gebhart/patrepeval huggingface dataset:
Death receptor 3 is essential for generating optimal protective CD41 T‐cell immunity against Salmonella (2012)

The TNF receptor superfamily member death receptor 3 (DR3) exacerbates Th2- and Th17-cell-mediated inflammatory and autoimmune conditions, yet no role in host defence has been reported. Here, we examined the role of DR3 during infection with Salmonella enterica serovar Typhimurium. Infection resulted in protracted expression of the DR3 ligand TL1A but not the related TNF superfamily proteins OX40L or CD30L. TL1A expression was localized to splenic F4/80(+) macrophages where S. enterica Typhimurium replicates, and temporally coincided with the onset of CD4(+) -cell expansion. To address the relevance of the TL1A-DR3 interaction, we examined immune responses to S. enterica Typhimurium in mice lacking DR3. Infected DR3(-/-) mice harboured reduced numbers of antigen-experienced and proliferating CD4(+) T cells compared with WT mice. Furthermore, the frequency of IFN-γ(+) CD4(+) T cells in DR3(-/-) mice was lower throughout the time of bacterial clearance. Importantly, bacterial clearance, which is dependent on Th1 cells, was also impaired in DR3(-/-) mice. This defect was intrinsic to CD4(+) T cells as evidenced by an increase in bacterial burden in RAG2-deficient mice receiving DR3(-/-) CD4(+) T cells compared with WT CD4(+) -cell recipients. These data establish for the first time a role for DR3 in a host defence response.
Maternal Cardiac Function and Uterine Artery Doppler at 11–14 Weeks in the Prediction of Preeclampsia in Nulliparous Women (2008)

It is clear that preeclampsia is not—as previously thought—a uniformly high-resistance, volume-contracted state. Instead, hemodynamic features range from a hyperdynamic state with elevated cardiac output (CO) and increased left ventricular (LV) function to a vasoconstrictive state with decreased CO and reduced LV function. Variable profiles of systemic resistance also have been described. This prospective observational study used two-dimensional and M-mode echocardiography as well as uterine artery Doppler studies, performed at 11 to 14 weeks’ gestation, to evaluate cardiac function in 534 nulliparous women with singleton pregnancies who presented consecutively to the maternity unit of a teaching hospital for routine antenatal care. In addition to 457 women having a normal outcome there were 8 with preeclampsia but not a small-for-gestational-age (SGA) infant, 19 with preeclampsia and SGA infant, and 50 with SGA infant but not with preeclampsia. The groups did not differ with respect to maternal age, height, or gestation at the time of enrollment. Women with preeclampsia and SGA infant included a disproportionately high number of black women and women having earlier gestations at delivery. Birth weight centile was significantly reduced in women having an SGA infant. Compared with women having a normal outcome, those with preeclampsia but not with SGA infant had increased CO and mean arterial pressure (MAP). MAP, total peripheral resistance, and the uterine artery pulsatility index (UAPI) were increased in the group with preeclampsia and SGA infant. Total peripheral resistance and UAPI were increased in women with SGA infant but not preeclampsia. Multiple logistic regression analysis identified MAP, stroke volume, and UAPI as independent predictors of preeclampsia. SV and UAPI also were independent predictors of SGA.
Extinction Coefficients of Triplet–Triplet Absorption Spectra of Organic Molecules in Condensed Phases: A Least-Squares Analysis (1987)

A global least-squares technique is developed to assist in the critical evaluation of data consisting of large sets of measurements. The technique is particularly designed to handle sets of data where many of the measurements are relative measurements. A linearization procedure is used to reduce the inherently nonlinear problem to a traditional multivariate linear regression. The technique developed here is used to evaluate extinction coefficients, ε’s, of triplet–triplet absorption (TTA) spectra of organic molecules in condensed phases. A previous assumption, that there are no solvent effects on the TTA spectra, is investigated and modified so that a group of compounds measured in benzene is treated separately. The set of 445 ε’s obtained from the global least-squares fit, including these solvent effects, is presented in the accompanying tables. How these least-squares results can be used in a hierarchy of TTA ε standards is discussed. Further solvent effects such as the separation of polar and nonpolar media and the influence of temperature are probed.
Revisión: Envasado activo de los alimentos / Review: Active food packaging (2000)

A great technological development for food packaging has been developed over the past few decades to satisfy consumer demands relating to more natural forms of preservation, and methods to control packaging and storage for assurance and food safety. Active packaging is, certainly, one of the most important innovations in this field. Active packages are designed to perform a role other than to provide an inert barrier between the product and the outside environment, using the possible interactions between food and package in a positive way to improve product quality and acceptability. Active food packaging is a heterogeneous concept involving a wide range of possibilities which globally can be grouped in two main goals: (i) to extend shelf life, and (ii) to facilitate processing and consumption of foods. In the first case, active packaging solutions include the systems studied to control the mechanisms of deterioration inside the package (i.e. oxygen scavengers, moisture absorbers or antimicrobial agents). In relation to the second goal, active packaging allows us to match the package to the properties of the food, to reduce costs of processing, or even to perform some processing operations in-package or to control the product history and quality. This paper reviews the different applications of active packaging and their commercial use, together with some legal aspects and future trends.
Polyfluorophores on a DNA Backbone: A Multicolor Set of Labels Excited at One Wavelength (2009)

We recently described the assembly of fluorescent deoxyriboside monomers ("fluorosides") into DNA-like phosphodiester oligomers (oligodeoxyfluorosides or ODFs) in which hydrocarbon and heterocyclic aromatic fluorophores interact both physically and electronically. Here we report the identification of a multicolor set of water-soluble ODF dyes that display emission colors across the visible spectrum, and all of which can be simultaneously excited by long-wavelength UV light at 340-380 nm. Multispectral dye candidates were chosen from a library of 4096 tetramer ODFs constructed on PEG-polystyrene beads using a simple long-pass filter to observe all visible colors at the same time. We resynthesized and characterized a set of 23 ODFs containing one to four individual chromophores and included 2-3 spacer monomers to increase aqueous solubility and minimize aggregation. Emission maxima of this set range from 376 to 633 nm, yielding apparent colors from violet to red, all of which can be visualized directly. The spectra of virtually all ODFs in this set varied considerably from the simple combination of monomer components, revealing extensive electronic interactions between the presumably stacked monomers. In addition, comparisons of anagrams in the set (isomers having the same components in a different sequence) reveal the importance of nearest-neighbor interactions in the emissive behavior. Preliminary experiments with human tumor (HeLa) cells, observing two ODFs by laser confocal microscopy, showed that they can penetrate the outer cellular membrane, yielding cytoplasmic localization. In addition, a set of four distinctly colored ODFs was incubated with live zebrafish embryos, showing tissue penetration, apparent biostability, and no apparent toxicity. The results suggest that ODF dyes may be broadly useful as labels in biological systems, allowing the simultaneous tracking of multiple species by color, and allowing visualization in moving systems where classical fluorophores fail.
Virological and immunological connotations of apoptotic and anti-apoptotic forces in neoplasia (2001)

Against the background of its earliest recognition, programmed cell death (PCD) or apoptosis (A) is presented in its fundamental biological contexts. Techniques of its demonstration are listed. Former original works of the authors encompass designs for genetically engineered oncolytic viruses. Presented here are observations on mesenchymal stromal cells of the bone marrow serving as feeder layers to chronic lymphocytic leukemia (CLL) cells (recently rediscovered elsewhere as subverted "nurse cells" protecting CLL cells from A). A-resistant human melanoma cells are shown to expropriate the Fas ligand to Fas receptor (CD95; APO-1) (FasL-->FasR) system for their autocrine growth loop not only in melanoma cells coexpressing CD95 and its ligand but also in CD95-positive melanoma cells undergoing divisions when exposed to CD95 ligand. Bi-directional A-induction is demonstrated upon the encounter of cytotoxic lymphocytes and targeted tumor cells as exemplified with lymphomas; and chemotherapy-induced A of malignant cells as exemplified by paclitaxel-induced PCD of Reed-Sternberg (RS) cells in a case of chemotherapy-resistant Hodgkin's disease (HD). A list of interventions capable of inducing A in tumor cells is provided. These interventions are of potential therapeutic value. The balance of apoptotic and anti-apoptotic forces in virally infected normal and malignant cells is discussed.
Moss–Burstein and plasma reflection characteristics of heavily doped n-type InxGa1−xAs and InPyAs1−y (1999)

Degenerately doped (&amp;gt;1019 cm−3) n-type InxGa1−xAs (x∼0.67) and InPyAs1−y (y∼0.65) possess a number of intriguing electrical and optical properties relevant to electro-optic devices and thermophotovoltaic devices in particular. Due to the low electron effective mass of these materials (m*&amp;lt;0.2) and the demonstrated ability to incorporate n-type dopants into the high 1019 cm−3 range, both the Moss–Burstein band gap shift and plasma reflection characteristics are particularly dramatic. For InGaAs films with a nominal undoped band gap of 0.6 eV and N=5×1019 cm−3, the fundamental absorption edge increased to 1.27 eV. InPAs films exhibit a shorter plasma wavelength (λp∼5 μm) in comparison to InGaAs films (λp∼6 μm) with similar doping concentrations. The behavior of the plasma wavelength and the fundamental absorption edge are investigated in terms of conduction band nonparabolicity and Γ-L valley separation using detailed band structure measurements and calculations.
GaAs-based near-infrared omnidirectional reflector (2003)

We introduce a compound-semiconductor-based omnidirectional reflector. A four-layer-pair stack of GaAs/AlAs was grown epitaxially using molecular-beam epitaxy, and was then converted to a GaAs/Al2O3 multilayer stack by selective oxidation of the AlAs layers. The resultant one-dimensional photonic crystal exhibited omnidirectional reflection properties in near-IR wavelength range below 1 μm. Reflectance spectra measured at various incidence angles and polarizations were observed to be in good agreement with theoretically simulated results.
Targeting TRAIL Death Receptor 4 with Trivalent DR4 Atrimer Complexes (2012)

TRAIL is a trimeric protein that potently induces apoptosis in cancer cells by binding to the trimeric death receptors (DR4 or DR5). Death receptors are attractive therapeutic targets through both the recombinant TRAIL ligand as well as receptor agonist monoclonal antibodies. Although efficacy of the ligand is hampered by its short half-life, agonistic antibodies have a much longer half-life and have shown some clinical efficacy as antitumor agents. However, the efficacy of these antibodies may be limited by their bivalent nature that does not optimally mimic the trimeric ligand. To overcome limitations of currently used death receptor-targeting agents, we engineered trimeric proteins called Atrimer complexes that selectively bind DR4 and potently induce apoptosis in a variety of cancer cells. Atrimer complexes are based on human tetranectin, a trimeric plasma protein of approximately 60 kDa. Loop regions within the tetranectin C-type lectin domains (CTLD) were randomized to create a large phage display library that was used to select DR4-binding complexes. A panel of unique and potent agonist DR4 Atrimer complexes with subnanomolar affinity to DR4 and no detectable binding to DR5 or the decoy receptors was identified. Mechanism of action studies with a selected Atrimer complex, 1G(2), showed that Atrimer complexes induce caspase-dependent and DR4-specific apoptosis in cancer cells while sparing normal human fibroblasts and, importantly, hepatocytes. This proof-of-principle study supports the use of alternative proteins engineered to overcome limitations of therapeutically desirable molecules such as TRAIL.
High viable cell concentration fed‐batch cultures of hybridoma cells through on‐line nutrient feeding (1995)

A hybridoma cell line was cultivated in fed-batch cultures using a low-protein, serum-free medium. On-line oxygen uptake rate (OUR) measurement was used to adjust the nutrient feeding rate based on glucose consumption, which was estimated on-line using the stoichiometric relations between glucose and oxygen consumption. Through on-line control of the nutrient feeding rate, not only sufficient were supplied for cell growth and antibody production, but also the concentrations of glucose and other important nutrients such as amino acids were maintained at low levels during the cell growth phase. During the cultivation, cell metabolism changed from high lactate production and low oxygen consumption to low lactate production and high oxygen consumption. As a result the accumulation of lactate was reduced and the growth phase was extended. In comparison with the batch cultures, in which cells reached a concentration of approximately 2 x 10(6) cells/mL, a very high concentration of 1.36 x 10(7) cells/mL with a high cell viability (>90%) was achieved in the fed-batch culture. By considering the consumption of glucose and amino acids, as well as the production of cell mass, metabolites, and antibodies, a well-closed material balance was established. Our results demonstrate the value of coupling on-line OUR measurement and the stoichiometric relations for dynamic nutrient feeding in high cell concentration fed batch cultures.
Markers of Collagen Remodeling Detect Clinically Significant Fibrosis in Chronic Hepatitis C Patients (2015)

The Pro-C3 protein fragment provided clinically relevant diagnostic accuracy as a single marker of liver fibrosis. A model combining Pro-C3 and C4M along with patient's age, body mass index and gender increased the diagnostic power for identifying clinically significant fibrosis.
A case for TCP Vegas in high-performance computational grids (2002)

Computational grids such as the Information Power Grid (Johnston et al., 1999), Particle Physics Data Grid , and Earth System Grid depend on TCP to provide reliable communication between nodes across a wide-area network (WAN). Of the available TCP implementations, TCP Reno and its variants are the most widely deployed; however, Reno's performance in computational grids is mediocre at best. Due to conflicting results in the evaluation of TCP implementations, we present a detailed simulation study that unifies the conflicting results and demonstrates the limitations of earlier work. We focus on the two most debated versions of TCP-Reno and Vegas. Using real traffic distributions, we show that Vegas performs well over modern high-performance links and better than Reno with the proper selection of the Vegas parameters /spl alpha/ and /spl beta/. Our results exhibit ways to significantly enhance the performance of distributed computational grids that rely on TCP.
The Tangier disease gene product ABC1 controls the cellular apolipoprotein-mediated lipid removal pathway (1999)

The ABC1 transporter was identified as the defect in Tangier disease by a combined strategy of gene expression microarray analysis, genetic mapping, and biochemical studies. Patients with Tangier disease have a defect in cellular cholesterol removal, which results in near zero plasma levels of HDL and in massive tissue deposition of cholesteryl esters. Blocking the expression or activity of ABC1 reduces apolipoprotein-mediated lipid efflux from cultured cells, and increasing expression of ABC1 enhances it. ABC1 expression is induced by cholesterol loading and cAMP treatment and is reduced upon subsequent cholesterol removal by apolipoproteins. The protein is incorporated into the plasma membrane in proportion to its level of expression. Different mutations were detected in the ABC1 gene of 3 unrelated patients. Thus, ABC1 has the properties of a key protein in the cellular lipid removal pathway, as emphasized by the consequences of its defect in patients with Tangier disease.
Local Drug Delivery to the Inner Ear Using Biodegradable Materials (2011)

The lack of an effective method of drug delivery has been a considerable obstacle in the development of novel therapeutics for inner ear diseases. However, several strategies have been investigated to achieve drug delivery to the inner ear, particularly for local application. Here, we review recent advances in the development of inner ear drug-delivery systems, focusing on biodegradable materials. Both synthetic and natural biodegradable materials have shown efficacy for inner ear drug delivery, resulting in an attenuation of hearing loss in animal models. We expect the further development of such drug-delivery systems to help translate the findings of experimental studies to clinical applications.
Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations (2010)

The Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) and the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) methods calculate binding free energies for macromolecules by combining molecular mechanics calculations and continuum solvation models. To systematically evaluate the performance of these methods, we report here an extensive study of 59 ligands interacting with six different proteins. First, we explored the effects of the length of the molecular dynamics (MD) simulation, ranging from 400 to 4800 ps, and the solute dielectric constant (1, 2, or 4) on the binding free energies predicted by MM/PBSA. The following three important conclusions could be observed: (1) MD simulation length has an obvious impact on the predictions, and longer MD simulation is not always necessary to achieve better predictions. (2) The predictions are quite sensitive to the solute dielectric constant, and this parameter should be carefully determined according to the characteristics of the protein/ligand binding interface. (3) Conformational entropy often show large fluctuations in MD trajectories, and a large number of snapshots are necessary to achieve stable predictions. Next, we evaluated the accuracy of the binding free energies calculated by three Generalized Born (GB) models. We found that the GB model developed by Onufriev and Case was the most successful model in ranking the binding affinities of the studied inhibitors. Finally, we evaluated the performance of MM/GBSA and MM/PBSA in predicting binding free energies. Our results showed that MM/PBSA performed better in calculating absolute, but not necessarily relative, binding free energies than MM/GBSA. Considering its computational efficiency, MM/GBSA can serve as a powerful tool in drug design, where correct ranking of inhibitors is often emphasized.
Peptide Vaccine: Progress and Challenges (2014)

Conventional vaccine strategies have been highly efficacious for several decades in reducing mortality and morbidity due to infectious diseases. The bane of conventional vaccines, such as those that include whole organisms or large proteins, appear to be the inclusion of unnecessary antigenic load that, not only contributes little to the protective immune response, but complicates the situation by inducing allergenic and/or reactogenic responses. Peptide vaccines are an attractive alternative strategy that relies on usage of short peptide fragments to engineer the induction of highly targeted immune responses, consequently avoiding allergenic and/or reactogenic sequences. Conversely, peptide vaccines used in isolation are often weakly immunogenic and require particulate carriers for delivery and adjuvanting. In this article, we discuss the specific advantages and considerations in targeted induction of immune responses by peptide vaccines and progresses in the development of such vaccines against various diseases. Additionally, we also discuss the development of particulate carrier strategies and the inherent challenges with regard to safety when combining such technologies with peptide vaccines.
Induction of the H-2 D antigen during B cell activation. (1989)

Mitogenic activation causes increased expression of class I Ag of the MHC in mouse B cells. The increased expression was seen in flow cytometry analysis for both K and D in k as well as d haplotypes. A more detailed molecular analysis was carried out for H-2Dd. Increased expression (10- to 20-fold) of the H-2 Dd gene was detected at both protein and messenger RNA levels, and the time course for the accumulation of H-2 Dd protein on the cell surface parallels the increase in the steady-state messenger RNA levels. The increase in H-2 Dd expression in small B cells stimulated with LPS is detectable after 10 h of culture. The present data provide molecular and serologic evidence about alterations in the expression of the H-2 Dd Ag, previously identified as a B cell activation antigen B7.2. Our results indicate a new significance for the function and regulation of the MHC during immune responses, and suggest that the class I molecules may serve some role in the B cell activation process.
Identification of Genes Encoding Adenylate Isopentenyltransferase, a Cytokinin Biosynthesis Enzyme, inArabidopsis thaliana (2001)

The initial step in the de novo biosynthesis of cytokinin in higher plants is the formation of isopentenyladenosine 5'-monophosphate (iPMP) from AMP and dimethylallylpyrophosphate (DMAPP), which is catalyzed by adenylate isopentenyltransferase (IPT). Although cytokinin is an essential hormone for growth and development, the nature of the enzyme for its biosynthesis in higher plants has not been identified. Herein, we describe the molecular cloning and biochemical identification of IPTs from Arabidopsis thaliana. Eight cDNAs encoding putative IPT, designated as AtIPT1 to AtIPT8, were picked up from A. thaliana. The Escherichia coli transformants expressing the recombinant proteins excreted cytokinin species into the culture medium except for that expressing AtIPT2 that is a putative tRNA IPT. A purified recombinant AtIPT1 catalyzed the formation of iPMP from DMAPP and AMP. These results indicate that the small multigene family contains both types of isopentenyltransferase, which could synthesize cytokinin and mature tRNA.
FBAR laterally Coupled Resonator Filter (2015)

A very attractive CRF (Coupled Resonator Filter) topology is to laterally couple thin film bulk acoustic resonators (FBAR). However, the filter band width is narrow because the coupling between conventional FBAR resonators is very weak. The coupling, and thus the bandwidth, may be increased by forming pairs of FBAR with an inter-digital coupling configuration. Both narrow electrode finger width and multiple coupled finger pairs enhance lateral acoustical coupling, resulting in filters with wider pass band. The finite element simulation and experimental results on LCRF structures show that the multiple acoustical modes can be combined to form a wider range of pass bands than available in a conventional ladder filter.