gebhart/patrepeval huggingface dataset:
Abstract 16030: M-Atrial Natriuretic Peptide: A Novel Renal Enhancing Therapeutic in a Model of Heart Failure and Acute Hypertension (2011)

Compartmentalization is vital for cell biological processes. The field of rule-based stochastic simulation has acknowledged this, and many tools and methods have capabilities for compartmentalization. However, mostly, this is limited to a static compartmental hierarchy and does not integrate compartmental changes. Integrating compartmental dynamics is challenging for the design of the modeling language and the simulation engine. The language should support a concise yet flexible modeling of compartmental dynamics. Our work is based on ML-Rules, a rule-based language for multi-level cell biological modeling that supports a wide variety of compartmental dynamics, whose syntax we slightly adapt. To develop an efficient simulation engine for compartmental dynamics, we combine specific data structures and new and existing algorithms and implement them in the Rust programming language. We evaluate the concept and implementation using two case studies from existing cell-biological models. The execution of these models outperforms previous simulations of ML-Rules by two orders of magnitude. Finally, we present a prototype of a WebAssembly-based implementation to allow for a low barrier of entry when exploring the language and associated models without the need for local installation.
Erratum to: Production of $${\pi ^0}$$ π 0 and $$\eta $$ η mesons up to high transverse momentum in pp collisions at 2.76 TeV (2017)

In the original version of this article unfortunately the copyright holder in the PDF was wrong. The original article has been corrected.
Development and Design of Laboratory and Pilot Scale Reactors for Microwave‐assisted Chemistry (2006)

This chapter contains sections titled: Introduction Basic Concepts for Reactions and Reactors in Organic Synthesis Methods for Enhancing the Rates of Organic Reactions Microwave-assisted Organic Syntheses (MAOS) Commercial Microwave Reactors-Market Overview Selected Equipment and Applications Qualification and Validation of Reactors and Results Conclusion and Future References
Oxidative Coupling of Methane by Adsorbed Oxygen Species on SrTi1-xMgxO3-δ Catalysts (1996)

It was found that ethane was formed by the stoichiometric reaction between methane and an adsorbed oxygen species on SrTi1-xMgxO3-δ with high selectivity (> 80 %) at much lower temperatures (550-750 K) than those typically used for the catalytic reaction. The properties of the adsorbed oxygen species were investigated by means of temperature programmed desorption, and the role of Mg2+ was studied using XRD, BET, and the measurements of the exchange rate between lattice oxide ions and gas phase oxygen. The added Mg2+ ions seem to be located at the surface and bulk Ti4+ site of Sr-Ti mixed oxides, where oxide ion defects are formed because of differences in ion charges. Surface oxide ion defects play an important role in oxygen adsorption, while bulk defects promote the mobility of oxide ions. SrTi0.5Mg0.5O3-δ was initially active for oxidative coupling of methane at low temperature (873 K), but combustion of methane predominated under steady state conditions, due to a change in adsorbed oxygen species induced by the adsorption of CO2.
Method combining acoustic emission and thermogravimetry for an improved evaluation of the high temperature corrosion (2006)

International audience
The aromatic cytokinins (1997)

After the discovery of kinetin (Miller et al. 1956, J. Am. Chem. Soc. 78: 1345–1350) there was a flurry of syntheses that led to the finding of 6‐benzylaminopurine (BA), an active and easily obtainable cytokinin. Much research into cytokinin physiology was subsequently done with this substance. Further, the isolation and unequivocal identification of natural BA and the high biological activity of its meta ‐hydroxylated analogues stimulated the search for other natural aromatic cytokinins. Screening was accomplished by ELISA of HPLC fractions using antisera against ortho ‐ and meta ‐hydroxybenzyladenosine. Subsequent isolation and decisive identification by mass spectrometry led to discovery of a broad spectrum of endogenous plant growth substances structurally similar to a highly active compound, meta ‐topolin (6‐[3‐hydroxybenzyl‐amino]purine), and to its less active analogue, ortho ‐topolin (6‐[2‐hydroxybenzyl‐amino]purine). The structures of such aromatic cytokinins suggest considerably different biosynthetic pathways from that of zeatin and related isoprenoid cytokinins. From a physiological viewpoint, aromatic cytokinin metabolism can be classified under four main headings analogous to isoprenoid cytokinins: interconversion, hydroxylation, conjugation, and oxidative degradation. This review attempts to put into context what is known about 9‐alkyl‐BAs and compares their metabolism in regard to the practical use of cytokinins in agriculture and biotechnology. The recently discovered unusual specificity of additionally C2,N9‐disubstituted aromatic cytokinins toward cell cycle kinases, suggests that these cytokinin‐derived growth regulators may selectively inhibit certain steps of the cell cycle. The functional overlap of the aromatic cytokinins with those of their isoprenoid counterparts and cytokinin inhibitors, in relation to growth and developmental processes in plants, has yet to be determined.
Hands‐on Wireless Communication Experience (2021)

This chapter introduces a wireless communication systems lab that will provide readers with the experience to design, test, and simulate wireless systems (along with wireless circuits) using modern instrumentation and computer-aided design software. The described laboratory based approach is developed in such a way that it can promote the understanding of other related wireless concepts at all levels: wireless systems, wireless networks, cognitive radio and software defined radio, digital baseband signal-processing algorithm development and hardware implementation, wireless circuits, wireless devices, and components. The chapter provides some examples for the co-simulation of system with hardware and test equipment, along with various device under test configurations. It also provides a model lab course as an example. The Wireless Communications Systems Laboratory course that has been offered at the electrical engineering department of University of South Florida is given as the example.
Inference for Generalized Linear Models via Alternating Directions and\n Bethe Free Energy Minimization (2015)

Generalized Linear Models (GLMs), where a random vector $\\mathbf{x}$ is\nobserved through a noisy, possibly nonlinear, function of a linear transform\n$\\mathbf{z}=\\mathbf{Ax}$ arise in a range of applications in nonlinear\nfiltering and regression. Approximate Message Passing (AMP) methods, based on\nloopy belief propagation, are a promising class of approaches for approximate\ninference in these models. AMP methods are computationally simple, general, and\nadmit precise analyses with testable conditions for optimality for large i.i.d.\ntransforms $\\mathbf{A}$. However, the algorithms can easily diverge for general\n$\\mathbf{A}$. This paper presents a convergent approach to the generalized AMP\n(GAMP) algorithm based on direct minimization of a large-system limit\napproximation of the Bethe Free Energy (LSL-BFE). The proposed method uses a\ndouble-loop procedure, where the outer loop successively linearizes the LSL-BFE\nand the inner loop minimizes the linearized LSL-BFE using the Alternating\nDirection Method of Multipliers (ADMM). The proposed method, called ADMM-GAMP,\nis similar in structure to the original GAMP method, but with an additional\nleast-squares minimization. It is shown that for strictly convex, smooth\npenalties, ADMM-GAMP is guaranteed to converge to a local minima of the\nLSL-BFE, thus providing a convergent alternative to GAMP that is stable under\narbitrary transforms. Simulations are also presented that demonstrate the\nrobustness of the method for non-convex penalties as well.\n
Neue Methoden zur Sequenzierung festphasengebunder Cyclopeptide (2009)

Cyclic peptides show a high biological activity and are widely used as model substances in SAR (structure activity relationship) studies. The split-mix synthesis is a very useful method for the preparation of big libraries of cyclic peptides. The post-screening sequence determination of cyclic "hit" peptides is a very challenging problem. In this thesis, a pre-analytical transformation of cyclic peptides into linear ones for an easier sequence determination is reported. Different concepts of selective ring-opening procedures have been investigated. Sequencing methods based on mass spectrometry and Edman degradation have been evaluated. By using a combination of partial Edman degradation (PED) and a chemical predetermined breaking point a reliable and efficient sequencing method for solid-phase bound cyclic peptides could be developed. After the synthesis and screening of a OBOC library containing 9800 cyclic peptides the method has been used to identify new Streptavidin ligands. Their binding affinities have been determined by surface plasmon resonance (SPR) experiments.
Active Sites for H2Adsorption and Activation in Au/TiO2and the Role of the Support (2009)

The catalytic activity toward H2 dissociation of several Au nanoparticles of different shape, supported on stoichiometric and reduced TiO2 surfaces, has been investigated by means of periodic DF calculations. Gold nanoparticles become positively charged when supported on stoichiometric TiO2 and negatively charged when adsorbed on the reduced surface, although this finding does not appear to be relevant for H2 dissociation activity. It is shown that Au atoms active for H2 dissociation must be neutral or with a net charge close to zero, and be located at corner or edge low coordinated positions and not directly bonded to the support. The particles with the largest number of potentially active sites for H2 dissociation are 2L isomers consisting of at least one bottom layer of gold atoms in contact with the support and therefore inactive, and one top layer with low coordinated gold atoms on which H2 is adsorbed and activated. The presence of Ovacancy defects in reduced surfaces preferentially stabilizes the most active 2L particles, while less active 1L isomers are the most stable on the stoichiometric surfaces.
Humidity Detection Using Metal Organic Framework Coated on QCM (2016)

Quartz crystal microbalance (QCM) coated with poly-4-vinylpyridine (PVP) and metal organic framework HKUST-1 are investigated and compared for humidity sensing. Drop casting method is employed to coat the PVP and HKUST-1 solutions onto the surface of a quartz crystal microbalance. The resonance frequencies of these sensors with varying relative humidity (RH) from 22% RH to 69% RH are measured using impedance analysis method. The sensitivity, humidity hysteresis, response, and recovery times of these sensors are studied. The sensitivities of uncoated, PVP, and HKUST-1 coated QCM sensors are 7 Hz, 48 Hz, and 720 Hz, respectively, in the range of 22% RH–69% RH. The extraction of desorption rate and adsorption energy associated with the adsorption and desorption of water molecules on these surfaces reveals that HKUST-1 has better sensing properties than PVP and uncoated QCM sensors. In this work, the HKUST-1 coated QCM is shown to be a promising material for moisture detection.
ChemInform Abstract: An Efficient Preparation of TIPS—Halofluoropropyne and Its Application to the Diastereoselective Synthesis of Propargylic Fluorohydrins. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
How does vacuum forming affect Pelite mechanical properties? (1994)

Pelite is a polyethylene closed cell foam commonly used as an interface material in prosthetics. Both normal and vacuum-formed Pelite were tested under compression and under shear loading. For shear testing, the results were not significantly different for normal and vacuum-formed Pelite. For normal Pelite, the slope of the stress-strain curve was 1.17MPa (+/- 0.14) while for vacuum-formed Pelite it was 1.24MPa (+/- 0.22). Compressive results, however, were significantly different. Below 80kPa of applied compression, the slope of the stress-strain curve for normal Pelite was 0.99MPa (+/- 0.11) while for vacuum formed Pelite it was 0.72MPa (+/- 0.12). Between 80kPa and 200kPa of applied compression, the slope of the stress-strain curve for normal Pelite was 0.45MPa (+/- 0.03) while for vacuum formed Pelite it was 0.55MPa (+/- 0.05). Reasons for the differences and their significance to interface mechanics and computer-aided prosthesis design are discussed.
PEDIATRIC RETROPERITONEOSCOPIC NEPHRECTOMY USING 2 MM. INSTRUMENTATION (1999)

Several modifications of the retroperitoneal approach, including the use of prone patient positioning and 2 mm. instrumentation for visualization and dissection, may improve the safety and efficacy of this technique in children.
ChemInform Abstract: THE ELECTROLUMINESCENCE OF COPPER, BROMINE DOPED ZINC SULFIDE PHOSPHOR (1982)

Abstract Der Einfluß der Gehalte an Cu und Br auf Leuchtkraft und Lebensdauer der Elektrolumineszenz im Phosphor ZnS wird untersucht.
PET Uptake Classification in Lymphoma and Lung Cancer using Deep Learning (2018)

325 Objectives: The interpretation of 18F-Fluorodeoxyglucose (FDG) PET/CT images is challenging given the sources of variability such as data acquisition, reconstruction methods and physiological tracer distribution. Recent advances in machine learning have enabled multi-parametric image classification with unprecedented accuracy. In this work, a convolutional neural network (CNN) was trained on PET/CT data to classify the malignancy of regions with increased uptake.
Methods PET/CT images of 628 patients with known lung cancer or lymphoma were analyzed by two experienced nuclear physicians: each uptake region was annotated in anatomical location and physiological characterization (e.g. benign, malignant) and served as ground truth for the CNN. The algorithm incorporated image features such as multi-planar PET and CT reconstructions focused around each region of uptake to describe the region and its local context. A non-rigid registration of a maximum intensity projection (MIP) PET image to an anatomical atlas was used to characterize the anatomical location. The network comprised a series of alternating convolutional and pooling layers to extract imaging features while fully connected layers integrated the non-imaging features into a single network. The available data were divided into training (60%), validation (20%) and testing (20%) subsets. The validation was used to guide the algorithm development and to select the algorithm hyper-parameters, while the test set was exclusively used to assess the final algorithm performance parameters.
Results A total of 12,959 PET regions of uptake were manually annotated from 302 lung cancer and 326 lymphoma cases resulting in 4,677 malignant lesions and 7,276 regions of physiological uptake. Characterization into benign or malignant classes using the CNN was shown to have an area under the ROC curve of 0.96 on the test subset demonstrating a good ability at discriminating benign versus malignant FDG uptake in this patient cohort. Furthermore, the MIP PET image proved to be useful to discriminate brown fat uptake and left-right symmetrical physiological uptake.
Conclusions In this study we have demonstrated that the characterization of lesions in patients with lung cancer or lymphoma can be successfully performed using a convolutional neural network. While further image data and refinement of algorithms will be required for the application of such technology in clinical decision making, there are several potential use cases using the presented technology: reading workflow could potentially be simplified by preprocessing PET/CT to more efficiently derive clinically relevant parameters such as automatic parametric lesion description (e.g., total lesion glycolysis or total metabolic tumor burden), lesion differential diagnosis and pre-population of appropriate reporting fields. Finally, the same technique could be expanded onto other PET indications.
Extended effects of a wearable sensory prosthesis on gait, balance function and falls after 26 weeks of use in persons with peripheral neuropathy and high fall risk—The walk2Wellness trial (2022)

ClinicalTrials.gov, identifier #NCT03538756.
Massive Machine-Type Communications (2017)

The articles in this special section address the techology and applications supported by machine-type communications (MTC). Here, MTC is characterized by fully automatic data generation, exchange, processing, and actuation among intelligent machines, without or with low intervention of humans. With the rapid penetration of embedded devices, MTC is becoming the dominant communication paradigm for a wide range of emerging smart services including healthcare, manufacturing, utilities, consumer goods, and transportation. Industry analysts predict that 50 billion devices will be connected to mobile networks worldwide by 2020. While mobile phone devices communicating among humans will still exist, machine-type devices sending bits of information to other machines, servers, clouds, or humans will account for a much larger proportion and thus create what is referred to as massive MTC (MMTC).
Scanning electron microscopical observations on the coastal marine nematode Epsilonema pustulatum (Gerlach, 1952) Lorenzen, 1973 (Nematoda: Epsilonematidae) (2000)

Abstract Additional detailed morphological information on features of the marine nematode Epsilonema pustulatum is presented for the first time. Lip structure, amphideal fovea, cuticular appendages (setae, spines, anal and copulatory thorns), annules and vacuoles, body inversion, setae ambulatoriae region, vulva, cloaca/anus and tail end are SEM studied and illustrated. Additionally, E. pustulatum (from Spain, Italy and Lebanon) is compared with other former Bathyepsilonema species. E. anulosum (Verschelde &amp; Vincx, 1992) is proposed as a junior synonym of E. pustulatum. Observations au microscope électronique à balayage sur le nématode marin côtier Epsilonema pustulatum (Gerlach, 1952) Lorenzen, 1973 (Nematoda: Epsilonematidae) - Des données morphologiques nouvelles concernant le nématode marin Epsilonema pustulatum sont présentées pour la première fois. Sont étudiés en microscopie électronique à balayage et illustrés des caractères tels que la structure labiale, les fovea amphidiales, les appendices cuticulaires (sétes, épines du corps, épines anales et copulatoires), anneaux et vacuoles, courbure du corps, région des sétes ambulatoires, vulve, cloaque/anus et extrémité de la queue. De plus, E. pustulatum (provenant d'Espagne, Italie et Liban) est comparé avec d'autres espèces auparavant placées dans le genre Bathyepsilonema. E. anulosum (Verschelde &amp; Vincx, 1992) est proposé comme synonyme mineur d'E. pustulatum.
Improved PET Detection of Focal Brain Activity Using Subset-dependent Relaxation `Dynamic' Row-action Maximum Likelihood Algorithm (DRAMA) (2006)

The SHR-7700 scanner (Hamamatsu Photonics, K.K.) is a high-resolution 20 cm bore research scanner that is used to acquiring images from both animals and human brains. The scanner has a reconstructed resolution of 2.5 mm and can image small amounts of tracer. To improve the recovery of low signals the DRAMA reconstruction method was implemented for the Hamamatsu scanner. To improve the signal-to-noise ratios the algorithm of subset-dependent relaxation 'dynamic' row-action maximum likelihood algorithm (DRAMA)[Tanaka, et al., -] was evaluated using a data set of three groups of subjects (n = 9, 9, and 8) received 5 mCi of [F-18] fluorodeoxyglucose at rest and during delayed recall task on 2 separate days. The optimum filter will be determined by varying the filter size. One filter has been evaluated and the resulting data was evaluated with a pixel wise one-sample t statistics were performed between task-resting conditions following pixel normalization and 3D Gaussian smoothing (9mm FWHM). Evoked brain activities were recorded with Z scores and spatial coordinates for comparisons. Significant task-evoked brain activities were detected by FBP and DRAMA (chi-square p < 0.001) in all 3 groups, but DRAMA produced 6.9 times more pixels than expected from random chance in comparison to 5.3 times by FBP. This method will be applied to the rest of the filter choices. This method will be also applied to a small animal study where the injected dose was only 15 to 25 muCi of activity to see if there is any improvement in the results. These results indicate a potential for DRAMA to improve the statistical power of brain-activation test.
Supplementary Table 1 from MYC Phosphorylation at Novel Regulatory Regions Suppresses Transforming Activity (2023)

&lt;p&gt;XLS file, 14K, Phosphopeptide analysis for ectopic MYC in 293Tv cells.&lt;/p&gt;
Use of a Common Table Architecture for Creating Hands Free, Eyes Free, Noisy Environment (Flex-Modal, Flex-Input) Interfaces (1997)

As we look to the design of nomadic systems, we need to find ways to create interfaces that the user can adapt to meet the constraints of different environments. We need to create interfaces that we can use whether we are walking down the hall driving the car, sitting at our workstation, or sitting in a meeting; that we can use when we're under stress or distracted; and that make it easy for us to locate and use new services. This requires an interface that at one point in the day can be used without using vision (e.g., when driving a car), but at other times may need to be totally visual (e.g., on a noisy prop airplane or in a meeting where you cannot use sound). It should also allow you to use a full keyboard and mouse (e.g., when seated) but not require use of these devices since they may not always be usable (e.g., while driving or while walking). Interestingly, this same interface flexibility (including the ability to change modalities) is what is needed to provide access to next generation systems by people with disabilities. That is, if we create fully nomadic systems we will have solved most of the problems and issues around providing access for people with disabilities, with reading problems and for those who are aging. The task in both of these pursuits is identifying ways to create interfaces that are Flex-Modal (the user can chose the sensory modality for information presentation) and Flex-Input (the user can chose which technique they use to input information to the device). Proposed is a method that uses a common table of semantic items that can be built in advance or on the fly. This can then be used as a basis for flex-modal and flex-input interface options.