gebhart/patrepeval huggingface dataset:
Quantifying nanoscale order in amorphous materials: simulating fluctuation electron microscopy of amorphous silicon (2007)

Fluctuation electron microscopy (FEM) is explicitly sensitive to 3- and 4-body atomic correlation functions in amorphous materials; this is sufficient to establish the existence of structural order on the nanoscale, even when the radial distribution function extracted from diffraction data appears entirely amorphous. However, it remains a formidable challenge to invert the FEM data into a quantitative model of the structure. Here, we quantify the FEM method for a-Si by forward simulating the FEM data from a family of high quality atomistic models. Using a modified WWW method, we construct computational models that contain 10–40 vol% of topologically crystalline grains, 1–3 nm in diameter, in an amorphous matrix and calculate the FEM signal, which consists of the statistical variance V (k) of the dark-field image as a function of scattering vector k. We show that V (k) is a complex function of the size and volume fraction of the ordered regions present in the amorphous matrix. However, the ratio of the variance peaks as a function of k affords the size of the ordered regions; and the magnitude of the variance affords a semi-quantitative measure of the volume fraction. We have also compared models that contain various amounts of strain in the ordered regions. This analysis shows that the amount of strain in realistic models is sufficient to mute variance peaks at high k. We conclude with a comparison between the model results and experimental data.
A Rigid Neutral Molecule Involving TTF and TCNQ Moieties with Intrinsic Charge‐ and Electron‐Transfer Properties that Depend on the Polarity of the Solvent (2005)

Eine Einkomponenten-Acceptor-Donor-Acceptor-Verbindung, die auf einem starren TCNQ-σ-TTF-σ-TCNQ-System beruht (siehe Bild), ist einzigartig wegen ihres intramolekularen Ladungs- und Elektronentransfers durch den Raum, der stark von der Polarität des Mediums abhängt. Die starke Abhängigkeit der elektronischen Struktur des Grundzustands von der Lösungsmittelpolarität bietet einen neuartigen Fall von Solvatochromie.
Selective Interactions between Vertebrate Polycomb Homologs and the SUV39H1 Histone Lysine Methyltransferase Suggest that Histone H3-K9 Methylation Contributes to Chromosomal Targeting of Polycomb Group Proteins (2002)

Polycomb group (PcG) proteins form multimeric chromatin-associated protein complexes that are involved in heritable repression of gene activity. Two distinct human PcG complexes have been characterized. The EED/EZH2 PcG complex utilizes histone deacetylation to repress gene activity. The HPC/HPH PcG complex contains the HPH, RING1, BMI1, and HPC proteins. Here we show that vertebrate Polycomb homologs HPC2 and XPc2, but not M33/MPc1, interact with the histone lysine methyltransferase (HMTase) SUV39H1 both in vitro and in vivo. We further find that overexpression of SUV39H1 induces selective nuclear relocalization of HPC/HPH PcG proteins but not of the EED/EZH2 PcG proteins. This SUV39H1-dependent relocalization concentrates the HPC/HPH PcG proteins to the large pericentromeric heterochromatin domains (1q12) on human chromosome 1. Within these PcG domains we observe increased H3-K9 methylation. Finally, we show that H3-K9 HMTase activity is associated with endogenous HPC2. Our findings suggest a role for the SUV39H1 HMTase and histone H3-K9 methylation in the targeting of human HPC/HPH PcG proteins to modified chromatin structures.
The Major Neutralizing Antigenic Site on Herpes Simplex Virus Glycoprotein D Overlaps a Receptor-Binding Domain (1999)

Herpes simplex virus (HSV) entry is dependent on the interaction of virion glycoprotein D (gD) with one of several cellular receptors. We previously showed that gD binds specifically to two structurally dissimilar receptors, HveA and HveC. We have continued our studies by using (i) a panel of baculovirus-produced gD molecules with various C-terminal truncations and (ii) a series of gD mutants with nonoverlapping 3-amino-acid deletions between residues 222 and 254. Binding of the potent neutralizing monoclonal antibody (MAb) DL11 (group Ib) was unaffected in forms of gD containing residues 1 to 250 but was greatly diminished in molecules truncated at residue 240 or 234. Both receptor binding and blocking of HSV infection were also affected by these C-terminal truncations. gD-1(234t) bound weakly to both HveA and HveC as determined by enzyme-linked immunosorbent assay (ELISA) and failed to block infection. Interestingly, gD-1(240t) bound well to both receptors but blocked infection poorly, indicating that receptor binding as measured by ELISA is not the only gD function required for blocking. Optical biosensor studies showed that while gD-1(240t) bound HveC with an affinity similar to that of gD-1(306t), the rates of complex formation and dissociation were significantly faster than for gD-1(306t). Complementation analysis showed that any 3-amino-acid deletion between residues 222 and 251 of gD resulted in a nonfunctional protein. Among this set of proteins, three had lost DL11 reactivity (those with deletions between residues 222 and 230). One of these proteins (deletion 222-224) was expressed as a soluble form in the baculovirus system. This protein did not react with DL11, bound to both HveA and HveC poorly as shown by ELISA, and failed to block HSV infection. Since this protein was bound by several other MAbs that recognize discontinuous epitopes, we conclude that residues 222 to 224 are critical for gD function. We propose that the potent virus-neutralizing activity of DL11 (and other group Ib MAbs) likely reflects an overlap between its epitope and a receptor-binding domain of gD.
Subcortical differentiation of stop consonants relates to reading and speech-in-noise perception (2009)

Children with reading impairments have deficits in phonological awareness, phonemic categorization, speech-in-noise perception, and psychophysical tasks such as frequency and temporal discrimination. Many of these children also exhibit abnormal encoding of speech stimuli in the auditory brainstem, even though responses to click stimuli are normal. In typically developing children the auditory brainstem response reflects acoustic differences between contrastive stop consonants. The current study investigated whether this subcortical differentiation of stop consonants was related to reading ability and speech-in-noise performance. Across a group of children with a wide range of reading ability, the subcortical differentiation of 3 speech stimuli ([ba], [da], [ga]) was found to be correlated with phonological awareness, reading, and speech-in-noise perception, with better performers exhibiting greater differences among responses to the 3 syllables. When subjects were categorized into terciles based on phonological awareness and speech-in-noise performance, the top-performing third in each grouping had greater subcortical differentiation than the bottom third. These results are consistent with the view that the neural processes underlying phonological awareness and speech-in-noise perception depend on reciprocal interactions between cognitive and perceptual processes.
The Impacts of Cellular Senescence in Elderly Pneumonia and in Age-Related Lung Diseases That Increase the Risk of Respiratory Infections (2017)

Pneumonia generates considerable negative impacts on the elderly. Despite the widespread uses of vaccines and appropriate antibiotics, the morbidity and mortality of elderly pneumonia are significantly higher compared to the counterparts of young populations. The definitive mechanisms of high vulnerability in the elderly against pathogen threats are unclear. Age-associated, chronic low-grade inflammation augments the susceptibility and severity of pneumonia in the elderly. Cellular senescence, one of the hallmarks of aging, has its own characteristics, cell growth arrest and senescence-associated secretory phenotype (SASP). These properties are beneficial if the sequence of senescence-clearance-regeneration is transient in manner. However, persisting senescent cell accumulation and excessive SASP might induce sustained low-grade inflammation and disruption of normal tissue microenvironments in aged tissue. Emerging evidence indicates that cellular senescence is a key component in the pathogenesis of chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF), which are known to be age-related and increase the risk of pneumonia. In addition to their structural collapses, COPD and IPF might increase the vulnerability to pathogen insults through SASP. Here, we discuss the current advances in understanding of the impacts of cellular senescence in elderly pneumonia and in these chronic lung disorders that heighten the risk of respiratory infections.
Emergence of polymyxin B-resistant Acinetobacter baumannii in hospitals in Rio de Janeiro Emergência de Acinetobacter baumannii resistente a polimixina B em hospitais do Rio de Janeiro (2016)

Introduction: Acinetobacter baumannii has been considered a prevalent pathogen in hospitals, raising concern in the medical community due to its broad spectrum of antimicrobial resistance. Since it is a subject that arouses much interest, it has been increasingly studied. Due to the emergence of multidrug-resistant (MDR) Gram-negative bacteria, the use of polymyxins was reestablished. The polymyxins have been considered the only option for the treatment of severe infections caused by MDR A. baumannii. Objective: To investigate the susceptibility profile of A. baumannii to polymyxin B. Material and method: 92 clinical isolates from two public hospitals in the Rio de Janeiro city were studied using broth microdilution method. Results: Most of the isolates were resistant to polymyxin B, 81.5% (n = 75), and minimum inhibitory concentration (MIC) values ranged between 4-64 mcg/ml. Conclusion: These results are a concern since currently the polymyxins have been considered the most effective therapeutic option against MDR isolates of A. baumannii.
Waterproof Flexible Polymer-Functionalized Graphene-Based Piezoresistive Strain Sensor for Structural Health Monitoring and Wearable Devices (2020)

In recent times, flexible piezoresistive polymer nanocomposite-based strain sensors are in high demand in wearable devices and various new age applications. In the polymer nanocomposite-based strain sensor, the dispersion of conductive nanofiller remains challenging due to the competing requirements of homogenized dispersion of nanofillers in the polymer matrix and retaining of the inherent characteristics of nanofillers. In the present work, waterproof and flexible poly(vinylidene difluoride) (PVDF) with a polymer-functionalized hydrogen-exfoliated graphene (HEG)-based piezoresistive strain sensor is developed and demonstrated. The novelty of the work is the incorporation of polystyrene sulfonate sodium salt (PSS) polymer-functionalized HEG in a PVDF-based flexible piezoresistive strain sensor. The PSS-HEG provides stable dispersion in the hydrophobic PVDF polymer matrix without sacrificing its inherent characteristics. The electrical conductivity of the PVDF/PSS-HEG-based strain sensor is 0.3 S cm<sup>-1</sup>, which is two orders of magnitude higher than the PVDF/HEG-based strain sensor. Besides, near the percolation region, the PVDF/PSS-HEG shows a maximum gauge factor of 10, which is about two times higher than the PVDF/HEG-based flexible strain sensor and 5-fold higher than the commercially available metallic strain gauge. The enhancement in the gauge factor is due to the stable dispersion of PSS-HEG in the PVDF matrix and electron conjugation caused by the adherence of negatively charged sulfonate functional groups on the HEG. The developed waterproof flexible strain sensor is demonstrated using portable wireless interfacing device for various applications. This work shows that the waterproof flexible PVDF/PSS-HEG-based strain sensor can be a potential alternative to the commercially available metallic strain gauge.
Detection of 2-chloroethyl ethyl sulfide and sulfonium ion degradation products on environmental surfaces using static SIMS (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetection of 2-chloroethyl ethyl sulfide and sulfonium ion degradation products on environmental surfaces using static SIMSGary S. Groenewold, Jani C. Ingram, Anthony D. Appelhans, James E. Delmore, and David A. DahlCite this: Environ. Sci. Technol. 1995, 29, 8, 2107–2111Publication Date (Print):August 1, 1995Publication History Published online1 May 2002Published inissue 1 August 1995https://doi.org/10.1021/es00008a033RIGHTS & PERMISSIONSArticle Views230Altmetric-Citations18LEARN 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 InReddit PDF (542 KB) Get e-Alertsclose Get e-Alerts
Improved osteoconduction of cortical bone grafts by biodegradable foam coating. (1999)

Alteration of the geometrical surface configuration of cortical bone allografts may improve incorporation into host bone. A porous biodegradable coating that would maintain immediate structural recovery and subsequently allow normal graft healing and remodeling by promoting bony ingrowth could provide an osteoconductive surface scaffold. We investigated the feasibility of augmenting cortical bone grafts with osteoconductive biodegradable polymeric scaffold coatings. Three types of bone grafts were prepared: Type I--cortical bone without coating (control), Type II--cortical bone coated with PLGA-foam, Type III--cortical bone coated with PPF-foam. The grafts were implanted into the rat tibial metaphysis (16 animals for each type of bone graft). Post-operatively the animals were sacrificed at 2 weeks and 4 weeks (8 animals for each type of bone graft at each time point). Histologic and histomorphometric analysis of grafts showed that the amount of new bone forming around the foam-coated grafts was significantly higher than in the control group (uncoated; p < 0.02). Although both foam formulations were initially equally osteoconductive, PLGA-based foam coatings appeared to have degraded at two weeks postoperatively, whereas PPF-based foam coatings were still present at 4 weeks postoperatively. While significant resorption was present in control allografts with little accompanying reactive new bone formation, PLGA-coated bone grafts showed evidence of bone resorption and subsequent bony ingrowth earlier than those coated with PPF-based foams suggesting that PPF-coated cortical bone grafts were longer protected against host reactions resulting in bone resorption.
Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F (2010)

Deregulation of cap-dependent translation is associated with cancer initiation and progression. The rate-limiting step of protein synthesis is the loading of ribosomes onto mRNA templates stimulated by the heterotrimeric complex, eukaryotic initiation factor (eIF)4F. This step represents an attractive target for anticancer drug discovery because it resides at the nexus of the TOR signaling pathway. We have undertaken an ultra-high-throughput screen to identify inhibitors that prevent assembly of the eIF4F complex. One of the identified compounds blocks interaction between two subunits of eIF4F. As a consequence, cap-dependent translation is inhibited. This compound can reverse tumor chemoresistance in a genetically engineered lymphoma mouse model by sensitizing cells to the proapoptotic action of DNA damage. Molecular modeling experiments provide insight into the mechanism of action of this small molecule inhibitor. Our experiments validate targeting the eIF4F complex as a strategy for cancer therapy to modulate chemosensitivity.
Genes and metals: a deadly combination. (2005)

Wilson's disease is an autosomal recessive disease of copper metabolism, with an estimated prevalence of 1:30000. The most common presentations of WD are liver disease and neurological disturbance. For many years the diagnosis was based on the results of several clinical and biochemical tests, for which several limitations had been reported. In recent years the developments of new techniques in genetic and molecular biology have provided useful tools in the diagnosis of Wilson's disease. However, the presence of several mutations and the fact that most patients are compound heterozygote means that the problem is not completely resolved. Chelators and zinc salts have been largely used in the treatment of WD patients with a favorable outcome, but the debate continues as to the agents of first choice. Liver transplantation is a cure for patients with decompensated liver disease but its effect on the neurological outcome is still not clear.
Chemical and thermal reduction of thin films of copper (<scp>II</scp>) oxide and copper (<scp>I</scp>) oxide (2001)

Chemical and thermal reduction of copper oxide thin films (∼20 Å) has been studied with x-ray photoelectron spectroscopy (XPS) and temperature programmed desorption (TPD) for application in microelectronic device interconnects. XPS showed that copper (I) oxide (Cu2O) and copper (II) oxide (CuO) were reduced to copper metal at 400 K within a 30 min exposure to deuterium atoms (D*) and molecules at 1×10−4 Torr. Similarly, XPS showed that Cu2O was reduced to copper metal at 400 K within a 30 min exposure to methyl radicals (CH3*) and acetone molecules at 1×10−4 Torr. After D* exposure, TPD showed O leaves the Cu2O surface as D2O from 400 K to 700 K with a peak desorption temperature of 510 K. After CH3* exposure, TPD showed O leaves the Cu2O surface as CO2 over a range from 400 to 700 K with a peak temperature at 590 K. With carbon impurity below the XPS detection limit, thermal reduction of CuO to Cu2O was verified by XPS near 890 K. TPD experiments showed that O leaves the CuO surface as O2 at 890 K. Without surface C, thermal reduction of Cu2O was not observed up to 1073 K. Reduction of Cu2O without reactive radical species (D* or CH3*) was negligible. These results suggest that thin films of copper oxide can be reduced at 400 K with D* and CH3*.
Antibodies to nuclear and smooth muscle antigens in multiple sclerosis and control patients (1982)

Serum and CSF specimens of 30 MS patients and 30 age- and sex-matched control patients with other neurological diseases were tested for autoantibodies. Indirect immunofluorescense was used to detect smooth muscle antibodies and antinuclear antibodies in the serum. Antibodies against DNA and RNA in the serum and CSF were tested by solid phase radioimmunoassays. No significant differences in autoantibody levels were found between MS and control patients.
Network Confinement and Heterogeneity Slows Nanoparticle Diffusion in Polymer Gels (2017)

Nanoparticle (NP) diffusion was measured in polyacrylamide gels (PAGs) with a mesh size comparable to the NP size, 21 nm. The confinement ratio (CR), NP diameter/mesh size, increased from 0.4 to 3.8 by increasing crosslinker density and from 0.4 to 2.1 by adding acetone, which collapsed the PAGs. In all gels, NPs either became localized, moving less than 200 nm, diffused microns, or exhibited a combination of these behaviors, as measured by single particle tracking. Mean squared displacements (MSDs) of mobile NPs decreased as CR increased. In collapsed gels, the localized NP population increased and MSD of mobile NPs decreased compared to crosslinked PAGs. For all CRs, van Hove distributions exhibited non-Gaussian displacements, consistent with intermittent localization of NPs. The non-Gaussian parameter increased from a maximum of 1.5 for crosslinked PAG to 5 for collapsed PAG, consistent with greater network heterogeneity in these gels. Diffusion coefficients decreased exponentially as CR increased for crosslinked gels; however, in collapsed gels, the diffusion coefficients decreased more strongly, which was attributed to network heterogeneity. Collapsing the gel resulted in an increasingly tortuous pathway for NPs, slowing diffusion at a given CR. Understanding how gel structure affects NP mobility will allow the design and enhanced performance of gels that separate and release molecules in membranes and drug delivery platforms.
Potential of SOI for analog and mixed analog-digital low-power applications (2002)

SOI technology offers significant assets for low-voltage, low-power high-speed logic. The steeper subthreshold slope of SOI MOSFETs not only improves design of low-voltage logic circuits, but also offers also opportunities for low-power analog design. Identical DC gains can be achieved in SOI and bulk either with less current or smaller geometries, or both. This is illustrated by plots of total area and stand-by current versus DC open-loop gain of two identical Miller op amps, one bulk and one SOI.
Using field evaluation and systematic iteration to rationalize the accumulation of omega‐3 long‐chain polyunsaturated fatty acids in transgenic <i>Camelina sativa</i> (2022)

The Brassicaceae Camelina sativa (gold of pleasure) is now an established niche crop and being used as a transgenic host for a range of novel seed traits. Most notable of these is the accumulation of omega-3 long-chain polyunsaturates such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), fatty acids normally only found in marine organisms. As part of continued efforts to optimize the accumulation of these non-native fatty acids via seed-specific expression of algal genes, a new series of iterative constructs was built and introduced into Camelina. Seed fatty acid composition was determined, and the presence of EPA and DHA was confirmed. To provide an additional level of evaluation, full environmental release was carried out on selected events, providing a real-world gauntlet against which to assess the performance of these novel lines. Composition of the seed oil triacylglycerol was determined by mass spectrometry, allowing for conclusions as to the contribution of different activities to the final accumulation of EPA and DHA. Since these data were derived from field-grown material, they also represent a robust demonstration of the stability of the omega-3 LC-PUFA trait in Camelina. We propose that field trialling should be routinely incorporated in the plant synthetic biology 'design-build-test-learn' cycle.