gebhart/patrepeval huggingface dataset:
Tissue Folding by Mechanical Compaction of the Mesenchyme (2017)

SUMMARY Many tissues fold during development into complex shapes. Engineering this process in vitro would represent an important advance for tissue engineering. We use embryonic tissue explants, finite element modeling, and 3D cell patterning techniques to show that a mechanical compaction of the ECM during mesenchymal condensation can drive tissue folding along programmed trajectories. The process requires cell contractility, generates strains at nearby tissue interfaces, and causes specific patterns of collagen alignment around and between condensates. Aligned collagen fibers support elevated tensions that promote the folding of interfaces along paths that can be predicted by finite element modeling. We demonstrate the robustness and versatility of this strategy for sculpting tissue interfaces by directing the morphogenesis of a variety of folded tissue forms from engineered patterns of mesenchymal condensates. These studies provide insight into the active mechanical properties of the embryonic mesenchyme and establish entirely new strategies for more robustly directing tissue morphogenesis ex vivo, without genetic engineering.
A different mechanism for the inhibition of the carboxyltransferase domain of acetyl-coenzyme A carboxylase by tepraloxydim (2009)

Acetyl-CoA carboxylases (ACCs) are crucial metabolic enzymes and are attractive targets for drug discovery. Haloxyfop and tepraloxydim belong to two distinct classes of commercial herbicides and kill sensitive plants by inhibiting the carboxyltransferase (CT) activity of ACC. Our earlier structural studies showed that haloxyfop is bound near the active site of the CT domain, at the interface of its dimer, and a large conformational change in the dimer interface is required for haloxyfop binding. We report here the crystal structure at 2.3 A resolution of the CT domain of yeast ACC in complex with tepraloxydim. The compound has a different mechanism of inhibiting the CT activity compared to haloxyfop, as well as the mammalian ACC inhibitor CP-640186. Tepraloxydim probes a different region of the dimer interface and requires only small but important conformational changes in the enzyme, in contrast to haloxyfop. The binding mode of tepraloxydim explains the structure-activity relationship of these inhibitors, and provides a molecular basis for their distinct sensitivity to some of the resistance mutations, as compared to haloxyfop. Despite the chemical diversity between haloxyfop and tepraloxydim, the compounds do share two binding interactions to the enzyme, which may be important anchoring points for the development of ACC inhibitors.
Monoclonal Antibodies to Human Parainfluenza Virus Type 1 Detect Major Antigenic Changes in Clinical Isolates (1991)

The extent of antigenic diversity within a population of human parainfluenza virus type 1 (HPIV-1) isolates collected over a 26-year period was investigated. Twenty-three monoclonal antibodies (MAbs) made to the hemagglutinin-neuraminidase protein (HN), fusion protein (F), phosphoprotein (P), and nucleoprotein (NP) of a 1957 type strain were compared in their ability to bind to the different clinical isolates in ELISA and hemagglutinin-inhibition (HI) assay. Four HN, one F, and two NP MAbs bound equally to all of the viruses tested, but six of the MAbs demonstrated significant antigenic heterogeneity. Most of these antigenic changes appeared stable over time and noncummulative. Four of the clinical isolates and the type virus had similar reactivity patterns (subtype A) to these MAbs, while the remaining 10 isolates may form a second group (subtype B). Children's sera demonstrated this same subtype specificity in HI assays. One neutralization site was present on the 1957 strain and not on any of the subsequent isolates. The possibility of two or more major subtypes of HPIV-1 should be considered in future epidemiologic, therapeutic, and vaccine-related work.
Large Grain Polycrystalline Silicon Film Produced by Nano-Aluminum-Enhanced Crystallization of Amorphous Silicon (2005)

This paper reports the results from an investigation of the effects of nanometer thick aluminum on aluminum-induced crystallization (AIC) of plasmas-enhanced chemical vapor deposited amorphous silicon (a-Si:H). Compared to traditional AIC, nano-aluminum-induced crystallization (nano-AIC) produces smooth polycrystalline silicon films with very large grains at significantly reduced temperatures. The average size of the five largest grains on the sample produced by nano-AIC at is , times larger than that produced by traditional AIC. To the authors' knowledge, these are the largest grains formed by AIC of a-Si:H at annealing temperatures as low as .
A novel coagulation assay incorporating adherent endothelial cells in thromboelastometry (2013)

Following vascular injury or activation, endothelial cells (ECs) participate in the modulation of haemostasis and fibrinolysis. Viscoelastic tests (VETs) are a potent bedside monitoring tool that reports haemostatic parameters in real time. However, VETs neglect the influence of the surrounding endothelium. Our aim was therefore to establish an assay that incorporates ECs in a whole blood VET and to assess the impact of ECs on coagulation parameters. Outgrowth endothelial cells (OECs) and human umbilical vein endothelial cells (HUVECs) were seeded onto microbeads to create transferable EC-microcarriers. Microbeads were then added to citrated whole blood in the measurement cup of a thromboelastometry device (ROTEM). After the addition of CaCl2 (star-TEM®) to the blood sample (NATEM assay), standard ROTEM parameters were analysed. Scanning electron microscopy (SEM) was carried out to visualise the interactions of the beads, whole blood components and the ROTEM pin after clotting. SEM showed that the added microbeads were effectively incorporated into the final blood clot. In the presence of activated ECs, the clotting time (CT) of the blood was shortened fourfold compared to that in uncoated control beads. A significant reduction in CT was also observed in the presence of unstimulated ECs. Interestingly, CT was also reduced by the addition of purified EC culture supernatant. CT shortening was prevented by incubating the supernatant with an inhibiting antibody against tissue factor (TF). Our findings demonstrate that ECs can be incorporated into a ROTEM assay via coated microbeads, and whole blood clotting initiation is accelerated by non-activated and activated ECs.
A study of process conditions for plasma ion implantation hydrogenation experiments (1995)

Summary form only given, as follows. Plasma Ion Implantation (PII) hydrogenation has recently been found to be an effective method for defect passivation in thin film transistors (TFTs). PII process conditions can have a profound effect on dose rate and device reliability. Charge accumulation during the time of the pulse can damage the gate oxide and reduce the sheath electric field, decreasing the dose-rate and average implant energy. In order to minimize these effects, the pulse width must be kept short. The resulting decrease in the duty factor must be compensated by increasing the pulse repetition frequency if the dose rate is to remain constant. However, there is an upper limit on pulse repetition frequency imposed by ion depletion around the target. Plasma heating must be regulated to aid diffusion in the device without causing damage. Hydrogen etching can alter device structure and remove hydrogen already implanted. Based upon theory and experimental measurements of these factors, we have identified a window of process parameters to maximize PII hydrogenation process efficiency. We have calculated the minimum required PII process time for device parameter saturation.
Experimental Verification of Ultra-Wide Bandwidth Spectra in Double-Clad Single-Mode Fiber (1982)

The low-loss and low-dispersion properties of single-mode fibers make them obvious choices for wide bandwidth system applications with very long repeater spans. This brief describes the fabrication procedure and transmission properties of a double-clad single-mode fiber which is capable of wide bandwidth (greater than 100 GHz-km for laser sources with 4-nm emission bandwidths) transmission over the widest wavelength range (1.45 μm to 1.73 μm) thus far reported in the literature. This range completely covers the lowest-loss wavelength window for fused-silica optical fibers. Double-clad lightguides <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1–4</sup> were formed by using an inner cladding to form an index well between the core and a pure silica outer cladding. A computer-aided analytical procedure was used to choose the proper fiber diameter so that waveguide dispersion effects could be used to cancel material dispersion at predetermined wavelengths. <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup>
CRISPR diagnostics (2021)

New CRISPR enzyme activities add to the nucleic acid detection arsenal
Line-Scan Hyperspectral Imaging Platform for Agro-Food Safety and Quality Evaluation: System Enhancement and Characterization (2011)

Line-scan-based hyperspectral imaging techniques have often served as a research tool to develop rapid multispectral methods based on only a few spectral bands for rapid online applications. With continuing technological advances and greater accessibility to and availability of optoelectronic imaging sensors and spectral imaging spectrographs, the range of implementation for hyperspectral imaging has been broadening across quality and safety inspection needs in the food and agricultural industries. We have developed a series of food inspection imaging systems based on hyperspectral line-scan imaging with the use of a low-light sensitive, electron-multiplying charge-coupled device (EMCCD). In this methodology article, the spectral and spatial system performance of the latest generation of the ARS hyperspectral imaging system, which is capable of reflectance and fluorescence measurements in the visible and near-infrared (NIR) spectral regions from 400 to 1000 nm, is evaluated. Results show that the spectral resolution of the system is 4.4 nm at full-width at half-maximum (FWHM) and 6 nm FWHM at our typical operation mode (6-pixel spectral binning). We enhanced the system throughput responses by using spectral weighting filters to better utilize the dynamic range of the analog-to-digital converter. With this system throughput adjustment, noise-equivalent reflectance measurements were significantly reduced by approximately 50% in the NIR region for a range of standard diffuse reflectance targets. The responsivity of the system from 450 to 950 nm was determined to be linear.
Isolation and Selection of Sulfur-oxidizing Bacteria for the Treatment of Sulfur-containing Hazardous Wastes (2013)

A total of 75 microorganisms were obtained from high-sulfur content environmental samples using different sulfur sources. Fifty-four of them had the ability to oxidize sulfur at 1% (w/v) in liquid culture, however only three of them AZCT-M125-5, AZCT-M125-6, and AZCT-M125-7 were able to grow autotrophycally using elemental sulfur at concentrations higher than 1 % and up to 9 % (w/v) as energy source. They produce more than 300 mg sulfate/L. Also, these microbial cultures were able to produce sulfate within pH 3 to 7. Analysis based on 16S rRNA gene sequences indicated that microbial cultures AZCT-M125-5 and AZCT-M125-6 were closely related to Acidithiobacillus thiooxidans while identification of AZCT-M125-7 was not possible. According to the results, these three microorganisms can be excellent candidates for the future development of alternative biotechnological processes for the treatment of hazardous wastes containing sulfur.
REMOTE ATTITUDE SENSING BASED ON HIGH-SPEED MUELLER MATRIX ELLIPSOMETRY (2020)

Abstract. The attitude metrology of moving objects has always been a hot topic in engineering applications. In this article, a novel optical method based on the high-speed Mueller matrix ellipsometry (MME) is proposed for real-time remote attitude sensing. With the help of an electric level, all the attitude angles of a free-moving object with a birefringent waveplate attached can be simultaneously extracted in real time. Compared with existing ellipsometry-based attitude metrology that can only be used in the transmission mode, the proposed method with the advantages of the high-speed MME can expand the application to both the transmission and reflection modes while maintaining higher accuracy and robustness in an ultra-large measurement range. The basic principle is presented via theoretical derivation, and the change in the Mueller matrix of the birefringent waveplate versus the attitude angles is explored in the simulated experiments. In a series of the dynamic experiments, with the extremely high temporal resolution and accuracy of the high-speed MME, an angular resolution up to 0.00022° and an angular accuracy better than 0.01° are achieved in the real-time attitude tracking of the free-moving object. As an additional benefit, the real-time angular velocity and acceleration of all the attitude angles can be obtained simultaneously. These experimental results demonstrate that the proposed attitude metrology is ready to be applied to the real-time remote attitude sensing with high angular resolution and accuracy.
LEM domain–containing protein 3 antagonizes TGFβ–SMAD2/3 signaling in a stiffness-dependent manner in both the nucleus and cytosol (2018)

Transforming growth factor-β (TGFβ) signaling through SMAD2/3 is an important driver of pathological fibrosis in multiple organ systems. TGFβ signaling and extracellular matrix (ECM) stiffness form an unvirtuous pathological circuit in which matrix stiffness drives activation of latent TGFβ, and TGFβ signaling then drives cellular stress and ECM synthesis. Moreover, ECM stiffness also appears to sensitize cells to exogenously activated TGFβ through unknown mechanisms. Here, using human fibroblasts, we explored the effect of ECM stiffness on a putative inner nuclear membrane protein, LEM domain-containing protein 3 (LEMD3), which is physically connected to the cell's actin cytoskeleton and inhibits TGFβ signaling. We showed that LEMD3-SMAD2/3 interactions are inversely correlated with ECM stiffness and TGFβ-driven luciferase activity and that LEMD3 expression is correlated with the mechanical response of the TGFβ-driven luciferase reporter. We found that actin polymerization but not cellular stress or LEMD3-nuclear-cytoplasmic couplings were necessary for LEMD3-SMAD2/3 interactions. Intriguingly, LEMD3 and SMAD2/3 frequently interacted in the cytosol, and we discovered LEMD3 was proteolytically cleaved into protein fragments. We confirmed that a consensus C-terminal LEMD3 fragment binds SMAD2/3 in a stiffness-dependent manner throughout the cell and is sufficient for antagonizing SMAD2/3 signaling. Using human lung biopsies, we observed that these nuclear and cytosolic interactions are also present in tissue and found that fibrotic tissues exhibit locally diminished and cytoplasmically shifted LEMD3-SMAD2/3 interactions, as noted <i>in vitro</i> Our work reveals novel LEMD3 biology and stiffness-dependent regulation of TGFβ by LEMD3, providing a novel target to antagonize pathological TGFβ signaling.
W-shaped common-path interferometer (2020)

We present a novel static W-shaped common-path interferometer. In particular, the W-shaped common-path corner-cube retroreflector interferometer (W-CPRI) is introduced via detailed analysis of its working principles and performance. It comprises two corner-cube retroreflectors (CCRs), a reflecting mirror (RM), and a beam splitter. For each interference output of an ideal W-CPRI, the two beams recombine and have the same output direction, including a tilted CCR. In a deformed W-CPRI structure, an optical path difference can be produced by inserting an optical element that changes the optical path in the interferometer arm of the W-CPRI. The posture deviations of the RM and the CCRs in the W-CPRI are analyzed. In addition, a proof-of-concept experiment is conducted, with the stability analyzed using the fringe similarity method. The average cosine similarity is 0.9953, revealing that this W-CPRI has high stability and strong coherence while avoiding the tilt and displacement of the interferometer arm.
Correction to “Nonviral Genome Editing Based on a Polymer-Derivatized CRISPR Nanocomplex for Targeting Bacterial Pathogens and Antibiotic Resistance” (2018)

ADVERTISEMENT RETURN TO ISSUEPREVCorrectionNEXTORIGINAL ARTICLEThis notice is a correctionCorrection to "Nonviral Genome Editing Based on a Polymer-Derivatized CRISPR Nanocomplex for Targeting Bacterial Pathogens and Antibiotic Resistance"Yoo Kyung KangYoo Kyung KangMore by Yoo Kyung Kang, Kyu KwonKyu KwonMore by Kyu Kwon, Jea Sung RyuJea Sung RyuMore by Jea Sung Ryu, Ha Neul LeeHa Neul LeeMore by Ha Neul Lee, Chankyu ParkChankyu ParkMore by Chankyu Park, and Hyun Jung Chung*Hyun Jung ChungMore by Hyun Jung Chunghttp://orcid.org/0000-0001-5055-902XCite this: Bioconjugate Chem. 2018, 29, 11, 3936Publication Date (Web):November 12, 2018Publication History Published online12 November 2018Published inissue 21 November 2018https://pubs.acs.org/doi/10.1021/acs.bioconjchem.8b00771https://doi.org/10.1021/acs.bioconjchem.8b00771correctionACS PublicationsCopyright © 2018 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views1332Altmetric-Citations4LEARN 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 PDF (187 KB) Get e-AlertscloseSUBJECTS:Antibiotic resistance,Genomics,Immunology,Targeting Get e-Alerts
Hippocampal Expression Analyses Reveal Selective Association of Immediate-Early, Neuroenergetic, and Myelinogenic Pathways with Cognitive Impairment in Aged Rats (2007)

Although expression of some genes is known to change during neuronal activity or plasticity, the overall relationship of gene expression changes to memory or memory disorders is not well understood. Here, we combined extensive statistical microarray analyses with behavioral testing to comprehensively identify genes and pathways associated with aging and cognitive dysfunction. Aged rats were separated into cognitively unimpaired (AU) or impaired (AI) groups based on their Morris water maze performance relative to young-adult (Y) animals. Hippocampal gene expression was assessed in Y, AU, and AI on the fifth (last) day of maze training (5T) or 21 d posttraining (21PT) and in nontrained animals (eight groups total, one array per animal; n = 78 arrays). ANOVA and linear contrasts identified genes that differed from Y generally with aging (differed in both AU and AI) or selectively, with cognitive status (differed only in AI or AU). Altered pathways/processes were identified by overrepresentation analyses of changed genes. With general aging, there was downregulation of axonal growth, cytoskeletal assembly/transport, signaling, and lipogenic/uptake pathways, concomitant with upregulation in immune/inflammatory, lysosomal, lipid/protein degradation, cholesterol transport, transforming growth factor, and cAMP signaling pathways, primarily independent of training condition. Selectively, in AI, there was downregulation at 5T of immediate-early gene, Wnt (wingless integration site), insulin, and G-protein signaling, lipogenesis, and glucose utilization pathways, whereas Notch2 (oligodendrocyte development) and myelination pathways were upregulated, particularly at 21PT. In AU, receptor/signal transduction genes were upregulated, perhaps as compensatory responses. Immunohistochemistry confirmed and extended selected microarray results. Together, the findings suggest a new model, in which deficient neuroenergetics leads to downregulated neuronal signaling and increased glial activation, resulting in aging-related cognitive dysfunction.
Isolation of Recombinant Protective <i>Helicobacter pylori</i> Antigens (1999)

A total of seven clones producing both new and previously described Helicobacter pylori proteins were isolated from a library of H. pylori genomic DNA. The screening approach by which these proteins were detected relied on the use of antisera raised in mice vaccinated with Helicobacter felis sonicate plus cholera toxin, a regimen which protects mice from H. pylori challenge. This strategy was designed to maximize the possibility of obtaining antigens which might be capable of conferring protection from H. pylori infection. Two of the clones were shown to encode the urease enzyme and the heat shock protein HspB, which have already been identified as protective antigens. The other five clones were sequenced, protein coding regions were deduced, and these sequences were amplified by PCR for incorporation into Escherichia coli expression vectors. The proteins produced from these expression systems were purified to allow testing for protective efficacy in an H. pylori mouse model. All five proteins were able to facilitate the clearance of a challenge with H. pylori, as judged by an assay of gastric urease activity and light microscopy on stomach sections. These results clearly indicate that the screening strategy has successfully identified candidate vaccine antigens.
Analysis of a simple smart antenna for CDMA wireless communications (2003)

The bit error rate (BER) of a code division multiple access (CDMA) system with a simple smart antenna is analyzed. The BER is also simulated and compared with the analysis. When the direction of the arrival angle (DOA) of the desired user signal is perturbed with a duty cycle, it is observed whether the smart antenna can track back the DOA of the desired user signal or not after perturbation. In addition its effects on BER results are presented.
Electrodeposition of Cobalt Using an Insoluble Anode (1976)

A method has been developed which permits the use of an insoluble anode to electrodeposit cobalt by the addition of a sufficient amount of an electrochemically active substance such as vanadium pentoxide to the cobalt sulfate plating solution. In the absence of such additions, formation of Co3+ ions and cobalt oxide at the platinum anode results during plating. The effects of the addition of vanadium pentoxide on the electrode process during plating have been investigated through the analyses of various electrolysis products as a function of additive concentration and plating time. The results show that besides cobalt deposition, vanadium ions of lower oxidation state (V++, V+++, ) are formed at the cathode and these ions seem to be responsible for the reduction and suppression of Co3+ ions and the oxide at the platinum anode. It has also been observed that the concentration of the added electrochemically active substance changed very little, indicating no incorporation of vanadium with the deposit during plating. The mechanical properties of the deposits prepared using an insoluble anode are compared with those obtained using a soluble anode.