gebhart/patrepeval huggingface dataset:
A Novel Route to Multiphase Polymer Systems Containing Nano‐Droplets: Radical Polymerization of Vinylic Monomers in Gelled Water‐in‐Oil Miniemulsions (2005)

Abstract Summary: A new strategy for the synthesis of composite polymers with larger volume fraction of aqueous inclusions less than 1 µm in diameter is presented. A water‐in‐oil miniemulsion of aqueous droplets in a continuous, cross‐linkable monomer phase is prepared. The addition of an organo‐gelator allows the immobilization of the droplets in a solid gel, thus avoiding the usual demixing upon polymerization of the continuous phase. This pregelled system is then converted into a composite polymer by photoinitiated free radical polymerization. Such coatings may be used for an improved climate control of buildings or as a deposit for the controlled release of actives from polar nano‐droplets. SEM image of a cross‐linked composite polymer showing controlled droplet inclusions with a maximal diameter of 500 nm. magnified image SEM image of a cross‐linked composite polymer showing controlled droplet inclusions with a maximal diameter of 500 nm.
A new mutation with a polycystin phenotypic spectrum in Caenorhabditis elegans (2017)

lov-1 and pkd-2, which encode the C. elegans orthologs of human polycystin-1 and -2, are necessary for three particular aspects of male mating behavior. In a screen for male mating defective mutants with similar spectrum of mating defects, we identified a mutation that apparently defines a new locus, lov-3. We isolated the sy682 mutation in an ethyl-methane sulphonate (EMS)-screen of Caenorhabditis elegans strain PS1395 [genotype: plg-1(e2001d); him-5(e1490)] for mutant males that do not mate efficiently and hence do not form plugs on hermaphrodites (Liu et al, 2017). sy682 is defective in the males’ response to contact with hermaphrodite and in vulval location (Table 1). The vulval location defect is failing to stop at the vulva. These two phenotypes are associated with lov-1 (Barr, 1999) and pkd-2 loss-of-function mutations (Barr et al. 2001; Whittaker et al., 2017). sy682 maps to the X chromosome and thus is distinct from lov-1 and pkd-2, so it defines a likely new locus, lov-3.
Abstract 21141: Cystathionine Gamma-Lyase Regulates Autophagy in Ischemic Endothelial Cells (2017)

Introduction: Peripheral arterial disease (PAD) is a chronic arterial occlusive disease leading to lower limb ischemia. Autophagy is a cell adaptive response associated with ischemic stress that may act as a double edged sword. It is essential during tissue ischemia, but may also phagocytize more organelles promoting cell death. Hydrogen sulfide (H 2 S), a gasotransmitter predominantly produced in the vasculature via cystathionine-γ-lyase (CSE), play a key regulatory role in the cardiovascular functions. However, role of H 2 S/CSE in autophagy, and its associated impact on ischemic injury is poorly understood. Objective: To investigate the role of CSE/H2S in the regulation of autophagy under ischemia using murine hind limb ischemia model and in vitro studies. Methods: Unilateral femoral artery ligation (FAL) was performed on C57BL/6J(WT) mice and tissue blood perfusion was measured using laser Doppler flowmetry. LC3B expression was measured in the skeletal muscle tissues by immunohistochemistry. We utilized mouse aortic endothelial cells (MAECs) isolated from WT and CSE deficient (CSEKO) mice respectively and immortalized them. We treated WT and CSE KO MAECs were subjected to normoxia and hypoxia with and without autophagy inhibitor bafilomycin and evaluated for LC3B. ROS levels were evaluated by DCFDH. Apoptosis was measured by LDH assay and cleaved caspase-3. Results: Compared to WT, CSEKO MAECs showed significant reduction in LC3B protein expression. Reduced LC3B and p62 mRNA expressions were also observed in CSEKO cells. In the WT mice subjected to FAL, blood perfusion was significantly reduced in the ligated limbs compared to non-ligated. Interestingly, LC3B was significantly higher in ischemic muscle compared to non-ischemic tissues. Additionally, CSE genetic deletion significantly increased ROS levels that lead to increased apoptosis. CSEKO MAECs showed increased LDH activity and elevated cleaved caspase-3 expression under hypoxia. Conclusions: Our study reveals for the first time that CSE/H 2 S regulates autophagy in ischemic endothelial cells. CSE/H 2 S may be used as a therapeutic agent to protect against ischemia injury by inhibiting autophagy during PAD.
Model for an inductively coupled Ar/c-C4F8 plasma discharge (2002)

This article describes a two-dimensional model for an inductively coupled Ar/c-C4F8 plasma discharge, which is widely used in the microelectronics industry for dielectric etching and polymerization. The chemical mechanism for c-C4F8 incorporates known information about electron impact dissociation, ionization, and attachment processes. Unknown details such as neutral dissociation byproducts have been empirically inferred using energetics analysis or diagnostic experiments. The mechanism also considers electron impact processes for neutral radicals (e.g., CF, CF2, CF3) and stable molecules (e.g., C2F4) produced in a c-C4F8 plasma. It is demonstrated in the article that the resulting neutral species densities, ion flux to the wafer, and electron characteristics are in good agreement with experiments in the Gaseous Electronics Conference reference cell. The validated model is used to understand the dynamics of an inductively coupled Ar/c-C4F8 plasma discharge, and the impact of various control parameters on plasma characteristics. Results indicate that CF2 is the dominant CFx radical in the c-C4F8 discharge and the plasma is mildly electronegative. Enhanced ionization and dissociation of c-C4F8 with increasing inductive power deposition leads to an increase in electron and CFx radical densities, and total ion flux to the wafer. Enhanced dissociative attachment at higher gas pressure decreases the electron density and increases the negative ion density. The plasma becomes more electropositive with decreasing c-C4F8 concentration in the gas mixture, which increases the total positive ion flux to the wafer.
Interaction of Bcl-2 with the Autophagy-related GABAA Receptor-associated Protein (GABARAP) (2013)

Apoptosis and autophagy are fundamental homeostatic processes in eukaryotic organisms fulfilling essential roles in development and adaptation. Recently, the anti-apoptotic factor Bcl-2 has been reported to also inhibit autophagy, thus establishing a potential link between these pathways, but the mechanistic details are only beginning to emerge. Here we show that Bcl-2 directly binds to the phagophore-associated protein GABARAP. NMR experiments revealed that the interaction critically depends on a three-residue segment (EWD) of Bcl-2 adjacent to the BH4 region, which is anchored to one of the two hydrophobic pockets on the GABARAP molecule. This is at variance with the majority of GABARAP interaction partners identified previously, which occupy both hydrophobic pockets simultaneously. Bcl-2 affinity could also be detected for GEC1, but not for other mammalian Atg8 homologs. Finally, we provide evidence that overexpression of Bcl-2 inhibits lipidation of GABARAP, a key step in autophagosome formation, possibly via competition with the lipid conjugation machinery. These results support the regulatory role of Bcl-2 in autophagy and define GABARAP as a novel interaction partner involved in this intricate connection.
Data from Application of Bayesian Modeling of Autologous Antibody Responses against Ovarian Tumor-Associated Antigens to Cancer Detection (2023)

&lt;div&gt;Abstract&lt;p&gt;Biomarkers for early detection of epithelial ovarian cancer (EOC) are urgently needed. Patients can generate antibodies to tumor-associated antigens (TAAs). We tested multiplex detection of antibodies to candidate ovarian TAAs and statistical modeling for discrimination of sera of EOC patients and controls. Binding of serum antibody of women with EOC or healthy controls to candidate TAA-coated microspheres was assayed in parallel. A Bayesian model/variable selection approach using Markov Chain Monte Carlo computations was applied to these data, and serum CA125 values, to determine the best predictive model. The selected model was subjected to area under the receiver-operator curve (AUC) analysis. The best model generated an AUC of 0.86 [95% confidence interval (95% CI), 0.78-0.90] for discrimination between sera of EOC patients and healthy patients using antibody specific to p53, NY-CO-8, and HOXB7. Inclusion of CA125 in the model provided an AUC of 0.89 (95% CI, 0.84-0.92) compared with an AUC of 0.83 (95% CI, 0.81-0.85) using CA125 alone. However, using TAA responses alone, the model discriminated between independent sera of women with nonmalignant gynecologic conditions and those with advanced-stage or early-stage EOC with AUCs of 0.71 (95% CI, 0.67-0.76) and 0.70 (95% CI, 0.48-0.75), respectively. Serum antibody to p53 and HOXB7 is positively associated with EOC, whereas NY-CO-8-specific antibody shows negative association. Bayesian modeling of these TAA-specific serum antibody responses exhibits similar discrimination of patients with early-stage and advanced-stage EOC from women with nonmalignant gynecologic conditions and may be complementary to CA125. (Cancer Res 2006; 66(3): 1792-8)&lt;/p&gt;&lt;/div&gt;
Stability of the Double Gyroid Phase in Bottlebrush Diblock Copolymer Melts (2021)

Bottlebrush block copolymers are emerging as promising materials for designing advanced materials with a number of unique properties engendered by densely grafted architectures. We used self-consistent field theory (SCFT) to determine how the stability of the double gyroid phase in a diblock copolymer melt is affected by converting one or both of the blocks of a linear diblock copolymer to a bottlebrush architecture. For architecturally symmetric polymers, the dominant effect of the bottlebrush is increasing segregation strength, whereupon the gyroid stability regions are effectively the same as linear diblock copolymers at equivalent segregation. In contrast, architectural asymmetry produced by coil–bottlebrush block polymers significantly impacts the gyroid stability region as a result of conformational asymmetry, which promotes spontaneous curvature. Gyroid is more stable when the coil blocks are in minority domains, which relieves packing frustration at the center of the gyroid nodes than in majority domains. Our results suggest that architectural asymmetry in bottlebrush block polymers can be a powerful design tool.
Effect of harvest stage on biomass and oil yield in different parts of Tagetes minuta L. (2018)

Growth and development studies in MAP have emerged as important sources of useful information for optimizing their harvesting stages. The economic utility of any MAP crop is governed by the quantum of the usable part and the active content. These studies become more important in such species where more than one plant part is the economic part yielding similar end product. Studies were conducted at monthly intervals during the growing period of its plants and the results suggested that Tagetes minuta can be harvested either at pre flowering stage (characterized by maximum leaf biomass) for getting leaf oil or at full flowering stage (characterized by negligible leaf biomass but maximum flower biomass) for getting flower oil.
Carrier heating dynamics in semiconductor waveguide saturable absorbers (1994)

Pump-probe measurements in GaAs/GaAlAs waveguide saturable absorbers reveal an ultrafast transient in the absorption recovery dynamics, and a second slower signal before the final recovery. We present a model of the differential transmission measurements which includes high field and space charge effects in addition to the spectral hole burning and carrier heating typically found in semiconductor amplifiers. The results of the model indicate that field-induced carrier heating strongly influences the absorption dynamics in saturable absorbers used for mode-locked diode lasers.
Structure and Function of the Type III Secretion System of Pseudomonas aeruginosa (2012)

Pseudomonas aeruginosa is a dangerous pathogen particularly because it harbors multiple virulence factors. It causes several types of infection, including dermatitis, endocarditis, and infections of the urinary tract, eye, ear, bone, joints and, of particular interest, the respiratory tract. Patients with cystic fibrosis, who are extremely susceptible to Pseudomonas infections, have a bad prognosis and high mortality. An important virulence factor of P. aeruginosa, shared with many other gram-negative bacteria, is the type III secretion system, a hollow molecular needle that transfers effector toxins directly from the bacterium into the host cell cytosol. This complex macromolecular machine works in a highly regulated manner and can manipulate the host cell in many different ways. Here we review the current knowledge of the structure of the P. aeruginosa T3SS, as well as its function and recognition by the immune system. Furthermore, we describe recent progress in the development and use of therapeutic agents targeting the T3SS.
Sketch-BERT: Learning Sketch Bidirectional Encoder Representation From Transformers by Self-Supervised Learning of Sketch Gestalt (2020)

Previous researches of sketches often considered sketches in pixel format and leveraged CNN based models in the sketch understanding. Fundamentally, a sketch is stored as a sequence of data points, a vector format representation, rather than the photo-realistic image of pixels. SketchRNN studied a generative neural representation for sketches of vector format by Long Short Term Memory networks (LSTM). Unfortunately, the representation learned by SketchRNN is primarily for the generation tasks, rather than the other tasks of recognition and retrieval of sketches. To this end and inspired by the recent BERT model, we present a model of learning Sketch Bidirectional Encoder Representation from Transformer (Sketch-BERT). We generalize BERT to sketch domain, with the novel proposed components and pre-training algorithms, including the newly designed sketch embedding networks, and the self-supervised learning of sketch gestalt. Particularly, towards the pre-training task, we present a novel Sketch Gestalt Model (SGM) to help train the Sketch-BERT. Experimentally, we show that the learned representation of Sketch-BERT can help and improve the performance of the downstream tasks of sketch recognition, sketch retrieval, and sketch gestalt.
Globally optimal line clustering and vanishing point estimation in Manhattan world (2012)

The projections of world parallel lines in an image intersect at a single point called the vanishing point (VP). VPs are a key ingredient for various vision tasks including rotation estimation and 3D reconstruction. Urban environments generally exhibit some dominant orthogonal VPs. Given a set of lines extracted from a calibrated image, this paper aims to (1) determine the line clustering, i.e. find which line belongs to which VP, and (2) estimate the associated orthogonal VPs. None of the existing methods is fully satisfactory because of the inherent difficulties of the problem, such as the local minima and the chicken-and-egg aspect. In this paper, we present a new algorithm that solves the problem in a mathematically guaranteed globally optimal manner and can inherently enforce the VP orthogonality. Specifically, we formulate the task as a consensus set maximization problem over the rotation search space, and further solve it efficiently by a branch-and-bound procedure based on the Interval Analysis theory. Our algorithm has been validated successfully on sets of challenging real images as well as synthetic data sets.
D-Peptide-Based Probe for CXCR4-Targeted Molecular Imaging and Radionuclide Therapy (2021)

Positron emission tomography (PET) imaging of the C-X-C chemokine receptor 4 (CXCR4) with [<sup>68</sup>Ga]PentixaFor has intrinsic diagnostic value and is used to select patients for personalized CXCR4-targeted radionuclide therapy with its therapeutic radiopharmaceutical companion [<sup>177</sup>Lu]PentixaTher. However, a CXCR4-targeting radiopharmaceutical labeled with fluorine-18 is still of high value due to its favorable characteristics over gallium-68. Furthermore, clinical results with [<sup>177</sup>Lu]PentixaTher are promising, but there is still room for improvement regarding pharmacokinetics and dosimetry profile. Therefore, this study aimed to develop innovative CXCR4-targeting radiopharmaceuticals, both for diagnostic and therapeutic purposes, starting from a D-amino acid-based peptide probe (DV1-k-(DV3)) that conserves high CXCR4 binding affinity after radiolabeling. AlF-NOTA-DV1-k-(DV3) showed similar in vitro binding affinity to human CXCR4 (hCXCR4) compared to [<sup>nat</sup>Ga]PentixaFor (half-maximal inhibitory concentration (IC<sub>50</sub>): 5.3 ± 0.9 nM and 8.6 ± 1.1 nM, respectively) and also binds to murine CXCR4 (mCXCR4) (IC<sub>50</sub>: 33.4 ± 13.5 nM) while [<sup>nat</sup>Ga]PentixaFor is selective for hCXCR4 (IC<sub>50</sub> > 1000 nM for mCXCR4). Both the diagnostic radiotracers based on the DV1-k-(DV3) vector platform, [<sup>18</sup>F]AlF-NOTA-DV1-k-(DV3) and [<sup>68</sup>Ga]Ga-DOTA-DV1-k-(DV3), and their therapeutic companion [<sup>177</sup>Lu]Lu-DOTA-DV1-k-(DV3) were successfully produced in high yield, demonstrated high in vitro and in vivo stability, and have the same favorable pharmacokinetic profile. Furthermore, in wild-type mice and a hCXCR4-expressing tumor model, [<sup>18</sup>F]AlF-NOTA-DV1-k-(DV3) shows CXCR4-specific targeting in mCXCR4-expressing organs such as liver (mean standardized uptake value (SUV<sub>mean</sub>) 8.2 ± 1.0 at 75 min post-injection (p.i.)), spleen (SUV<sub>mean</sub> 2.5 ± 1.0 at 75 min p.i.), and bone (SUV<sub>mean</sub> 0.4 ± 0.1 at 75 min p.i., femur harboring bone marrow) that can be blocked with the CXCR4 antagonist AMD3100. However, in a hCXCR4-expressing tumor model, tumor uptake of [<sup>18</sup>F]AlF-NOTA-DV1-k-(DV3) was significantly lower (SUV<sub>mean</sub> 0.6 ± 0.2) compared to [<sup>68</sup>Ga]PentixaFor (SUV<sub>mean</sub> 2.9). This might be explained by the high affinity of [<sup>18</sup>F]AlF-NOTA-DV1-k-(DV3) toward both mCXCR4 and hCXCR4. High mCXCR4 expression in mouse liver results in a large fraction of [<sup>18</sup>F]AlF-NOTA-DV1-k-(DV3) that is sequestered to the liver, resulting despite its similar in vitro affinity for hCXCR4, in lower tumor accumulation compared to [<sup>68</sup>Ga]PentixaFor. As CXCR4 is not expressed in healthy human liver, the findings in mice are not predictive for the potential clinical performance of this novel class of CXCR4-targeting radiotracers. In conclusion, the DV1-k-(DV3) scaffold is a promising vector platform for translational CXCR4-directed research.
Cell position fates and collective fountain flow in bacterial biofilms revealed by light-sheet microscopy (2020)

Bacterial biofilms represent a basic form of multicellular organization that confers survival advantages to constituent cells. The sequential stages of cell ordering during biofilm development have been studied in the pathogen and model biofilm-former <i>Vibrio cholerae</i> It is unknown how spatial trajectories of individual cells and the collective motions of many cells drive biofilm expansion. We developed dual-view light-sheet microscopy to investigate the dynamics of biofilm development from a founder cell to a mature three-dimensional community. Tracking of individual cells revealed two distinct fates: one set of biofilm cells expanded ballistically outward, while the other became trapped at the substrate. A collective fountain-like flow transported cells to the biofilm front, bypassing members trapped at the substrate and facilitating lateral biofilm expansion. This collective flow pattern was quantitatively captured by a continuum model of biofilm growth against substrate friction. Coordinated cell movement required the matrix protein RbmA, without which cells expanded erratically. Thus, tracking cell lineages and trajectories in space and time revealed how multicellular structures form from a single founder cell.
Implications of decreased serum adiponectin for type IIb hyperlipidaemia and increased cholesterol levels of very-low-density lipoprotein in type II diabetic patients (2005)

The present study was performed to investigate the relevance of cholesterol levels of plasma lipoproteins [HDL (high-density lipoprotein), LDL (low-density lipoprotein), IDL (immediate-density lipoprotein), VLDL (very-LDL) and chylomicrons] determined by a novel HPLC method, with adiponectin, which is decreased in Type II diabetes and assumed to be involved in dysregulated metabolism and atherogenesis. Type II diabetic patients who were not treated with insulin, statins and fibrates were enrolled. Study subjects included Type II diabetic patients with normolipidaemia (DM-NL; n=15), type 4 hyperlipidaemia (DM-T4HL; n=13), Type IIa hyperlipidaemia (DM-T2aHL; n=15) and Type IIb hyperlipidaemia (DM-T2bHL; n=13). Fasting blood samples were collected. The serum adiponectin level was lower in DM-T2bHL than in any of the other groups. Cholesterol levels of each lipoprotein fraction, serum triacylglycerol (triglyceride), remnant-like particle-cholesterol, fasting plasma glucose, HbA1c (glycated haemoglobin), age, gender difference and BMI (body mass index) were incorporated into a stepwise regression analysis as independent variables. VLDL-cholesterol correlated inversely with adiponectin independently of age, BMI, gender difference and glycaemic control. Although the mechanisms remain to be explored, serum adiponectin was reduced particularly in Type II diabetics with type IIb hyperlipidaemia and correlated inversely with VLDL-cholesterol. Measuring VLDL-cholesterol may be helpful for understanding the pathological features of diabetic dyslipidaemia.
The vacuolar ATPase proton pump is present on intracellular vacuoles induced by Helicobacter pylori (1996)

Cytotoxic strains of Helicobacter pylori cause an intense vacuolar degeneration of cells, due to the enlargement of late endosomes in the presence of membrane permeant weak bases. Bafilomycins, specific inhibitors of the vacuolar-type (V-) ATPase proton pump, prevent vacuole formation. The presence of the V-ATPase on vacuolar membranes was demonstrated by immunofluorescence with a monoclonal antibody (MAb) specific for the human 116-kDa regulatory subunit. The V-ATPase co-localised with the late endosomal marker rab7 on vacuolar membranes. In contrast, the early recycling endosomal compartment was not altered by the VacA cytotoxin, although it was endowed with the V-ATPase. Endocytosis of a MAb against the 116-kDa regulatory subunit of V-ATPase blocked endosomal acidification in HeLa cells and prevented VacA action. These results indicate that selective swelling of late endosomes, due to accumulation of osmotically active weak bases driven by the V-ATPase, is essential for vacuole formation.
Improved cost-effectiveness of the block co-polymer anneal process for DSA (2016)

This manuscript first presents a cost model to compare the cost of ownership of DSA and SAQP for a typical front end of line (FEoL) line patterning exercise. Then, we proceed to a feasibility study of using a vertical furnace to batch anneal the block co-polymer for DSA applications. We show that the defect performance of such a batch anneal process is comparable to the process of record anneal methods. This helps in increasing the cost benefit for DSA compared to the conventional multiple patterning approaches.