gebhart/patrepeval huggingface dataset:
Germline mosaic transmission of a novel duplication of PXDN and MYT1L to two male half-siblings with autism (2011)

Autism is a neurodevelopmental disorder with a strong genetic component to susceptibility. In this study, we report the molecular characterization of an apparent de-novo 281 kb duplication of chromosome 2p25.3 in two male half-siblings with autism. The 2p25.3 duplication was first identified through a low-density microarray, validated with fluorescent in-situ hybridization, and duplication breakpoints were delineated using an Affymetrix 6.0 single-nucleotide polymorphism microarray. The fluorescent in-situ hybridization results validated the novel copy number variant and revealed the mother to be mosaic, with ∼33% of her lymphoblast cells carrying the duplication. Therefore, the duplication was transmitted through the mechanism of germline mosaicism. In addition, duplication breakpoints were refined and showed that PXDN is fully duplicated, whereas seven exons of the terminal portion of the 25 exon gene MYT1L are within the duplicated region. MYT1L, a gene predominately expressed in the brain, has recently been linked with other neuropsychiatric illness such as schizophrenia and depression. Results from this study indicate that the 2p25.3 duplication disrupting PXDN and MYT1L is a potential autism-causing variant in the pedigree reported here and should receive further consideration as a candidate for autism.
Relative Placement of Benefit and Risk Information in Direct-to-Consumer Advertisements of Prescription Drugs on the World Wide Web (2001)

This research was conducted to determine how risk information is presented within direct-to-consumer (DTC) drug advertisements on the World Wide Web (WWW). Twenty prescription drug manufacturers' web sites were examined with respect to risk and benefit information placement. Measured were (a) the number of clicks required to view the benefit and risk information from the home page, (b) the number of clicks to the risk information from the benefit information, (c) the number of clicks to the benefit information from the risk information, (d) and whether scrolling was required to view both benefit and risk information. Also measured were whether the benefit and risk information was on the same page and whether a separate file reader was needed to view the risk information. Results indicated that the risk information is more difficult to find on DTC prescription medication web site advertisements compared to benefits. More clicks from the home page were required to find the risk information than the benefits. Also, scrolling was required more often to find the risk information compared to the benefits. Implications of these results are discussed with respect to the equal balance of risk and benefit information that is required by U.S. Federal Regulations.
Amphiphilic triblock copolymers with PEGylated hydrocarbon structures as environmentally friendly marine antifouling and fouling-release coatings (2014)

The ideal marine antifouling (AF)/fouling-release (FR) coating should be non-toxic, while effectively either resisting the attachment of marine organisms (AF) or significantly reducing their strength of attachment (FR). Many recent studies have shown that amphiphilic polymeric materials provide a promising solution to producing such coatings due to their surface dual functionality. In this work, poly(ethylene glycol) (PEG) of different molecular weights (Mw = 350, 550) was coupled to a saturated difunctional alkyl alcohol to generate amphiphilic surfactants (PEG-hydrocarbon-OH). The resulting macromolecules were then used as side chains to covalently modify a pre-synthesized PS8 K-b-P(E/B)25 K-b-PI10 K (SEBI or K3) triblock copolymer, and the final polymers were applied to glass substrata through an established multilayer surface coating technique to prepare fouling resistant coatings. The coated surfaces were characterized with AFM, XPS and NEXAFS, and evaluated in laboratory assays with two important fouling algae, Ulva linza (a green macroalga) and Navicula incerta, a biofilm-forming diatom. The results suggest that these polymer-coated surfaces undergo surface reconstruction upon changing the contact medium (polymer/air vs polymer/water), due to the preferential interfacial aggregation of the PEG segment on the surface in water. The amphiphilic polymer-coated surfaces showed promising results as both AF and FR coatings. The sample with longer PEG chain lengths (Mw = 550 g mol(-1)) exhibited excellent properties against both algae, highlighting the importance of the chemical structures on ultimate biological performance. Besides reporting synthesis and characterization of this new type of amphiphilic surface material, this work also provides insight into the nature of PEG/hydrocarbon amphiphilic coatings, and this understanding may help in the design of future generations of fluorine-free, environmentally friendly AF/FR polymeric coatings.
Dynamic crushing of auxetic open-cell polyurethane foam (2002)

A high strain rate compression test with a constant speed of 1.5 m/s has been performed on samples of negative Poisson's ratio and normal open-cell polyurethane foam. The tests show that the transformation of the normal foam into the auxetic phase greatly increases the crashworthiness qualities of the open-cell foam.
Slotted ALOHA and code division multiple access techniques for land-mobile satellite personal communications (1995)

The throughput and delay characteristics of a land-mobile satellite channel are analyzed for both slotted ALOHA. And slotted direct-sequence CDMA (code division multiple access), using binary phase shift keying (BPSK) modulation and forward error correction coding (FEC). In the case of CDMA, the application of path diversity techniques-maximal ratio combining and selection diversity-is also taken into account. Packet success probabilities are derived for both slow and fast fading, in order to evaluate the throughput and delay. Numerical results are presented for arbitrary code lengths and for specific values of the number of resolvable paths. It is shown that CDMA can offer a substantial improvement over slotted ALOHA, especially when the chip time is less than the delay spread.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Analytic Modeling for Nanoscale Resistive Filament Variation in ReRAM With Stochastic Differential Equation (2017)

Nanoscale filament is the active area in oxygen vacancy type resistance random access memory (ReRAM), which is formed stochastically during electric test after being fabricated in a clean room. That is, the filament dimension cannot be controlled with a designed mask pattern. Here, we introduce a formula to describe the current cycle-to-cycle trajectories based on a stochastic differential equation (SDE) with microscopic structure parameters: filament dimension and oxygen vacancy concentration. Since ReRAM conduction follows hopping, the filament can be described by a random resistance network (RRN). The stochastic configuration of an RRN follows the Brownian motion, which is the key parameter in the diffusion of SDE. The formula provides a practically quantitative filament characterization method, which is verified by direct observation of the filament in actual devices. Based on the formula, we can predict ReRAM endurance with the given microscopic structure parameters.
Sequences Just Upstream of the Simian Immunodeficiency Virus Core Enhancer Allow Efficient Replication in the Absence of NF-κB and Sp1 Binding Elements (1998)

Large deletions of the upstream U3 sequences in the long terminal repeats (LTRs) of human immunodeficiency virus and simian immunodeficiency virus (SIV) accumulate in vivo in the absence of an intact nef gene. In the SIV U3 region, about 65 bp just upstream of the single NF-kappaB binding site always remained intact, and some evidence for a novel enhancer element in this region exists. We analyzed the transcriptional and replicative capacities of SIVmac239 mutants containing deletions or mutations in these upstream U3 sequences and/or the NF-kappaB and Sp1 binding sites. Even in the absence of 400 bp of upstream U3 sequences, the NF-kappaB site and all four Sp1 binding sites, the SIV promoter maintained about 15% of the wild-type LTR activity and was fully responsive to Tat activation in transient reporter assays. The effects of these deletions on virus production after transfection of COS-1 cells with full-length proviral constructs were much greater. Deletion of the upstream U3 sequences had no significant influence on viral replication when either the single NF-kappaB site or the Sp1 binding sites were intact. In contrast, the 26 bp of sequence located immediately upstream of the NF-kappaB site was essential for efficient replication when all core enhancer elements were deleted. A purine-rich site in this region binds specifically to the transcription factor Elf-1, a member of the ets proto-oncogene-encoded family. Our results indicate a high degree of functional redundancy in the SIVmac U3 region. Furthermore, we defined a novel regulatory element located immediately upstream of the NF-kappaB binding site that allows efficient viral replication in the absence of the entire core enhancer region.
Community-based benchmarking improves spike rate inference from two-photon calcium imaging data (2018)

In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. However, the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators. Different algorithms for estimating spike rates from noisy calcium measurements have been proposed in the past, but it is an open question how far performance can be improved. Here, we report the results of the spikefinder challenge, launched to catalyze the development of new spike rate inference algorithms through crowd-sourcing. We present ten of the submitted algorithms which show improved performance compared to previously evaluated methods. Interestingly, the top-performing algorithms are based on a wide range of principles from deep neural networks to generative models, yet provide highly correlated estimates of the neural activity. The competition shows that benchmark challenges can drive algorithmic developments in neuroscience.
Interaction of pertussis toxin with human T lymphocytes (1992)

The binding of pertussis toxin (PT) to the human T-cell line Jurkat was examined by using flow cytometry. Fluorescein isothiocyanate (FITC)-labeled PT bound rapidly to the cells in a specific manner as determined by blocking experiments with unlabeled toxin, B oligomer, and the S2-S4 and S3-S4 dimers. Monoclonal antibodies against the S3 subunit of the toxin also significantly inhibited the binding of FITC-PT. Sialidase treatment of the cells resulted in decreased binding of FITC-PT, indicating that sialic acid residues are involved in the binding process. In addition, we studied the effect of PT binding on the expression of cell surface molecules. On binding of PT to the cell surface, a rapid down-regulation of the T-cell receptor (TCR)-CD3 complex was observed. The modulation of the TCR-CD3 complex was independent of the toxin's enzymatic activity, as the B oligomer and a nonenzymatic toxin mutant induced modulation comparable to that caused by the native holotoxin. Isolated dimers did not cause down-regulation. Stimulation of the TCR-CD3 complex, leading to reduced cell surface expression of this complex, provides a possible explanation for the second messenger production associated with the interaction of PT or B oligomer with T lymphocytes. We therefore conclude that PT activates T cells by divalent binding to the TCR-CD3 complex itself or by binding a structure closely associated with it.
Recipes for synthesizing polyolefins with tailor-made molecular weight, polydispersity index, long-chain branching frequencies, and chemical composition using combined metallocene catalyst systems in a CSTR at steady state (1999)

Polymerization of ethylene in a CSTR using a combined metallocene catalyst system (combination of an open-face catalyst, such as Constrained Geometry Catalyst, and a conventional metallocene catalyst) was studied. Using the model developed by Soares and Hamielec, and expanded by Beigzadeh et al., a steady-state simulator was prepared. The effects of different process parameters (such as reactor residence time) and kinetic parameters of the combined catalyst system on steady-state values of molecular weight, polydispersity index, long-chain branching frequency, and copolymer composition (in the case of copolymerization with α-olefins) were investigated. It was shown how recipes for synthesizing polyolefins with tailor-made MWD, CCD, and LCB frequencies can be designed. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 71: 1753–1770, 1999
Has Conduction to the Pulmonary Vein Recovered? (2008)

Case Reports
Faculty Opinions recommendation of Altered DNA methylation profile in idiopathic pulmonary fibrosis. (2012)

RATIONALE: DNA methylation is an important epigenetic mechanism, which often occurs in response to environmental stimuli and is crucial in regulating gene expression. It is likely that epigenetic alterations contribute to pathogenesis in idiopathic pulmonary fibrosis (IPF).OBJECTIVES: To determine the DNA methylation changes in IPF and their effects on gene expression.METHODS: Total DNA methylation and DNA methyltransferase expression were compared in IPF and normal control lung tissues. IPF and normal tissues were subjected to comparative analysis of genome-wide DNA methylation and RNA expression using DNA hybridization to the Illumina HumanMethylation27 BeadChip and RNA hybridization to Illumina HumanHT-12 BeadChip. Functional analyses of differentially expressed and differentially methylated genes were done. Selected genes were validated at DNA, RNA, and protein levels.MEASUREMENTS AND MAIN RESULTS: DNA methylation status was altered in IPF. IPF samples demonstrated higher DNA methyltransferase expression without observed alterations in global DNA methylation. Genome-wide differences in DNA methylation status and RNA expression were demonstrated by array hybridization. Among the genes whose DNA methylation status and RNA expression were both significantly altered, 16 genes were hypermethylated in DNA associated with decreased mRNA expression or vice versa. We validated CLDN5, ZNF467, TP53INP1, and DDAH1 genes at the level of DNA methylation status, RNA, and protein-level expression.CONCLUSIONS: Changes in DNA methylation correspond to altered mRNA expression of a number of genes, some with known and others with previously uncharacterized roles in IPF, suggesting that DNA methylation is important in the pathogenesis of IPF. PMID: 22700861 Funding information This work was supported by: PHS HHS, United States Grant ID: AHA09SDG2260095 NHLBI NIH HHS, United States Grant ID: R01HL067967 NHLBI NIH HHS, United States Grant ID: R01 HL082818 NHLBI NIH HHS, United States Grant ID: R01HL082818 NHLBI NIH HHS, United States Grant ID: R03 HL097006 NHLBI NIH HHS, United States Grant ID: R01 HL067967 NHLBI NIH HHS, United States Grant ID: R01HL092906 NHLBI NIH HHS, United States Grant ID: R01 HL092906 NHLBI NIH HHS, United States Grant ID: R03HL097006 More Less keyboard_arrow_down
The Receptor-Like Kinase SERK3/BAK1 Is Required for Basal Resistance against the Late Blight Pathogen Phytophthora infestans in Nicotiana benthamiana (2011)

We demonstrated that N. benthamiana NbSERK3 significantly contributes to resistance to P. infestans and regulates the immune responses triggered by the P. infestans PAMP protein INF1. In the future, the identification of novel surface receptors that associate with NbSERK3A and/or NbSERK3B should lead to the identification of new receptors that mediate recognition of oomycete PAMPs, such as INF1.
Anomalous bulk modulus in vanadate spinels (2016)

All single-valent oxide spinels are insulators. The relatively small activation energy in the temperature dependence of resistivity in vanadate spinels led to the speculation that the spinels are near the crossover from localized to itinerant electronic behavior, and the crossover could be achieved under pressure. We have performed a number of experiments and calculations aimed at obtaining information regarding structural changes under high pressure for the whole series of vanadate spinels, as well as transport and magnetic properties under pressure for $\mathrm{Mg}{\mathrm{V}}_{2}{\mathrm{O}}_{4}$. We have also studied the crystal structure under pressure of wide-gap insulators $A\mathrm{C}{\mathrm{r}}_{2}{\mathrm{O}}_{4}$ ($A=\phantom{\rule{0.16em}{0ex}}\mathrm{Mg}$, Mn, Fe, Zn) for comparison. Moreover, the relationship between the bulk modulus and the cell volume of $A{\mathrm{V}}_{2}{\mathrm{O}}_{4}$ ($A=\phantom{\rule{0.16em}{0ex}}\mathrm{Mg}$, Mn, Fe, Co, Zn) has been simulated by a density functional theory calculation. The proximity of $A{\mathrm{V}}_{2}{\mathrm{O}}_{4}$ spinels to the electronic state crossover under high pressure has been tested by three criteria: (1) a predicted critical V-V bond length, (2) the observation of a sign change in the pressure dependence of N\'eel temperature, and (3) measurement of a reduced bulk modulus. The obtained results indicate that, although the crossover from localized to itinerant \ensuremath{\pi} bonding $\text{V-}3d$ electrons in the $A{\mathrm{V}}_{2}{\mathrm{O}}_{4}$ spinels is approached by reducing under pressure the V-V separation $R$, the critical separation ${R}_{\mathrm{c}}$ is not reached by 20 GPa in $\mathrm{Co}{\mathrm{V}}_{2}{\mathrm{O}}_{4}$, which has the smallest V-V separation in the $A{\mathrm{V}}_{2}{\mathrm{O}}_{4}$ ($A=\phantom{\rule{0.16em}{0ex}}\mathrm{Mg}$, Mn, Fe, Co, Zn) spinels.
Chemoprevention of Colorectal Cancer by Anthocyanidins and Mitigation of Metabolic Shifts Induced by Dysbiosis of the Gut Microbiome (2019)

Diets rich in fat, smoking, as well as exposure to environmental pollutants and dysbiosis of gut microbiota, increase the risk of developing colorectal cancer. Much progress has been made in combating colorectal cancer. However, options for chemoprevention from environmental insult and dysbiosis of gut microbiota remain elusive. We investigated the influence of berry-derived anthocyanidins (Anthos), with and without encapsulating them in bovine milk-derived exosomes (ExoAnthos), on the chemoprevention of bacteria-driven colon tumor development. Anthos and ExoAnthos treatment of colon cancer cells showed dose-dependent decreases in cell viability. Calculated selectivity index (SI) values for Anthos and ExoAnthos suggest that both treatments selectively targeted cancer over normal colon cells. In addition, ExoAnthos treatment yielded higher SI values than Anthos. Anthos and ExoAnthos treatment of Apc<sup>Min/+</sup> mice inoculated with enterotoxigenic <i>Bacteriodes fragilis</i> (ETBF) bacteria led to significant decreases in colon tumor numbers over mice receiving vehicle treatments. Western blot analysis of normal colon, colon tumor, and liver tissue lysates showed that mice inoculated with ETBF featured increased expression of phase I enzymes in normal colon tissue and decreased expression of phase II enzymes in liver tissue. Treatment with the Anthos and ExoAnthos reverted the modulation of phase I and phase II enzymes, respectively; no significant changes in phase II enzyme expression occurred in colon tumor tissue. Treatment of HCT-116 cells with the ubiquitous carcinogen, benzo[a]pyrene (B[<i>a</i>]P) led to similar modulation of phase I and II enzymes, which was partially mitigated by treatment with Anthos. These results provide a promising outlook on the impact of berry Anthos for prevention and treatment of bacteria- and B[<i>a</i>]P-driven colorectal cancer.
(010) $\beta$-Ga2O3 Metal Oxide Catalyzed Epitaxy (MOCATAXY) growth and Sn doping in plasma-assisted molecular beam epitaxy (2019)

Metal Oxide Catalyzed Epitaxy (MOCATAXY) of (010) β-Ga <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> was investigated using In as a catalyst in plasma-assisted molecular beam epitaxy. Expansion of the (010) β-Ga <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> growth regime to higher growth temperatures and Ga fluxes was demonstrated. A maximum growth rate of 5 nm/min was achieved, doubling that of conventional growth. Smooth surface morphology of a 1.6 μm film with root mean squared roughness of 0.12 nm was shown. Sn doping of MOCATAXY (010) β-Ga <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> was demonstrated up to concentrations of 4 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">18</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> .
Intradural Spinal Cord Stimulation: Performance Modeling of a New Modality (2019)

<b>Introduction:</b> Intradural spinal cord stimulation (SCS) may offer significant therapeutic benefits for those with intractable axial and extremity pain, visceral pain, spasticity, autonomic dysfunction and related disorders. A novel intradural electrical stimulation device, limited by the boundaries of the thecal sac, CSF and spinal cord was developed to test this hypothesis. In order to optimize device function, we have explored finite element modeling (FEM). <b>Methods:</b> COMSOL<sup>®</sup>Multiphysics Electrical Currents was used to solve for fields and currents over a geometric model of a spinal cord segment. Cathodic and anodic currents are applied to the center and tips of the T-cross component of the electrode array to shape the stimulation field and constrain charge-balanced cathodic pulses to the target area. <b>Results:</b> Currents from the electrode sites can move the effective stimulation zone horizontally across the cord by a linear step method, which can be diversified considerably to gain greater depth of penetration relative to standard epidural SCS. It is also possible to prevent spread of the target area with no off-target action potential. <b>Conclusion:</b> Finite element modeling of a T-shaped intradural spinal cord stimulator predicts significant gains in field depth and current shaping that are beyond the reach of epidural stimulators. Future studies with <i>in vivo</i> models will investigate how this approach should first be tested in humans.
Outcomes of surgical resection for pulmonary metastasis from pancreatic cancer (2023)

A long-term prognosis may be expected in some cases with a disease-free interval of ≥ 15 months. Our findings suggest that the disease-free interval may influence the prognosis.