gebhart/patrepeval huggingface dataset:
Asymmetry of the brain surface from deformation field analysis (2003)

The detection of asymmetry of exposed brain surfaces is examined, and a new method, deformation-based asymmetry (DBA), is introduced. DBA is based on analysis of two high-resolution magnetic resonance brain images, each with features representative of the subject group from which they were derived. Warping of individual brain images to their group representative image using octree spatial normalization provides sets of displacement vectors that are used in estimating deformation variance. For DBA group-representative left and right hemisphere images are compared. Representative hemisphere images are warped to each other and asymmetry analyzed using standardized d-values calculated as the ratio of displacement vector magnitude to the estimated component of variance in the direction of the displacement vector for each surface voxel. D-values were calculated within hemispheres by dividing subjects into two equal groups and comparing left-to-left and right-to-right. D-values from this ipsilateral hemisphere grouping were pooled. D-values from contralateral hemispheres were compared with the pooled ipsilateral hemisphere data. The proportion of d-values above a fixed level was used to test for difference between the two groups. High-resolution magnetic resonance (MR) images from 20 young, right-handed males were studied using DBA. No significant differences were seen between sub-grouped ipsilateral d-values (P > 0.10). Highly significant asymmetries (P < 0.0001) were found between hemispheres, and in each lobe. Common right frontal and left occipital petalias were seen. The DBA method can theoretically be applied to any two groups of globally similar structures where analysis of dissimilarity of regional features is sought.
Quantum-Confined Stark Effect of Lead Halide Perovskite Quantum Dots in a Mixed Dimensional van der Waals Heterostructure (2019)

We demonstrate quantum-confined Stark effect in Perovskite quantum dots by employing a voltage-tunable vertically stacked van der Waals heterostructure with 2D materials. A spectral shift of 10 meV was observed for the exciton peak. © 2019 The Author(s)
Efficacy of the MDM2 Inhibitor SAR405838 in Glioblastoma Is Limited by Poor Distribution Across the Blood–Brain Barrier (2018)

Controversy exists surrounding whether heterogeneous disruption of the blood-brain barrier (BBB), as seen in glioblastoma (GBM), leads to adequate drug delivery sufficient for efficacy in GBM. This question is especially important when using potent, targeted agents that have a poor penetration across an intact BBB. Efficacy of the murine double minute-2 (MDM2) inhibitor SAR405838 was tested in patient-derived xenograft (PDX) models of GBM. <i>In vitro</i> efficacy of SAR405838 was evaluated in PDX models with varying MDM2 expression and those with high (GBM108) and low (GBM102) expression were evaluated for flank and orthotopic efficacy. BBB permeability, evaluated using TexasRed-3 kDa dextran, was significantly increased in GBM108 through VEGFA overexpression. Drug delivery, MRI, and orthotopic survival were compared between BBB-intact (GBM108-vector) and BBB-disrupted (GBM108-VEGFA) models. MDM2-amplified PDX lines with high MDM2 expression were sensitive to SAR405838 in comparison with MDM2 control lines in both <i>in vitro</i> and heterotopic models. In contrast with profound efficacy observed in flank xenografts, SAR405838 was ineffective in orthotopic tumors. Although both GBM108-vector and GBM108-VEGFA readily imaged on MRI following gadolinium contrast administration, GBM108-VEGFA tumors had a significantly enhanced drug and gadolinium accumulation, as determined by MALDI-MSI. Enhanced drug delivery in GBM108-VEGFA translated into a marked improvement in orthotopic efficacy. This study clearly shows that limited drug distribution across a partially intact BBB may limit the efficacy of targeted agents in GBM. Brain penetration of targeted agents is a critical consideration in any precision medicine strategy for GBM. <i>Mol Cancer Ther; 17(9); 1893-901. ©2018 AACR</i>.
Electrically detected magnetic resonance and near-zero field magnetoresistance in 28Si/28SiO2 (2021)

We report on electrically detected magnetic resonance (EDMR) and near-zero-field magnetoresistance (NZFMR) measurements observed through spin-dependent trap-assisted-tunneling on unpassivated Si/SiO2 metal–insulator–semiconductor capacitors comparing those containing silicon of natural isotopic abundance and silicon depleted of 29Si. Although our measurements involve monitoring the spin-dependence of the trap-assisted-tunneling current responsible for leakage across the oxide, the EDMR spectra resemble that of a combination of Pb0 and Pb1 silicon dangling bonds sites at the Si/SiO2 interface. Additionally, we observe a substantial narrowing of the NZFMR response with the removal of 29Si nuclei. The breadth of the NZFMR response is strongly influenced by hyperfine interactions. Since superhyerfine interactions between 29Si nuclei and silicon dangling bonds at the Si/SiO2 interface are a full order of magnitude stronger than such interactions involving silicon dangling bonds defects (E′ centers) within the oxide, the NZFMR results also strongly suggest a response dominated by Si/SiO2 interface trap defects. These results collectively suggest very strongly that the leakage currents that we observe involve tunneling from Si/SiO2 Pb dangling bonds to defects within the oxide. Our results thus offer fundamental insight into technologically important phenomena involving oxide leakage currents in metal–oxide–semiconductor devices such as stress induced leakage currents and time dependent dielectric breakdown.
A novel iso-thermal intermetallic compound insertion bonding approach to improve throughput for 3D die to wafer stacking (2020)

In this paper, we present a novel approach using preformed IMC layer to mechanically attach two dies at low temperatures and fast time followed by underfilling process. An isothermal bonding profile with a constant arm temperature was developed to save TCB bonding time. At optimized TCB bonding recipe, IMC insertion bonding offers a very short bonding time in the range of 2-5s for each die. The bonding interface temperature is around 150°C. The electrical test results and cross-section images show high stacking yield in the range of 95% and the void-free interface is obtained for a 20μm pitch microbump.
Mechanochemistry (2006)

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.
Oleanolic Acid Acetate Exerts Anti-Inflammatory Activity via IKKα/β Suppression in TLR3-Mediated NF-κB Activation (2019)

Oleanolic acid acetate (OAA), a major triterpenoid compound of <i>Vigna angularis</i> (azuki bean, <i>V. angularis</i>), has been shown to downregulate inflammatory responses in macrophages. Here, we show the molecular basis for the effect of OAA on Toll-like receptor (TLR) downstream signaling. OAA treatment significantly inhibited the secretion of embryonic alkaline phosphatase (SEAP) induced by polyinosinic acid (poly(I), TLR3 ligand) in a dose-dependent manner and without cytotoxicity in THP1-XBlue cells. In addition, OAA downregulated the gene expression of poly(I) induced pro-inflammatory cytokines and chemokines genes such as MCP-1, IL-1β, IL-8, VCAM-1 and ICAM-1. Furthermore, we found that the inhibition activity of OAA was accompanied by decreased activation of not only nuclear factor-kappa B (NF-κB) signaling but also mitogen-activated protein kinase (MAPK) signaling upon stimulation with the TLR3 agonist. Interestingly, the interaction of OAA with IκB kinase α/β (IKKα/β) strongly attenuated the production of certain proteins and inflammatory cytokines in the TLR3 signaling pathway, such as nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (IkBα), extracellular regulated kinases (ERK), and p38, in an in vitro model. The action of OAA was regulated by TLR3, demonstrating that TLR3 plays a critical role in mediating the physiologically-relevant anti-inflammatory action of OAA and that the interaction with IKKα/β is modulated through TLR3. These results reveal new insight into the understanding of the regulatory mechanisms of the downstream TLR3 signaling pathway and consequent inflammatory responses that are involved in the development and progression of inflammatory diseases.
Adaptive matched field processing in an uncertain propagation environment (1992)

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution January 1992
Effects of vacuum conditions on low frequency noise in silicon field emission devices (2002)

The effects of pressure on emission current noise have been studied. Field emission currents from silicon devices were observed over a range of pressures. The current fluctuations were analyzed in both the time and frequency domain. Signal to noise ratios between 0.9 and 6.9 were observed. These values appear to be more dependent on operation time than on pressures. Spectral density coefficients of low frequency measurements range from -1.37 to -1.81. Some pressure dependence is suggested in the lower pressure ranges. At higher pressures emission currents seem to be reduced and the current is cut off completely above a threshold pressure which is somewhere in the 10's of Torr.
EPSTEIN BARR VIRUS ENCODED LATENT MEMBRANE PROTEIN 1 ACTIVATES THE JAK/STAT PATHWAY INDIRECTLY THROUGH PRODUCTION OF IFN-G (2008)

Martinez, O1,2; Vaysberg, M1,2; Lambert, S1,2; Kra, S1,2; Esquivel, C1 Author Information
Supplementary Figures 1-7 from Genome-Wide Interrogation of Human Cancers Identifies EGLN1 Dependency in Clear Cell Ovarian Cancers (2023)

&lt;p&gt;Supplementary Figure 1 identifies EGLN1 as a cancer dependency in RNAi and CRISPR datasets and contains all significant associations. Supplementary Figure 2 is a lineage analysis of EGLN1 dependency within RNAi dataset. Supplementary Figure 3 is an immunoblot showing EGLN1 knockout in EGLN1-insensitive cell line. Supplementary Figure 4 shows pan-EGLN inhibition affects proliferation and apoptosis. Supplementary Figure 5 shows specific EGLN1 inhibitor IOX2 and VHL inhibitor VH298 inhibit proliferation. Supplementary Figure 6 shows differentially expressed genes in EGLN1-KO cells. Supplementary Figure 7 shows increased apoptosis in vivo when inhibiting EGLN1 or VHL.&lt;/p&gt;
Optical pumping and tunable laser spectroscopy of the ν2 band of D2O (1975)

Absorption resonances in the ν2 band of D2O in near coincidence with CO2 laser lines are reported and assigned. Optical pumping induces strong laser emission at new submillimeter wavelengths, confirming the assignments. Acousto−optic modulation is used to tune the R (22) line of the CO2 laser into coincidence with the 000,533−010,422 D2O transition. Its center frequency is 1079.8628 cm−1; the linewidth (HWHM) due to collisional broadening is 13 MHz/Torr. D2S and HDS transitions in near coincidence with CO2 laser lines are also reported.
Distinct Subsets of Syt-IV/BDNF Vesicles Are Sorted to Axons versus Dendrites and Recruited to Synapses by Activity (2012)

BDNF plays a critical role in the regulation of synaptic strength and is essential for long-term potentiation, a phenomenon that underlies learning and memory. However, whether BDNF acts in a diffuse manner or is targeted to specific neuronal subcompartments or synaptic sites to affect circuit function remains unknown. Here, using photoactivation of BDNF or syt-IV (a regulator of exocytosis present on BDNF-containing vesicles) in transfected rat hippocampal neurons, we discovered that distinct subsets of BDNF vesicles are targeted to axons versus dendrites and are not shared between these compartments. Moreover, syt-IV- and BDNF-harboring vesicles are recruited to both presynaptic and postsynaptic sites in response to increased neuronal activity. Finally, using syt-IV knockout mouse neurons, we found that syt-IV is necessary for both presynaptic and postsynaptic scaling of synaptic strength in response to changes in network activity. These findings demonstrate that BDNF-containing vesicles can be targeted to specific sites in neurons and suggest that syt-IV-regulated BDNF secretion is subject to spatial control to regulate synaptic function in a site-specific manner.
Development of a Rapid Salivary Proteomic Platform for Oral Feeding Readiness in the Preterm Newborn (2017)

Oral feeding competency is a major determinant of length of stay in the neonatal intensive care unit. An infant must be able to consistently demonstrate the ability to take all required enteral nutrition by mouth before discharge home. Most infants born prematurely (<37 weeks) will require days, if not weeks, to master this oral feeding competency skill. Inappropriately timed feeding attempts can lead to acute and long-term morbidities, prolonged hospitalizations, and increased health-care costs. Previously, a panel of five genes involved in essential developmental pathways including sensory integration (<i>nephronophthisis 4, Plexin A1</i>), hunger signaling [<i>neuropeptide Y2 receptor</i> (<i>NPY2R</i>), <i>adenosine-monophosphate-activated protein kinase</i> (<i>AMPK</i>)], and facial development (<i>wingless-type MMTV integration site family, member 3</i>) required for oral feeding success were identified in neonatal saliva. This study aimed to translate these five transcriptomic biomarkers into a rapid proteomic platform to provide objective, real-time assessment of oral feeding skills, to better inform care, and to improve neonatal outcomes. Total protein was extracted from saliva of 10 feeding-successful and 10 feeding-unsuccessful infants matched for age, sex, and post-conceptional age. Development of immunoassays was attempted for five oral feeding biomarkers and two reference biomarkers (GAPDH and YWHAZ) to normalize for starting protein concentrations. Normalized protein concentrations were correlated to both feeding status at time of sample collection and previously described gene expression profiles. Only the reference proteins and those involved in hunger signaling were detected in neonatal saliva at measurable levels. Expression patterns for NPY2R and AMPK correlated with the gene expression patterns previously seen between successful and unsuccessful feeders and predicted feeding outcome. Salivary proteins associated with hunger signaling are readily quantifiable in neonatal saliva and may be utilized to assess oral feeding readiness in the newborn. This study lays the foundation for the development of an informative, rapid, proteomic platform to assess neonatal oral feeding maturation.
Dose Response to Transnasal Pulmonary Administration of Bronchodilator Aerosols via Nasal High-Flow Therapy in Adults with Stable Chronic Obstructive Pulmonary Disease and Asthma (2019)

With a nasal cannula at 15-20 L/min, transnasal pulmonary delivery of 1.5 mg albuterol resulted in similar bronchodilator response as 4 actuations of MDI + VHC.
A Side-and Rear-View Image Registration System for Eliminating Blind Spots (2009)

In this paper, we propose a blind spots elimination system using three cameras. A wide-angle camera is attached on trunk for eliminating blind spots of a rear-view mirror and two cameras are attached on each side-view mirror for eliminating blind spots of vehicle's sides. In order to eliminate blind spots efficiently, we suggest a method to build a panoramic mosaic view with two side images and one wide-angle rear image. First, we obtain an undistorted image from a wide-angle camera of rear-view and calculate the focus-of-contraction (FOC) in undistorted images of rear-view while the car is moving straight forward. Second, we compute a homography among side-view images and an undistorted image of rear-view in flat road scenes. Next, we perform an image registration process after road and background region segmentation. Finally, we generate various views such as a cylinder panorama view, a top view and an information panoramic mosaic view.
Flexible dye solar cells (2004)

Strategies towards flexible solid state solar cells based on nanocrystalline titanium oxide and organic hole conductor were investigated. For the flexible cell geometry a metal foil was used as substrate and a semi-transparent gold layer as counter electrode which allows light transmission (back illumination). The device performance of solid state cells based on SnO<sub>2</sub>:F coated glass on the one hand and a metal foil on the other hand were characterized and compared by measuring the current voltage curves on back and front illumination.
Synthesis and structure–activity relationship (SAR) studies of 1,2,3-triazole, amide, and ester-based benzothiazole derivatives as potential molecular probes for tau protein (2023)

The pyridinyl-butadienyl-benzothiazole (PBB3 15) scaffold was used to develop tau ligands with improved <i>in vitro</i> and <i>in vivo</i> properties for imaging applications to provide insights into the etiology and characteristics of Alzheimer's disease. The photoisomerisable <i>trans</i>-butadiene bridge of PBB3 was replaced with 1,2,3-triazole, amide, and ester moieties and <i>in vitro</i> fluorescence staining studies revealed that triazole derivatives showed good visualisation of Aβ plaques, but failed to detect the neurofibrillary tangles (NFTs) in human brain sections. However, NFTs could be observed using the amide 110 and ester 129. Furthermore, the ligands showed low to high affinities (<i>K</i><sub>i</sub> = >1.5 mM-0.46 nM) at the shared binding site(s) with PBB3.
Somatotopically Inappropriate Projections from Thalamocortical Neurons to the SI Cortex of the Cat Demonstrated by the Use of Intracortical Microstimulation (1988)

Single thalamocortical neurons with receptive fields on the toes were antidromically activated by the passage of 300-microseconds, 0.5- to 10-microA pulses through glass micropipette electrodes placed within somatotopically identified regions of the digit representation of the cat first somatosensory (SI) cortex. The somatotopy of the cortex was determined using recordings from single cortical neurons (see "Methods"), and the positions of the all tracks were marked on an enlarged photograph of the postcruciate cortex. In two of the three protocols, a very precise map of the boundary between two adjacent toes was produced prior to attempting intracortical microstimulation. Slopes of the threshold-distance curves at the sites of the lowest recorded thresholds were on the order of 0.8 microA/10 micron. This value, together with information on the anatomy of the cortical arborizations of thalamocortical neurons (Landry and Deschenes, 1981), suggested that currents of 2 and 5 microA would not activate the cortical processes of thalamocortical neurons at distances greater than 50 and 90 microns, respectively. With currents below 5 microA, thalamocortical neurons could be antidromically activated at a number of sites at depths between 340 and 930 microns (layer IV and upper layer III) and between 1,050 and 1,460 microns (layer VI). A total of 13 thalamocortical neurons could be antidromically activated using current pulses of between 0.8 and 5.0 microA, from within tracks at tangential distances of 250-830 microns from the nearest track through the somatotopically appropriate region. Within somatotopically inappropriate regions, cortical neurons frequently had receptive fields on a toe adjacent to that bearing the receptive field of the thalamic neuron(s) under study. The possible relationship of somatotopically inappropriate projections to the reorganization of cortical somatotopy following digit amputation, paw amputation, and nerve section is discussed.
Age-Adjusted D-Dimer Cutoff Levels to Rule Out Pulmonary Embolism (2014)

clinicaltrials.gov Identifier: NCT01134068.
Amino acids and proteomic acclimation of Staphylococcus aureus when incubated in a defined minimal medium supplemented with 5% sodium chloride (2019)

Staphylococcus aureus is a versatile bacterium that can adapt to survive and grow in a wide range of salt concentrations. This study investigated whether the cells could mount a response to survive a challenge of 5% NaCl in a minimal incubation medium that would not support cell replication. Cells were grown in liquid culture, washed and then incubated for 90 min at 37°C in a medium that contained only glycine and glucose as substrates in PBS plus trace elements. The control cells were compared with a treatment group which was incubated with an additional 5% NaCl. Significantly more glycine was taken up by the cells exposed to 5% NaCl compared with control cells, and both groups consumed 99% of the glucose supplied. The NaCl treated cells had significantly higher cytoplasmic levels of proline and glutamic acid as well as lower levels of alanine and methionine compared with the controls (p < 0.05). The levels of the two major cytoplasmic amino acids, aspartic acid and glycine, remained constant in control and treated cells. Proteomic analyses revealed that 10 proteins showed differential responses between the control and treatment groups. The reductions in proteins were primarily associated with processes of protein biosynthesis, pathogenicity, and cell adhesion. Since cell numbers remained constant during the incubation period in minimal medium, it was concluded that there was no cell division to support population growth. The results provided evidence that the cells in the minimal medium exposed to the NaCl treatment underwent in situ homeostatic changes to adjust to the new environmental conditions. It was proposed that this represented a phenotypic shift to form cells akin to small colony variants, with lower metabolic rates and lower levels of key proteins associated with pathogenicity.
Stiffness of Hydrogels Regulates Cellular Reprogramming Efficiency Through Mesenchymal‐to‐Epithelial Transition and Stemness Markers (2016)

Frontispiece: Physical signals at the interface between cell and substrate can be used as a potent regulator to promote cell fate changes associated with reprogramming into pluripotent stem cells (iPSCs) via increased mesenchymalto- epithelial transition activity and stemness marker expression. This study can lead to effective and reproducible iPSC-production. Further details can be found in the article by B. Choi, K.-S. Park, J.-H. Kim, K.-W. Ko, J.-S. Kim, D. K. Han, S.-H. Lee on page 199.
Photon statistics of amplified spontaneous emission in a dense wavelength-division multiplexing regime (2003)

The photon statistics of amplified spontaneous emission in the few-modes regime and in single mode, conditions that are typical of dense wavelength-division multiplexing transmission, have been experimentally proved by direct detection. The dependence of the degeneracy factor for the Bose-Einstein distribution on the degree of second-order coherence of light is stated. The theoretical dependence of the number of amplified spontaneous emission modes on the ratio between the optical channel and the detector bandwidths has also been confirmed by experiments, thus quantifying the loss of validity of asymptotic approximations when they are extended to the few-modes regime.