gebhart/patrepeval huggingface dataset:
Computational Studies of Solubilities of LiO2and Li2O2in Aprotic Solvents (2017)

Knowledge of the solubilities of Li<sub>2</sub>O<sub>2</sub> and LiO<sub>2</sub> in aprotic solvents is important for insight into the discharge and charge processes of Li-O<sub>2</sub> batteries, but these quantities are not well known. In this contribution, the solvation free energies of molecular LiO<sub>2</sub> and Li<sub>2</sub>O<sub>2</sub> in various organic solvents were calculated using various explicit and implicit solvent models, as well as ab initio molecular dynamics (AIMD) methods. Best estimates for the solvation energies from these calculations along with calculated lattice energies of Li<sub>2</sub>O<sub>2</sub> and LiO<sub>2</sub> were used to determine the solubility of bulk LiO<sub>2</sub> and Li<sub>2</sub>O<sub>2</sub>. The computed solubility of LiO<sub>2</sub> (1.8 × 10<sup>-2</sup> M) is about 15 orders higher than that of Li<sub>2</sub>O<sub>2</sub> (2.0 × 10<sup>-17</sup> M) due to a much less negative lattice energy of bulk LiO<sub>2</sub> compared to that of Li<sub>2</sub>O<sub>2</sub>. The difference in solubilities between LiO<sub>2</sub> and Li<sub>2</sub>O<sub>2</sub> likely will affect the nucleation and growth mechanisms and resulting morphologies of the products formed during battery discharge, influencing the performance of the battery cell. In conclusion, the calculated LiO<sub>2</sub> and Li<sub>2</sub>O<sub>2</sub> solubilities provide important information for fundamental studies of discharge and charge chemistries in Li-O<sub>2</sub> batteries.
Scalable Dense Linear Algebra on Heterogeneous Hardware (2013)

Design of systems exceeding 1 Pflop/s and the push toward 1 Eflop/s, forced a dramatic shift in hardware design. Various physical and engineering constraints resulted in introduction of massive parallelism and functional hybridization with the use of accelerator units. This paradigm change brings about a serious challenge for application developers, as the management of multicore proliferation and heterogeneity rests on software. And it is reasonable to expect, that this situation will not change in the foreseeable future. This chapter presents a methodology of dealing with this issue in three common scenarios. In the context of shared-memory multicore installations, we show how high performance and scalability go hand in hand, when the well-known linear algebra algorithms are recast in terms of Direct Acyclic Graphs (DAGs), which are then transparently scheduled at runtime inside the Parallel Linear Algebra Software for Multicore Architectures (PLASMA) project. Similarly, Matrix Algebra on GPU and Multicore Architectures (MAGMA)schedules DAG-driven computations on multicore processors and accelerators. Finally, Distributed PLASMA (DPLASMA), takes the approach to distributed-memory machines with the use of automatic dependence analysis and the Direct Acyclic Graph Engine (DAGuE) to deliver high performance at the scale of many thousands of cores.
Asymmetric Synthesis of Octahedral Coordination Complexes (2011)

Abstract In contrast to stereoselective organic chemistry, which has established sophisticated synthetic strategies to control the relative and absolute configuration at tetrahedral carbon atoms, the stereochemical control of octahedral coordination spheres is much less understood. This microreview reflects on the state of the art of asymmetric coordination chemistry of octahedral complexes within the historical context, including asymmetric coordination chemistry evolved by nature, the predetermination of metal‐centered chirality with tailored chiral ligands, chiral‐anion‐mediated asymmetric synthesis, chiral‐auxiliary‐mediated asymmetric coordination chemistry, and finally, very recent work on the catalytic asymmetric synthesis of an octahedral coordination complex. The stereocontrolled synthesis of octahedral metal complexes is an important problem of contemporary coordination chemistry and will ultimately provide the necessary synthetic tools to fully exploit the opportunities provided by the rich stereochemistry of octahedral coordination geometries.
Quantification of Three-Dimensional Motion of the Renal Arteries Using Image-Based Modeling Techniques (2007)

Stents implanted to treat renal artery stenosis are vulnerable to stent fracture and thrombosis [1–3]. We hypothesize that the motion of the renal arteries during respiration is a possible cause of stent fracture or in-stent restenosis. However, the respiratory motion of the renal arteries and the kidneys is poorly understood. Using magnetic resonance imaging data we previously quantified the two-dimensional deformation of the renal arteries and demonstrated that respiration-induced kidney motion results in vessel bending near the ostia [4]. In this study we quantified the complex three-dimensional motion of the renal arteries and kidneys over the respiratory cycle using magnetic resonance angiography data and imaged-based modeling methods. We provide quantitative information on anatomic changes to the renal arteries that may provide data to design improved pre-clinical, benchtop tests for renal stents.
Consultant and Critics on the Couch (2008)

The process of situating the “client on the couch” also entails the seating of “consultant and critics on the couch” as they participate in a self-reflective and dialectical process. The author argues the importance of strategic use of the “toxicity” metaphor and the central role of an initially qualitative lens via corporate cases and narrative investigations into dark side, destructive behavior in companies. Central to the study of toxicity is the blending of micro and macro, as individual psychology and systemic company-wide perspectives are fused into consulting and coaching hybrids. The patience of an anthropologist is required for the consultant facing thick, textured cases of organizational and leadership toxicity, and similar emotional intelligence is depicted as essential for a bridging of both qualitative and metric-driven streams of consultation and research.
Advanced Cell Mapping Visualizations for Single Cell Functional Proteomics Enabling Patient Stratification (2020)

Highly multiplexed single-cell functional proteomics has emerged as one of the next-generation toolkits for a deeper understanding of functional heterogeneity in cell. Different from the conventional population-based bulk and single-cell RNA-Seq assays, the microchip-based proteomics at the single-cell resolution enables a unique identification of highly polyfunctional cell subsets that co-secrete many proteins from live single cells and most importantly correlate with patient response to a therapy. The 32-plex IsoCode chip technology has defined a polyfunctional strength index (PSI) of pre-infusion anti-CD19 chimeric antigen receptor (CAR)-T products, that is significantly associated with patient response to the CAR-T cell therapy. To complement the clinical relevance of the PSI, a comprehensive visualization toolkit of 3D uniform manifold approximation and projection (UMAP) and t-distributed stochastic neighbor embedding (t-SNE) in a proteomic analysis pipeline is developed, providing more advanced analytical algorithms for more intuitive data visualizations. The UMAP and t-SNE of anti-CD19 CAR-T products reveal distinct cytokine profiles between nonresponders and responders and demonstrate a marked upregulation of antitumor-associated cytokine signatures in CAR-T cells from responding patients. Using this powerful while user-friendly analytical tool, the multi-dimensional single-cell data can be dissected from complex immune responses and uncover underlying mechanisms, which can promote correlative biomarker discovery, improved bioprocessing, and personalized treatment development.
Utilizing Spherical Resonances for Microwave Breast Cancer Detection (2023)

In this paper, we investigate if external resonances created at a spherical tumor model can be utilized to increase the contrast between the tumor and background field in a simple microwave breast imaging scenario. Numerical simulations are being performed for two cases, low-adipose and high-adipose average breast tissue, exhibiting high and low permittivity and dielectric losses, respectively. The electric field is probed along the breast surface with and without a spherical tumor model present, and the relative tumor signal with respect to the background field is separated into a surface-normal and surface-parallel component. It is shown that in the high-adipose case, an external spherical resonance is created at the tumor, whereas no clear resonance occurs in the low-adipose case. In both cases is the contrast between the tumor signal and the background field stronger in the surface-normal than in the surface-parallel component. The external tumor resonance could directly be observed in the high-adipose case as a decrease of field strength close to the tumor if placed in close proximity to the breast surface.
Marfan Database (second edition): software and database for the analysis of mutations in the human FBN1 gene (1997)

Fibrillin is the major component of extracellular microfibrils. Mutations in the fibrillin gene on chromosome 15 (FBN1) were described at first in the heritable connective tissue disorder, Marfan syndrome (MFS). More recently, FBN1 has also been shown to harbor mutations related to a spectrum of conditions phenotypically related to MFS. These mutations are private, essentially missense, generally non-recurrent and widely distributed throughout the gene. To date no clear genotype/phenotype relationship has been observed excepted for the localization of neonatal mutations in a cluster between exons 24 and 32. The second version of the computerized Marfan database contains 89 entries. The software has been modified to accomodate new functions and routines.
Digital beamforming algorithm for 5G low-SHF-band massive MIMO with intersite coordination (2017)

Massive multiple-input multiple-output (Massive MIMO) beamforming (BF) is an important technology to utilize higher frequency bands effectively. Fully-digital Massive MIMO BF can be applied for low-SHF-band, and joint processing of digital fixed BF and channel state information (CSI)-based precoding (Digital FBCP) is proposed as one of the fully-digital algorithms. Additionally, it is assumed that multiple sites with low-SHF-band cover continuous areas in the early fifth-generation (5G) mobile communication system. New BF algorithm for multi-site Massive MIMO is required to enable to transmit effectively multiple streams with intersite interference reduction. In this paper, we propose three types of Digital FBCP algorithm with intersite coordination. Throughput performances are shown by link level simulation, and we clarify that the proposed schemes can improve throughput performance compared to that without intersite coordination.
Identification of a new intestinal spirochete with pathogenicity for chickens (1995)

Two intestinal spirochete isolates obtained from chickens with diarrhea were examined by electron microscopy, biochemical tests, rRNA gene restriction pattern analysis, and multilocus enzyme electrophoresis. One isolate (strain 91-1207/C1) was pathogenicity tested in vivo in chickens. The chicken spirochetes were morphologically indistinguishable from Serpulina innocens and Serpulina hyodysenteriae and phenotypically similar to S. innocens. However, the chicken spirochetes could be distinguished from S. innocens, S. hyodysenteriae, and other swine intestinal spirochetes by rRNA gene restriction pattern analysis and multilocus enzyme electrophoresis. In pathogenicity tests in 1-day-old chicks and 14-month-old hens, chicken spirochete 91-1207/C1 produced pale-yellow, watery cecal contents and mild lymphocytic typhlitis. These findings support the conclusion that avian intestinal spirochetes can be pathogenic to commercial poultry and that the microorganisms are different from intestinal spirochetes that infect pigs.
Expanding homogeneous culture of human primordial germ cell-like cells maintaining germline features without serum or feeder layers (2022)

In vitro expansion of human primordial germ cell-like cells (hPGCLCs), a pluripotent stem cell-derived PGC model, has proved challenging due to rapid loss of primordial germ cell (PGC)-like identity and limited cell survival/proliferation. Here, we describe long-term culture hPGCLCs (LTC-hPGCLCs), which actively proliferate in a serum-free, feeder-free condition without apparent limit as highly homogeneous diploid cell populations maintaining transcriptomic and epigenomic characteristics of hPGCLCs. Histone proteomics confirmed reduced H3K9me2 and increased H3K27me3 marks in LTC-hPGCLCs compared with induced pluripotent stem cells (iPSCs). LTC-hPGCLCs established from multiple human iPSC clones of both sexes were telomerase positive, senescence-free cells readily passaged with minimal cell death or deviation from the PGC-like identity. LTC-hPGCLCs are capable of differentiating to DAZL-positive M-spermatogonia-like cells in the xenogeneic reconstituted testis (xrTestis) organ culture milieu as well as efficiently producing fully pluripotent embryonic germ cell-like cells in the presence of stem cell factor and fibroblast growth factor 2. Thus, LTC-hPGCLCs provide convenient access to unlimited amounts of high-quality and homogeneous hPGCLCs.
Proceedings of the 2014 International SPIN Symposium on Model Checking of Software (2014)

Techniques and tools for verification of multi-threaded programs must cope with the huge number of possible thread interleavings. Tools based on systematic exploration of a program state space employ partial order reduction to avoid redundant thread ...
Decoding Energy Estimation of an HEVC Hardware Decoder (2018)

This paper investigates the energy a hardware decoder needs for decoding and displaying an HEVC-coded bit stream. Therefore, energy measurements are performed on a high amount of different bit streams. The results are used to validate the estimation accuracy of various decoder energy models. Furthermore, from power measurements, two new models are derived and proposed. The results show that all models are capable of estimating the decoding energy with a mean estimation error below 5%, where the lowest error of 1.04% was found for one of the proposed models. Furthermore, trained parameter values are given quantifying the influence of various sequence properties on the decoding energy: the resolution, the frame rate, the playback time, and the file size of the bit stream.
Identifying cis-Acting DNA Elements within a Control Region (2012)

Computational methods can be used to identify DNA sequence motifs that have been conserved through evolution, as well as motifs that correspond to recognition sites for known DNA-binding proteins. These computational methods, when combined with chromatin immunoprecipitation and other basic experiments, can provide preliminary insight into the elements and factors that regulate a gene of interest. When pursuing a more complete understanding of a control region of interest, a comprehensive mutant analysis should generally be performed as a critical step toward more advanced functional studies. This article describes strategies for such a comprehensive analysis. It also summarizes the insights provided by a comprehensive mutant analysis versus a phylogenetic analysis.
Two-photon absorption spectra of CdTe quantum dots (2005)

Both degenerate and nondegenerate two-photon absorption (2PA) spectra are studied in two different samples of CdTe quantum-dots in borosilicate glass hosts. One sample (CdTe-600) contains quantum-dots of radius 3.2 ± 0.2 nm and has its absorption edge at 600nm. The other sample (CdTe-750) contains quantum-dots of radius 6.6 ± 0.9 nm and absorption edge at 750nm. CdTe-600 contains quantum-dots with a narrower size distribution than CdTe-750. Consequently, the peaks corresponding to discrete transitions are more clearly visible in CdTe-600 than in CdTe-750. Both nondegenerate and degenerate spectra for these samples show a marked difference from bulk CdTe. In CdTe-750 the two-photon absorption spectrum has a shape similar to that for bulk solids but for CdTe-600 the 2PA spectrum is somewhat different from that expected for the bulk. In the Z-scan measurements we also observed a photo-darkening effect, which is accompanied by an increase in the measured effective 2PA coefficient. All results suggest that 2PA cannot be predicted by the bulk theory especially near to the 2PA edge, that the 2PA in quantum dots is generally smaller than would be expected for the same volume of bulk semiconductor with the same band edge, and that the quantum-dot size and size distribution play important roles in the 2PA spectral behavior and magnitude.
Thermoreversible sol–gel transition of an aqueous solution of polyrotaxane composed of highly methylated α-cyclodextrin and polyethylene glycol (2006)

Novel thermo-gelling aqueous solution systems are developed with a polyrotaxane, consisting of methylated alpha-cyclodextrin and polyethylene glycol, based on the slide-ring properties of the macrocycles along the linear chain.
OSSO: Obtaining Skeletal Shape from Outside (2022)

We address the problem of inferring the anatomic skeleton of a person, in an arbitrary pose, from the 3D surface of the body; i.e. we predict the inside (bones) from the outside (skin). This has many applications in medicine and biomechanics. Existing state-of-the-art biomechanical skeletons are detailed but do not easily generalize to new subjects. Additionally, computer vision and graphics methods that predict skeletons are typically heuristic, not learned from data, do not leverage the full 3D body surface, and are not validated against ground truth. To our knowledge, our system, called OSSO (Obtaining Skeletal Shape from Outside), is the first to learn the mapping from the 3D body surface to the internal skeleton from real data. We do so using 1000 male and 1000 female dual-energy X-ray absorptiometry (DXA) scans. To these, we fit a parametric 3D body shape model (STAR) to capture the body surface and a novel part-based 3D skeleton model to capture the bones. This provides inside/outside training pairs. We model the statistical variation of full skeletons using PCA in a pose-normalized space and train a regressor from body shape parameters to skeleton shape parameters. Given an arbitrary 3D body shape and pose, OSSO predicts a realistic skeleton inside. In contrast to previous work, we evaluate the accuracy of the skeleton shape quantitatively on held out DXA scans, outperforming the state-of-the art. We also show 3D skeleton prediction from varied and challenging 3D bodies. The code to infer a skeleton from a body shape is available at https://osso.is.tue.mpg.de, and the dataset of paired outer surface (skin) and skeleton (bone) meshes is available as a Biobank Returned Dataset. This research has been conducted using the UK Biobank Resource.
Active reduced-size hexapeptide analogs of luteinizing hormone-releasing hormone (1989)

A series of reduced-size hexapeptide analogues of LH-RH were synthesized that contain the residues corresponding to amino acid positions 4-9 and are linked to various carboxylic acids in place of residue 3. These compounds were tested in vitro in the rat pituitary receptor binding and LH release assays. A wide range of binding affinities was obtained up to and exceeding that of LH-RH. Both agonists and antagonists were obtained. From the SAR studies, it appears that a very precise size, length, and shape of the substituent at position 3 is required to achieve agonist activity, whereas the structural requirements for antagonist activity appear to be much less stringent. Depending on the nature of the substituent at positions 6 and 4, the biological response switches from antagonist to agonist or vice versa. The results suggest that conformational changes at position 6 or 4 feed back to the substituent at position 3, which induces the change from agonist to antagonist. The most potent compounds in the series were tested in vivo and found to be active.
MO‐FF‐A2‐03: A Method for Measuring X‐Ray Beam Profiles Using a Flat Panel Detector (2010)

Purpose : Many digital x‐ray imaging applications require knowledge of the spatial distribution of the incident x‐ray flux intensity (beam profile), which is often obtained through Monte Carlo simulations or dedicated measuring equipment such as point detector that is raster scanned. Direct measurement of flux intensities using an area detector is difficult due to detector gain variations. We present a method to separate detector gain variations from flux intensity variations thus providing a practical means for efficient measurement of beam profiles using area detectors. Method and Materials : A flat panel imager is used to acquire at least two unattenuated intensity images at slightly shifted positions. Signal intensity differences read from the same pixel are assumed to be due to flux intensity variations while differences measured at a same spatial location are assumed to be due to gain variations. Detector gain maps and flux intensity maps are then created by mathematically decoupling the flux and gain intensity components from the readings. The process is repeated in the other in‐plane direction to generate 2‐D maps. To test the method, a Varian Paxscan 4030CB was used to measure the beam profile produced by a Varian G242 tube. Results were compared to Monte Carlo simulations and raster‐scanned photodiode measurements. Results : The detector gain of the imager and the beam profile of the source were separated. The beam profiles measured using the propose method were independent of how prior gain calibrations were performed and matched well with Monte Carlo predictions and photodiode measurements. Conclusions : A robust method to measure the beam profile of an x‐ray field using an area detector is presented. The method also generates a detector gain map that is independent of flux intensity variations. Employees of Varian Medical Systems.
Trinucleotide repeat expansion and human disease (1995)

Trinucleotide repeat expansions have been identified as the underlying mutation in an increasing number of human genetic diseases, such as fragile site syndromes, myotonic dystrophy and several neurodegenerative disorders including Huntington's disease. By an unknown mechanism, polymorphic GC-rich triplet repeats expand in all these diseases. The expansions of a CCG repeat in fragile-site-associated disorders and the CTG repeat (in the 3'-untranslated region of the myotonin kinase gene) causing myotonic dystrophy are very large, whereas small expansions of CAG repeats have been identified in the open reading frame of genes in a number of neurological genetic disorders.
The Determination of the Thermal History in a One-Dimensional Freezing System by a Perturbation Method (1979)

A perturbation method is employed to determine the thermal history of a biological organ frozen with a constant cooling rate at its outer surface. Solutions were obtained for the time history of the propagating phase front and the distribution of cooling rates within the organ. By means of a one-dimensional analysis, a new dimensionless group has been found to correlate the range of cooling rates in a frozen organ of complex shape. The analytical model has been confirmed by experimental measurements on a one-dimensional freezing system. The results of this treatment are useful in the design and analysis of experiments dealing with freezing in one dimension, particularly in the preservation of organs by freezing.