gebhart/patrepeval huggingface dataset:
Optimal strategies for imaging thick biological specimens: exit wavefront reconstruction and energy‐filtered imaging (1996)

In transmission electron microscopy (TEM) of thick biological specimens, the relationship between the recorded image intensities and the projected specimen mass density is distorted by incoherent electron-specimen interactions and aberrations of the objective lens. It is highly desirable to develop a strategy for maximizing and extracting the coherent image component, thereby allowing the projected specimen mass density to be directly related to image intensities. For this purpose, we previously used exit wavefront reconstruction to understand the nature of image formation for thick biological specimens in conventional TEM. Because electron energy-loss filtered imaging allows the contributions of inelastically scattered electrons to be removed, it is potentially advantageous for imaging thick, biological samples. In this paper, exit wavefront reconstruction is used to quantitatively analyse the imaging properties of an energy-filtered microscope and to assess its utility for thick-section microscopy. We found that for imaging thick biological specimens (> 0.5 microns) at 200 keV, only elastically scattered electrons contribute to the coherent image component. Surprisingly little coherent transfer was seen when using energy-filtering at the most probable energy loss (in this case at the first plasmon energy-loss peak). Furthermore, the use of zero-loss filtering in combination with exit wavefront reconstruction is considerably more effective at removing the effects of multiple elastic and inelastic scattering and microscope objective lens aberrations than either technique by itself. Optimization of the zero-loss signal requires operation at intermediate to high primary voltages (> 200 keV). These results have important implications for the accurate recording of images of thick biological specimens as, for instance, in electron microscope tomography.
Modulation of intracranial field potential responses in the human large-scale attention network during a spatial attention task (2015)

Spatial attention is mediated through a large-scale network that includes occipital, temporal, parietal and frontal cortical regions. While the network architecture has been well characterized using neuroimaging methods, less is known about the temporal dynamics in local regions and across the network. Here, we explored the modulatory effects of spatial attention throughout this cortical network by analyzing intracranial field potentials recorded from 538 ECoG electrodes implanted in 6 epilepsy patients. We examined the effects of attention using a variant of the Eriksen flanker task, where subjects were cued by an exogenous stimulus to the spatial location of an upcoming target stimulus which, after a variable delay period, was presented embedded in a circular array of shapes. Subjects had to differentiate between barrel or bowtie target stimuli flanked either by congruent or incongruent shapes. Using our probabilistic atlas of the human visual system, we localized the recorded ECoG signals to topographically organized brain areas and linked them to functional brain imaging data from normal subjects. We found spatially constrained visual response fields in 175 electrodes, as indicated by differential cue-related activity, obtained from both induced broadband power and evoked potentials. We examined response modulation from those electrodes during the delay period of the task when subjects either attended to or away from the response field. Further, we related these results to changes in the BOLD signal measured in normal subjects performing the same task. We found that covert spatial attention affected evoked event-related potentials and induced low frequency (4-20Hz) and broadband high gamma (50-200Hz) power differentially along the dorsal pathway through nodes of the fronto-parietal attention network, from V1 through intraparietal sulcus areas IPS0-IPS5 and the frontal eye fields. Meeting abstract presented at VSS 2015
The evolution of universal adaptations of life is driven by universal properties of matter: energy, entropy, and interaction (2020)

The evolution of multicellular eukaryotes expresses two sorts of adaptations: local adaptations like fur or feathers, which characterize species in particular environments, and universal adaptations like microbiomes or sexual reproduction, which characterize most multicellulars in any environment. We reason that the mechanisms driving the universal adaptations of multicellulars should themselves be universal, and propose a mechanism based on properties of matter and systems: <i>energy</i>, <i>entropy</i>, and <i>interaction</i>. <i>Energy</i> from the sun, earth and beyond creates new arrangements and interactions. Metabolic networks channel some of this energy to form cooperating, interactive arrangements. <i>Entropy</i>, used here as a term for all forces that dismantle ordered structures (rather than as a physical quantity), acts as a selective force. Entropy selects for arrangements that resist it long enough to replicate, and dismantles those that do not. <i>Interactions</i>, energy-charged and dynamic, restrain entropy and enable survival and propagation of integrated living systems. This fosters <i>survival-of-the-fitted</i> - those entities that resist entropic destruction - and not only of the fittest - the entities with the greatest reproductive success. The "unit" of evolution is not a discrete entity, such as a gene, individual, or species; what evolves are collections of related interactions at multiple scales. Survival-of-the-fitted explains universal adaptations, including resident microbiomes, sexual reproduction, continuous diversification, programmed turnover, seemingly wasteful phenotypes, altruism, co-evolving environmental niches, and advancing complexity. Indeed survival-of-the-fittest may be a particular case of the survival-of-the-fitted mechanism, promoting local adaptations that express reproductive advantages in addition to resisting entropy. Survival-of-the-fitted accounts for phenomena that have been attributed to neutral evolution: in the face of entropy, there is no neutrality; all variations are challenged by ubiquitous energy and entropy, retaining those that are "fit enough". We propose experiments to test predictions of the survival-of-the-fitted theory, and discuss implications for the wellbeing of humans and the biosphere.
Transcribed and non-transcribed regions ofTetrahymenaribosomal gene chromatin have different accessibilities to micrococcal nuclease (1983)

DNA renaturation kinetics was used to examine the relative accessibility of various regions of the Tetrahymena ribosomal RNA gene (rDNA) chromatin to micrococcal nuclease. In nuclei from cells active in rRNA transcription, the transcribed region of the rDNA chromatin was as much as 5-fold more accessible than the average of the total chromatin. As few as 20% inactive genes in the population could have accounted for all of the hybridization, so the transcribed region of the active units may be totally unprotected from nuclease degradation. The terminal non-transcribed spacer downstream from the transcription unit was also preferentially digested, but to a smaller degree. The central non-transcribed spacer was degraded to the same extent as total chromatin after a high degree of nuclease digestion. In nuclei from starved cells, which have 96% reduced rRNA transcription, the transcribed and terminal spacer regions of the rDNA were again more accessible than the total chromatin from the same nuclei, but the difference did not exceed 2-fold. We conclude that transcriptional activation is accompanied by major changes in the structure of the ribosomal gene chromatin, and that the extent and/or type of structural alteration differs in each functionally defined region of the rDNA.
Current Concepts on Action of Synthetic Thrombin Inhibitors (1978)

The development of synthetic inhibitors of thrombin and of related arginine-specific esteroproteases is reviewed. The superiority of bis- and tris-benzamidines over benzamidine is disccussed and related to the presence on the enzyme of secondary binding sites beyond the specificity pocket. It is demonstrated that inhibitors with marked specificity for a single enzyme can be produced, and with the help of such selective compounds it is shown that inhibition of factor Xa is more significant for overall anticoagulant effect than inhibition of thrombin.
An Enantiomerically Pure Tetracoordinate Boron Compound:  Stereochemistry of Substitution Reactions at the Chirogenic Boron Atom (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTAn Enantiomerically Pure Tetracoordinate Boron Compound: Stereochemistry of Substitution Reactions at the Chirogenic Boron AtomTsuneo Imamoto and Hideaki MorishitaView Author Information Department of Chemistry, Faculty of Science Chiba University, Yayoi-cho, Inage-ku Chiba 263-8522, Japan Cite this: J. Am. Chem. Soc. 2000, 122, 26, 6329–6330Publication Date (Web):June 17, 2000Publication History Received4 April 2000Published online17 June 2000Published inissue 1 July 2000https://pubs.acs.org/doi/10.1021/ja0011764https://doi.org/10.1021/ja0011764rapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views1008Altmetric-Citations41LEARN 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 Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information SUBJECTS:Absolute configuration,Boron,Lithium,Molecular structure,Substitution reactions Get e-Alerts
Hard X-ray photoelectron spectroscopy on ultra shallow plasma-doped silicon layers (2007)

Recently, we have shown that hard X‐ray photoemission spectroscopy (HX‐PES) using undulator X‐rays at SPring‐8 is quite feasible with both high resolution and high throughput. Here we report an application of HX‐PES to the characterization of electronic and chemical states of ultra shallow plasma doped samples. We found that the shift in chemical binding energy by impurity activation can be measured with high accuracy. The binding energy of Si 1s changes according to the shift in Fermi level as the carrier concentration varies. Thus, the active carrier concentration of ultra‐shallow junction region can be measured by non‐destructive HX‐PES with high accuracy.
Non‐lithographic SERS Substrates: Tailoring Surface Chemistry for Au Nanoparticle Cluster Assembly (2012)

Near-field plasmonic coupling and local field enhancement in metal nanoarchitectures, such as arrangements of nanoparticle clusters, have application in many technologies from medical diagnostics, solar cells, to sensors. Although nanoparticle-based cluster assemblies have exhibited signal enhancements in surface-enhanced Raman scattering (SERS) sensors, it is challenging to achieve high reproducibility in SERS response using low-cost fabrication methods. Here an innovative method is developed for fabricating self-organized clusters of metal nanoparticles on diblock copolymer thin films as SERS-active structures. Monodisperse, colloidal gold nanoparticles are attached via a crosslinking reaction on self-organized chemically functionalized poly(methyl methacrylate) domains on polystyrene-block-poly(methyl methacrylate) templates. Thereby nanoparticle clusters with sub-10-nanometer interparticle spacing are achieved. Varying the molar concentration of functional chemical groups and crosslinking agent during the assembly process is found to affect the agglomeration of Au nanoparticles into clusters. Samples with a high surface coverage of nanoparticle cluster assemblies yield relative enhancement factors on the order of 10⁹ while simultaneously producing uniform signal enhancements in point-to-point measurements across each sample. High enhancement factors are associated with the narrow gap between nanoparticles assembled in clusters in full-wave electromagnetic simulations. Reusability for small-molecule detection is also demonstrated. Thus it is shown that the combination of high signal enhancement and reproducibility is achievable using a completely non-lithographic fabrication process, thereby producing SERS substrates having high performance at low cost.
Compass: A scalable simulator for an architecture for cognitive computing (2012)

Inspired by the function, power, and volume of the organic brain, we are developing TrueNorth, a novel modular, non-von Neumann, ultra-low power, compact architecture. TrueNorth consists of a scalable network of neurosynaptic cores, with each core containing neurons, dendrites, synapses, and axons. To set sail for TrueNorth, we developed Compass, a multi-threaded, massively parallel functional simulator and a parallel compiler that maps a network of long-distance pathways in the macaque monkey brain to TrueNorth. We demonstrate near-perfect weak scaling on a 16 rack IBM® Blue Gene®/Q (262144 CPUs, 256 TB memory), achieving an unprecedented scale of 256 million neurosynaptic cores containing 65 billion neurons and 16 trillion synapses running only 388x slower than real time with an average spiking rate of 8.1 Hz. By using emerging PGAS communication primitives, we also demonstrate 2x better real-time performance over MPI primitives on a 4 rack Blue Gene/P (16384 CPUs, 16 TB memory).
Severe Multifocal Form of Buruli Ulcer after Streptomycin and Rifampin Treatment: Comments on Possible Dissemination Mechanisms (2010)

Buruli ulcer (BU), a disease caused by Mycobacterium ulcerans, leads to the destruction of skin and sometimes bone. Here, we report a case of severe multifocal BU with osteomyelitis in a 6-year-old human immunodeficiency virus (HIV)-negative boy. Such disseminated forms are poorly documented and generally occur in patients with HIV co-infection. The advent of antibiotic treatment with streptomycin (S) and rifampin (R) raised hope that these multifocal BU cases could be reduced. The present case raises two relevant points about multifocal BU: the mechanism of dissemination that leads to the development of multiple foci and the difficulties of treatment of multifocal forms of BU. Biochemical (hypoproteinemia), hematological (anemia), clinical (traditional treatment), and genetic factors are discussed as possible risk factors for dissemination.
IPv6 Multicast VPN (MVPN) Support Using PIM Control Plane and Selective Provider Multicast Service Interface (S-PMSI) Join Messages (2012)

The specification for Multicast Virtual Private Networks (MVPN)
contains an option that allows the use of PIM as the control protocol
between provider edge routers. It also contains an option that allows
UDP-based S-PMSI Join messages to be used to bind particular
customer multicast flows to particular tunnels through a service
provider's network. This document extends the MVPN specification so
that these options can be used when the customer multicast flows are
IPv6 flows.
Role of Gap Junctional Intercellular Communication and NO Signaling in Low-Dose Radiation Hypersensitivity (2008)

In the cells irradiated at low density, U87 cell line has shown a highly distinguishable HRS/IRR response (Chandna et al, Radiat Res, 157, 516-525, 2002), which was mitigated at higher density. In order to understand the basis of increased cellular lethality at low doses as well as the density-mediated suppression of HRS/IRR response, effect of low gamma radiation doses was studied using additional parameters including micronucleation, apoptosis induction and cell cycle progression delay in the absence and presence of inhibitors of gap junctional intercellular communication (GJIC) and NO signaling. Cells plated/ seeded at high cell multiplicity or density were pre-treated with phorbol ester PMA (phorbyl myristate acetate) and/or the NOS inhibitor LNMMA from 2h pre-irradiation, and treatment continued till 1h post-irradiation, after which cells were incubated in fresh growth medium. The low dose of 20cGy induced significant micronucleation in cells, and inhibition of GJIC by PMA (5nM) significantly enhanced this radiation-induced micronucleation in high density cultures. On the other hand, the NOS inhibitor LNMMA reduced micronucleation induced at 20cGy, and also significantly mitigated the PMA-induced enhancement of radiation-induced micronucleation. Interestingly, PMA could induce relatively larger number of binucleated cells, which indicates abrogation of G2/M checkpoint and might explain the higher induction of micronuclei in irradiated cells pre-treated with this agent. In contrast to PMA that enhanced micronucleation and reduced irradiated cell survival at low doses, LNMMA inhibited the micronucleation and enhanced survival in the irradiated cells, indicating the role of nitrosative stress in low-dose sensitivity of cells. A small but significant proportion of cells also showed nuclear fragmentation typical of apoptosis when pre-treated with PMA prior to irradiation at 20cGy. Further, a significant proportion of micronuclei induced at 20cGy were relatively larger in size, possibly indicating the induction of chromosome laggards due to spindle disturbances during the cell division. In this study, inhibition of GJIC significantly enhanced low dose lethality in the high density tumour cell cultures, whereas NOS inhibition reversed this effect. Indeed, the cell density mediated abrogation of HRS/IRR was significantly reversed in the presence of PMA, indicating protective role of gap junctional communication in HRS/IRR response. The study further indicated that PMA induced enhancement of radiation lethality could be effected through abrogation of G2/M cell cycle checkpoint.
Case Report: Abnormalities of sperm motility and morphology in a patient with Leber hereditary optic neuropathy: Improvement after idebenone therapy (2023)

This case confirms the possibility of sperm dysfunction in Leber hereditary optic neuropathy and the interest of idebenone as a treatment for infertility due to mtDNA mutations in human.
Putting language into language modeling (1999)

In this paper we describe the statistical Structured Language Model (SLM) that uses grammatical analysis of the hypothesized sentence segment (prefix) to predict the next word. We first describe the operation of a basic, completely lexicalized SLM that builds up partial parses as it proceeds left to right. We then develop a chart parsing algorithm and with its help a method to compute the prediction probabilities P (wi+1jWi): We suggest useful computational shortcuts followed by a method of training SLM parameters from text data. Finally, we introduce more detailed parametrization that involves non-terminal labeling and considerably improves smoothing of SLM statistical parameters. We conclude by presenting certain recognition and perplexity results achieved on standard corpora.
AAA in a Cloud-Based Virtual DIME Network Architecture (DNA) (2011)

The design of a cloud architecture can be difficult according the business logic complexity which Cloud Service Providers (SPs) want to achieve. This paper describes a possible solution for simplifying the design of cloud-based services exploiting a DIME Network Architecture (DNA). More specifically, exploiting the signaling channel and FCAPS of DIMEs, we discuss an approach for the management of SSO Authentication, Authorization, and Accounting in cloud-based services.
Rimless wheel with radially expanding spokes: dynamics, impact, and stable gait (2004)

This paper describes the dynamics and intermittent impact model of a novel rimless wheel with radially expanding spokes confined to move in a vertical plane. The wheel has two degrees of freedom, namely rotation in the plane and change of radius. The system has intermittent impacts with the ground and its mathematical model is discontinuous. The motions of the wheel on a horizontal and an inclined plane are investigated. The contact point of the wheel with the ground is assumed to have no slip. We derive the equations of motion in between the collisions and velocity change before and after the wheel impact. We construct the return map of its cyclic motion and plan the motion in between impacts to obtain a stable gait. Dynamic simulations are performed using MATLAB and are presented in the paper.
Health-related quality of life and economic impact of urinary incontinence due to detrusor overactivity associated with a neurologic condition: a systematic review (2013)

Incontinent patients with underlying neurologic conditions have impaired HRQoL as well as substantial economic burden attributable to UI due to NDO. There is a need for urgency UI treatments that improve HRQoL of these patients and alleviate the economic burden of this condition.