gebhart/patrepeval huggingface dataset:
Synergistic Antitumor Effects of Immune Cell-Viral Biotherapy (2006)

Targeted biological therapies hold tremendous potential for treatment of cancer, yet their use has been limited by constraints on delivery and effective tumor targeting. We combined an immune effector cell population [cytokine-induced killer (CIK) cells] with an oncolytic viral therapy to achieve directed delivery to, and regression of, tumors in both immunodeficient and immunocompetent mouse models. Preinfection of CIK cells with modified vaccinia virus resulted in a prolonged eclipse phase with the virus remaining hidden until interaction with the tumor. Whole-body imaging revealed that the cells retained their ability to traffic to and to infiltrate the tumor effectively before releasing the virus. These results illustrate the potential of combining biotherapeutics for synergistic effects that more effectively treat cancer.
Analysis of a continuous‐culture technique for the selection of mutants tolerant to extreme environmental stress (1999)

An analysis is presented of a continuous-culture technique named “Brown and Oliver Interactive-Continuous Selection” (BOICS; Brown and Oliver, 1982), that was devised for the selection of microbial mutants tolerant to extreme environmental stress. The case in which the stress is due to a growth inhibitor is considered. The possible steady outcomes of competition between mutants in BOICS are analyzed under the assumption that the specific growth rates of the competing mutants depend only on the inhibitor concentration. The analysis indicates that BOICS selects mutants that sustain a given specific growth rate (equal to the dilution rate in the selection experiment) at an increased concentration of the inhibitor. Simulation results support the steady-state analysis. Further simulation results show that BOICS may fail if the specific growth rate of a mutant has to be considered to depend on a factor beside the inhibitor concentration. The choice of experimental conditions that promote the success of BOICS is discussed. An interpretation of BOICS emerges from the analysis. Namely, that BOICS implements (at least approximately) a strategy for the selection of tolerant mutants in which (1) all factors in the growth environment, beside the stress of interest (inhibitor concentration) are maintained constant, and (2) the stress is adjusted as the culture evolves so that it is always maximized subject to a specified minimum value of the mean specific-growth rate being maintained. This interpretation suggests new (possibly improved) ways of implementing essentially the same selection technique. It is noted that a chemostat implements the same strategy in the case that the stress is due to the lack of a growth-rate-limiting nutrient. The outcome of selection for inhibitor tolerant mutants in chemostats, turbidostats, and in BOICS is compared. Only BOICS selects specifically for mutants tolerant to extreme concentrations of the inhibitor. © 1999 John Wiley & Sons, Inc. Biotechnol Bioeng 65: 397–406, 1999.
Parameterized unit testing (2010)

Unit testing has been widely recognized as an important and valuable means of improving software reliability, as it exposes bugs early in the software development life cycle. However, manual unit testing is often tedious and insufficient. Testing tools can be used to enable economical use of resources by reducing manual effort. Recently parameterized unit testing has emerged as a very promising and effective methodology to allow the separation of two testing concerns or tasks: the specification of external, black-box behavior (i.e., assertions or specifications) by developers and the generation and selection of internal, white-box test inputs (i.e., high-code-covering test inputs) by tools. A parameterized unit test (PUT) is simply a test method that takes parameters, calls the code under test, and states assertions. PUTs have been supported by various testing frameworks. Various open source and industrial testing tools also exist to generate test inputs for PUTs.
Co-culture of Umbilical Cord Blood CD34þ Cells with Human Mesenchymal Stem Cells (2006)

Insufficient numbers of hematopoietic stem cells (HSCs) and hematopoietic progenitor cells (HPCs) sometimes limit allogenic transplantation of umbilical cord blood (UCB). Ex vivo expansion may overcome this limitation. Mesenchymal stem cells (MSCs), as non-hematopoietic, well-characterized skeletal and connective-tissue progenitor cells within the bone marrow stroma, have been investigated as support cells for the culture of HSCs/HPCs. MSCs are attractive for the rich environmental signals that they provide and for immunological compatibility in transplantation. Thus far, HSC/MSC co-cultures have mainly been performed in 2-dimensional (2D) configuration. We postulate that a 3-dimensional (3D) culture environment that resembles the natural in vivo hematopoietic compartment might be more conducive for regulating HSC expansion. In this study, we compared the co-culture of HSCs and MSCs in 2D and 3D configurations. The results demonstrated the benefit of MSC inclusion in HSC expansion ex vivo. Direct contact between MSCs and HSCs in 3D cultures led to statistically significantly higher expansion of cord blood CD34+ cells than in 2D cultures (891- versus 545-fold increase in total cells, 96- versus 48-fold increase of CD34+ cells, and 230- versus 150-fold increase in colony-forming cell assay [CFC]). Engraftment assays in non-obese diabetic/severe combined immunodeficiency mice also indicated a high success rate of hematopoiesis reconstruction with these expanded cells.
Light-Emitting Electrochemical Cells Based on Hybrid Lead Halide Perovskite Nanoparticles (2015)

Methylammonium lead bromide (MAPbBr3) perovskite nanoparticles (NPs) have been recently proposed as a new material for light-emitting diodes, as well as a new paradigm to elucidate the operational mechanism in perovskite solar cells. Here, we have expanded the synthesis concept to fabricate NPs based on formamidinium lead bromide (FAPbBr3). Importantly, we have demonstrated that the photophysical features of this novel material can be easily tuned by exchanging the organic cation, achieving lower radiative bimolecular recombination rate for FAPbBr3 NPs. Additionally, we report for the first time light-emitting electrochemical cells (LECs) based on perovskite NPs by an easily up-scalable spray-coating technique. Stable luminance of 1–2 cd/m2 at low driving currents was achieved for both types of materials. Overall, this work opens a new avenue of research into the field of organic–inorganic metal halide nanoparticles bearing different alkyl ammonium groups and their application in the developing field of thin-film lighting devices.
Reovirus as a novel oncolytic agent (2000)

Reovirus is a double-stranded RNA-containing virus that possesses the distinctive ability to replicate in transformed cells while sparing normal cells, both in vitro and in vivo, in rodent models of cancer. The discovery of this property only arose through years of basic research on the biology of reovirus infection. Upon elucidation of the intracellular factors that govern cellular susceptibility, it became clear that reovirus Type 3 Dearing was capable of replicating in cells with an activated Ras signaling pathway, whereas normal, untransformed cells were unable to support reovirus infection (1). Because normal cells are resistant to reovirus, it is not surprising that reovirus infection in humans is usually subclinical (2, 3). Altogether, the potential impact of such findings is impressive when one considers that activating mutations in the ras genes alone contribute to more than 30% of all human cancers and that many other mutations in elements of the Ras pathway can also contribute to oncogenesis (4, 5). Recently, research using murine cancer models has revealed that this genetically unmodified laboratory strain of reovirus can indeed selectively destroy tumor cells, with no manifestations of animal morbidity or mortality (6). This has led the way to investigation into its therapeutic potential in human cancer.
Differences in DNA methylation during oogenesis and spermatogenesis and their persistence during early embryogenesis in the mouse. (1987)

We have examined the relative methylation levels of several dispersed repeated and low-copy-number gene sequences during gametogenesis and early embryogenesis. Southern blot analyses revealed that L1, intercisternal A particle (IAP), and major urinary protein (MUP) sequences were undermethylated extensively at MspI sites in DNA from diplotene oocytes. In contrast, the same sequences were highly methylated in DNA from pachytene spermatocytes, round spermatids, and epididymal sperm. These results indicate that there are genome-wide DNA methylation differences between oogenesis and spermatogenesis. Repeated sequences in DNA from cleavage-stage embryos and inner cell masses (ICM) were methylated at intermediate levels, consistent with transient maintenance of gametic methylation levels during early embryogenesis. Gametic differences in DNA methylation observed here indicate that methylation could provide a mechanism for imprinting maternal and paternal genomes resulting in differential regulation of parental genomes during early development.
Cerebrospinal fluid CXCL13 in multiple sclerosis: a suggestive prognostic marker for the disease course (2010)

Background: Levels of CXCL13, a potent B-cell chemoattractant, are elevated in the cerebrospinal fluid (CSF) during multiple sclerosis (MS) and are associated with markers of MS activity. Levels decrease upon effective treatments. Objective: Here we validate the potential role of CSF CXCL13 as a biomarker for aspects of MS in a large amount of clinical material, the majority collected at early diagnostic work-up. Methods: CXCL13 was measured by ELISA in 837 subjects: relapsing–remitting MS (RRMS; n = 323), secondary progressive MS (SPMS; n = 40), primary progressive MS (PPMS; n = 24), clinically isolated syndrome (CIS; n = 79), other neurological diseases (ONDs; n = 181), ONDs with signs of inflammation or viral/bacterial infections (iONDs; n = 176) and healthy controls ( n = 14). Results: Subjects with viral/bacterial infections had extremely high CXCL13 levels compared to all included groups ( p &lt; 0.0001). CXCL13 was otherwise significantly higher in MS compared to the remaining controls ( p &lt; 0.0001), and CIS ( p &lt; 0.01). A significant and positive correlation between CXCL13 and relapse rate, the results obtained for the Expanded Disability Status Scale (EDSS) and the number of lesions detected by MRI was demonstrated. CXCL13 was increased in CIS conversion to clinically definite MS ( p &lt; 0.001). Oligoclonal immunoglobulin band (OCB)-positive CIS or MS had significantly increased CXCL13 levels compared to OCB-negative CIS or MS ( p &lt; 0.001 and p &lt; 0.0001, respectively). Conclusion: CXCL13 was associated with disease exacerbations and unfavourable prognosis in RRMS. Increased CXCL13 was not specific for MS since subjects with viral/bacterial infections exhibited even higher levels. High levels predicted CIS conversion to MS. We suggest that measurement of CSF CXCL13 can be part of the armamentarium in the diagnostic and prognostic work-up in MS and be of help in future treatment decisions.
Triggering of OX40 (CD134) on CD4+CD25+ T cells blocks their inhibitory activity: a novel regulatory role for OX40 and its comparison with GITR (2005)

OX40 (CD134) is a member of the tumor necrosis factor (TNF) receptor family that is transiently expressed on T cells after T-cell receptor (TCR) ligation. Both naive and activated CD4(+)CD25+ regulatory T cells (T reg's) express OX40 but its functional role has not been determined. Since glucocorticoid-induced tumor necrosis factor receptor (GITR), a related TNF receptor family member, influences T reg function, we tested whether OX40 might have similar effect. Triggering either GITR or OX40 on T reg's using agonist antibodies inhibited their capacity to suppress and restored effector T-cell proliferation, interleukin-2 (IL-2) gene transcription and cytokine production. OX40 abrogation of T reg suppression was confirmed in vivo in a model of graft-versus-host disease (GVHD). In a fully allogeneic C57BL/6>BALB/c bone marrow transplantation, GVHD was lethal unless T reg's were cotransferred with the bone marrow and effector T cells. Strikingly, T reg suppression of GVHD was abrogated either by intraperitoneal injection of anti-OX40 or anti-GITR monoclonal antibodies (mAbs) immediately after transfer, or by in vitro pretreatment of T reg's with the same mAbs before transfer. Cumulatively, the results suggest that in addition to controlling memory T-cell numbers, OX40 directly controls T reg-mediated suppression.
Field-induced nucleation in phase change memory (2008)

A theory of field-induced crystal nucleation is developed and verified experimentally for the case of switching in nanoglasses of phase change memory. For symmetry-breaking strong electric fields, it predicts needle-shaped crystallites with nucleation barriers lower than that of spherical nuclei and a strong field dependent. We have observed bias dependent switching for times and temperatures far beyond those typically reported and supportive of our predictions, in particular, switching time exponential in voltage and temperature.
MoSe 2 layer formation at Cu(In,Ga)Se 2/Mo Interfaces in High Efficiency Cu(In1- xGa x)Se 2 Solar Cells (1998)

MoSe 2 layers formed at the interface between Cu-In-Ga-Se and Mo layers were studied by X-ray diffraction and high resolution transmission electron microscopy. Various composition Cu-In-Ga-Se films such as Se, Cu-Se, In-Ga-Se and Cu-rich Cu-In-Ga-Se were deposited on Mo coated glass substrates by physical vapor deposition. For the case of the Se/Mo interface, a MoSe 2 layer of about 100 Å thickness was observed. The c -axis of the MoSe 2 grains were found to be oriented normal to the surface of Mo layer. For the Cu-Se/Mo and Cu-rich Cu-In-Ga-Se/Mo structures, the thickness of the MoSe 2 layers found at the interface was thin. For the case of the In-Ga-Se/Mo structure, a 0.1 µm thick interfacial MoSe 2 layer was observed whose c -axis was oriented parallel to the Mo surface. The microstructure of the In-Ga-Se/Mo film was similar to that of the device quality CIGS/Mo structure deposited by the “3-stage” process. A formation mechanism for the MoSe 2 layers occurring during the “3-stage” process is proposed.
Topogenesis of membrane proteins: determinants and dynamics (2001)

For targeting and integration of proteins into the mammalian endoplasmic reticulum, two types of signals can be distinguished: those that translocate their C-terminal sequence (cleavable signals and signal-anchors) and those that translocate their N-terminus (reverse signal-anchors). In addition to the well established effect of flanking charges, also the length and hydrophobicity of the apolar core of the signal as well as protein folding and glycosylation contribute to orienting the signal in the translocon. In multi-spanning membrane proteins, topogenic determinants are distributed throughout the sequence and may even compete with each other. During topogenesis, segments of up to 60 residues may move back and forth through the translocon, emphasizing unexpected dynamic aspects of topogenesis.
Spin polarized tunneling in reactively sputtered tunnel junctions (1997)

In order to study spin-polarized electron tunneling, we have grown MOM junctions where M is a magnetic transition metal (Co, Fe or CoFe) and O a reactively sputtered oxide (CoO, NiO, Ta2O5, MgO, HfO2). The oxide thickness ranged between 20 and 300 Å. The structural, magnetic, and transport properties of these junctions have been investigated. Among these various oxides, large magnetoresistance due to spin-polarized tunneling effects have been observed in MgO on the order of 20% at 77 K, and a maximum of 31% has been observed in HfO2 based junctions at 30 K. The other oxides had a much higher tendency to form pinholes and had smaller dielectric breakdown thresholds.
Catalytic reaction of methanol with a series of ruthenium(II) complexes and the mechanism of the formation of acetic acid from methanol alone (1994)

The catalytic abilities of a series of ruthenium(II) complexes containing zero, one and two SnCl3– ligands, [RuCl2{P(OMe)3}4]1, [RuCl(SnCl3){P(OMe)3}4]2 and [Ru(SnCl3)2{P(OMe)3}3]3, have been compared in the reaction of methanol to form acetic acid (and/or methyl acetate due to esterification), as well as their reactions with the possible intermediates (formaldehyde, methyl formate) in the overall reaction. It was found that the formation of acetic acid from methanol occurred only with 3, which also converted paraformaldehyde or methyl formate into acetic acid. Complex 1 showed only a catalytic activity for the Tischenko-type dimerization (2HCHO → HCO2Me), and 2 exhibited an intermediate character, being able to catalyse the two reactions (2HCHO → HCO2Me, HCO2Me → MeCO2H) but unable to react with methanol. Based on kinetic results for the reaction of methanol with 3, a possible reaction pathway is proposed where methyl formate and acetic acid are formed from formaldehyde competitively sharing a common reaction path. For the isomerization of methyl formate as a substrate a separate reaction path is suggested, where the RuII–SnII bimetallic centre of 2 and 3 converts the co-ordinated HCO2Me into a five-membered acetate bridge.
Realization of power spectra from partial covariance sequences (1987)

In this paper, we address the problem of realization of a spectral density function from incomplete information about the underlying stochastic process. The standing assumption is the availability of an (incomplete) partial sequence of covariance samples of the process. We study the set of rational extensions of this finite sequence to an infinite covariance function that agrees with the available samples. The classical theory of orthogonal polynomials (with respect to the unit circle) and the theory of moments have been utilized extensively in a variety of engineering problems, including the one we are dealing with. These have been known to provide a unifying framework for a variety of current spectral estimation techniques (maximum entropy method, Pisarenko's harmonic decomposition, etc.). In this work, we consider and study the set of all covariance realizations of dimension lower than or equal to the length of the partial sequence (and equal to the dimension of the maximum entropy realization). The ME solution is a point in this set. Other points correspond to "pole-zero" models. A general formula is obtained for recursively updated "pole-zero" models of dimension increasing with the data record. Information about the "zeros" is obtained from the asymptotic behavior of the "partial autocorrelation coefficients." Our approach combines techniques from the theory of orthogonal polynomials on the unit circle, the theory of moments, and also techniques from degree theory/topology. Our objective is to develop a theory that will provide a frame for constructing recursively "pole-zero" realizations of increasing dimension.
High sensitivity assays for docetaxel and paclitaxel in plasma using solid-phase extraction and high-performance liquid chromatography with UV detection (2006)

We have developed an HPLC method using UV detection capable of quantifying 1 nM of docetaxel in plasma samples. The method should be useful for pharmacokinetic determinations at all relevant doses of docetaxel. Using a similar methodology paclitaxel can be quantified down to a concentration of 1.2 nM in plasma with acceptable accuracy and precision. We further demonstrate that the previously reported negative influence of Cremophor EL on assay performance may be overcome by degradation of the detergent by incubation with lipase.
Immunoregulatory circuits among T-cell sets. I. T-helper cells induce other T-cell sets to exert feedback inhibition. (1978)

These experiments test the hypothesis that cells carrying the Ly1+23- surface phenotype are programmed exclusively for helper and not suppressive activity regardless of external conditions such as the mode or type of antigen stimulation. To this end, we have stimulated purified populations of Ly1 cells with antigen in vitro using conditions devised to induce unselected T cells to express optimal levels of antigen specific T-suppressor activity. We find that after such stimulation, Ly1 cells generate SRBC-specific T-helper activity but not T-suppressive activity. These findings establish that the Ly1.2+,2.2/3.2- surface phenotype is a stable, and probably invariant, marker of T cells that are programmed to express only helper activity and have lost the capacity to directly suppress the antibody response. These findings support the concept that the genetic program for a single differentiated set of cells combines information for cell surface phenotype and function. We also demonstrate that antigen-stimulated Ly1 cells, in addition to inducing B cells to secrete antibody, can induce or activate other sets of resting T cells to develop profound suppressive effects. The surface phenotype of this feedback suppressive T-cell set is shown to be: Ly1+2+3+Qa1+. These findings, taken together, indicate that activation of resting Ly123 cells by immune Ly1 TH cells may represent an important homeostatic immunoregulatory mechanism.
Graft versus Host Disease in the Bone Marrow, Liver and Thymus Humanized Mouse Model (2012)

Mice bearing a "humanized" immune system are valuable tools to experimentally manipulate human cells in vivo and facilitate disease models not normally possible in laboratory animals. Here we describe a form of GVHD that develops in NOD/SCID mice reconstituted with human fetal bone marrow, liver and thymus (NS BLT mice). The skin, lungs, gastrointestinal tract and parotid glands are affected with progressive inflammation and sclerosis. Although all mice showed involvement of at least one organ site, the incidence of overt clinical disease was approximately 35% by 22 weeks after reconstitution. The use of hosts lacking the IL2 common gamma chain (NOD/SCID/γc(-/-)) delayed the onset of disease, but ultimately did not affect incidence. Genetic analysis revealed that particular donor HLA class I alleles influenced the risk for the development of GVHD. At a cellular level, GVHD is associated with the infiltration of human CD4+ T cells into the skin and a shift towards Th1 cytokine production. GVHD also induced a mixed M1/M2 polarization phenotype in a dermal murine CD11b+, MHC class II+ macrophage population. The presence of xenogenic GVHD in BLT mice both presents a major obstacle in the use of humanized mice and an opportunity to conduct preclinical studies on GVHD in a humanized model.
Pharmaceutical particulate carriers : Therapeutic applications (1993)

Pharmaceutical particulate carriers : Therapeutic applications , Pharmaceutical particulate carriers : Therapeutic applications , کتابخانه دیجیتال جندی شاپور اهواز
Improving Antibiotic Selection (2006)

Multidimensional interventions using audit and feedback to improve antibiotic selection were less effective than interventions using clinician education alone. Although confounding may partially account for this finding, our results suggest that enhancing the intensity of a focused intervention may be preferable to a less intense, multidimensional approach.