gebhart/patrepeval huggingface dataset:
CoCoA: Conditional Correlation Models with Association Size (2022)

S ummary Many scientific questions can be formulated as hypotheses about conditional correlations. For instance, in tests of cognitive and physical performance, the trade-off between speed and accuracy motivates study of the two variables together. A natural question is whether speed-accuracy coupling depends on other variables, such as sustained attention. Classical regression techniques, which posit models in terms of covariates and outcomes, are insufficient to investigate the effect of a third variable on the symmetric relationship between speed and accuracy. In response, we propose CoCoA (Conditional Correlation Model with Association Size), a likelihood-based statistical framework to estimate the conditional correlation between speed and accuracy as a function of additional variables. We propose novel measures of the association size, which are analogous to effect sizes on the correlation scale, while adjusting for confound variables. In simulation studies, we compare likelihood-based estimators of conditional correlation to semi-parametric estimators adapted from genome association studies, and find that the former achieves lower bias and variance under both ideal settings and model assumption misspecification. Using neurocognitive data from the Philadelphia Neurodevelopmental Cohort, we demonstrate that greater sustained attention is associated with stronger speed-accuracy coupling in a complex reasoning task while controlling for age. By highlighting conditional correlations as the outcome of interest, our model provides complementary insights to traditional regression modelling and partitioned correlation analyses.
Measurement of scattered light Wigner functions by phase space tomography and implications for parallel OCT (2003)

We demonstrate phase space tomography for the measurement of the transversal spatial coherence function of light after propagation through a scattering medium. The results of this approach are compared to measurements performed with shearing-interferometry. Implications for parallel Optical Coherence Tomography will be briefly discussed.
Choledochal cysts: comparison of findings at MR cholangiopancreatography and endoscopic retrograde cholangiopancreatography in eight patients. (1998)

MRCP provides information equivalent to that provided with ERCP, without potential complications, for the preoperative assessment of choledochal cysts. Dynamic secretin-stimulated MRCP studies might help better understand the pathophysiologic characteristics of this entity.
The Electronic Structure of Iron Corroles: A Combined Experimental and Quantum Chemical Study (2008)

There is a longstanding debate in the literature on the electronic structure of chloroiron corroles, especially for those containing the highly electron-withdrawing meso-tris(pentafluorophenyl)corrole (TPFC) ligand. Two alternative electronic structures were proposed for this and the related [FeCl(tdcc)] (TDCC=meso-tris(2,6-dichlorophenyl)corrole) complex, namely a high-valent ferryl species chelated by a trianionic corrolato ligand ([Fe(IV)(Cor)(3-)](+)) or an intermediate-spin (IS) ferric ion that is antiferromagnetically coupled to a dianionic pi-radical corrole ([Fe(III)(Cor)(.2-)](+)) yielding an overall triplet ground state. Two series of corrole-based iron complexes ([Fe(L)(Cor)], in which L=F, Cl, Br, I, and Cor=TPFC, TDCC) have been investigated by a combined experimental (Mössbauer spectroscopy) and computational (DFT) approach in order to differentiate between the two possible electronic-structure descriptions. The experimentally calibrated conclusions were reached by a detailed analysis of the Kohn-Sham solutions, which successfully reproduce the experimental structures and spectroscopic parameters: the electronic structures of [Fe(L)(Cor)] (L=F, Cl, Br, I, Cor=TPFC, TDCC) are best formulated as ([IS-Fe(III)(Cor)(.2-)](+)), similar to chloroiron corrole complexes containing electron-rich corrole ligands. The antiferromagnetic pathway is composed of singly occupied Fe d(z(2) ) and corrole a(2u)-like pi orbitals, with coupling constants that exceed those of analogous porphyrin systems by a factor of 2-3. In the corroles, the combination of lower symmetry, extra negative charge, and smaller cavity size (relative to the porphyrins) leads to exceptionally strong iron-corrole sigma bonds. Hence, the Fe d(x(2)-y(2) )-based molecular orbital is unavailable in the corrole complexes (contrary to the porphyrin case), and the local spin states are S(Fe)=3/2 in the corroles versus S(Fe)=5/2 in the porphyrins. The consequences of this qualitative difference are discussed for spin distributions and magnetic properties.
Collagen II Promoter and Enhancer Interact Synergistically Through Sp1 and Distinct Nuclear Factors (1995)

The collagen II gene is expressed primarily in chondrocytes. Its transcription is activated through the interaction of cell type-specific regulatory elements located in the promoter region and in the first intron. In this study, we found that a short promoter sequence including two GC boxes was required for efficient enhancer-mediated transcription. Gel-shift analysis, site mutations, and footprint analysis showed that one of the GC boxes bound functionally to an Sp1-related factor and that an oligonucleotide containing this GC box did interact with an enhancer-nuclear factor complex. Additionally, an enhancer-derived oligonucleotide was found to complex CIIZFP, a zinc-finger protein that binds to the enhancer within the first intron and Sp1, but only in presence of CIIZFP. Antibodies against Sp1 specifically inhibited the formation of this complex. Western/Southwestern analysis also showed that a protein complex including Sp1 was able to bind the enhancer and the promoter regions in non-denaturing conditions. This complex was dissociated by denaturation. These results suggest that the formation of a nuclear protein-mediated loop structure between the promoter and enhancer may regulate transcription of the collagen II gene transcription.
Visualization of Various Supramolecular Assemblies of Oligo(para‐phenylenevinylene)–Melamine and Perylene Bisimide (2008)

A melamine derivative has been covalently equipped with two oligo(para-phenylenevinylene) (OPV) chromophores. This procedure yields a bifunctional molecule with two hydrogen-bonding arrays available for complementary binding to perylene bisimide derivatives. Depending on the solvent, hydrogen-bonded trimers, tetramers, and dimers on a graphite surface are observed for pure OPV-melamine by using scanning tunneling microscopy (STM). Upon the addition of perylene bisimide, linear tapes of perylene bisimide, 12-membered rosettes that consist of alternating hydrogen-bonded OPV-melamine and perylene bisimide moieties are visualized. These results provide direct evidence for the possible modes of hydrogen bonding within a supramolecular co-assembly in solution. Subsequently, the optical properties of pure OPV-melamine and co-assemblies with a perylene bisimide derivative were characterized in solution. In an apolar solvent, OPV-melamine self-assembles into chiral superstructures. Disassembly into molecularly dissolved species is reversibly controlled by concentration and temperature. Complementary hydrogen bonding to a perylene bisimide derivative in an apolar solvent yields multicomponent, pi-stacked dye assemblies of enhanced stability that are characterized by fluorescence quenching of the constituent chromophores. Titration experiments reveal that a mixture of hydrogen-bonded oligomers is present in solution, rather than a single discrete assembly. The solution experiments are consistent with the STM results, which revealed various supramolecular assemblies. Our system is likely not to be optimally programmed to obtain a discrete co-assembled structure in quantitative yield.
Modeling the Dynamics of Nonenzymatic and Enzymatic Nucleotide Processes by Fractal Dimension (1998)

We introduce here D as a fractal dimension according to Mandelbrot [5] for multicyclic nucleotide processes producing variabilities, where M (l,N) is the probability density of truncated, deleted and point-mutated sequence variabilities (l) as net term of the deterministic processes in the two-dimensional embedding space. The very generality of this result holds for all fractal sets of cumulative sequence variabilities. The minimal requirements sufficient to produce, or to degrade, a target DNA sequence N are multistep additions, recombinations or degradations of some monomeric or oligomeric building blocks with the propagation probability function d = d i at cycle i. Our fractal dimension D can be obtained from the scaling with respect to the largest nucleotide lengths of interest, N. The scaling behaviour of suitable examples of quantified experiments is experimentally analysed for the first time in the following systems, ordered by increasing complexity: (i) chemical, solid-phase oligodeoxyribonucleotide synthesis, (ii) incorporation of fluorescently-labeled deoxyuri-dine 5′-triphosphate by different DNA polymerases and reverse transcriptases, and (iii) characteristic restriction endonuclease patterns for a few typical genes within the genome of herpes simplex virus type 1. Under different experimental conditions, D extends the interpretation to a short-term synthesis pattern of variability of oligonucleotide populations, to characteristics of DNA polymerase and reverse transcriptase activities, and to typical intrinsic long-term variability as shown by enzymatic degradation of viral DNA strains studied.
Intra-Node B Orthogonal Pilot Channel Structure for OFDM Radio Access in Evolved UTRA Downlink (2006)

This paper proposes an intra-node B orthogonal pilot channel structure employing a sector-specific orthogonal sequence and cell-specific (node B-specific) scrambling code for orthogonal frequency division multiplexing (OFDM)-based radio access in the E-UTRA downlink. This paper also proposes a sophisticated orthogonal pilot channel employing code division multiplexing (CDM) to separate sectored beams and distributed frequency division multiplexing (FDM) to separate streams (transmission antennas) in MIMO channel transmissions simultaneously. Successive simulation results verify the effectiveness of the proposed orthogonal pilot channel structures using distributed FDM among multiple streams and CDM between sectored beams. Furthermore, the simulation results also show that the average packet error rate (PER) performance using the proposed intra-node B orthogonal pilot channel is significantly improved compared to that of the conventional structure employing a random sequence, particularly for 16QAM and 64QAM modulations under high intra-node B interference-to-desired signal power ratio conditions
Design of a Database-Driven Assist Control for a Hydraulic Excavator Considering Human Operation (2023)

In recent years, there has been strong focus on sustainable development goals (SDGs). In Japan, Society 5.0, which is proposed as a future vision to be achieved towards the realization of SDGs, is being promoted by various organizations. In particular, “i-Construction” is being promoted in the construction industry. As a result, hydraulic excavators are becoming increasingly automated and semi-automated. Furthermore, if operators achieve high productivity, it helps them maintain a sense of accomplishment and motivation to work. In this study, a control system that results in the desired output is proposed for a hydraulic excavator; in this system, the degree of interference depends on the human input and controller input. Attachments on hydraulic excavators cause interference owing to the characteristics of the hydraulic system. Therefore, a control system that can adaptively adjust the controller input to the human operation, considering the interference with information caused by human operation stored in the database, was constructed. The proposed method was implemented on a hydraulic excavator and its effectiveness was verified.
Spirometer-controlled cine magnetic resonance imaging used to diagnose tracheobronchomalacia in paediatric patients (2013)

Tracheobronchomalacia (TBM) is defined as an excessive collapse of the intrathoracic trachea. Bronchoscopy is the gold standard for diagnosing TBM; however it has major disadvantages, such as general anaesthesia. Cine computed tomography (CT) is a noninvasive alternative used to diagnose TBM, but its use in children is restricted by ionising radiation. Our aim was to evaluate the feasibility of spirometer-controlled cine magnetic resonance imaging (MRI) as an alternative to cine-CT in a retrospective study. 12 children with a mean age (range) of 12 years (7-17 years), suspected of having TBM, underwent cine-MRI. Static scans were acquired at end-inspiration and expiration covering the thorax using a three-dimensional spoiled gradient echo sequence. Three-dimensional dynamic scans were performed covering only the central airways. TBM was defined as a decrease of the trachea or bronchi diameter >50% at end-expiration in the static and dynamic scans. The success rate of the cine-MRI protocol was 92%. Cine-MRI was compared with bronchoscopy or chest CT in seven subjects. TBM was diagnosed by cine-MRI in seven (58%) out of 12 children and was confirmed by bronchoscopy or CT. In four patients, cine-MRI demonstrated tracheal narrowing that was not present in the static scans. Spirometer controlled cine-MRI is a promising technique to assess TBM in children and has the potential to replace bronchoscopy.
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1 (2010)

We have created a high-quality mouse genome-scale metabolic reconstruction, iMM1415 (Mus Musculus, 1415 genes). We demonstrate that the mouse model can be used to perform phenotype simulations, similar to models of microbe metabolism. Since the mouse is an important experimental organism, this model should become an essential tool for studying metabolic phenotypes in mice, including outcomes from drug screening.
Validation and Use of SIMULINK Integrated, High Fidelity, Engine-In-Vehicle Simulation of the International Class VI Truck (2000)

&lt;div class="htmlview paragraph"&gt;This work presents the development, validation and use of a SIMULINK integrated vehicle system simulation composed of engine, driveline and vehicle dynamics modules. The engine model links the appropriate number of single-cylinder modules, featuring thermodynamic models of the in-cylinder processes with transient capabilities to ensure high fidelity predictions. A detailed fuel injection control module is also included. The engine is coupled to the driveline, which consists of the torque converter, transmission, differential and prop shaft and drive shafts. An enhanced version of the point mass model is used to account for vehicle dynamics in the longitudinal and heave directions. A vehicle speed controller replaces the operator and allows the feed-forward simulation to follow a prescribed vehicle speed schedule. For the particular case reported here, the simulation is configured for the International 4700 series, Class VI, 4×2 delivery truck powered by a V8 turbocharged, intercooled diesel engine. The integrated vehicle simulation is validated against transient data measured on the proving ground. Comparisons of predicted and measured responses of engine and vehicle variables during vehicle acceleration from 0 to 60 mph and from 30 to 50 mph show very good agreement. The simulation is also used to study trade-offs involved in redesigning control strategies for improved performance of the vehicle system.&lt;/div&gt;
The effect of different powder particle size on mechanical properties of sintered alumina, resin‐ and glass‐infused alumina (2008)

In this study, the compaction and sintering behavior of fine alumina powders of different particle sizes and the effect of matrix particle size on biaxial strength and fracture toughness of infused matrices were investigated. Three different alumina powders, In-Ceram alumina, A16SG, and RC172 were selected, representing a range of particle size and shape. RC172 and A16SG were dry-pressed. In-Ceram alumina was slip-cast following manufacturer's recommendations. Dry-pressed ceramic blocks were sectioned into disks with a thickness of 1.5-mm. Uninfused disks were sintered at four temperatures between 1250 degrees C and 1400 degrees C. For glass or resin infused specimens, alumina disks were sintered at 1250 degrees C for 2 h and separated into two groups for glass infusion and resin (UDMA/TEGDMA) infusion. Disks were tested for biaxial flexural strength with a universal testing machine (Instron) at 0.5-mm/min crosshead speeds. One-way ANOVA and Duncan's multiple range tests revealed that alumina disks with different smaller particle sizes have significantly higher biaxial strength (p < 0.05). The strength of the alumina matrix was greatly increased by glass and resin infusion. The biaxial strength of resin-infused alumina increased as particle size decreased, whereas strength of glass-infused alumina was constant.
A Novel Texture Improving Young’s Modulus in Rolling Direction of Hot Rolled Low Carbon Sheet Steel (2017)

A novel texture, which improves Young’s modulus in rolling direction, has been found in a hot rolled low carbon sheet steel. This unique texture is observed in sheet surface area, which consists of sharply developed {110}<111>–{110}<112> fiber without {110}<001>. Together with {112}<111> orientation, this fiber can significantly contribute to increase Young’s modulus in rolling direction. The measured Young’s modulus in rolling direction in the present material is 236 GPa, which is more than 10% increase, compared to the one in conventional steels.
Genomics and Weeds: A Synthesis (2009)

This chapter contains sections titled: From Fundamental Information to Practical Solutions Where Do We Go from Here? References
Emerging Spintronic Memories (2019)

Spintronic memories are emerging as one of the next generation storage technologies to replace hard disk drives and current solid state memories. This chapter reviews the underlying physics, and the state of the technology of these emerging spintronic memories. Most conventional solid state memories require one or more transistors or switches per data bit, to a large extent, by the size of a single transistor, the number of transistors needed per memory cell, and the cell layout and architecture. The target market of the domain wall (DW)-motion Magnetic random access memory (MRAM) is high-speed memory macros embedded in a next generation System on a Chip. Compared with conventional MRAM, including spin transfer torque MRAM, the main advantage of DW-motion MRAM is the separation of the writing and read-out circuits and thus, the larger margin for the read-out levels. The racetrack memory is conceptually very different from MRAM.
2-Azido-2-deoxy-2,4-C-dimethyl-3,4-O-isopropylidene-L-ribono-1,5-lactone (2007)

The relative configuration of the title lactone, C10H15N3O4, a compound of value in the synthesis of complex pyrrolidines, was determined by X-ray crystallographic analysis.
New Cell Biology Assays Using a Stabilized Luciferase Exhibiting Red Luminescence (2012)

Bioluminescence is the light produced in certain organisms as a result of luciferase enzyme mediated oxidation of a luciferin substrate. This oxidation is linearly dependent on the presence of adenosine tri‐phosphate (ATP). We have recently developed a codon‐optimized luciferase based upon the gene sequence of the natural luciferase isolated from Luciola cruciata (Japanese firefly). This new gene codes for a modified amino acid sequence which exhibits improved expression levels in mammalian cells, red‐shifted emission wavelengths (560 to 619 nm) as well as improved thermal stability, while still utilizing D‐luciferin and ATP as substrates. This new recombinant enzyme was purified to 98% homogeneity from both transfected E . coli bacteria and HEK 293 mammalian cells using Ni +2 ‐affinity chromatography as the His6‐tagged protein. Enzymes isolated from either source were found to have equivalent activity in ATP dependent assays. The purified recombinant luciferase was used to develop a number of ultrasensitive biological assays useful in measuring cell number, cell viability as well as the cytotoxicity effects of several chemotherapeutic drugs (Etoposide and Doxorubicin) when added to murine NIH3T3 cells in culture. We also utilized the purified enzyme to sensitively detect bacterial cell number down to 1 × 10 2 cells and adapted the methods for use in high‐throughput antibiotic screening protocols. By cloning the luciferase downstream of TFkB responsive elements, the activation of TF‐κB (with stimulation by TNFα) in human HEK 293 cells could be quantitated by directly monitoring the increase in luminescence from activation of luciferase expression. Finally, since this new luciferase has a red‐shift in light emission, it was utilized in multiplexed assay conditions with other green (firefly) or blue‐emitting (Renilla) luciferases in a number of coupled biological assays. Moreover, application of this new luciferase for use in in vivo imaging was explored.
Analysis of immune responses in the sheep to synthetic peptides of foot-and-mouth disease virus using ovine polyclonal and monoclonal antibodies. (1990)

A 40-residue peptide incorporating residues 200-213 and 141-158 of foot-and-mouth disease virus VP1 capsid protein strain O1 Kaufbeuren was injected uncoupled into sheep, and the immune responses analysed. Direct-binding and inhibition experiments showed that the polyclonal antibody response was directed mainly against epitopes unique to the 40-residue peptide but absent from the constituent peptides containing residues 200-213 or 141-158, respectively. Further confirmation of the presence of unique epitopes on the 40-residue peptide was obtained from similar experiments performed with sheep monoclonal antibodies generated through the use of an aminopterin-sensitive sheep/mouse heterohybridoma cell line as a fusion partner. The sheep polyclonal antisera to the 40-residue peptide had high neutralization titres and were fully active in a mouse protection assay, whereas none of the sheep monoclonal antibodies conferred protection. The results suggest that the conformation of the 40-residue peptide is important for its ability to induce neutralizing antibodies.
Depleting Mycobacterium tuberculosis of the transcription termination factor Rho causes pervasive transcription and rapid death (2017)

Rifampicin, which inhibits bacterial RNA polymerase, provides one of the most effective treatments for tuberculosis. Inhibition of the transcription termination factor Rho is used to treat some bacterial infections, but its importance varies across bacteria. Here we show that Rho of Mycobacterium tuberculosis functions to both define the 3' ends of mRNAs and silence substantial fragments of the genome. Brief inactivation of Rho affects over 500 transcripts enriched for genes of foreign DNA elements and bacterial virulence factors. Prolonged inactivation of Rho causes extensive pervasive transcription, a genome-wide increase in antisense transcripts, and a rapid loss of viability of replicating and non-replicating M. tuberculosis in vitro and during acute and chronic infection in mice. Collectively, these data suggest that inhibition of Rho may provide an alternative strategy to treat tuberculosis with an efficacy similar to inhibition of RNA polymerase.