gebhart/patrepeval huggingface dataset:
Single-beam squeezed-state generation in semiconductor waveguides with X^(3) nonlinearity at below half-band gap (1995)

We analyze a new scheme for generating squeezed states in a short semiconductor AlxGa1−xAs waveguide with χ(3) nonlinearity at below half the band-gap energy. We find that for a Gaussian pulse the amount of squeezing achievable is limited by the squeezed-state detection phase mismatch caused by the pump self-phase modulation and is also degraded slightly by the pump–probe phase mismatch that is due to the different nonlinear refractive indices experienced by the pump and the probe beams. We show theoretically that the amount of squeezing observed can be increased by use of either a short pulse or a pulse with matched phase variation as the local oscillator. In a centimeter-long AlxGa1−xAs waveguide more than 85% (8.2 dB) of squeezing potentially can be obtained, limited mainly by two-photon absorption.
A Systematic Literature Review of Curcumin with Promising Antileishmanial Activity (2020)

This review indicated that CUR derivatives, instead of CUR alone showed a high potential to serve as an effective herbal drug against leishmaniasis. Moreover, we concluded that the antileishmanial activity of CUR/bioactive compounds is mostly due to increased oxidative stress and apoptosis.
Annexin A2: biology and relevance to the antiphospholipid syndrome (2008)

Antiphospholipid antibodies (aPL), the majority of which are directed against beta(2)-glycoprotein I (beta(2)GPI), are associated with an increased incidence of venous and arterial thrombosis. The pathogenesis of antiphospholipid/anti-beta(2)GPI-associated thrombosis has not been defined, and is likely multifactorial. However, accumulating evidence suggests an important role for endothelial cell activation with the acquisition of a procoagulant phenotype by the activated endothelial cell. Previous work demonstrated that endothelial activation by antiphospholipid/anti-beta(2)GPI antibodies is beta(2)GPI-dependent. We extended these observations by defining annexin A2 as an endothelial beta(2)GPI binding site. We also observed that annexin A2 plays a critical role in endothelial cell activation induced by anti-beta(2)GPI antibodies, and others have described direct endothelial activation by anti-annexin A2 antibodies in patients with aPL . Similar findings have been reported using human monocytes, which also express annexin A2. Because annexin A2 is not a transmembrane protein, how binding of beta(2)GPI/anti-beta(2)GPI antibodies, or anti-annexin A2 antibodies, to endothelial annexin A2 causes cellular activation is unknown. Recent studies, however, suggest an important role for the Toll-like receptor family, particularly TLR4. In this article, we review the role of these interactions in the activation of endothelial cells by aPL . The influence of these antibodies on the ability of annexin A2 to enhance t-PA-mediated plasminogen activation is also discussed.
Live Cell Imaging of In Vitro Human Trophoblast Syncytialization1 (2014)

Human trophoblast syncytialization, a process of cell-cell fusion, is one of the most important yet least understood events during placental development. Investigating the fusion process in a placenta in vivo is very challenging given the complexity of this process. Application of primary cultured cytotrophoblast cells isolated from term placentas and BeWo cells derived from human choriocarcinoma formulates a biphasic strategy to achieve the mechanism of trophoblast cell fusion, as the former can spontaneously fuse to form the multinucleated syncytium and the latter is capable of fusing under the treatment of forskolin (FSK). Live-cell imaging is a powerful tool that is widely used to investigate many physiological or pathological processes in various animal models or humans; however, to our knowledge, the mechanism of trophoblast cell fusion has not been reported using a live- cell imaging manner. In this study, a live-cell imaging system was used to delineate the fusion process of primary term cytotrophoblast cells and BeWo cells. By using live staining with Hoechst 33342 or cytoplasmic dyes or by stably transfecting enhanced green fluorescent protein (EGFP) and DsRed2-Nuc reporter plasmids, we observed finger-like protrusions on the cell membranes of fusion partners before fusion and the exchange of cytoplasmic contents during fusion. In summary, this study provides the first video recording of the process of trophoblast syncytialization. Furthermore, the various live-cell imaging systems used in this study will help to yield molecular insights into the syncytialization process during placental development.
Hardware realisable models of neural processing (1989)

Summary form only given. An identity that has been recently established by D. Gorse and J.G. Taylor (Phys. Lett., vol.A131, p.326, 1988) between a certain class of neural model (originally proposed by Taylor) and a simple piece of electronic hardware, the probabilistic random-access memory (pRAM) holds out the possibility of mimicking physiological nets in hardware. The Taylor model has recently been extended to examine in more detail the pre- and postsynaptic processes that lead up to neural firing. The extended model retains the successful features of the original, but by operating at much shorter time scales (on the order of the lifetime of a quantum of neurotransmitter in the synaptic cleft) it allows higher order statistical information to be retrieved from the simulated spike train. It is capable of incorporating a great deal of biological detail, including effects associated with the mechanism of summation of postsynaptic potentials (PSPs), cell surface geometry, and axo-axonal interactions. Like its predecessor the new model has a straightforward hardware implementation as a pRAM, in which parameters relating to PSP summation and firing behavior can be changed by simply writing to the appropriate set of memory locations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Lethal effect of the expression of a killer gene SMK1 in Saccharomyces cerevisiae (2000)

Expression of the SMK1 gene which encodes the yeast killer toxin SMKT is lethal in Saccharomyces cerevisiae. Effects of deletion and site-directed mutagenesis of SMK1 on the lethality and the secretion of the gene products were examined. Deletion of the interstitial gamma peptide or the C-terminal loop from Ala208 to the C-terminal Asp222 had no effect on the lethality. Those SMK1 products that lacked either the gamma peptide or the C-terminal loop were expressed in the cells but were not secreted into the culture medium, suggesting that these peptides may have a role in secretion or in protein stability. On the other hand, deletion of the signal sequence resulted in complete loss of the lethal activity. Entering the secretory pathway may be critical for the lethality. Further, deletion of the region from the C-terminus to Leu207 resulted in loss of the lethal activity. Leu207 is located at the C-terminus of the central strand of the beta-sheet structure of SMKT and its side chain is thrust into a hydrophobic environment between the beta-sheet and the alpha-helices. The result obtained upon substitutions of Ala, Ser or Glu for Leu207 suggested that the side chain of Leu207 stabilizes the hydrophobic environment that contributes to the overall structure of the SMK1 product.
Reactivity with a specific epitope of outer surface protein A predicts protection from infection with the Lyme disease spirochete, Borrelia burgdorferi (1997)

The response to recombinant vaccines for Lyme disease was studied to determine serum antibody levels effective in protecting against tick-transmitted infection. Data presented here demonstrate a significant correlation between antibody to an epitope on outer surface protein A (OspA) and protection against infection with Borrelia burgdorferi in canines and mice. A competitive enzyme-linked immunosorbent assay was developed to measure antibody to a site on OspA, defined by monoclonal antibody LA-2. Comparison of LA-2 titers against infection of canines and mice following vaccination and challenge established a predicted value for LA-2 titers. The statistical relationship between serum antibody levels and protection was calculated by logistic regression analysis. The statistical model predicted that an LA-2 titer of 0.32 microg equivalents (eq) per ml correlated to an 80% predicted probability of protection for both mice and dogs. This value was used to classify mice and dogs as to their protected status at the time of tick exposure. The LA-2 cutoff titer (0.32 microg eq/ml) correctly classified all dogs (n = 13) and mice (n = 44) that failed to become infected. By contrast, 20 of 22 dogs and 28 of 31 mice with titers of less than 0.32 microg eq/ml became infected. On the basis of these results, we conclude that an LA-2 titer is a reliable indicator of immune status for estimating immune protection following use of OspA-based vaccines for B. burgdorferi sensu stricto.
Claudin-6: a novel receptor for CPE-mediated cytotoxicity in ovarian cancer (2012)

Claudins are integral tight junction proteins that are responsible for maintaining the integrity of epithelial cell architecture and cell polarity. Claudin-3 and -4 are overexpressed in several cancers and have been shown to act as receptors for the Clostridium perfringens enterotoxin (CPE), a toxin that causes rapid cell lysis. CPE has demonstrated effectiveness in treating several different cancers in mouse models, provided that these cancers express claudin-3 or claudin-4. Here, we show that claudin-3/4 expression is not an absolute requirement for CPE action and, through overexpression and knockdown experiments, we identify claudin-6 as a novel functional receptor for CPE. Indeed, UCI-101, an ovarian cancer cell line highly sensitive to CPE, does not express claudin-3/4 and knockdown of claudin-6 in these cells decreases CPE sensitivity. Moreover, two different ovarian cell lines that are resistant to the effects of CPE can be made sensitive through claudin-6 overexpression. Binding assays show that CPE can indeed bind claudin-6 in cells and that this binding is associated with CPE cytotoxicity. Multicellular tumor spheroids experiments demonstrate that claudin-6 can also be a target of CPE in three-dimensional cultures. Our data establish claudin-6 as a novel receptor for CPE and introduces the possibility of a novel targeted therapeutic for ovarian and other cancers that express claudin-6.
Calmodulin Remains Extended upon Binding to Smooth Muscle Caldesmon:  A Combined Small-Angle Scattering and Fourier Transform Infrared Spectroscopy Study (2000)

We show that calmodulin (CaM) has an extended conformation in its complexes with sequences from the smooth muscle thin filament protein caldesmon (CaD) by using small-angle X-ray and neutron scattering with contrast variation. The CaD sequences used in these experiments were a C-terminal fragment, 22kCaD, and a smaller peptide sequence within this fragment, MG56C. Each of these sequences contains the CaM-binding sites A and B previously shown to interact with the C- and N-terminal lobes of CaM, respectively [Wang et al. (1997) Biochemistry 36, 15026]. By modeling the scattering data, we show that the majority of the MG56C sequence binds to the N-terminal domain of CaM. FTIR data on CaM complexed with 22kCaD or with MG56C peptide show the 22kCaD sequence contains unordered, helix, and extended structures, and that the extended structures reside primarily in the MG56C portion of the sequence. There are small changes in secondary structure, involving approximately 12 residues, induced by CaM binding to CaD. These changes involve a net decrease in extended structures accompanied by an increase in alpha-helix, and they occur within the CaM and/or in the MG56C sequence.
Positive Regulation of Sugar Catabolic Pathways in the Cyanobacterium Synechocystis sp. PCC 6803 by the Group 2 σ Factor SigE (2005)

The sigE gene of Synechocystis sp. PCC 6803 encodes a group 2 sigma factor for RNA polymerase and has been proposed to function in transcriptional regulation of nitrogen metabolism. By using microarray and Northern analyses, we demonstrated that the abundance of transcripts derived from genes important for glycolysis, the oxidative pentose phosphate pathway, and glycogen catabolism is reduced in a sigE mutant of Synechocystis maintained under the normal growth condition. Furthermore, the activities of the two key enzymes of the oxidative pentose phosphate pathway, glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase, encoded by the zwf and gnd genes were also reduced in the sigE mutant. The dark enhancements in both enzyme activity and transcript abundance apparent in the wild type were eliminated by the mutation. In addition, the sigE mutant showed a reduced rate of glucose uptake and an increased intracellular level of glycogen. Moreover, it was unable to proliferate under the light-activated heterotrophic growth conditions. These results indicate that SigE functions in the transcriptional activation of sugar catabolic pathways in Synechocystis sp. PCC 6803.
Enhanced Waypoint Graph for Path Planning in Virtual Worlds (2012)

Our research focuses on the problem of path planning, which often occurs in virtual world applications. We propose an automatic generation of enhanced waypoint graph, which is a graph data structure consisting of point nodes, which describe the corner features in the virtual world, as well as edges connecting those nodes. Given a polygon soup representation of a virtual world, for every character radius, the proposed algorithm starts by constructing a discrete distance field, consisting of regularly sampled points in 3D space. Corner detection and clustering are then done with respect to the points whose distance values are slightly larger than the character size to get the waypoints. These waypoints are further sparsely connected using traversability test, taking into account their distances to nearby obstacles. The resulting enhanced waypoint graph is sparse but has regularly distributed edges emanating from each waypoint. In addition, the graph is also able to handle different types of motions for characters with various sizes.
Elevated vascular angiotensin converting enzyme mediates increased neointima formation after balloon injury in spontaneously hypertensive rats (1997)

Neointima formation after balloon angioplasty in SHR is increased compared with that in normotensive SD rats. This is due mainly to there being a higher degree of activation of the renin-angiotensin system in the aorta of the SHR before and after balloon injury compared with that in normotensive SD rats measured in terms of the increased vascular ACE concentrations. Blood pressure alone had only a moderate effect on neointima formation.
Single-cell nucleic acid profiling in droplets (SNAPD) enables high-throughput analysis of heterogeneous cell populations (2021)

Experimental methods that capture the individual properties of single cells are revealing the key role of cell-to-cell variability in countless biological processes. These single-cell methods are becoming increasingly important across the life sciences in fields such as immunology, regenerative medicine and cancer biology. In addition to high-dimensional transcriptomic techniques such as single-cell RNA sequencing, there is a need for fast, simple and high-throughput assays to enumerate cell samples based on RNA biomarkers. In this work, we present single-cell nucleic acid profiling in droplets (SNAPD) to analyze sets of transcriptional markers in tens of thousands of single mammalian cells. Individual cells are encapsulated in aqueous droplets on a microfluidic chip and the RNA markers in each cell are amplified. Molecular logic circuits then integrate these amplicons to categorize cells based on the transcriptional markers and produce a detectable fluorescence output. SNAPD is capable of analyzing over 100,000 cells per hour and can be used to quantify distinct cell types within heterogeneous populations, detect rare cells at frequencies down to 0.1% and enrich specific cell types using microfluidic sorting. SNAPD provides a simple, rapid, low cost and scalable approach to study complex phenotypes in heterogeneous cell populations.
Studies of reactions with polymers. II. The reaction of maleic anhydride with acrylonitrile onto PVA and the properties of the resultant (1985)

Abstract Graft terpolymers were prepared by graft polymerization of a mixture of acrylonitrile (AN) and maleic anhydride (MA) onto PVA in DMSO solution using KPS as an initiator. Structure and solubility of graft terpolymers varied with the concentrations of KPS and MA. Both lower and upper critical values of KPS concentration varied with MA concentration, and the resulting reaction could be divided into three regions—crosslinked, hydrophobic, and hydrophilic regions. Structures of graft terpolymers were considered to be composed of homopolymer side chain grafted onto PVA while gelation occurred from the surplus radicals in PVA backbone to carry on the coupling reaction. The mechanical properties and viscosities increased with the increase of the wt % of AN in graft terpolymers; however, to increase AN content in PVA by increasing KPS concentration would bring about the oxidation scission and do damage to mechanical properties. Thus it becomes obvious that KPS can only be used at a suitable amount.
Site‐specific enzymatic cleavage of TMV RNA directed by deoxyribo‐ and chimeric (deoxyribo‐ribo)oligonucleotides (1988)

The TMV RNA molecule can be cleaved at a single site by RNase H directed by chimeric oligo(deoxyribo-ribo)nucleotide with an internucleotide pyrophosphate bond.
Automated robust generation of compact 3D statistical shape models (2004)

Ascertaining the detailed shape and spatial arrangement of anatomical structures is important not only within diagnostic settings but also in the areas of planning, simulation, intraoperative navigation, and tracking of pathology. Robust, accurate and efficient automated segmentation of anatomical structures is difficult because of their complexity and inter-patient variability. Furthermore, the position of the patient during image acquisition, the imaging device and protocol, image resolution, and other factors induce additional variations in shape and appearance. Statistical shape models (SSMs) have proven quite successful in capturing structural variability. A possible approach to obtain a 3D SSM is to extract reference voxels by precisely segmenting the structure in one, reference image. The corresponding voxels in other images are determined by registering the reference image to each other image. The SSM obtained in this way describes statistically plausible shape variations over the given population as well as variations due to imperfect registration. In this paper, we present a completely automated method that significantly reduces shape variations induced by imperfect registration, thus allowing a more accurate description of variations. At each iteration, the derived SSM is used for coarse registration, which is further improved by describing finer variations of the structure. The method was tested on 64 lumbar spinal column CT scans, from which 23, 38, 45, 46 and 42 volumes of interest containing vertebra L1, L2, L3, L4 and L5, respectively, were extracted. Separate SSMs were generated for each vertebra. The results show that the method is capable of reducing the variations induced by registration errors.
A software design and implementation for filtering, forwarding and ciphering in a secure bridge (2003)

The authors present the development and the methodology to implement the software of a secure learning-bridge which has the ability to filter, to forward, and to cipher frames in an extended Ethernet environment. The implemented security system was basically built up with three subsystems. These were a management subsystem, a supervision center, and a set of secure bridges, whose functions were filtering the network data traffic and ciphering/deciphering the sensitive data. These devices, called CryptoNets, are described. The algorithm for data ciphering is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Enhanced Immunogenicity of a Genetic Chimeric Protein Consisting of Two Virulence Antigens of<i>Streptococcus mutans</i>and Protection against Infection (2002)

The saliva-binding region (SBR) of the cell surface antigen I/II (AgI/II) and the glucan-binding region (GLU) of the glucosyltransferase enzyme of Streptococcus mutans have been implicated in the initial adherence of S. mutans to saliva-coated tooth surfaces and the subsequent sucrose-dependent accumulation of S. mutans, respectively. Here, we describe the construction and characterization of a genetic chimeric protein consisting of the two virulence determinants SBR and GLU (SBR-GLU). The effectiveness of this construct in inducing mucosal and systemic immune responses to each virulence determinant following intranasal immunization was compared to that of each antigen alone or an equal mixture of SBR and GLU (SBR+GLU) in a mouse model. Furthermore, the ability of antibodies induced to SBR-GLU to protect against S. mutans infection was also investigated. Immunization of mice with the chimeric protein SBR-GLU resulted in significantly enhanced (P < 0.001) levels of serum immunoglobulin G (IgG) anti-SBR antibody activity compared to those in the SBR and SBR+GLU groups. The SBR-GLU-immunized mice also demonstrated a significant (P < 0.05) increase in salivary and vaginal IgA antibody responses to SBR and GLU. Analysis of the serum IgG subclass responses to SBR in mice immunized with SBR alone indicated a mixed IgG1 and IgG2a response. A preferential IgG1 response compared to an IgG2a anti-GLU response was induced in mice immunized with GLU alone. Similarly, a preferential IgG1 response was also induced to SBR when GLU was present in either a mixed or conjugated form. Finally, a significant reduction (P < 0.05) in S. mutans colonization was observed only in mice immunized with the SBR-GLU chimeric protein. Taken together, our results indicate that the chimeric protein SBR-GLU significantly enhanced mucosal immune responses to SBR and GLU and systemic immune responses to SBR. The ability of SBR-GLU to induce responses effective in protection against colonization of S. mutans suggests its potential as a vaccine antigen for dental caries.
Antiangiogenic Therapy for Ischemic Retinopathies (2012)

Neovascularization is a common pathological process in various retinal vascular disorders including diabetic retinopathy (DR), age-related macular degeneration (AMD) and retinal vein occlusion (RVO). The development of neovascular vessels may lead to complications such as vitreous hemorrhage, fibrovascular tissue formation, and traction retinal detachments. Ultimately, irreversible vision loss may result. Various proangiogenic factors are involved in these complex processes. Different antiangiogenic drugs have been formulated in an attempt treat these vascular disorders. One factor that plays a major role in the development of retinal neovascularization is vascular endothelial growth factor (VEGF). Anti-VEGF agents are currently FDA approved for the treatment of AMD and RVO. They are also extensively used as an off-label treatment for diabetic macular edema (DME), proliferative DR, and neovascular glaucoma. However, at this time, the long-term safety of chronic VEGF inhibition has not been extensively evaluated. A large and rapidly expanding body of research on angiogenesis is being conducted at multiple centers across the globe to determine the exact contributions and interactions among a variety of angiogenic factors in an effort to determine the therapeutic potential of antiangiogenic agent in the treatment of a variety of retinal diseases.