ions were generated by dissociation of the steroidal A- and B-ring retaining the introduced charge within the pyrazole function of stanozolol and by elimination of A- and B-ring fractions including the pyrazole residue. In addition, a charge-remote fragmentation causing the neutral loss of methanol was observed, which was suggested to be composed by the methyl residue at C-18 and the hydroxyl function located at C-17.
Extreme infrared variables from UKIDSS – I. A concentration in star-forming regions (2014)

We present initial results of the first panoramic search for high-amplitude near-infrared variability in the Galactic Plane. We analyse the widely separated two-epoch K-band photometry in the 5th and 7th data releases of the UKIDSS Galactic Plane Survey. We find 45 stars with \Delta K > 1 mag, including 2 previously known OH/IR stars and a Nova. Even though the mid-plane is not yet included in the dataset, we find the majority (66%) of our sample to be within known star forming regions (SFRs), with two large concentrations in the Serpens OB2 association (11 stars) and the Cygnus-X complex (12 stars). Sources in SFRs show spectral energy distributions (SEDs) that support classification as Young Stellar Objects (YSOs). This indicates that YSOs dominate the Galactic population of high amplitude infrared variable stars at low luminosities and therefore likely dominate the total high amplitude population. Spectroscopic follow up of the DR5 sample shows at least four stars with clear characteristics of eruptive pre-main-sequence variables, two of which are deeply embedded. Our results support the recent concept of eruptive variability comprising a continuum of outburst events with different timescales and luminosities, but triggered by a similar physical mechanism involving unsteady accretion. Also, we find what appears to be one of the most variable classical Be stars.
QueSTR probes: Quencher-labeled RNase H2-dependent probes for Short Tandem Repeat genotyping (2022)

Forensic Short Tandem Repeat (STR) genotyping is almost exclusively performed by capillary electrophoresis (CE) in specialized laboratories. As an alternative to CE, and to enable miniaturized lab-on-a-chip STR profiling, we developed the QueSTR probes, a hybridization-based genotyping assay that relies on the recognition and cleavage of an RNA:DNA duplex by the RNase H2 enzyme. For each STR allele to be genotyped, a matching DNA probe containing one RNA moiety is designed. After performing asymmetric STR PCR, a hybridization curve analysis indicates the matching probe(s), and thus indicates the allele(s) present in the sample. Accurate genotyping of 13 samples was obtained using the QueSTR probes for three CODIS core loci (D16S539, D7S820, and TH01). A probe corresponding to the TH01 9.3 allele was included to demonstrate accurate genotyping, even in the presence of a partial repeat. The QueSTR probes are a valuable option to miniaturize STR genotyping in lab-on-a-chip devices that cannot harbor a CE analysis.
Mitogen-Activated Protein Kinases (Erk1,2) Phosphorylate Lys-Ser-Pro (KSP) Repeats in Neurofilament Proteins NF-H and NF-M (1998)

Mammalian neurofilament proteins, particularly midsized (NF-M) and heavy (NF-H) molecular weight neurofilament proteins, are highly phosphorylated in axons. Neurofilament function depends on the state of phosphorylation of the numerous serine/threonine residues in these proteins. Most phosphorylation occurs in the lys-ser-pro (KSP) repeats in the C-terminal tail domains of NF-H and NF-M. In our previous study, cyclin-dependent kinase 5 (cdk5) was shown to phosphorylate specifically the KSPXK repeats in rat NF-H. Because 80% of the repeats are of the KSPXXXK type, it was of interest to determine which kinase phosphorylates these motifs. Using a synthetic KSPXXXK peptide to screen for a specific kinase, we fractionated rat brain extracts by column chromatography and identified extracellular signal-regulated kinase (Erk2) activated by an upstream activator, the mitogen-activated protein kinase kinase MAPKK (MEK), by Western blot analysis, sequence identification, and inhibition by a specific MEK inhibitor (PD 98059). The fraction containing Erk2, as well as bacterially expressed Erk1 and Erk2, phosphorylated all types of KSP motifs in peptides (KSPXK, KSPXXK, KSPXXXK, and KSPXXXXK) derived from NF-M and NF-H. They also phosphorylated an expressed 24 KSPXXXK repeat NF-H polypeptide, an expressed NF-H as well as dephosphorylated native rat NF-H, and NF-M proteins with accompanying decreases in their respective electrophoretic mobilities. A comparative kinetic study of Erk2 and cdk5 phosphorylation of KSPXK and KSPXXXK peptides revealed that, in contrast to cdk5, which phosphorylated only the KSPXK peptide, Erk2 could phosphorylate both. The preferred substrate for Erk2 was KSPXXXK peptide. The MEK inhibitor PD 98059 also inhibited phosphorylation of NF-H, NF-M, and microtubule-associated protein (MAP) in primary rat hippocampal cells and caused a decrease in neurite outgrowth, suggesting that Erk1,2 may play an important role in neurite growth and branching. These data suggest that neuronal Erk1 and Erk2 are capable of phosphorylating serine residues in diverse KSP repeat motifs in NF-M and NF-H.
On the Complexity of the Constrained Input Selection Problem for\n Structural Linear Systems (2014)

This paper studies the problem of, given the structure of a linear-time\ninvariant system and a set of possible inputs, finding the smallest subset of\ninput vectors that ensures system's structural controllability. We refer to\nthis problem as the minimum constrained input selection (minCIS) problem, since\nthe selection has to be performed on an initial given set of possible inputs.\nWe prove that the minCIS problem is NP-hard, which addresses a recent open\nquestion of whether there exist polynomial algorithms (in the size of the\nsystem plant matrices) that solve the minCIS problem. To this end, we show that\nthe associated decision problem, to be referred to as the CIS, of determining\nwhether a subset (of a given collection of inputs) with a prescribed\ncardinality exists that ensures structural controllability, is NP-complete.\nFurther, we explore in detail practically important subclasses of the minCIS\nobtained by introducing more specific assumptions either on the system dynamics\nor the input set instances for which systematic solution methods are provided\nby constructing explicit reductions to well known computational problems. The\nanalytical findings are illustrated through examples in multi-agent\nleader-follower type control problems.\n
EXPERIMENTAL VERIFICATION OF FREQUENCY EFFECTS IN TILTING PAD JOURNAL BEARING DYNAMIC COEFFICIENTS (2020)

In this paper, vibrational frequency effect in dynamic coefficients of tilting pad journal bearing is verified experimentally. Tilting pad journal bearings (TPJB) is applied in various turbomachinery. Accurate evaluation of the bearing characteristics of TPJB is very important to ensure reliability of rotating machinery. To evaluate the stability of such rotating machinery for sub-synchronous vibration accurately, examination of damped vibrational frequency effects in dynamic coefficients of TPJB under various bearing load condition is necessary. In this study, excitation test with test rig of 4pad TPJB with two types of preload or pad offset ratio is carried out in various load condition. Especially, the test condition where the influence of fluid inertia is small is focused. Frequency effect in dynamic coefficients of TPJB is verified experimentally under the test condition. And, thermo-elastic-hydrodynamic-lubrication (TEHL) analysis is carried out. By comparing analytical results to experimental results, good agreement with experimental result and TEHL analytical result is confirmed. In addition, the influence of bearing load, load direction, pre-load or pad offset ratio on frequency effect is confirmed experimentally and analytically. The results that the frequency effect is larger as bearing load is lower (Sommerfeld number is larger), and the influence of pre-load of bearing on frequency effect is small and that of pad offset ratio (pivot position) is large is obtained.
Computational approaches to predict drug metabolism (2009)

Although considerable progress has been made, the results of the calculations still need careful inspection. The domain of applicability of the models as well as methodological limitations have to be taken into account.
Finding optimum parallel coprocessor design for genus 2 hyperelliptic curve cryptosystems (2004)

Hardware accelerators are often used in cryptographic applications for speeding up the highly arithmetic-intensive public-key primitives, e.g. in high-end smart cards. One of these emerging and very promising public-key schemes is based on hyperelliptic curve cryptosystems (HECC). In the open literature only a few considerations deal with hardware implementation issues of HECC. Our contribution appears to be the first one to propose architectures for the latest findings in efficient group arithmetic on HEC. The group operation of HECC allows parallelization at different levels: bit-level parallelization (via different digit-sizes in multipliers) and arithmetic operation-level parallelization (via replicated multipliers). We investigate the trade-offs between both parallelization options and identify speed and time-area optimized configurations. We found that a coprocessor using a single multiplier (D=8) instead of two or more is best suited. This coprocessor is able to compute group addition and doubling in 479 and 334 clock cycles, respectively. Providing more resources it is possible to achieve 288 and 248 clock cycles, respectively.
Limited feedback with joint CSI quantization for multicell cooperative generalized eigenvector beamforming (2010)

Existing work on limited feedback for cooperative multicell beamforming quantizes the desired and interfering channel state information (CSI) using separate codebooks. In this paper, it is shown that comparatively higher sum-rates can be obtained by jointly quantizing the desired and interfering CSI using a single codebook. A selection criterion is developed for random vector quantization (RVQ) to show that joint quantization with RVQ yields higher sum-rates than those obtained using separate codebooks. The generalized Lloyd algorithm is then used to generate codebooks using the codeword design strategy proposed in this paper. Simulations are used to show that the proposed joint quantization approaches perform almost as well as the full CSI case.
Combination anti-CD74 (milatuzumab) and anti-CD20 (rituximab) monoclonal antibody therapy has in vitro and in vivo activity in mantle cell lymphoma (2011)

Mantle cell lymphoma (MCL) is an aggressive B-cell malignancy with a median survival of 3 years despite chemoimmunotherapy. Rituximab, a chimeric anti-CD20 monoclonal antibody (mAb), has shown only modest activity as single agent in MCL. The humanized mAb milatuzumab targets CD74, an integral membrane protein linked with promotion of B-cell growth and survival, and has shown preclinical activity against B-cell malignancies. Because rituximab and milatuzumab target distinct antigens and potentially signal through different pathways, we explored a preclinical combination strategy in MCL. Treatment of MCL cell lines and primary tumor cells with immobilized milatuzumab and rituximab resulted in rapid cell death, radical oxygen species generation, and loss of mitochondrial membrane potential. Cytoskeletal distrupting agents significantly reduced formation of CD20/CD74 aggregates, cell adhesion, and cell death, highlighting the importance of actin microfilaments in rituximab/milatuzumab-mediated cell death. Cell death was independent of caspase activation, Bcl-2 family proteins or modulation of autophagy. Maximal inhibition of p65 nuclear translocation was observed with combination treatment, indicating disruption of the NF-κB pathway. Significant in vivo therapeutic activity of combination rituximab and milatuzumab was demonstrated in a preclinical model of MCL. These data support clinical evaluation of combination milatuzumab and rituximab therapy in MCL.
Metagenomic and Metatranscriptomic Insights into Population Diversity of Microcystis Blooms: Spatial and Temporal Dynamics of mcy Genotypes, Including a Partial Operon That Can Be Abundant and Expressed (2022)

Cyanobacterial harmful algal blooms (cyanoHABs) degrade freshwater ecosystems globally. Microcystis aeruginosa often dominates cyanoHABs and produces microcystin (MC), a class of hepatotoxins that poses threats to human and animal health. Microcystin toxicity is influenced by distinct structural elements across a diversity of related molecules encoded by variant <i>mcy</i> operons. However, the composition and distribution of <i>mcy</i> operon variants in natural blooms remain poorly understood. Here, we characterized the variant composition of <i>mcy</i> genes in western Lake Erie <i>Microcystis</i> blooms from 2014 and 2018. Sampling was conducted across several spatial and temporal scales, including different bloom phases within 2014, extensive spatial coverage on the same day (2018), and frequent, autonomous sampling over a 2-week period (2018). Mapping of metagenomic and metatranscriptomic sequences to reference sequences revealed three <i>Microcystis mcy</i> genotypes: complete (all genes present [<i>mcyA-J</i>]), partial (truncated <i>mcyA</i>, complete <i>mcyBC</i>, and missing <i>mcyD-J</i>), and absent (no <i>mcy</i> genes). We also detected two different variants of <i>mcyB</i> that may influence the production of microcystin congeners. The relative abundance of these genotypes was correlated with pH and nitrate concentrations. Metatranscriptomic analysis revealed that partial operons were, at times, the most abundant genotype and expressed <i>in situ</i>, suggesting the potential biosynthesis of truncated products. Quantification of genetic divergence between genotypes suggests that the observed strains are the result of preexisting heterogeneity rather than <i>de novo</i> mutation during the sampling period. Overall, our results show that natural <i>Microcystis</i> populations contain several cooccurring <i>mcy</i> genotypes that dynamically shift in abundance spatiotemporally via strain succession and likely influence the observed diversity of the produced congeners. <b>IMPORTANCE</b> Cyanobacteria are responsible for producing microcystins (MCs), a class of potent and structurally diverse toxins, in freshwater systems around the world. While microcystins have been studied for over 50 years, the diversity of their chemical forms and how this variation is encoded at the genetic level remain poorly understood, especially within natural populations of cyanobacterial harmful algal blooms (cyanoHABs). Here, we leverage community DNA and RNA sequences to track shifts in <i>mcy</i> genes responsible for producing microcystin, uncovering the relative abundance, expression, and variation of these genes. We studied this phenomenon in western Lake Erie, which suffers annually from cyanoHAB events, with impacts on drinking water, recreation, tourism, and commercial fishing.
Spontaneous three-dimensional nanostructure formation of perfluoroalkyl terminated liquid crystal: A molecular dynamics simulation study (2004)

Structure formation of a perfluoroalkyl terminated liquid crystal molecule was studied by molecular dynamics simulations. Two distinct structures with smectic-C-like layers and with bundles (blocks) of collapsed layers were spontaneously formed depending on the simulation temperatures. The bundles in the latter structure were somewhat positionally ordered (with respect to the small angle spots in its structure function) and orientationally isotropic overall even though the molecules making each bundle were well oriented. These characteristics of the simulated system well correspond to the cubic phase of the real system, and an even more precisely correspond to the proposed cubic structure model with respect to its hierarchical structure.
Magnetic Heating of Fe–Co Ferrites — Experiments and Modeling (2016)

Magnetic nanoparticle hyperthermia uses magnetically-induced heat to kill cancer cells. In an alternating magnetic field, the induced heat depends strongly on particles' absorption properties. In order to achieve and maintain therapeutic temperatures inside a tumor and to minimize damage to normal tissues due to induced eddy currents, there is a need to develop new magnetic nanoparticles with improved heating characteristics. This paper investigates the magnetic heating properties of composite iron-cobalt ferrite nanoparticles Co <i><sub>x</sub></i> Fe<sup>II</sup><sub>1-</sub><i><sub>x</sub></i> Fe<sup>III</sup><sub>2</sub>O<sub>4</sub> with 0≤<i>x</i>≤1. These composite materials are synthesized using a precipitation method. First, the Fe-Co nanoparticle synthesis is described, then their structure, size, magnetic and heating properties are measured and analyzed. The resulting nanoparticles were treated at temperatures 100-600°C in order to study any structural transformations and changes of physical properties. Finally, an empirical model is used to calculate both the nanoparticles' coercivity and their specific absorption rates for different Co concentrations.