gebhart/patrepeval huggingface dataset:
Category Theory Approach to Solution Searching Based on Photoexcitation Transfer Dynamics (2017)

Solution searching that accompanies combinatorial explosion is one of the most important issues in the age of artificial intelligence. Natural intelligence, which exploits natural processes for intelligent functions, is expected to help resolve or alleviate the difficulties of conventional computing paradigms and technologies. In fact, we have shown that a single-celled organism such as an amoeba can solve constraint satisfaction problems and related optimization problems as well as demonstrate experimental systems based on non-organic systems such as optical energy transfer involving near-field interactions. However, the fundamental mechanisms and limitations behind solution searching based on natural processes have not yet been understood. Herein, we present a theoretical background of solution searching based on optical excitation transfer from a category-theoretic standpoint. One important indication inspired by the category theory is that the satisfaction of short exact sequences is critical for an adequate computational operation that determines the flow of time for the system and is termed as “short-exact-sequence-based time.” In addition, the octahedral and braid structures known in triangulated categories provide a clear understanding of the underlying mechanisms, including a quantitative indication of the difficulties of obtaining solutions based on homology dimension. This study contributes to providing a fundamental background of natural intelligence.
Vertically stacking 10 periods of self-assembled InAs/InP quantum wires (2003)

Summary form only given. Additional confinement in semiconductor quantum wires is expected to significantly improve the performances of semiconductor devices due to the increased density of states at the band edge. We report our result on the fabrication of self-assembled InAs/InP quantum wires (QWRs) with single and 10 vertical-periods. Our InAs QWRs were grown on InP [001] substrates in a Riber 32 MBE system at the temperature of 430/spl deg/C and a growth rate of 0.3 ML/s. The photoluminescence (PL) spectra and PL polarizations of the two samples were investigated at different pump wavelengths, different pump intensities and sample temperatures. Our results exhibited unique behaviors, especially on the stacked quantum wires. Following our detailed analyses, we determined the structure of the stacked quantum wires from the bottom to the top, which is different from the designed one. Furthermore, we have provided a new design that will result in the narrowing of the PL linewidth for the stacked self-assembled quantum wires.
Supplementary Figure 5 from Human Breast Cancer Cells Harboring a Gatekeeper T798M Mutation in HER2 Overexpress EGFR Ligands and Are Sensitive to Dual Inhibition of EGFR and HER2 (2023)

&lt;p&gt;Supplementary Figure 5 - PDF file 77K, HER3 expression is required for growth of T798M mutant-expressing cells&lt;/p&gt;
Dependency of tonality perception on frequency, bandwidth and duration (2013)

Psychoacoustic studies show that a narrowband noise masker exhibits a stronger simultaneous masking effect than a tonal masker with the same signal power placed at the noise center frequency. Consequently, perceptual audio codecs commonly incorporate some sort of tonality estimation as part of their perceptual model. However, common tonality estimation techniques do not necessarily reflect the perception of tonality by human listeners. As long as the tone and narrowband noise signals are long enough, they are easily distinguishable for normal hearing listeners. However, if the stimulus duration decreases, both signal types approach the shape of impulses and therefore, at some point become audibly identical. Consequently, at a given frequency and noise bandwidth, there is a duration threshold below which the signals cannot be distinguished. A series of so-called "2-AFC 3-step up-down" psychoacoustic tests are designed and carried out to investigate the frequency and bandwidth dependency of these duration thresholds. The test results, collected from 32 listeners, are statistically evaluated and confirm a decreasing threshold for increasing center frequency and bandwidth. These results can be used to improve psychoacoustic models for audio codecs by using tonality estimators with frequency and bandwidth adapted temporal resolution.
Gut microbes and food reward: From the gut to the brain (2022)

Inappropriate food intake behavior is one of the main drivers for fat mass development leading to obesity. Importantly the gut microbiota-mediated signals have emerged as key actors regulating food intake acting mainly on the hypothalamus, and thereby controlling hunger or satiety/satiation feelings. However, food intake is also controlled by the hedonic and reward systems leading to food intake based on pleasure (i.e., non-homeostatic control of food intake). This review focus on both the homeostatic and the non-homeostatic controls of food intake and the implication of the gut microbiota on the control of these systems. The gut-brain axis is involved in the communications between the gut microbes and the brain to modulate host food intake behaviors through systemic and nervous pathways. Therefore, here we describe several mediators of the gut-brain axis including gastrointestinal hormones, neurotransmitters, bioactive lipids as well as bacterial metabolites and compounds. The modulation of gut-brain axis by gut microbes is deeply addressed in the context of host food intake with a specific focus on hedonic feeding. Finally, we also discuss possible gut microbiota-based therapeutic approaches that could lead to potential clinical applications to restore food reward alterations. Therapeutic applications to tackle these dysregulations is of utmost importance since most of the available solutions to treat obesity present low success rate.
<i>Scytalidium dimidiatum</i> Causing Recalcitrant Subcutaneous Lesions Produces Melanin (2004)

Scytalidium dimidiatum is a pigmented dematiaceous coelomycete that typically causes chronic superficial skin diseases and onychomycosis, as well as deeper infections, such as subcutaneous abscesses, mycetoma, and even fungemia in immunocompromised patients. A second species, Scytalidium hyalinum, has hyaline hyphae and arthroconidia and is considered by some authors to be an albino mutant of S. dimidiatum. This study aimed to confirm the presence of melanin or melanin-like compounds (which have been previously implicated in the virulence of other fungal pathogens) in S. dimidiatum from a patient with multiple subcutaneous nodules. Treatment of the hyphae and arthroconidia with proteolytic enzymes, denaturant, and concentrated hot acid yielded dark particles, which were stable free radicals, consistent with their identification as melanins. Extracted melanin particles from S. dimidiatum cultures were labeled by melanin-binding monoclonal antibodies (MAbs) from Sporothrix schenckii, Aspergillus fumigatus, and Cryptococcus neoformans. Lesional skin from the patient infected with S. dimidiatum contained fungal cells that were labeled by melanin-binding MAbs, and digestion of the tissue yielded dark particles that were also reactive. S. hyalinum was also subjected to the melanin extraction protocol, but no dark particles were yielded.
Structural Equation Modeling of Cover Crop Effects on Soil Nitrogen and Dry Bean (2017)

Core Ideas Structural equation modeling is utilized to explore how cover crops influence dry beans. Cover crop C/N ratio and incorporation timing can indirectly affect dry bean yield. Cover crops quality needs to be managed to benefit cash crops. The direct impact of cover crops on nutrient cycling and yield has been studied in many different systems, however limited datasets have prevented larger scale modeling of the complex relationships among these variables. The reduced model generated from this analysis demonstrated that in an organic dry bean system, both higher cover crop C/N ratio and shorter time from cover crop incorporation until dry bean planting could negatively affect yield through lower soil inorganic N availability at the time of bean planting (mid‐ to late June). Days between cover crop incorporation and dry bean planting ranged from 1 to 64, with the model showing that less time also reduced yield through reduced dry bean population. These findings support the premise that cover crop quality and time for decomposition are important parameters to manage to benefit the subsequent cash crop.
Supplementary Table 3 from A Susceptibility Locus for Papillary Thyroid Carcinoma on Chromosome 8q24 (2023)

Supplementary Table 3 from A Susceptibility Locus for Papillary Thyroid Carcinoma on Chromosome 8q24
Predictors of Tonsillectomy after Previous Adenoidectomy for Upper Airway Obstruction (2011)

Patients undergoing adenoidectomy for upper airway obstruction are likely to be at an increased risk of subsequent tonsillectomy when compared with those with other indications. Within this subgroup of patients with upper airway obstruction, young age, female sex, and large tonsil size may further increase the risk of subsequent tonsillectomy.
Investigations of mode control in proton-implanted and oxide-confined VCSELs using PBGs: modelling and experiment (2004)

We have investigated theoretically the influence on transverse optical modes of a two-dimensional photonic crystal (PC) defect waveguide embedded into a vertical-cavity surface-emitting laser. In gain-guided structures, where the index profile is weak, the effect of the PC is efficient. In the oxide-confined structures, where the index guidance provided by the oxide is larger, this is not the case, but the efficiency of the PC can be increased by oxide in the node position. It is shown that the thermal lensing effect leads to increased sensitivity of the single-mode conditions on the current injection change.
The implementation of adaptive elements into an experimental high‐rise building (2018)

Abstract Dedicated to our speaker, Prof. Werner Sobek, in honour of his 65 th birthday In 2017, the University of Stuttgart started a Collaborative Research Centre with the title Adaptive Skins and Structures for the Built Environment of Tomorrow. The goal of this research project is to find an answer to today's most urgent social and ecological questions as the global population continuously increases and the available resources remain limited. As the central approach to the solution of this problem, adaptive elements will be included in the structure, the interior and the façade of an experimental 37 m tall building. This paper introduces the topic of adaptivity in building structures and provides an overview of the research topics applied in this globally unique adaptive high‐rise building. Due to the complexity of research topics of this Collaborative Research Centre, this paper only covers the research concerning the experimental high‐rise building.
Anti-Tuberculous Activity of Treponemycin Produced by a Streptomyces Strain MS-6-6 Isolated from Saudi Arabia (2015)

A Streptomyces strain MS-6-6 with promising anti-tuberculous activity was isolated from soil samples in Saudi Arabia. The nucleotide sequence of its 16S rRNA gene (1426 bp) evidenced a 100% similarity to Streptomyces mutabilis. Through an anti-tuberculous activity-guided approach, a polyketide macrolide was isolated and identified as treponemycin (TP). The structure of the isolated compound was determined by comprehensive analyses of its 1D and 2D NMR as well as HRESI-MS. In addition to the promising anti-tuberculous activity (MIC = 13.3 µg/mL), TP showed broad spectrum of activity against the Gram positive, Gram negative strains, and Candida albicans. Improvement of TP productivity (150%) was achieved through modification in liquid starch nitrate medium by replacing KNO3 with corn steep liquor and yeast extract or tryptone, and removing CaCO3 and K2HPO4. The follow up of TP percentage as well as its metabolites profile for each media was assessed by LC/DAD/MS.
Compact microwave applicator for thermal therapy of breast cancer: Comparative assessment of arrays operating at 434 and 915 MHz (2016)

The objective of this study was to design a comfortable, compact, wearable and easy-to-manufacture microwave applicator affording conformal thermal therapy of breast tumors. Several configurations of patch antenna arrays operating at 434 and 915 MHz were evaluated in terms of average power absorption (aPA) ratio in target tumors and impedance matching. Models incorporated breast tissue and simulated target tumors of varying size positioned at several location within breast tissue. Single antenna simulations show that the performance at the two frequencies is dependent on the model dimensions. However, multiple element arrays at 915 MHz can achieve greater aPA ratio levels (up to 60%) than arrays at 434 MHz for deep targets in large breast models.
Piezoresistive cantilever integrated microfluidic channel for measuring cellular properties (2016)

We propose a microfluidic device that has piezoresistive cantilever on the bottom wall of its microchannel to measure cellular mechanical property. This sensor allows us to measure force applied to the wall of microfluidic channel directly with high sensitivity and high temporal resolution. Moreover, feedback from the sensor can be used to control liquid flow above the cantilever. We demonstrate that our device is able to detect the force acting on the channel bottom wall during the passing-through of mammalian cells by the piezoresistive cantilever.
Measurement and use of Formation Fluid, Saturate, and Aromatic Content, With Wireline Formation Testers (2015)

The measurement of the composition of a formation fluid can provide great insight for petrophysical, geochemical, and phase behavior interpretation. Laboratory analyses of bottomhole samples have historically provided much of this required compositional data. The delay in providing this critical information for decision making can range from weeks to months. By the time evaluation occurs, the opportunity to collect additional samples is lost, and any ambiguities regarding the sampled fluids may not be resolved. Providing formation fluid characterization in situ and in real time by means of wireline formation testers can enhance formation characterization and sampling programs. However, direct single station fluid compositional analysis measurements by wireline formation testers have historically been limited to gas components C1-C5 and bulk oil C6+. Although some multistation extrapolation can provide information regarding asphaltene content, no direct assay of bulk oil C6+ into measured components has been available. New measurement technology based on a multivariate optical computing technique has provided evidence of saturate and aromatics content. The bulk residual of a single-phase oil with respect to the directly measured gas, saturates, and aromatic fraction represents the non-polar resins and asphaltene fraction of the oil. A comparison of tool response to laboratory values for eight formation fluids validates the measurements of gas/oil ratio (GOR), C1, saturates, and aromatics concentration. The bulk difference with measured density corresponds well with resin and asphaltene content. Because of the high associated aromatic character of fluids in and near tar mat zones, the measurement of aromatic content can be useful for pinpointing the locations of such zones. SATURATES AROMATICS RESINS
Dynamic interference management (2013)

A linear interference network is considered. Long-term fluctuations (shadow fading) in the wireless channel can lead to any link being erased with probability p. Each receiver is interested in one unique message that can be available at M transmitters. In a cellular downlink scenario, the case where M = 1 reflects the cell association problem, and the case where M > 1 reflects the problem of setting up the backhaul links for Coordinated Multi-Point (CoMP) transmission. For M = 1, we characterize the average per user DoF, and identify the optimal assignment of messages to transmitters at each value of p. For general values of M, we show that there is no strategy for assigning messages to transmitters in large networks that is optimal for all values of p.
The development and characterization of a 57<scp>K</scp> single nucleotide polymorphism array for rainbow trout (2014)

In this study, we describe the development and characterization of the first high-density single nucleotide polymorphism (SNP) genotyping array for rainbow trout. The SNP array is publically available from a commercial vendor (Affymetrix). The SNP genotyping quality was high, and validation rate was close to 90%. This is comparable to other farm animals and is much higher than previous smaller scale SNP validation studies in rainbow trout. High quality and integrity of the genotypes are evident from sample reproducibility and from nearly 100% agreement in genotyping results from other methods. The array is very useful for rainbow trout aquaculture populations with more than 40 900 polymorphic markers per population. For wild populations that were confounded by a smaller sample size, the number of polymorphic markers was between 10 577 and 24 330. Comparison between genotypes from individual populations suggests good potential for identifying candidate markers for populations' traceability. Linkage analysis and mapping of the SNPs to the reference genome assembly provide strong evidence for a wide distribution throughout the genome with good representation in all 29 chromosomes. A total of 68% of the genome scaffolds and contigs were anchored through linkage analysis using the SNP array genotypes, including ~20% of the genome assembly that has not been previously anchored to chromosomes.
SPATIOTEMPORAL AVERAGING METHOD FOR ENHANCEMENT OF REVERBERANT SPEECH (2010)

We present a reverberant speech enhancement algorithm which, operating on the linear prediction residual of spatially averaged multimicrophone observations, utilizes temporal averaging of neighbouring larynx cycles. The enhanced larynx cycles are used to design an equalization filter, which is applied in order to dereverberate both voiced and unvoiced speech. The DYPSA algorithm is employed and evaluated for larynx cycle segmentation of reverberant speech. Simulation results show reverberation reduction with up to 5 dB in terms of segmental signal-to-reverberant ratio and 0.34 in terms of normalized Bark spectral distortion score. Index Terms — Speech dereverberation, GCI identification 1.
Lateral clay injection into normal faults (2003)

ABSTRACT The clay content of fault gouge is one of the main factors controlling transport and mechanical properties of a fault zone. This paper addresses the process of lateral clay injection into normal faults, which is one of the many processes contributing to the development of clay smear, and can lead to local enrichment of clay in a fault gouge. We combined field observations with geomechanical models to quantify the parameters leading to lateral clay injection into fault zones. Detailed field study shows that a releasing fault bend in a clay layer is required for clay injection to occur. The clay injection process is often associated with the formation of a branch in the fault and the development of a “squeezing block” which injects the clay into the fault zone. A simple analytical model predicts the onset of clay injection when C = σ'v (1 - sin ϕ) / (2 cos ϕ), where C is cohesion (MPa), σ'v is vertical stress (MPa) and ϕ (°) is friction angle. More detailed analysis using 2-D geomechanical finite element models is in good agreement with the analytical models and allows study of the system at higher fault throw. Results of sandbox models containing layers of an elastoplastic clay analogue also compare well with field observations and numerical models, and show the initiation of the releasing step and the evolution of the clay injection process with increasing fault throw. Using our results it is possible to predict the likelihood of lateral clay injection in the subsurface, in settings like the Gharif formation of the Haushi group of Central and South Oman or the Natih formation of North Oman. This requires an estimation of the mechanical properties of the clays at the time of faulting; data which can be obtained from wireline logs and cuttings. This approach to fault seal analysis emphasizes the mechanical aspects of the clay smear process, in addition to the kinematics which were considered in previous analyses. Its application should lead to improved prediction of fault seal processes in the subsurface.
Is there an “ACE” in the hole for postcoronary artery bypass graft myocardial dysfunction? * (2003)

Parrish, J. S. CAPT (S) MC USN, FCCP; Amundson, Dennis E. CAPT MC USN, FACP, FCCM, FCCP Author Information
Genetically encoded intrabody sensors report the interaction and trafficking of β-arrestin 1 upon activation of G-protein–coupled receptors (2020)

Agonist stimulation of G-protein-coupled receptors (GPCRs) typically leads to phosphorylation of GPCRs and binding to multifunctional proteins called β-arrestins (βarrs). The GPCR-βarr interaction critically contributes to GPCR desensitization, endocytosis, and downstream signaling, and GPCR-βarr complex formation can be used as a generic readout of GPCR and βarr activation. Although several methods are currently available to monitor GPCR-βarr interactions, additional sensors to visualize them may expand the toolbox and complement existing methods. We have previously described antibody fragments (FABs) that recognize activated βarr1 upon its interaction with the vasopressin V2 receptor C-terminal phosphopeptide (V2Rpp). Here, we demonstrate that these FABs efficiently report the formation of a GPCR-βarr1 complex for a broad set of chimeric GPCRs harboring the V2R C terminus. We adapted these FABs to an intrabody format by converting them to single-chain variable fragments and used them to monitor the localization and trafficking of βarr1 in live cells. We observed that upon agonist simulation of cells expressing chimeric GPCRs, these intrabodies first translocate to the cell surface, followed by trafficking into intracellular vesicles. The translocation pattern of intrabodies mirrored that of βarr1, and the intrabodies co-localized with βarr1 at the cell surface and in intracellular vesicles. Interestingly, we discovered that intrabody sensors can also report βarr1 recruitment and trafficking for several unmodified GPCRs. Our characterization of intrabody sensors for βarr1 recruitment and trafficking expands currently available approaches to visualize GPCR-βarr1 binding, which may help decipher additional aspects of GPCR signaling and regulation.