gebhart/patrepeval huggingface dataset:
Automatic design of graphical presentations (1987)

This dissertation describes research on the graphical presentation of relational information. It presents theoretical results about graphical languages and a program that incorporates these results.
According to the theory, a graphical language is a set of graphical sentences (such as bar charts, scatter plots, or connected graphs), each of which is a two dimensional arrangement of pixel objects. These languages are evaluated on the basis of two graphic design criteria: expressiveness is an indication of the kinds of relational information that can be expressed in a language, and effectiveness deals with the relative desirability of sentences from alternative graphical languages. A composition algebra is also developed that can be used to systematically generate a wide variety of graphical languages from a small set of primitives.
These theoretical results are incorporated into a graphical presentation program called APT (A Presentation Tool). APT is unique in that its designs are sensitive to both the structure of the information and the output medium. The design process has three parts. First, the information is divided into components, each of which satisfies the expressiveness criterion for a primitive graphical language. Next, effectiveness criteria are used to select the most effective primitive graphical language for each component. Finally, composition operators are used to compose the individual designs into a unified presentation of all of the information. Even though only a few primitives are implemented, APT can synthesize a wide variety of designs that express information effectively.
Image Processing Chains for ALOS and EnMAP Data: Similarities and Differences (2013)

The Earth Observation Center (EOC) of DLR realizes processors for ALOS and EnMAP high-resolution optical remote sensing satellite missions. The functional and developmental similarities and differences of the DLR processors are analyzed. It turns out that despite or precisely because of pan-chromatic and multispectral versus hyperspectral imaging as well as the post- versus pre-launch establishment of the DLR processing chains, both activities strongly benefit from each other.
Comment on "Observer Stabilization of Singularly Perturbed Systems" (1980)

Comparison with Optimal Controller It is interesting to note that the vertical channel is optimal in a larger sense. In the vertical channel, the control variables were constrained to be the simple functions of the measurement variable given in Eq. (3). Can a more complicated compensation connecting the measurement and control variables provide smaller mean-square errors? It is well known that optimal control is provided by feedback compensation that is the cascade combination of the KalmanBucy filter and the state-feedback optimal regulator. The filter was given in Eq. (11). The regulator is
Structure of the NheA Component of the Nhe Toxin from Bacillus cereus: Implications for Function (2013)

The structure of NheA, a component of the Bacillus cereus Nhe tripartite toxin, has been solved at 2.05 Å resolution using selenomethionine multiple-wavelength anomalous dispersion (MAD). The structure shows it to have a fold that is similar to the Bacillus cereus Hbl-B and E. coli ClyA toxins, and it is therefore a member of the ClyA superfamily of α-helical pore forming toxins (α-PFTs), although its head domain is significantly enlarged compared with those of ClyA or Hbl-B. The hydrophobic β-hairpin structure that is a characteristic of these toxins is replaced by an amphipathic β-hairpin connected to the main structure via a β-latch that is reminiscent of a similar structure in the β-PFT Staphylococcus aureus α-hemolysin. Taken together these results suggest that, although it is a member of an archetypal α-PFT family of toxins, NheA may be capable of forming a β rather than an α pore.
Flexible and reusable cap-like thin Fe2O3 film for SERS applications (2018)

Cap-like α-Fe2O3 films are fabricated and deposited onto quartz fabric by using radio frequency magnetron sputtering and annealing. The treated fabric sample in this study shows highly sensitive surface-enhanced Raman scattering (SERS) and excellent flexibility, reproducibility and stability. In addition, the sample can be recovered after a washing process with an organic solvent and repeatedly used. The sensitive SERS performance is attributed to chemical enhancement through a charge transfer process. Moreover, the SERS performance is also found to be dependent on the light coupling effect. When the light absorbance rate of the α-Fe2O3 films increases at a wavelength near that of laser light, the film shows excellent sensitivity due to light coupling effect.
Multiscale molecular simulations to investigate adenylyl cyclase‐based signaling in the brain (2022)

Abstract Adenylyl cyclases (ACs) play a key role in many signaling cascades. ACs catalyze the production of cyclic AMP from ATP and this function is stimulated or inhibited by the binding of their cognate stimulatory or inhibitory Gα subunits, respectively. Here we used simulation tools to uncover the molecular and subcellular mechanisms of AC function, with a focus on the AC5 isoform, extensively studied experimentally. First, quantum mechanical/molecular mechanical free energy simulations were used to investigate the enzymatic reaction and its changes upon point mutations. Next, molecular dynamics simulations were employed to assess the catalytic state in the presence or absence of Gα subunits. This led to the identification of an inactive state of the enzyme that is present whenever an inhibitory Gα is associated, independent of the presence of a stimulatory Gα. In addition, the use of coevolution‐guided multiscale simulations revealed that the binding of Gα subunits reshapes the free‐energy landscape of the AC5 enzyme by following the classical population‐shift paradigm. Finally, Brownian dynamics simulations provided forward rate constants for the binding of Gα subunits to AC5, consistent with the ability of the protein to perform coincidence detection effectively. Our calculations also pointed to strong similarities between AC5 and other AC isoforms, including AC1 and AC6. Findings from the molecular simulations were used along with experimental data as constraints for systems biology modeling of a specific AC5‐triggered neuronal cascade to investigate how the dynamics of downstream signaling depend on initial receptor activation. This article is categorized under: Structure and Mechanism &gt; Computational Biochemistry and Biophysics Molecular and Statistical Mechanics &gt; Molecular Dynamics and Monte‐Carlo Methods Software &gt; Molecular Modeling
Editorial (2006)

The editorial teams of Blood and the British Journal of Haematology recently became aware of an attempt at duplicate publication involving both journals. Regrettably, as a sanction for this unacceptable behaviour, the two journals have combined to exclude the authors from submitting to the journals for 2 years. Both journals take their responsibilities to maintain widely accepted scientific publishing standards very seriously, and this sanction reflects this responsibility. Based on this episode, both journals wish to make our readers aware of the serious breach of scientific and publishing standards that dual publication represents. In future, attempts at duplicate publication may be treated more severely including retraction of the article. We hope that this editorial note acts as a timely reminder to us of all the high value that should be placed on good scientific publication ethics.
Figure S9 from UNC-45A Is a Novel Microtubule-Associated Protein and Regulator of Paclitaxel Sensitivity in Ovarian Cancer Cells (2023)

&lt;p&gt;Effects on UNC-45A loss on SKOV-3 ovarian cancer cells&lt;/p&gt;
Effective dynamic scheduling and memory management on parallel processing systems (2003)

An effective dynamic processor self-scheduling scheme is presented for general parallel program constructs in a restructuring compiler. In the program constructs, parallel loops, serial loops, if-then-else constructs and a generalization of fork-joins can be nested in an arbitrary order, and procedure calls can be involved in any level of the nested constructs. In parallel programs, a piece of the program code, such as loop iterations, is called a chore, which is considered to be a work unit in the program. In this scheme, processors schedule themselves to the chores dynamically at execution time without involving the operating system. Memory management is another issue addressed. Efficiency concerns dictate treating chore locality differently from procedure locality. As a corollary, the number of call frames required at any one time for a nonrecursive procedure is bounded by the number of processors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
PTU-128 Novel insights into metastatic spread of oesophageal adenocarcinoma from whole genome sequencing data (2015)

<h3>Introduction</h3> The evolution of metastatic oesophageal adenocarcinoma (OAC) is poorly understood. Whole genome sequencing (WGS) across multiple metastatic sites provides the unique opportunity to study clonal evolution of OAC. <h3>Method</h3> 2 cases of junctional OAC were extensively sampled at autopsy within 4 h of death. At presentation case 1 was palliative, case 2 had potentially curative disease but progressed during treatment. 20 fresh frozen tumour samples from primary tumour and multiple metastases (adrenal, liver, pancreas, station 102, left gastric and para-aortic lymph nodes) underwent WGS. Clonal analysis involved estimating copy number status and tumour purity, followed by point mutation clustering based on allele frequency (proportion of tumour cells harbouring a mutation); clusters were referred to as clones and were annotated with driver events of clonal progression (single nucleotide variants (SNVs) and copy number events). <h3>Results</h3> 11 clones spanned all samples in case 1 compared to 5 in case 2. Median SNVs per clone were 5885 in case 1 (range 1091–29883) and 2149 (range 424–27031) in case 2. The founding clone in both cases contained the bulk of the SNVs and key potential drivers of carcinogenesis (case 1:KRAS and GATA4 amplification, case 2:TP53 mutation). Metastases in case 1 had a branching pattern of evolution; 6 clones were unique to individual metastases and only 1 was shared across sites. Clones were on average 9363 (+/-5827) SNVs distant from the founder clone demonstrating continuing evolution in metastases. Para-aortic nodal metastasis preceded local lymph node metastasis. In contrast case 2 demonstrated linear evolution with just 2 metastatic clones that were on average 1286 (+/-1219) SNVs distinct from the primary tumour; 1 was only in the adrenal, the second was shared across multiple sites suggestive of an embolic pattern of tumour seeding. The liver metastasis was identical to the primary founder clone demonstrating that metastasis to the liver was the initial event, even prior to local lymph node metastasis. <h3>Conclusion</h3> Metastases can result from contrasting patterns of clonal evolution. Both cases demonstrate the striking phenomenon of early distant metastases, prior to the development of local lymph node metastases thus challenging our traditional algorithms of tumour staging and prognostication. Additional cases are being analysed to support our findings. <h3>Disclosure of interest</h3> None Declared.
Development of a Food Freshness Indicator for Monitoring Spoilage of Chicken Breast Using a Porous Substrate (2017)

To visually identify the spoilage of chicken breasts, a three layered freshness indicator consisting of PET/bromocresol green (BCG)-ethylene vinyl acetate (EVA)-acetic acid (AA) composite layer/porous substrates was successfully prepared and their performance were simulated at 20% of CO2 and 4 different trimethylamine (TMA) concentrations to evaluate color change at minimal spoilage level. The visibility and range of color changes of the as-prepared indicators responding to TMA concentration as a simulant were strongly dependent on the concentrations of BCG and AA. As the BCG content increased, the visibility of color change in the freshness indicators was apparently improved and the range of color change could be controlled by contents of AA. Among the as-prepared freshness indicators, ‘G0.12_A0.5’ which consisting 0.12g of BCG and 0.5g of AA was selected as an optimum composition due to the highest visibility at TMA 20 mg% corresponding to the minimal spoilage level. The color of the indicator changed from yellow to green for spoilage indication of chicken breast, which could be easily seen with the naked eyes and well consistent with the simulation results. It is expected that our developed freshness indicator can be useful in monitoring various food freshness and quality.
Technological properties ofOenococcus oenistrains isolated from typical southern Italian wines (2010)

The results reported are useful for the selection of indigenous MLF starter cultures with desired oenological traits from typical regional wines. It should be the base for the improvement in organoleptic quality of typical red wine.
Targeting Realistic Geometry in Tokamak Code Gysela★ (2018)

In magnetically confined plasmas used in Tokamak, turbulence is respon-sible for specific transport that limits the performance of this kind of reactors. Gyroki-netic simulations are able to capture ion and electron turbulence that give rise to heat losses, but require also state-of-the-art HPC techniques to handle computation costs. Such simulations are a major tool to establish good operating regime in Tokamak such as ITER, which is currently being built. Some of the key issues to address more re- alistic gyrokinetic simulations are: efficient and robust numerical schemes, accurate geometric description, good parallelization algorithms. The framework of this work is the Semi-Lagrangian setting for solving the gyrokinetic Vlasov equation and the Gy-sela code. In this paper, a new variant for the interpolation method is proposed that can handle the mesh singularity in the poloidal plane at r = 0 (polar system is used for the moment in Gysela). A non-uniform meshing of the poloidal plane is proposed instead of uniform one in order to save memory and computations. The interpolation method, the gyroaverage operator, and the Poisson solver are revised in order to cope with non-uniform meshes. A mapping that establish a bijection from polar coordinates to more realistic plasma shape is used to improve realism. Convergence studies are provided to establish the validity and robustness of our new approach.
The preterm piglet as an animal model for bronchopulmonary dysplasia: preliminary findings (2020)

<b>Background:</b> BPD is a common complication of preterm birth. Animal models, such as the preterm piglet, remain imperative to study local tissue changes, but little is known about their lung development beyond the first 48 hours of life. However, this wider time frame is crucial when studying BPD pathophysiology. <b>Aim:</b> To determine whether lung changes comparable to human BPD occur in preterm piglets of different ages. <b>Methods:</b> Preterm piglets were surgically delivered at 90% gestation and compared to term newborn SGA piglets (n=7). Preterm animals were euthanized at 4 (pD4; n=14) and 5 days (pD5; n=46) postnatally. After perfusion with saline, the left lung was fixed and stained for histological assessment and the right lung was sampled for qPCR. KW and appropriate posthoc tests were used for statistical analysis. <b>Results:</b> pD4 and pD5 piglets showed less advanced alveolarization and septation and a thicker and more cellular interstitium than term piglets. TNFα levels were higher in both preterm groups combined than in the term controls. IL6 was higher in control and pD4 piglets compared to pD5 piglets; while IL1β was different between pD4 and pD5. IL10 was upregulated in the pD5 piglets compared to pD4 piglets and controls. <b>Conclusion:</b> Our results show evolution in inflammatory cytokine levels, as in human preterm infants. Despite variation, less advanced alveolarization and septation in preterm piglets was evidently present.
Abstract 3050: Imaging tissue extracellular pH for the differential diagnosis of coccidioidomycosis and lung cancer (2018)

Abstract Introduction: Our objective was to determine whether acidoCEST MRI—a novel, non-invasive MRI method that measures extracellular pH (pHe)—can differentiate between lung tumors and coccidioidomycosis (valley fever) granulomas within in vivo mouse models of lung cancer and valley fever. Methods: To develop a spontaneous murine lung tumor model, A/J mice received orthotopic injections of urethane to induce formation of lung adenocarcinomas. The Valley Fever Center for Excellence at the University of Arizona infected SW mice with a BSL 2-compatible mutant Coccidioides strain, Δcps1, to develop our preclinical valley fever model. All scans were performed with a Bruker BioSpin 7T MRI system. For all MRI scans, mice were anesthetized with 2.0% isofluorane, respiration and body temperature were monitoreduring scans, and body temperature was maintained at 37 °C. Respiration-triggering (gating) was used in all imaging sequences to compensate for motion artifacts in the lung. For optimal gating, the mouse's respiration rate was maintained at &amp;lt; 50 breaths per minute. Each mouse was scanned with acidoCEST MRI using 370 mg/mL Iopamidol (200 μL IV bolus, 400 μL/hr IV infusion). AcidoCEST MRI (3.5 μT, 300 ms imaging time, 6000 ms presaturation pulse) was performed according to previously published methods, updated with improved respiration gating. For acidoCEST MRI, the saturation pulse continued until terminated by the gating trigger. Spatial pHe maps of tumor and granuloma ROI were produced using Bloch fitting in Matlab 2014a. Average lesion pHe and iopamidol concentration we also recorded. Results: AcidoCEST MRI was successfully applied to the in vivo imaging of murine lung tumors and coccidioidomycosis granulomas. Lung tumors demonstrated successful uptake of the iopamidol contrast agent, with an average concentration of approximately 40 mM. pHe values in the tumor ROI ranged from 6.5 to 7.2 with an average value of 6.64. Granulomas demonstrated successful uptake of iopamidol with an average concentration of about 75 mM. pHe values in granulomas ranged from 7.2 to 7.4 with an average value of 7.29. Conclusion: AcidoCEST MRI may be used to quantify the pHe of murine lung tumors and coccidioidomycosis granulomas in vivo. Our results show that pHe is a promising biomarker for the differential diagnosis of coccidioidomycosis and lung cancer. Citation Format: Leila Renee Lindeman, Edward A. Randtke, Lisa F. Shubitz, Christine M. Howison, Kyle M. Jones, Mark D. Pagel. Imaging tissue extracellular pH for the differential diagnosis of coccidioidomycosis and lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3050.
Computing the mind (2008)

This brief overview course states and motivates the observation that cognition is fundamentally a computational process and explores the implications of this idea [12]. Students are introduced to a number of conceptual tools for thinking about cognitive information processing, including statistical learning from experience and the use of patterns distilled from past experience in guiding future actions. The application of these tools to the understanding of natural minds and to advancing the goals of artificial intelligence is illustrated on selected examples drawn from the domains of perception, memory, motor control, language, action planning, problem solving, decision making, reasoning, creativity, and consciousness. The material is aimed at advanced undergraduate students, as well as graduate students from computer science and natural sciences. The recommended textbook for the course is Computing the Mind: How the Mind Really Works (Oxford University Press, 2008). Additional readings (in PDF) will be made available as needed.
Structural Characterization of Lead Zirconate Titanate Film Synthesized by Hydrothermal Method (2007)

The structural properties of a hydrothermally deposited lead zirconate titanate (PZT) film have been investigated. The deposited film exhibited a tetragonal perovskite structure with a Zr/Ti ratio of 12/88 in the region between the surface and the depth of 6 µm. The lattice parameters and Curie temperature of the film were measured to be a=3.948 Å, c=4.141 Å, and TC=520 °C, respectively, which were different from those reported for bulk PZT. Furthermore, potassium was detected in the film with a K/Pb ratio of 1.4/98.6 because potassium hydroxide was used as a mineralizer for the hydrothremal reaction. Consequently, we conclude that the differences in the lattice parameters of the film from those of the bulk PZT are attributed to K+ ions incorporated into the PZT crystal, and the high Curie temperature resulted from the polarization pinning effect induced by K+ substituents and oxygen vacancies.
1-Oxabicyclic β-lactams as new inhibitors of elongating MPT–a key enzyme responsible for assembly of cell-surface phosphoglycans of Leishmania parasite (2005)

New iminosugars (1-oxabicyclic β-lactam disaccharides) have been synthesized as inhibitors of elongating α-D-mannosyl phosphate transferase (eMPT), a key enzyme involved in the iterative biosynthesis of cell-surface phosphoglycans of the Leishmania parasite. The design is based on a transition-state model for this remarkable enzyme that transfers intact α-D-mannosyl-phosphate from GDP-Man. Since these phosphoglycans are unique to Leishmania and are essential for its infectivity and survival, their biosynthetic pathway has emerged as a novel target for anti-leishmanial drug and vaccine design.
Applications of phase-contrast X-ray microscopy in an SEM (2003)

We have developed a new approach to SEM-based X-ray projection microscopy which utilises phase contrast to enhance the quality and information content of images. The development of SEMs based on high-brightness field emission guns and highly sensitive CCD cameras enables us to produce an extremely fine microfocus source with sufficient flux for imaging. By combining this fine source with an appropriate imaging geometry, phase contrast arising from Fresnel diffraction at edges and boundaries within the sample leads to images with greatly enhanced edge detail. We have also developed phase-retrieval algorithms for quantitative determination of the projected phase shift in the object-plane from either a single image or multiple images acquired at different energies or magnifications. These developments have been realised in an instrument, dubbed the X-ray ultramicroscope (XuM), which has enabled us to acquired images down to -200nm resolution. Examples of applications of the XuM are described here including the use of phase-retrieval algorithms and microtomography.
Electron microscopic studies of growth of nanoscale catalysts and soot particles in a candle flame (2012)

Scanning electron microscopy and high-resolution transmission electron microscopy have been used to investigate non-classic crystal growth of catalytic nanoparticles, such as zeolites, perovskites, metal and alloy particles. Growth mechanisms of some crystals with novel morphologies, for example, BiOBr flower-like particles and ZnO twin-crystals, have also been studied. A development of sampling method for soot particles inside a candle flame allows us to reveal all four well-known carbon forms, amorphous, graphitic, fullerenic and nanodiamond particles. This article demonstrates that electron microscopy is a powerful tool to study the microstructures of small particles, giving us more freedom to develop new materials.
NEREL-BIO: a dataset of biomedical abstracts annotated with nested named entities (2023)

The dataset and annotation guidelines are freely available at https://github.com/nerel-ds/NEREL-BIO.