gebhart/patrepeval huggingface dataset:
Data mining and the human genome (2000)

As genomics research moves from an era of data acquisition to one of both acquisition and interpretation, new methods are required for organizing and prioritizing the data. These methods would allow an initial level of data analysis to be carried out before committing resources to a particular genetic locus. This JASON study sought to delineate the main problems that must be faced in bioinformatics and to identify information technologies that can help to overcome those problems. While the current influx of data greatly exceeds what biologists have experienced in the past, other scientific disciplines and the commercial sector have been handling much larger datasets for many years. Powerful datamining techniques have been developed in other fields that, with appropriate modification, could be applied to the biological sciences.
Advances and Innovations in Ablative Head and Neck Oncologic Surgery Using Mixed Reality Technologies in Personalized Medicine (2022)

The benefit of computer-assisted planning in head and neck ablative and reconstructive surgery has been extensively documented over the last decade. This approach has been proven to offer a more secure surgical procedure. In the treatment of cancer of the head and neck, computer-assisted surgery can be used to visualize and estimate the location and extent of the tumor mass. Nowadays, some software tools even allow the visualization of the structures of interest in a mixed reality environment. However, the precise integration of mixed reality systems into a daily clinical routine is still a challenge. To date, this technology is not yet fully integrated into clinical settings such as the tumor board, surgical planning for head and neck tumors, or medical and surgical education. As a consequence, the handling of these systems is still of an experimental nature, and decision-making based on the presented data is not yet widely used. The aim of this paper is to present a novel, user-friendly 3D planning and mixed reality software and its potential application for ablative and reconstructive head and neck surgery.
The15O Steady-State Method: Correction for Variation in Arterial Concentration (1988)

One of the factors limiting the accuracy of the 15O steady-state method for the measurement of regional cerebral blood flow and oxygen metabolism is the requirement that a constant arterial blood concentration be maintained over long periods. A new method has been developed to correct for the variation of the arterial concentration in the C15O2 and 15O2 steady-state inhalation technique. The time course of the arterial activity is obtained by multiple sampling over the study period. The same 15O model as is used in the steady-state method is employed but is solved without assuming equilibrium. Look-up tables are generated to relate flow and oxygen extraction fraction to tissue activity, and from them the regional parameters are estimated. Theory and simulation studies suggest that substantial improvement in accuracy can be obtained with no increase in statistical error. The validity of the method was checked experimentally by making repeated measurements in the same subject after perturbing the gas delivery. The conventional steady-state method showed significantly larger deviations in repeat measurement than did the new method. Thus, it is concluded that the proposed method is superior.
Platelet Protein Disulfide Isomerase Promotes Glycoprotein Ibα–Mediated Platelet-Neutrophil Interactions Under Thromboinflammatory Conditions (2019)

Our results demonstrate that PDI-facilitated cleavage of the allosteric disulfide bonds tightly regulates GPIbα function, promoting platelet-neutrophil interactions, vascular occlusion, and tissue damage under thromboinflammatory conditions.
Applications of hydrothermal time to quantifying and modeling seed germination and dormancy (2002)

Abstract Knowledge and prediction of seasonal weed seedling emergence patterns is useful in weed management programs. Seed dormancy is a major factor influencing the timing of seedling emergence, and once dormancy is broken, environmental conditions determine the rate of germination and seedling emergence. Seed dormancy is a population-based phenomenon, because individual seeds are independently sensing their environment and responding physiologically to the signals they perceive. Mathematical models based on characterizing the variation that occurs in germination times among individual seeds in a population can describe and quantify environmental and after-ripening effects on seed dormancy. In particular, the hydrothermal time model can describe and quantify the effects of temperature and water potential on seed germination. This model states that the time to germination of a given seed fraction is inversely proportional to the amount by which a given germination factor (e.g., temperature or water potential) exceeds a threshold level for that factor. The hydrothermal time model provides a robust method for understanding how environmental factors interact to result in the germination phenotype (i.e., germination pattern over time) of a seed population. In addition, other factors that influence seed dormancy and germination act by causing the water potential thresholds of the seed population to shift to higher or lower values. This relatively simple model can describe and quantify the germination behavior of seeds across a wide array of environmental conditions and dormancy states, and can be used as an input to more general models of seed germination and seedling emergence in the field.
Neuroregulatory Events Follow Adaptive Immune-Mediated Elimination of HIV-1-Infected Macrophages: Studies in a Murine Model of Viral Encephalitis (2004)

HIV-1-specific cellular immunity serves to eliminate infected cells and disease. However, how this process specifically affects the CNS is poorly understood. To mirror the regulatory events that occur in human brain after HIV-1 infection, a murine model of viral encephalitis was used to study relationships, over time, among lymphocyte-mediated infected cell elimination, innate immune responses, and neuropathology. Nonobese diabetic SCID mice were reconstituted with human PBL and a focal encephalitis induced by intracranial injection of autologous HIV-1-infected, monocyte-derived macrophages (MDM). On days 7, 14, and 21 after MDM injection into the basal ganglia, the numbers of human lymphocytes and mouse monocytes, virus-infected MDM, glial (astrocyte and microglial) responses, cytokines, inducible NO (iNOS), neurotrophic factors, and neuronal Ags were determined in brain by immunohistochemistry, real-time PCR, and Western blot assays. Microglia activation, astrocytosis, proinflammatory cytokines, and iNOS expression accompanied the loss of neuronal Ags. This followed entry of human lymphocytes and mouse monocytes into the brain on days 7 and 14. Elimination of virus-infected human MDM, expression of IL-10, neurotropins, and a down-regulation of iNOS coincided with brain tissue restoration. Our results demonstrate that the degree of tissue damage and repair parallels the presence of infected macrophages and effectors of innate and adaptive immunity. This murine model of HIV-1 encephalitis can be useful in elucidating the role played by innate and adaptive immunity in disease progression and resolution.
Investigation of the low-field leakage through high-k interpoly dielectric stacks and its impact on nonvolatile memory data retention (2006)

We describe the low-field leakage through high-k interpoly dielectric stacks in floating gate nonvolatile memories with an inelastic trap-assisted tunneling model, which accounts for arbitrary trap distributions in both energy and space. A systematic investigation of the impact of trap parameters, stack composition, bias and temperature on the leakage is presented, focusing on Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> -based stacks. Room- and high-temperature retention data indicate charge loss/gain due to bulk traps in Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2 </sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , with an average depth of 2.2 eV and a spread of plusmn0.3 eV. Scalability of Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> IPD stacks below 6.5 nm EOT may be achieved by reducing the trap density by at least 1 order of magnitude
The Redistribution ofDrosophilaVesicular Monoamine Transporter Mutants from Synaptic Vesicles to Large Dense-Core Vesicles Impairs Amine-Dependent Behaviors (2014)

Monoamine neurotransmitters are stored in both synaptic vesicles (SVs), which are required for release at the synapse, and large dense-core vesicles (LDCVs), which mediate extrasynaptic release. The contributions of each type of vesicular release to specific behaviors are not known. To address this issue, we generated mutations in the C-terminal trafficking domain of the Drosophila vesicular monoamine transporter (DVMAT), which is required for the vesicular storage of monoamines in both SVs and LDCVs. Deletion of the terminal 23 aa (DVMAT-Δ3) reduced the rate of endocytosis and localization of DVMAT to SVs, but supported localization to LDCVs. An alanine substitution mutation in a tyrosine-based motif (DVMAT-Y600A) also reduced sorting to SVs and showed an endocytic deficit specific to aminergic nerve terminals. Redistribution of DVMAT-Y600A from SV to LDCV fractions was also enhanced in aminergic neurons. To determine how these changes might affect behavior, we expressed DVMAT-Δ3 and DVMAT-Y600A in a dVMAT null genetic background that lacks endogenous dVMAT activity. When expressed ubiquitously, DVMAT-Δ3 showed a specific deficit in female fertility, whereas DVMAT-Y600A rescued behavior similarly to DVMAT-wt. In contrast, when expressed more specifically in octopaminergic neurons, both DVMAT-Δ3 and DVMAT-Y600A failed to rescue female fertility, and DVMAT-Y600A showed deficits in larval locomotion. DVMAT-Y600A also showed more severe dominant effects than either DVMAT-wt or DVMAT-Δ3. We propose that these behavioral deficits result from the redistribution of DVMAT from SVs to LDCVs. By extension, our data suggest that the balance of amine release from SVs versus that from LDCVs is critical for the function of some aminergic circuits.
Synthesis of TiN Nanoparticles by Pulsed Laser Ablation for Photothermal and Photodynamic Therapy (2020)

Spherical titanium nitride (TiN) nanoparticles (NPs) (&lt;50 nm) demonstrating high quality plasmon resonances are synthesized from commercially available much larger TiN NPs using pulsed laser ablation with an 800 nm femtosecond laser.
MADE (2018)

Enterprises are targeted by various malware activities at a staggering rate. To counteract the increased sophistication of cyber attacks, most enterprises deploy within their perimeter a number of security technologies, including firewalls, antivirus software, and web proxies, as well as specialized teams of security analysts forming Security Operations Centers (SOCs).
Supplementary Figure S3 from Genetic Heterogeneity and Tissue-specific Patterns of Tumors with Multiple <i>PIK3CA</i> Mutations (2023)

&lt;p&gt;Patterns of mutual exclusivity as well as co-occurrence between multi-PIK3CA mutations and alterations in other cancer associated genes.&lt;/p&gt;
Deferred Data Structuring (1988)

We consider the problem of answering a series of on-line queries on a static data set. The conventional approach to such problems involves a preprocessing phase which constructs a data structure with good search behavior. The data structure representing the data set then remains fixed throughout the processing of the queries. Our approach involves dynamic or query-driven structuring of the data set; our algorithm processes the data set only when doing so is required for answering a query. A data structure constructed progressively in this fashion is called a deferred data structure. We develop the notion of deferred data structures by solving the problem of answering membership queries on an ordered set. We obtain a randomized algorithm which achieves asymptotically optimal performance with high probability. We then present optimal deferred data structures for the following problems in the plane: testing convex-hull membership, half-plane intersection queries and fixed-constraint multi-objective linear programming. We also apply the deferred data structuring technique to multi-dimensional dominance query problems.
Hierarchical power distribution in large scale computing systems (2023)

Techniques for managing power distribution amongst processors in a massively parallel computer architecture are disclosed. The techniques utilize a hierarchy that organizes the various processors of the massively parallel computer architecture. The hierarchy groups numbers of the processors at the lowest level. When processors complete tasks, the power assigned to those processors is distributed to other processors in the same group so that the performance of those processors can be increased. Hierarchical organization simplifies the calculations required for determining how and when to distribute power, because when tasks are complete and power is available for distribution, a relatively small number of processors are available for consideration to receive that power. The number of processors that are grouped together can be adjusted in real time based on performance factors to improve the trade-off between calculation speed and power distribution efficacy.
Dual Serotonin Transporter/Histamine H3 Ligands: Optimization of the H3 Pharmacophore. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Experimental and theoretical study of magnetodonors in GaAs and InP at megagauss fields (1994)

Donor states in GaAs and InP at megagauss magnetic fields are studied experimentally and theoretically. The data allow us to investigate the magnetodonors for values of \ensuremath{\gamma}=\ensuremath{\Elzxh}${\mathrm{\ensuremath{\omega}}}_{\mathit{c}}$/2 ${\mathrm{Ry}}^{\mathrm{*}}$\ensuremath{\approxeq}10, unattainable until now in these materials. The observations are described by a theoretical model, which uses variational atomic-magnetic wave functions and accounts for the band nonparabolicity within an effective two-band k\ensuremath{\cdot}p formalism. The theory describes well the absolute values and field dependences of energy shifts between the cyclotron resonance (CR) transitions and the corresponding magnetodonor impurity cyclotron resonance (ICR) transitions in both materials. Spin doublets of CR and ICR transitions are considered; they are shown to be related to a variation of the spin g value with the energy. It is argued that the spin-doublet splittings at high fields should be considerably larger in GaAs than in InP. This conclusion agrees with the observations.
Multimorphic Materials: Spatially Tailoring Mechanical Properties via Selective Initiation of Interpenetrating Polymer Networks (2022)

Access to multimaterial polymers with spatially localized properties and robust interfaces is anticipated to enable new capabilities in soft robotics, such as smooth actuation for advanced medical and manufacturing technologies. Here, orthogonal initiation is used to create interpenetrating polymer networks (IPNs) with spatial control over morphology and mechanical properties. Base catalyzes the formation of a stiff and strong polyurethane, while blue LEDs initiate the formation of a soft and elastic polyacrylate. IPN morphology is controlled by when the LED is turned "on", with large phase separation occurring for short time delays (≈1-2 min) and a mixed morphology for longer time delays (>5 min), which is supported by dynamic mechanical analysis, small angle X-ray scattering, and atomic force microscopy. Through tailoring morphology, tensile moduli and fracture toughness can be tuned across ≈1-2 orders of magnitude. Moreover, a simple spring model is used to explain the observed mechanical behavior. Photopatterning produces "multimorphic" materials, where morphology is spatially localized with fine precision (<100 µm), while maintaining a uniform chemical composition throughout to mitigate interfacial failure. As a final demonstration, the fabrication of hinges represents a possible use case for multimorphic materials in soft robotics.
FEP-Guided Selection of Bicyclic Heterocycles in Lead Optimization for Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase [J. Am. Chem. Soc. 2006, 128, 15372−15373]. (2007)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionFEP-Guided Selection of Bicyclic Heterocycles in Lead Optimization for Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase [J. Am. Chem. Soc.2006, 128, 15372−15373].Joseph T. Kim, Andrew D. Hamilton, Christopher M. Bailey, Robert A. Domaoal, Ligong Wang, Karen S. Anderson, and William L. JorgensenCite this: J. Am. Chem. Soc. 2007, 129, 10, 3027Publication Date (Web):February 15, 2007Publication History Published online15 February 2007Published inissue 1 March 2007https://pubs.acs.org/doi/10.1021/ja076881shttps://doi.org/10.1021/ja076881scorrectionACS PublicationsCopyright © 2007 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views698Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (11 KB) Get e-Alertsclose Get e-Alerts
Fast parallel simulation of fiber optical communication systems accelerated by a graphics processing unit (2010)

A parallel implementation of the split-step Fourier method utilizing the general purpose parallel computing architecture for graphics processing units CUDA is presented. Results of the GPU-implementation are compared to a conventional CPU-based approach regarding computation time and accuracy. We developed a novel implementation with a significantly higher accuracy than the CUDA intrinsic FFT in single precision mode yielding a high speed-up factor of up to 144 compared to a CPU implementation.
SMC with adaptive resampling: Large sample asymptotics (2009)

A longstanding problem in sequential Monte Carlo (SMC) is to mathematically prove the popular belief that resampling does improve the performance of the estimation (this of course is not always true, and the real question is to clarify classes of problems where resampling helps). A more pragmatic answer to the problem is to use adaptive procedures that have been proposed on the basis of heuristic considerations, where resampling is performed only when it is felt necessary, i.e. when some criterion (effective number of particles, entropy of the sample, etc.) reaches some prescribed threshold. It still remains to mathematically prove the efficiency of such adaptive procedures. The contribution of this paper is to propose an approach, based on a representation in terms of multiplicative functionals (in which importance weights are treated as particles, roughly speaking) to obtain the asymptotic variance of adaptive resampling procedures, when the sample size goes to infinity. It is then possible to see the impact of the threshold on the asymptotic variance, at least in the Gaussian case, where the resampling criterion has an explicit expressions in the large sample asymptotics.
Synthesis of Novel Fluorinated [sgrave]-Conjugated Silicon-Containing Polymers: Polysilynes and Polysilanes (1992)

Abstract The synthesis of fluorinated polysilynes, a new class of silicon-silicon network materials, has been achieved by reductive coupling of fluorinated trichlorosilanes with molten sodium in a mixture of toluene and diglyme (4:1) as a new synthetic route. Homopolysilynes containing fluorinated organogroups were insoluble in organic solvents due to side reactions. To improve solubility, copolysilynes were synthesized by co-polymerization of fluorinated trichlorosilanes with cyclohexyltrichlorosi-lane. All spectroscopic data indicate that the structure of the resulting fluorinated copolysilynes is a rigid, irregular network of monoalkyl sp 3-hybridized silicon units which exhibit extensive Si-Si [sgrave]-delocalization. They are more thermally stable than unfluorinated polysilynes. Upon exposure to deep-UV radiation in air, they undergo photooxidative crosslinking to give insoluble glass-like materials. This photooxidation process is accompanied by a large decrease in refractive index from n = 1.61 to n = 1.485. These results suggest that their potential applications include photoresists and optical waveguides. In order to understand the mechanism of reductive coupling of fluorinated trichlorosilanes, fluorinated linear polysilanes were also prepared.
ChemInform Abstract: The Zirconocene Induced Coupling of Benzyne with Nitriles: Synthesis, Structure, and Reactions of Novel Azametallacyclopentenes. (1987)

Abstract Dicyclopentadienylzirconium dichloride (I) reacts with benzene (II) to give the aryne complex (III) which undergoes cyclization with the nitriles (IV), yielding the benzofused azazirconiacyclopentenes (V).
Histopathological and morphometric analyses of late rectal injury after irradiation (2000)

The aim of the present study was to assess and quantify changes in the structural components of the rectal wall after irradiation with varying single doses of x-rays. A total of 70 CDF1/Bom male mice were irradiated at a selective 1.5 cm of the distal rectum with varying single doses of 0-30 Gy. At 32 weeks postirradiation the mice were sacrificed and the rectum was removed. Sampling of the specimens was based on unbiased stereological principles using systematic random sampling. Vertical tissue sections were used to estimate mucosal surface area density and to measure the thickness and volume fraction of the different intestinal wall layers. The surface area density decreased with increasing dose (p<0.02) due to pronounced injury of the crypts and mucosal morphology. The thickness and the volume fraction of the submucosa were significantly increased in the 20, 25 and 30 Gy treatment groups (p<0.0001 and p<0.0001), whereas the thicknesses of the mucosa, the lamina muscularis propria and the serosa did not change after irradiation. It is concluded that irradiation causes histopathological changes in the rectal mucosa and submucosa, and changes in the thickness of the submucosal intestinal layer. These changes were found to be dose-dependent.