gebhart/patrepeval huggingface dataset:
Modelling contractile ring formation and division to daughter cells for simulating proliferative multicellular dynamics (2023)

Abstract Cell proliferation is a fundamental process underlying embryogenesis, homeostasis, wound healing, and cancer. The process involves multiple events during each cell cycle, such as cell growth, contractile ring formation, and division to daughter cells, which affect the surrounding cell population geometrically and mechanically. However, existing methods do not comprehensively describe the dynamics of multicellular structures involving cell proliferation at a subcellular resolution. In this study, we present a novel model for proliferative multicellular dynamics at the subcellular level by building upon the nonconservative fluid membrane (NCF) model that we developed in earlier research. The NCF model utilizes a dynamically-rearranging closed triangular mesh to depict the shape of each cell, enabling us to analyze cell dynamics over extended periods beyond each cell cycle, during which cell surface components undergo dynamic turnover. The proposed model represents the process of cell proliferation by incorporating cell volume growth and contractile ring formation through an energy function and topologically dividing each cell at the cleavage furrow formed by the ring. Numerical simulations demonstrated that the model recapitulated the process of cell proliferation at subcellular resolution, including cell volume growth, cleavage furrow formation, and division to daughter cells. Further analyses suggested that the orientation of actomyosin stress in the contractile ring plays a crucial role in the cleavage furrow formation, i.e., circumferential orientation can form a cleavage furrow but isotropic orientation cannot. Furthermore, the model replicated tissue-scale multicellular dynamics, where the successive proliferation of adhesive cells led to the formation of a cell sheet and stratification on the substrate. Overall, the proposed model provides a basis for analyzing proliferative multicellular dynamics at subcellular resolution.
Analysis of pediatric adverse reactions to transfusions (2017)

Pediatric patients had double the rate of transfusion reactions compared to adults. The nationally reported data on reaction rates are consistent with this study's findings in adults but much lower than the observed rates for pediatric patients. Future studies are needed to address the differences in reaction rates, particularly in allergic and febrile reactions, and to further address blood transfusion practices in the pediatric patient population.
Whole-Brain Functional and Diffusion Tensor MRI in Human Participants with Metallic Orthodontic Braces (2019)

Background MRI performed with echo-planar imaging (EPI) sequences is sensitive to susceptibility artifacts in the presence of metallic objects, which presents a substantial barrier for performing functional MRI and diffusion tensor imaging (DTI) in patients with metallic orthodontic material and other head implants. Purpose To evaluate the ability to reduce susceptibility artifacts in healthy human participants wearing metallic orthodontic braces for two alternative approaches: T2-prepared functional MRI and diffusion-prepared DTI with three-dimensional fast gradient-echo readout. Materials and Methods In this prospective study conducted from February to September 2018, T2-prepared functional MRI and diffusion-prepared DTI were performed in healthy human participants. Removable dental braces with bonding trays were used so that MRI could be performed with braces and without braces in the same participants. Results were evaluated in regions with strong (EPI dropout regions for functional MRI and the inferior fronto-occipital fasciculus for DTI) and minimal (motor cortex for functional MRI and the posterior limb of internal capsule for DTI) susceptibility artifacts. Signal-to-noise ratio (SNR), contrast-to-noise ratio for functional MRI, apparent diffusion coefficient and fractional anisotropy for DTI, and degree of distortion (quantified with the Jaccard index, which measures the similarity of geometric shapes) were compared in regions with strong or minimal susceptibility effects between the current standard EPI sequences and the proposed alternatives by using paired <i>t</i> test. Results Six participants were evaluated (mean age ± standard deviation, 40 years ± 6; three women). In brain regions with strong susceptibility effects from the metallic braces, T2-prepared functional MRI showed significantly higher SNR (37.8 ± 2.4 vs 15.5 ± 5.3; <i>P</i> < .001) and contrast-to-noise ratio (0.83 ± 0.16 vs 0.29 ± 0.10; <i>P</i> < .001), whereas diffusion-prepared DTI showed higher SNR (5.8 ± 1.5 vs 3.8 ± 0.7; <i>P</i> = .03) than did conventional EPI methods. Apparent diffusion coefficient and fractional anisotropy were consistent with the literature. Geometric distortion was substantially reduced throughout the brain with the proposed methods (significantly higher Jaccard index, 0.95 ± 0.12 vs 0.81 ± 0.61; <i>P</i> < .001). Conclusion T2-prepared functional MRI and diffusion-prepared diffusion tensor imaging can acquire functional and diffusion MRI, respectively, in healthy human participants wearing metallic dental braces with less susceptibility artifacts and geometric distortion than with conventional echo-planar imaging. © RSNA, 2019 <i>Online supplemental material is available for this article.</i> See also the editorial by Dietrich in this issue.
Collagen analysis of mesenchymal stromal cell assisted hernial scar repair (2012)

Mesenchymal stem cells (MSC) migrate to the site of injury to promote tissue remodeling and cellular re‐organization. In this study we use a hernia repair model in rats to investigate how MSCs and platelet rich plasma (PRP) influence collagen deposition in hernial scars. A midline incision in 21 age‐matched Lewis rats was repaired using one of 3 protocols: 1) standard suture repair (control) 2) platelet‐rich plasma embedded in a collagen matrix (PRP) and 3) platelet‐rich plasma and mesenchymal stem cells embedded in a collagen matrix (MSC+PRP). At 4 weeks post surgery, 0.15 mm scar tissue was harvested and analyzed for collagen content and phenotype. Results showed that collagen content was greater in MSC‐treated rats. Total collagen in MSC+PRP scars was 394.2 % greater than controls (p=0.003) and 250.4% greater than PRP scars (p=0.004). Collagen concentration (per mg scar protein) was significantly higher in MSC+PRP scars than in controls (p=.012) and there was no significant difference between control and PRP scars. A comparison of collagen I/III ratios in scar tissue using 2Dgel analysis of CnBr treated scar tissue indicated that the relative proportion of Col III was higher in MSC+PRP treated scars than in control. The results of this study show that MSC therapy can enhance hernial scar integrity by increasing collagen content and decreasing the Col I/III ratio. Supported by the American Hernia Society.
Electron microscopic evidence on the acrosomal status of bound sperm and their penetration into human hemizonae pellucida after storage in a buffered salt solution* (2009)

The hemizona assay (HZA) was developed to evaluate sperm binding potential using microbisected human zona pellucida. In this study, eight human oocytes stored in a buffered salt solution for 60 days were bisected into two identical hemispheres (hemizonae) and coincubated with the spermatozoa from a fertile man. All evaluated spermatozoa were tightly bound to the outer surface or had begun penetration into the zona pellucida. The hemizonae with bound spermatozoa were prepared and fixed for transmission electron microscopy (TEM) using standard techniques. Among the 108 sperm bound to the zone we were able to evaluate 25 by TEM. Twenty (80%) of the zona bound spermatozoa were partially or completely acrosome reacted, while six (20%) of the zona bound sperm had intact acrosomes. Acrosome intact, partially acrosome reacted and completely reacted spermatozoa were observed within the zona. Penetration pathways or tunnels were seen within the zona matrix. The results illustrate, that typically spermatozoa tightly bound the human zona pellucida show induction of the acrosome reaction. Importantly, following storage of human eggs in salt solution (buffered to 7.4), the zona pellucida retain their biological and functional characteristics for at least 90 days.
Active matrix CdSe TFT addresses electroluminescent displays (2003)

The authors show that the classical double-insulator thin-film (electroluminescent) EL display can be driven by a CdSe thin-film transistor (TFT) matrix. Both the display and the TFTs can be fabricated by thin-film technology. The active matrix EL-display concept is outlined. A comparison is made of passive versus active EL-displays. The TFT requirements are derived, and their measured performance is described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Effects of Excess Manganese on the Xylem Sap Protein Profile of Tomato (Solanum lycopersicum) as Revealed by Shotgun Proteomic Analysis (2020)

Metal toxicity is a common problem in crop species worldwide. Some metals are naturally toxic, whereas others such as manganese (Mn) are essential micro-nutrients for plant growth but can become toxic when in excess. Changes in the composition of the xylem sap, which is the main pathway for ion transport within the plant, is therefore vital to understanding the plant's response(s) to metal toxicity. In this study we have assessed the effects of exposure of tomato roots to excess Mn on the protein profile of the xylem sap, using a shotgun proteomics approach. Plants were grown in nutrient solution using 4.6 and 300 µM MnCl<sub>2</sub> as control and excess Mn treatments, respectively. This approach yielded 668 proteins reliably identified and quantified. Excess Mn caused statistically significant (at <i>p</i> ≤ 0.05) and biologically relevant changes in relative abundance (≥2-fold increases or ≥50% decreases) in 322 proteins, with 82% of them predicted to be secretory using three different prediction tools, with more decreasing than increasing (181 and 82, respectively), suggesting that this metal stress causes an overall deactivation of metabolic pathways. Processes most affected by excess Mn were in the oxido-reductase, polysaccharide and protein metabolism classes. Excess Mn induced changes in hydrolases and peroxidases involved in cell wall degradation and lignin formation, respectively, consistent with the existence of alterations in the cell wall. Protein turnover was also affected, as indicated by the decrease in proteolytic enzymes and protein synthesis-related proteins. Excess Mn modified the redox environment of the xylem sap, with changes in the abundance of oxido-reductase and defense protein classes indicating a stress scenario. Finally, results indicate that excess Mn decreased the amounts of proteins associated with several signaling pathways, including fasciclin-like arabinogalactan-proteins and lipids, as well as proteases, which may be involved in the release of signaling peptides and protein maturation. The comparison of the proteins changing in abundance in xylem sap and roots indicate the existence of tissue-specific and systemic responses to excess Mn. Data are available via ProteomeXchange with identifier PXD021973.
Identité, islam et catholicisme allemand (2018)

This papers analyses the speech by Benedict XVI at the University of Ratisbonne. I focus on a often overlooked aspect of this speech: the critic of Modernity and the general perspective for the future of religions. Benedict XVI develops an analysis of the place of the Church through the concepts of ‘faith’, ‘reason’, ‘violence’. The apologetic tone is clear: only the Catholic Church has maintened a “reasonable religion“ according to the Pope. But he defends an international perspective for the Church in a globalised world and sketch a manifesto for Catholicism in a multicultural civilisation.
Update on the Scientific Status of the Plasma Focus (2021)

This paper is a sequel to the 1998 review paper “Scientific status of the Dense Plasma Focus” with 16 authors belonging to 16 nations, whose initiative led to the establishment of the International Center for Dense Magnetized Plasmas (ICDMP) in the year 2000. Its focus is on understanding the principal defining characteristic features of the plasma focus in the light of the developments that have taken place in the last 20 years, in terms of new facilities, diagnostics, models, and insights. Although it is too soon to proclaim with certainty what the plasma focus phenomenon is, the results available to date conclusively indicate what it is demonstrably not. The review looks at the experimental data, cross-correlated across multiple diagnostics and multiple devices, to delineate the contours of an emerging narrative that is fascinatingly different from the standard narrative, which has guided the consensus in the plasma focus community for several decades, without invalidating it. It raises a question mark over the Fundamental Premise of Controlled Fusion Research, namely, that any fusion reaction having the character of a beam-target process must necessarily be more inefficient than a thermonuclear process with a confined thermal plasma at a suitably high temperature. Open questions that need attention of researchers are highlighted. A future course of action is suggested that individual plasma focus laboratories could adopt in order to positively influence the future growth of research in this field, to the general benefit of not only the controlled fusion research community but also the world at large.
Structure-Activity Relationship Study of Biflavonoids on the Dengue Virus Polymerase DENV-NS5 RdRp (2013)

Dengue virus is the world's most prevalent human pathogenic arbovirus. There is currently no treatment or vaccine, and solutions are urgently needed. We previously demonstrated that biflavonoids from Dacrydium balansae, an endemic gymnosperm from New Caledonia, are potent inhibitors of the Dengue virus NS5 RNA-dependent RNA polymerase. Herein we describe the structure-activity relationship study of 23 compounds: biflavonoids from D. balansae (1-4) and from D. araucarioides (5-10), hexamethyl-amentoflavone (11), cupressuflavone (12), and apigenin derivatives (13-23). We conclude that 1) over the four different biflavonoid skeletons tested, amentoflavone (1) and robustaflavone (5) are the most promising ones for antidengue drug development, 2) the number and position of methyl groups on the biflavonoid moiety modulate their inhibition of Dengue virus NS5 RNA-dependent RNA polymerase, and 3) the degree of oxygenation of flavonoid monomers influences their antidengue potential. Sotetsuflavone (8), with an IC50 = 0.16 µM, is the most active compound of this series and is the strongest inhibitor of the Dengue virus NS5 RNA-dependent RNA polymerase described in the literature.
A scanning Kelvin probe study of charge trapping in zone-cast pentacene thin film transistors (2008)

We have used scanning Kelvin probe microscopy (SKPM) as a local probe to study charge trapping in zone-cast pentacene field effect transistors on both SiO(2) and benzocyclobutene (BCB) substrates. Annealing at 130 degrees C was found to reduce the threshold voltage, susceptibility to negative gate bias stress and trapping of positive charges within single pentacene grains. We conclude that oxygen is able to penetrate and disassociatively incorporate into crystalline pentacene, chemically creating electrically active defect states. Screening of a positive gate bias caused by electron injection from Au into pentacene was directly observed with SKPM. The rate of screening was found to change significantly after annealing of the film and depended on the choice of gate dielectric.
Degradation of carbon reinforced polymer composites under galvanic coupling conditions (1992)

Carbon re inforced polyes ter and vinyl e s t e r composi tes form blisters when galvanically coupled. S c a n n i n g e l e c t r o n m i c r o s c o p e s t u d i e s r e v e a l d e b o n d i n g a t f ibe r lmat r ix in te r face which is related to cathodic reaction(s) at the interface. A cathode with a polymer f i lm on i t can produce galvanic b l i s t e r s w h i c h e l i m i n a t e s t h e influence of coupling agents, etc. on the blistering. Polymer degradation on platinum cathode suggests that the polymer may involve in the blistering reaction. Electrochemical s tudies reveal that at a s ing le potential, the cathodic current under polymer f i lm is two orders of magni tude l o w e r than tha t o n uncoated carbon fiber. Even the low current density is sufficient to cause galvanic degradation. The t ime for b l is ter ing i s sens i t ive to smal l changes in galvanic currents.
Impact of mask making imperfections on the performance of matching critical sub-circuit blocks (2012)

In this paper, we present an investigation of the impact of mask making imperfections on matching. Comparing optically measured and electrically derived data for line width errors allows pinpointing whether or not the mask limits the best achievable device matching. Treating matching critical sub-circuit blocks themselves as test structures, we demonstrate a direct methodology for assessing the impact of process and mask on the performance of high-precision analog products.
Structural and catalytic properties of a deletion derivative (delta 133-157) of Escherichia coli adenylate kinase (1991)

Escherichia coli adenylate kinase (AKe) as well as the enzyme from yeast and mitochondria differs from the muscle cytosolic variant (AK1) by an insertion of 25 amino acid residues that are missing in AK1. The extra sequence, highly homologous in "large" size variants, is situated between residues 133 and 157 in AKe. Removal of 25 codons in the corresponding adk gene resulted in expression of a modified form of adenylate kinase (delta 133-157 AKe) which still conserved 7% of the maximal activity of the wild-type protein. The apparent Km for nucleotide substrates was increased by a factor of 4.6 (ADP), 23 (ATP) or 43 (AMP) in delta 133-157 AKe when compared with the wild-type enzyme. The secondary structure of delta 133-157 AKe, as well as its thermal stability were very similar to the parent protein. However, the deleted protein was much more sensitive than the wild-type enzyme to inactivation by trypsin. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of trypsin digested delta 133-157 AKe revealed accumulation of several well defined fragments which were not observed in the case of wild-type enzyme. We conclude that the additional sequence, although necessary for expression of full activity in AKe, is not critical for catalysis. It is perhaps responsible for interaction of enzyme with other cellular components although a different mechanism of water shielding for large and small size variants of AK can be also envisaged.
Structural basis of synergistic neutralization of Crimean-Congo hemorrhagic fever virus by human antibodies (2022)

Crimean-Congo hemorrhagic fever virus (CCHFV) is the most widespread tick-borne zoonotic virus, with a 30% case fatality rate in humans. Structural information is lacking in regard to the CCHFV membrane fusion glycoprotein Gc—the main target of the host neutralizing antibody response—as well as antibody–mediated neutralization mechanisms. We describe the structure of prefusion Gc bound to the antigen-binding fragments (Fabs) of two neutralizing antibodies that display synergy when combined, as well as the structure of trimeric, postfusion Gc. The structures show the two Fabs acting in concert to block membrane fusion, with one targeting the fusion loops and the other blocking Gc trimer formation. The structures also revealed the neutralization mechanism of previously reported antibodies against CCHFV, providing the molecular underpinnings essential for developing CCHFV–specific medical countermeasures for epidemic preparedness.
Gray codes for Spatial Modulation systems: An open research issue (2017)

Due to the high spectral efficiency of Spatial Modulation (SM) systems, an increasing attention is being paid to investigate SM as a potential candidate for future wireless transmission. Large amount of research has been dedicated for SM performance compared to the current transmission systems. However, the problem of bit to symbol mapping in SM has been rarely investigated in the literature. Unlike other systems, the applied bit to symbol mapping in SM cannot satisfy Gray code principle, which, in turn, degrades the error performance. This article sheds light on this problem as an open research issue. The article starts by exploring the problem, discussing the encountering challenges for potential solutions, and including some expected results, aiming at motivating researchers to handle the problem.
Conserved effects and altered trafficking of Cetuximab antibodies conjugated to gold nanoparticles with precise control of their number and orientation (2017)

Gold nanoparticles (17 nm) have been functionalized with the antiangiogenic monoclonal antibody drug Cetuximab at a well-defined orientation and coverage density of antibodies. Functionalization has been carried out through site-directed chemistry via the selective oxidation of the carbohydrate moiety of antibodies linked to a thiolated hydrazide. A431 tumor cells have been exposed to these conjugates for in vitro evaluation of their effects. In addition to epithelial growth factor receptor blocking, trafficking and signaling alterations were also observed. Thus, the blocking effects of Cetuximab were increased and sustained for a longer time when associated with the nanoparticles. Enhancing antibody therapy effects by decreasing the needed dose and prolonging its effect by avoiding receptor recycling may serve to obtain increased therapeutic benefits for immunotherapy.
Probing the Halide Effect in the δ-Bond with One- and Two-Photon Spectroscopy (2022)

Two electrons in two orbitals give rise to four states. When the orbitals are weakly coupled as in the case for the d<sub><i>xy</i></sub> orbitals of quadruple bond species, two of the states are diradical in character with electrons residing in separate orbitals and two of the states are zwitterionic with electrons paired in one orbital or the other. By measuring one-and two-photon spectra, the one-electron (ΔW) and two-electron (K) energies may be calculated, which are the determinants of the state energies of the four-state model for the two-electron bond. The K energy is thus especially sensitive to the size of the orbital as K is dependent on the distance between electrons. To this end, one- and two-photon spectra of Mo<sub>2</sub>X<sub>4</sub>(PMe<sub>3</sub>)<sub>4</sub> are sensitive to secondary bonding interactions of the δ-orbital manifold with the halide orbitals, as reflected in decreasing K energies along the series Cl > Br > I. Additionally, the calculated one-electron energies have been verified with the spectroelectrochemical preparation of the Mo<sub>2</sub>X<sub>4</sub>(PMe<sub>3</sub>)<sub>4</sub><sup>+</sup> complexes, where the δ bond is a one-electron bond, and K is thus absent. The δ → δ* transition shifts over 10,000 cm<sup>-1</sup> upon oxidation of Mo<sub>2</sub>X<sub>4</sub>(PMe<sub>3</sub>)<sub>4</sub> to Mo<sub>2</sub>X<sub>4</sub>(PMe<sub>3</sub>)<sub>4</sub><sup>+</sup>, establishing that transitions within the two-electron δ bond are heavily governed by the two-electron exchange energy.
MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes (2023)

The MultiomicsTracks96 workflow is well suited for high dimensional multi-omics studies - for instance, multiorgan animal models of disease, drug toxicities, environmental exposure, and aging as well as large-scale clinical investigations involving the use of biospecimens from existing tissue repositories.