gebhart/patrepeval huggingface dataset:
Abstract MP58: Motor Cortex and Spinal Cord Transcriptome After Post-Stroke Optogenetic Neuronal Stimulation (2021)

Background: Post-stroke brain stimulation is a promising neurorestorative technique to promote recovery. However, the underlying molecular mechanisms driving recovery are still unclear. Here we investigate the molecular changes in both the primary motor cortex and the cervical spinal cord after large cortical stroke in mice receiving repeated optogenetic stimulations in the ipsilateral primary motor cortex (iM1). Methods: C57Bl6 male mice (8 weeks) underwent stereotaxic surgery to express Channelrhodopsin2 in excitatory neurons in iM1, with optical fiber implanted in the same location. After five weeks the mice underwent a transient middle cerebral artery occlusion to induce stroke. Optogenetic stimulations were given daily from post-stroke days (PD) 5-14. Non-stimulated mice were used as controls. Rotating beam test was used to evaluate functional recovery after stroke. At PD 7 and 15, ipsi- and contralesional primary motor cortex (iM1 and cM1) and cervical spinal cords (iSp and cSp) were dissected and processed for RNA sequencing. Results: Repeated iM1 stimulations resulted in a robust recovery on the rotating beam test at PD14, with significant improvement in distance traveled (p&lt;0.05). RNA sequencing analysis (stimulated vs non-stimulated mice) revealed differential transcriptome in both motor cortex and spinal cord. Higher number of differentially expressed genes (DEGs) were observed in the ipsilesional regions (iM1 and iSp). At PD 7, stimulated mice exhibited upregulation of activity-dependent and neuroplasticity-related genes in iM1. Interestingly, at PD15, cholesterol metabolism and neuroinflammatory related genes in iM1 were downregulated. The expressions of the genes were negatively correlated with behavioral recovery. Higher number of DEGs were altered in the spinal cord than motor cortex, suggesting more dynamic molecular changes occur in this area during the post-stroke reinnervation processes. Expressions of synaptogenesis related genes were altered in both iSp and cSp at both timepoints. Conclusions: These transcriptome data reveal important insights into the molecular signaling involved in post-stroke stimulation-induced recovery and provide potential drug targets for enhancing recovery in stroke patients.
A novel family of plant nuclear envelope-associated proteins (2016)

This paper describes the characterisation of a new family of higher plant nuclear envelope-associated proteins (NEAPs) that interact with other proteins of the nuclear envelope. In the model plant Arabidopsis thaliana, the family consists of three genes expressed ubiquitously (AtNEAP1-3) and a pseudogene (AtNEAP4). NEAPs consist of extensive coiled-coil domains, followed by a nuclear localisation signal and a C-terminal predicted transmembrane domain. Domain deletion mutants confirm the presence of a functional nuclear localisation signal and transmembrane domain. AtNEAP proteins localise to the nuclear periphery as part of stable protein complexes, are able to form homo- and heteromers, and interact with the SUN domain proteins AtSUN1 and AtSUN2, involved in the linker of nucleoskeleton and cytoskeleton (LINC) complex. An A. thaliana cDNA library screen identified a putative transcription factor called AtbZIP18 as a novel interactor of AtNEAP1, which suggest a connection between NEAP and chromatin. An Atneap1 Atneap3 double-knockout mutant showed reduced root growth, and altered nuclear morphology and chromatin structure. Thus AtNEAPs are suggested as inner nuclear membrane-anchored coiled-coil proteins with roles in maintaining nuclear morphology and chromatin structure.
High resolution holographic imaging with a robot scanner and its applications (2015)

The high spatial resolution offered by the holographic radar operating in the frequency range 2GHz–8GHz can be fully exploited in field surveys if the radar head can scan large areas with spatial resolution and accuracy corresponding to a fraction of the wavelength. For the typical operating frequencies this requires a millimeter resolution of the acquisition system. For achieving these requirements a robot scanner is proposed and the realization of the main blocks is described. The advantage of this approach for fast and accurate subsurface imaging is demonstrated with laboratory experiments for the detection of defects on the bonding of thermal insulating material on a metal sheet. For more complex environments like natural soil a multisensory system is proposed and a low cost range meter with special design of the ultrasonic transducers is proposed. The profile of the surface is an important information for obtaining the best resolution of buried object underneath irregular surfaces.
Uncovering Effects of Ex Vivo Protease Activity during Proteomics and Peptidomics Sample Extraction in Rat Brain Tissue by Oxygen-18 Labeling (2014)

In biological samples, proteins and peptides are altered by proteolytic activity. The actual ex vivo form of the peptidome or proteome analyzed, therefore, does not always reflect the natural in vivo state. Sample stabilization and sample treatment are thereby decisive for how far these two states diverge. To assess ex vivo formation of peptides, we used enzymatic incorporation of oxygen-18 water during proteolysis (PALeO approach) to label ex-vivo-formed peptides in rodent brain tissue. Rates of ex-vivo-formed peptides were determined in 25 samples that were stabilized and treated by six different protocols, whereby samples were subjected to different conditions such as temperature, urea concentration, and duration of treatment. Samples were measured by nano LC-Orbitrap-MS, and incorporation of oxygen-18 was determined by MS/MS database search and analysis of the precursor isotope pattern. Extent of ex vivo degradations was affected relevantly by the sample treatment protocol applied and stopped almost completely by heat stabilization. Determination of the formation state by oxygen-18 incorporation by MS/MS database search correlated well to more elaborate analysis of the MS isotope pattern. Overall, oxygen-18 labeling in combination with shotgun data-acquisition and MS/MS database search offers an adjuvant and easily applicable tool to monitor sample quality and fidelity in peptide and neuropeptide sample preparations.
Mesoscopic Heterogeneity in the Curing Process of an Epoxy–Amine System (2019)

Epoxy resins are composed of a three-dimensional network formed by chemical reactions between epoxy and amino compounds, which plays an important role in the mechanical properties. Thus, to use epoxy resins in various applications, it is necessary to gain a better understanding of their network structure. Here, we study the structural heterogeneity evolved in an epoxy–amine mixture during the curing process on the basis of a particle tracking technique, in which the thermal motion of probe particles in the mixture was tracked, small-angle X-ray scattering measurements in conjunction with coarse-grained molecular dynamics simulation. The heterogeneous environment was generated even at the initial stage of the curing process. Notably, the characteristic length scale was on the order of several hundreds of nanometers down to several tens of nanometers, depending on the extent of curing. Once a reaction occurs between a pair of epoxy and amino groups, the temperature at the site is locally elevated due to the heat of formation, accelerating a subsequent reaction nearby. Repeating such a situation, actively and scarcely reacted domains are formed. This is the main origin of the structural heterogeneity in epoxy resins.
Efficient synthesis and biological evaluation of epiceanothic acid and related compounds (2020)

Epiceanothic acid (1) is a naturally occurring, but very rare pentacyclic triterpene with a unique pentacyclic triterpene (PT) structure. An efficient synthesis of 1 starting from betulin (3) has been accomplished in 12 steps with a total yield of 10% in our study. Compound 1 and selected synthetic intermediates were further evaluated as anti-HIV-1 agents, inhibitors of glycogen phosphorylase (GP), and cytotoxic agents. Compound 1 exhibited moderate HIV-1 inhibition. Most importantly, compound 5, with an opened A-ring, showed significant GP inhibitory activity with an IC50 of 0.21 μM, suggesting a potential for development as an anti-diabetic agent. On the other hand, compound 12, with a closed A-ring, showed potent cytotoxicity against A549 and MCF-7 human tumor cell lines, with IC50 values of 0.89 and 0.33 μM, respectively. These results suggest that the A-ring of PTs is an important pharmacophore that could be modified to involve different biological activities.
Concentrations of tumor-associated trypsin inhibitor and C-reactive protein in serum in acute pelvic inflammatory disease. (1989)

We measured tumor-associated trypsin inhibitor (TATI) and C-reactive protein (CRP) in serum of 29 patients with proven pelvic inflammatory disease (PID). TATI values were increased in seven (24%), paralleling increases in CRP. TATI was increased by about 3.5-fold in seven of eight patients with CRP concentrations greater than 90 mg/L, but in none of 21 patients with CRP concentrations less than 90 mg/L. TATI concentration and severity of PID as determined by laparoscopy or endometrial biopsy were not correlated. These results suggest that, in severe infections, regulation of TATI synthesis resembles that of acute-phase proteins.
VLSI design synthesis with testability (1988)

A VLSI design synthesis approach with testability, area, and delay constraints is presented. This research differs from other synthesizers by implementing testability as part of the VLSI design solution. A binary tree data structure is used throughout the testable design search. Its bottom up and top down tree algorithms provide datapath allocation, constraint estimation, and feedback for design exploration. The partitioning and two dimensional characteristics of the binary tree structure provide VLSI design floorplans and global information for test incorporation. An elliptical wave filter example was used to illustrate the design synthesis with testability constraints methodology. Test methodologies such as multiple chain scan paths and BIST with different test schedules were explored. Design Scores comprised of area, delay, fault coverage, and test length were computed and graphed. Results show that the 'best' testable design solution is not always the same as that obtained from the 'best' design solution of an area and delay based synthesis search.
A dietary phytochemical blend prevents liver damage associated with adipose tissue mobilization in ovariectomized rats (2014)

Adverse hepatic effects secondary to ovariectomy were mitigated through the inclusion of a dietary phytochemical blend in aged ovariectomized rats. The use of such compounds may not only help with weight management and disease risk in menopausal women, but may also prevent the lipotoxicity in NAFLD.
RRAM Crossbar Array With Cell Selection Device: A Device and Circuit Interaction Study (2012)

The resistive random access memory (RRAM) crossbar array has been extensively studied as one of the most promising candidates for future high-density nonvolatile memory technology. However, some problems caused by circuit and device interaction, such as sneak leakage paths, result in limited array size and large power consumption, which degrade the array performance significantly. Thus, the analysis on circuit and device interaction issue is imperative. In this paper, a simulation method is developed to investigate the critical issues correlated with the interaction between devices and the circuit. The simulations show that a large off/on ratio of resistance states of RRAM is beneficial for large readout margin (i.e., array size). The existence of the selector connected in series with an RRAM device can eliminate the need for high <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</sub> resistance, which is critical for the array consisted of only RRAM cells. The readout margin is more sensitive to the variation of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</sub> and is determined by the nonlinearity of the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</i> - <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</i> characteristics of RRAM, whereas the nonlinear characteristics of the selector device are beneficial for a larger readout margin. An optimal design scheme for turn-on voltage and conductance of the selector is proposed based on the simulation.
Analysis of Hydroxylamine Glycosidic Linkages: Structural Consequences of the NO Bond in Calicheamicin (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAnalysis of Hydroxylamine Glycosidic Linkages: Structural Consequences of the NO Bond in CalicheamicinSuzanne Walker, Varsha Gupta, Daniel Kahne, and David GangeCite this: J. Am. Chem. Soc. 1994, 116, 8, 3197–3206Publication Date (Print):April 1, 1994Publication History Published online1 May 2002Published inissue 1 April 1994https://pubs.acs.org/doi/10.1021/ja00087a005https://doi.org/10.1021/ja00087a005research-articleACS PublicationsRequest reuse permissionsArticle Views257Altmetric-Citations47LEARN 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-Alertsclose Get e-Alerts
A Phase II Study of 5-Fluorouracil/Leucovorin in Combination with Paclitaxel and Oxaliplatin as First-Line Treatment for Patients with Advanced Gastric Cancer (2008)

The objective of this study was to evaluate the efficacy and safety of the POF regimen (biweekly 5-fluorouracil/leucovorin combined with paclitaxel and oxaliplatin) as first-line treatment for advanced gastric cancer (AGC). Twenty-seven previously untreated patients with advanced adenocarcinoma of the gastric or gastroesophageal junction were eligible for this study. The chemotherapy regimen consisted of a 3-hour infusion of paclitaxel (135 mg/m(2)) followed by oxaliplatin (85 mg/m(2)) and leucovorin (400 mg/m(2)), administered simultaneously over a 2-hour infusion period, followed by an infusion of 5-fluorouracil (2400 mg/m(2)) over a 46-hour period. Twenty-one patients had measurable lesions: four complete responses, eight partial responses and seven stable diseases. At a median follow-up of 610 days, median survival was 348 days. Frequent grade 3 to 4 toxicities were: neutropenia (29.6%), stomatitis (7.4%), nausea (7.4%), vomiting (7.4%), hepatic dysfunction (3.7%), and fatigue (18.5%). No treatment-related deaths occurred. The POF regimen appears to be efficacious and is well tolerated in patients with AGC.
The Gene Ontology Handbook (2016)

This book is open access under a CC BY 4.0 license. This book provides a practical and self-contained overview of the Gene Ontology (GO), the leading project to organize biological knowledge on genes
Suppression of a Pituitary-Ovarian Axis by Chronic Oral Administration of a Novel Nonpeptide Gonadotropin-Releasing Hormone Antagonist, TAK-013, in Cynomolgus Monkeys (2003)

TAK-013 is a novel nonpeptide and orally active GnRH antagonist. We first examined the effect of TAK-013 on GnRH-stimulated LH release using primary-cultured pituitary cells of cynomolgus monkeys. TAK-013 suppressed LH release to below basal levels at concentrations higher than 100 nM with the IC(50) value of 36 nM. Next, we examined the effect of chronic oral administration of TAK-013 on serum hormone levels in regularly cycling female cynomolgus monkeys. TAK-013 administered at 90 mg/kg x d (30 mg/kg 3 times daily) for approximately 80 d continued to suppress LH, estradiol, and progesterone, but not FSH. The suppressive effect was reversible, in that normal profiles of sex steroids were observed immediately after discontinuation of the TAK-013 treatment. Interestingly, the suppressive effect of TAK-013 was not observed in marmoset monkeys. In summary, TAK-013 by oral administration suppresses a pituitary-ovarian axis continuously and reversibly in cynomolgus monkeys. Considering that TAK-013 has more potent antagonistic properties for human GnRH receptor than for monkey receptor, our data suggest that TAK-013 would be effective for reproductive disorders such as endometriosis and uterine leiomyoma and useful for assisted reproductive technology procedures.
Optical Clearing of Fixed Brain Samples Using SeeDB (2014)

Large-scale three-dimensional fluorescence imaging is essential for comprehensive and quantitative understanding of neuronal circuitry. We describe a water-based optical clearing agent, SeeDB, which clears fixed brain samples in a few days leaving many types of fluorescent dyes unquenched, including fluorescent proteins and lipophilic neuronal tracers. This method maintains a constant sample volume during the clearing procedure, an important factor to keep cellular morphology intact. After optical clearing with SeeDB, we can reach a depth of >1000 µm with confocal microscopy. When combined with two-photon microscopy, SeeDB allows us to image fixed mouse brains at millimeter-scale level.
Design and performance of wideband GaAs MMIC's for high-speed optical communication systems (1992)

Advanced design techniques for GaAs wideband direct-coupled amplifiers are described. The amplifier achieved a 20 dB gain with a 3 dB bandwidth of 13 GHz and a 5-7 dB noise figure. An equalizing amplifier module consisting of amplifier and variable attenuator monolithic microwave integrated circuits (MMICs) exhibited a high gain of 43 dB over a 10 GHz band with a controllable gain of 20-43 dB.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Downregulation of SF3B2 protects CNS neurons in models of multiple sclerosis (2022)

Together, these findings suggest that the downregulation of SF3B2 is a novel potential therapeutic target to prevent secondary neurodegeneration in MS.
An Image Encryption Algorithm Based on Random Hamiltonian Path (2020)

In graph theory, Hamiltonian path refers to the path that visits each vertex exactly once. In this paper, we designed a method to generate random Hamiltonian path within digital images, which is equivalent to permutation in image encryption. By these means, building a Hamiltonian path across bit planes can shuffle the distribution of the pixel's bits. Furthermore, a similar thought can be applied for the substitution of pixel's grey levels. To ensure the randomness of the generated Hamiltonian path, an adjusted Bernoulli map is proposed. By adopting these novel techniques, a bit-level image encryption scheme was devised. Evaluation of simulation results proves that the proposed scheme reached fair performance. In addition, a common flaw in calculating correlation coefficients of adjacent pixels was pinpointed by us. After enhancement, correlation coefficient becomes a stricter criterion for image encryption algorithms.
Identification of epithelial and mesenchymal circulating tumor cells in clonal lineage of an aggressive prostate cancer case (2022)

Little is known about the complexity and plasticity of circulating tumor cell (CTC) biology in different compartments of the fluid microenvironment during tumor metastasis. Here we integrated phenomics, genomics, and targeted proteomics to characterize CTC phenotypic and genotypic heterogeneity in paired peripheral blood (PB) and bone marrow aspirate (BMA) from a metastatic prostate cancer patient following the rapid disease progression, using the High-Definition Single Cell Assay 3.0 (HDSCA3.0). Uniquely, we identified a subgroup of genetically clonal CTCs that acquired a mesenchymal-like state and its presence was significantly associated with one subclone that emerged along the clonal lineage. Higher CTC abundance and phenotypic diversity were observed in the BMA than PB and differences in genomic alterations were also identified between the two compartments demonstrating spatial heterogeneity. Single cell copy number profiling further detected clonal heterogeneity within clusters of CTCs (also known as microemboli or aggregates) as well as phenotypic variations by targeted proteomics. Overall, these results identify epithelial and mesenchymal CTCs in the clonal lineage of an aggressive prostate cancer case and also demonstrate a single cell multi-omic approach to deconvolute the heterogeneity and association of CTC phenotype and genotype in multi-medium liquid biopsies of metastatic prostate cancer.
Design, tolerance analysis, fabrication, and testing of a 6-in. dual-wavelength transmission sphere for a Fizeau interferometer (2017)

This paper presents the validation of the design of a 6-in. f/2.2 dual-wavelength transmission sphere (TS) based on the Fizeau interferometer. The TS was verified at a wavelength of 632.8 nm and is compatible for measuring the transmitted wavefront error of an i-line lithography lens. The achromatic design is imperative for a dual wavelength TS and requires more lenses for correcting the chromatic focal shift. Because the overall weight of the TS should be controlled within the load range of the piezoelectric transducers of the interferometer, the fabrication and mounting of lenses with high aspect ratios are challengeable. The mounting of the reference surface based on three-point mounting was successful for the residual reference wavefront error under peak-to-valley (PV) λ/10. Furthermore, the reference wavefront is typically restricted within PV 5λ to avoid distorted interference fringes. Therefore, we built a double-pass interferometer model for tolerance analysis, and the error budget facilitated decision-making regarding the suitable specifications of lens manufacturing and assembly for cost efficiency. The test results demonstrated that the deformation of the reference wavefront and the residual reference wavefront error met the critical specification at 632.8 nm and that the achromatic TS is compatible for measuring i-line lithography lenses.