gebhart/patrepeval huggingface dataset:
Transformation of Soybean (Glycine max) via Agrobacterium tumefaciens and Analysis of Transformed Plants (2003)

The transfer of genetic material into soybean (Glycine max L. Merr.) plant tissues has been accomplished by several methods: electroporation (1), microprojectiles (2), and by the more widely used Agrobacterium-mediated T-DNA transfer (3,4). The transformation of soybean by electroporation-mediated gene transfer appears to be efficient for obtaining stable transformants in soybean cells (1). However, the disadvantage of this method is that the efficiency is affected by many variables, such as voltage, duration, and spacing of electrical pulses, size and number of protoplasts, buffer composition, temperature, concentration, and form of DNA. Thus, optimum electroporation must be determined for each protoplast type. The transformation of soybean by particle bombardment (2), in which the microprojectiles are used to transfer the genetic material into meristematic cells of immature seeds, appears to be simple and very effective. However, it requires a knowledge of the design of the acceleration instruments for those who wish to build their own, or at least access to an instrument that can control the acceleration of microprojectiles. These limitations presently restrict genetic engineering of soybean to some university and corporate laboratories.
Cloning and Functional Analysis of Cyclin A Gene in Pig (2010)

The study was aimed at cloning porcine Cyclin A gene and expressing it in swine umbilicus veins endothelial cell(SUVEC)to verify its functionality.The human Cyclin A gene was utilized as the informational probe to e-clone the pigs Cyclin A gene.Reverse transcription polymerase chain reaction(RT-PCR)was used to identify the products in silico cloned,and the bioinformatics methods was used to analyze structure characteristics of the gene,RT-PCR,Western blot were employed for investigating its expression in SUVEC.Subcellular localization of Cyclin A was analyzed by confocal microscope,and the flow cytometry was used to analyze the cell cycle,and MTS was used to detect the proliferation of the cells.The results proved that the product of RT-PCR was consistent with that of silico cloning.This cDNA contains the complete open reading frame(ORF)of 1 299 bp coding 432 amino acid residues,and NCBI BLAST analysis indicated that the gene is located in swine on chromosome 8.Western blot manifested that molecular size of Cyclin A protein was about 40 kDa,and subcellular localization showed that this protein was localized in nuclear.The flow cytometry analysis showed that cell lines SUVEC-CycAGFP of G1 phase cells increased by 15% to 20%,while those in S phase decreased about 18% compared with that of the control cells.MTS assay showed that the proliferative activity of cell lines SUVEC-CycAGFP was significantly higher than that of the control groups.Our results indicate that Cyclin A gene of pig was successfully cloned and its biological function was also confirmed,which will provide a foundation for further research on the impact of virus infection on the Cyclin A.
New approach to the growth of low dislocation relaxed SiGe material (1994)

In this growth process a new strain relief mechanism operates, whereby the SiGe epitaxial layer relaxes without the generation of threading dislocations within the SiGe layer. This is achieved by depositing SiGe on an ultrathin silicon on insulator (SOI) substrate with a superficial silicon thickness less than the SiGe layer thickness. Initially, the thin Si layer is put under tension due to an equalization of the strain between the Si and SiGe layers. Thereafter, the strain created in the thin Si layer relaxes by plastic deformation. Since the dislocations are formed and glide in the thin Si layer, no threading dislocation is ever introduced in to the upper SiGe material, which appeared dislocation free to the limit of the cross sectional transmission electron microscopy analysis. We thus have a method for producing very low dislocation, relaxes SiGe films with the additional benefit of an SOI substrate.
IL-12 protects bone marrow from and sensitizes intestinal tract to ionizing radiation. (1994)

IL-12, a potent stimulator of hemopoietic progenitor cells, was evaluated as a potential protector against 60Co-gamma radiation-induced lethal hemopoietic syndrome in mice. Administration of IL-12 before lethal irradiation of genetically distinct strains of mice, B6D2F1 and C3H/HeJ, protected a significant fraction of both strains of mice from death. Radioprotection was associated with a fivefold increase in the number of bone marrow cells at 6 days after irradiation. Even at supralethal doses of radiation (1200 cGy), the number of c-kit+ bone marrow cells 3 days after irradiation was twofold greater in IL-12-treated mice than in saline-treated mice. However, mice that received IL-12 and 1200 cGy (B6D2F1) or 900 cGy (C3H/HeJ) died of the gastrointestinal syndrome, as was evident by gross necroscopy and histologic evaluation, within 4 to 6 days after irradiation. Induction of the gastrointestinal syndrome in mice not treated with IL-12 required radiation doses of 1500 cGy or greater in both strains. Thus, at doses of radiation at which IL-12 still protects c-kit+ hemopoietic cells, it sensitizes the intestinal tract to damage. Radioprotection with IL-12 was abrogated by anti-IL-1R or anti-stem cell factor Ab. Anti-IFN-gamma Ab did not affect IL-12-induced hemopoietic radioprotection, but abrogated sensitization of the intestinal tract by IL-12. The sensitizing effect of IL-12 may be related to its ability to prime mice to subsequent inflammatory challenge, as demonstrated by an almost 100-fold increase in circulating TNF and IL-6 levels in normal B6D2F1 mice challenged with IL-12 and LPS. This priming effect of IL-12 also was abrogated by anti-IFN-gamma Ab.
Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network. (1998)

vladimir@wehi.edu. au
Mucosally Delivered Dendritic Cells Activate T Cells Independently of IL-12 and Endogenous APCs (2008)

In vitro manipulated dendritic cells (DC) have increasingly been used as a promising vaccine formulation against cancer and infectious disease. However, improved understanding of the immune mechanisms is needed for the development of safe and efficacious mucosal DC immunization. We have developed a murine model of respiratory mucosal immunization by using a genetically manipulated DC vaccine. Within 24 h of intranasal delivery, the majority of vaccine DCs migrated to the lung mucosa and draining lymph nodes and elicited a significant level of T cells capable of IFN-gamma secretion and CTL in the airway lumen as well as substantial T cell responses in the spleen. And such T cell responses were associated with enhanced protection against respiratory mucosal intracellular bacterial challenge. In comparison, parenteral i.m. DC immunization did not elicit marked airway luminal T cell responses and immune protection regardless of strong systemic T cell activation. Although repeated mucosal DC delivery boosted Ag-specific T cells in the airway lumen, added benefits to CD8 T cell activation and immune protection were not observed. By using MHC-deficient vaccine DCs, we further demonstrated that mucosal DC immunization-mediated CD8 and CD4 T cell activation does not require endogenous DCs. By using IL-12-deficient vaccine DCs, we also observed that IL-12(-/-) DCs failed to migrate to the lymph nodes but remained capable of T cell activation. Our observations indicate that mucosal delivery of vaccine DCs represents an effective approach to enhance mucosal T cell immunity, which may operate independent of vaccine IL-12 and endogenous DCs.
Waveguide-Plasmon Polaritons Enhance Transverse Magneto-Optical Kerr Effect (2013)

Properties of light propagating in some materials can be influenced by a static magnetic field. Such magneto-optical effects are useful, but their strength is limited traditionally by the materials used. Scientists demonstrate that a hybrid structure of a magneto-optical photonic waveguide with plasmonic (gold) nanowires significantly boosts an important effect, the so-called transverse magneto-optical Kerr effect, through resonant interaction between the waveguide photons and the plasmons.
Telomeric site position heterogeneity in macronuclear DNA ofParamecium primaurelia (1987)

In Paramecium primaurelia, the macronuclear gene encoding the G surface protein is located near a telomere. In this study, multiple copies of this telomere have been isolated and the subtelomeric and telomeric regions of some of them have been sequenced. The telomeric sequences consist of tandem repeats of the hexanucleotides C4A2 or C3A3. We show that the location where these repeats are added, which we call the telomeric site, is variable within a 0.6-0.8-kb region. These results are discussed in relation with the formation of macronuclear DNA.
Insulin Antibodies in Insulin-Dependent Diabetics Before Insulin Treatment (1983)

A sensitive assay was used to measure the binding of iodine-125-labeled insulin in serum obtained from 112 newly diagnosed insulin-dependent diabetics before insulin treatment was initiated. Two groups of nondiabetics served as controls: children with a variety of diseases other than diabetes and nondiabetic siblings of insulin-dependent diabetics. Eighteen of the diabetics were found to have elevated binding and 36 were above the 95th percentile of control values. The insulin-binding protein is precipitated by antibody to human immunoglobulin G, has a displacement curve that is parallel and over the same concentration range as serum from long-standing insulin-dependent diabetics, and elutes from a Sephacryl S-300 column at the position of gamma globulin. These insulin antibodies are present in a large percentage of newly diagnosed, untreated diabetics and may be an immune marker of B-cell damage.
Controlled Chemical Routes to Nanotube Architectures, Physics, and Devices (1999)

This article presents our recent work in the controlled synthesis of multiwalled (MWNT) and single-walled nanotubes (SWNT) with ordered architectures. The general synthesis approach involves chemical vapor deposition using rationally designed catalyst and substrates. The results include self-oriented MWNTs, individual SWNTs grown from controlled surface sites, and structures of suspended SWNTs along well-defined directions. The chemically derived nanotube architectures have opened up new possibilities in fundamental characterization and potential applications of nanotube materials. Systematic electron transport measurements are carried out to elucidate the electrical properties of various classes of SWNTs and to explore the physics in one-dimensional systems. High-performance electrical devices based on individual SWNTs are enabled by combining synthesis and microfabrication approaches.
Rapid Microbial Sample Preparation from Blood Using a Novel Concentration Device (2015)

Appropriate care for bacteremic patients is dictated by the amount of time needed for an accurate diagnosis. However, the concentration of microbes in the blood is extremely low in these patients (1-100 CFU/mL), traditionally requiring growth (blood culture) or amplification (e.g., PCR) for detection. Current culture-based methods can take a minimum of two days, while faster methods like PCR require a sample free of inhibitors (i.e., blood components). Though commercial kits exist for the removal of blood from these samples, they typically capture only DNA, thereby necessitating the use of blood culture for antimicrobial testing. Here, we report a novel, scaled-up sample preparation protocol carried out in a new microbial concentration device. The process can efficiently lyse 10 mL of bacteremic blood while maintaining the microorganisms' viability, giving a 30-μL final output volume. A suite of six microorganisms (Staphylococcus aureus, Streptococcus pneumoniae, Escherichia coli, Haemophilus influenzae, Pseudomonas aeruginosa, and Candida albicans) at a range of clinically relevant concentrations was tested. All of the microorganisms had recoveries greater than 55% at the highest tested concentration of 100 CFU/mL, with three of them having over 70% recovery. At the lowest tested concentration of 3 CFU/mL, two microorganisms had recoveries of ca. 40-50% while the other four gave recoveries greater than 70%. Using a Taqman assay for methicillin-sensitive S. aureus (MSSA)to prove the feasibility of downstream analysis, we show that our microbial pellets are clean enough for PCR amplification. PCR testing of 56 spiked-positive and negative samples gave a specificity of 0.97 and a sensitivity of 0.96, showing that our sample preparation protocol holds great promise for the rapid diagnosis of bacteremia directly from a primary sample.
Correlation of high lactate levels in head and neck tumors with incidence of metastasis. (1997)

Using quantitative bioluminescence imaging, tissue concentrations of ATP, glucose, and lactate were registered in biopsies that were taken from primary tumors of human head and neck at the time of first cancer diagnosis. From 15 patients investigated at present, 6 had locoregional lymph node metastasis, 6 had no detectable metastatic spread, 2 biopsies contained dysplasias, and 1 biopsy consisted exclusively of normal mucosal and submucosal tissue. There was no correlation between staging or grading and any of the metabolic parameters measured. Mean lactate concentrations (+/-SD) were significantly higher and scattered over a wider range in tumors with metastatic spread (12.3 +/- 3.3 mumol/g) in comparison with malignancies in patients without metastasis (4.7 +/- 1.5 mumol/g). Despite the low number of patients, these differences were statistically highly significant (P < 0.005; Mann-Whitney). Neither ATP nor glucose contents showed such a correlation with the emergence of metastasis. Mean lactate contents of the two dysplasias were 0.1 and 3.5 mumol/g; that of the normal tissue was 0.1 mumol/g. Although these findings have to be verified in a higher number of patients, the present data indicate that elevated lactate levels in primary tumors of head and neck may be associated with a high risk of metastatic spread. With the underlying mechanisms remaining to the investigated, lactate imaging is possibly useful as an early indicator of the malignant potential of tumors in patients.
Development of tumor-infiltrating lymphocytes in breast cancer after neoadjuvant paclitaxel chemotherapy. (2001)

These results suggest that development of TILs after treatment correlates with clinical response to neoadjuvant paclitaxel therapy. The possible mechanism(s) whereby neoadjuvant chemotherapy may lead to induction of antitumor T cells is discussed. Immunological processes may influence the response of breast cancer patients to neoadjuvant treatment.
Three-month stability of delay and probability discounting measures. (2006)

Psychopharmacologists are interested in delay and probability discounting because the tendency to discount the value of future and uncertain rewards has been linked with drug dependency. However, relatively little is known about the long-term stability of discounting measures typically studied in clinical psychopharmacology. To evaluate the stability of discounting over a 3-month period, the authors compared points of subjective equality (indifference points) with those collected from the same subjects 3 months earlier. Seven delay periods, ranging from 1 week to 25 years, and 7 probability values, ranging from .95 to .05, were assessed in an undergraduate sample (n=22, delay discounting; n=18, probability discounting). The authors examined both differential stability (stability of individual differences) and absolute stability (stability of the group mean) of delay and probability discounting measures as well as their respective indifference points. The results demonstrate that standard delay and probability discounting parameters (e.g., hyperbolic k and area under the curve) had both differential stability and absolute stability across 3 months. Moreover, most indifference points in the delay and probability discounting tasks demonstrated both differential and absolute stability. All together, these results suggest that delay and probability parameters are stable enough to predict future behavior, such as substance abuse. Additional findings indicated that a hyperbolic function fitted the data better than an exponential function and that delay and probability discounting parameters were not significantly correlated.
Single-layer white light-emitting organic electroluminescent devices based on dye-dispersed poly(N-vinylcarbazole) (1995)

Bright single-layer white light-emitting organic electroluminescent devices were developed by using dye-dispersed poly(N-vinylcarbazole) (PVK). The active layer consists only of one polymer layer that is simply sandwiched between two electrodes, indium-tin oxide, and Mg:Ag. In order to achieve bipolarity in the single polymer emitter layer, PVK was molecularly dispersed with electron-transporting additives such as 2-(4-biphenyl)-5-(4-tert-butylphenyl)-1,3,4-oxadiazole. In addition, several fluorescent dyes, having different emission colors, were dispersed as emitting centers. By adjusting the concentration of the fluorescent dyes, white light with a maximum luminescence of 4100 cd/m2 was obtained, which is the brightest white light ever observed for organic electroluminescent devices.
Photochemical Studies of the Esters of Aroylphosphonic Acids (1970)

Abstract The photochemical behavior of several dialkyl benzoylphosphonates and para-substituted benzoylphosphonates in various solvents has been studied using product isolation, ultravioletspectral change, the electron spin resonance (ESR) technique, and quantum yield measurements. Upon irradiation to a degassed solution of these benzoylphosphonates through a Pyrex filter, the photo-pinacolization reaction was observed, except in the case of diethyl benzoylphosphonate; it was effectively quenched by 1,3-pentadiene or oxygen. On the other hand, the ESR spectra of photo-irradiated aroylphosphonates at 77°K have a large anisotropic doublet of 53–128 gauss separation; this separation is thought to be due to the interaction between an unpaired electron and the phosphorus nucleus. The structure of these radicals is also discussed. From these observations, it can be considered that the photochemical reaction proceeds via the ketyl radical formed by the hydrogen abstraction of the lowest excited triplet state of these aroylphosphonates. Irradiation to the diethyl benzoylphosphonate solutions in various solvents gave, not the pinacolized product, but 2,4,6-triphenyl-2,4,6-tris[diethylphosphoryl]-1,3,5-trioxane almost quantitatively. The quantum yields (Φ) of the disappearance of several para-substituted derivatives are highly sensitive to the electron-inductive abilities of the substituents; that is, Φ drops from 2.10 in the p-methoxybenzoylphosphonate derivative to 1.79 in the p-chloro derivative at room temperature. Such a substituent effect can be considered to result in the difference in the conformation between the carbonyl and phosphoryl groups. On the basis of these studies, the mechanism of the photochemical reaction of aroylphosphonates is described and discussed.
Alternative Random Initialization in Genetic Algorithms. (1997)

Though unanimously recognized as a crucial step in Evolutionary Algorithms, initialization procedures have not been paid much attention so far. In bitstring Genetic Algorithms, for instance, the standard 0/1 equiprobable choice for every bit is rarely discussed, as the resulting distribution probability over the whole bitstring space is uniform. However, uniformity is relative to a measure on the search space. First, considering the measure given by the density of 1&amp;apos;s, the Uniform Covering initialization procedure is naturally designed. Second, taking into account the probability of appearance of sequences of identical bits leads to design another alternative initialization procedure, the Homogeneous Block procedure. These procedures are compared with the standard initialization procedure on several problems. A priori comparison is achieved using FitnessDistance Correlation. Actual experiments demonstrate the accuracy of these FDCbased comparisons, and emphasize the usefulness of the two proposed procedure. 1
Efficient System for Directed Integration into the Lactobacillus acidophilus and Lactobacillus gasseri Chromosomes via Homologous Recombination (2001)

An efficient method is described for the generation of site-specific chromosomal integrations in Lactobacillus acidophilus and Lactobacillus gasseri. The strategy is an adaptation of the lactococcal pORI system (K. Leenhouts, G. Venema, and J. Kok, Methods Cell Sci. 20:35-50, 1998) and relies on the simultaneous use of two plasmids. The functionality of the integration strategy was demonstated by the insertional inactivation of the Lactobacillus acidophilus NCFM lacL gene encoding beta-galactosidase and of the Lactobacillus gasseri ADH gusA gene encoding beta-glucuronidase.
Adiponectin Is a Negative Regulator of NK Cell Cytotoxicity (2006)

NK cells are a key component of innate immune systems, and their activity is regulated by cytokines and hormones. Adiponectin, which is secreted from white adipose tissues, plays important roles in various diseases, including hypertension, cardiovascular diseases, inflammatory disorders, and cancer. In this study the effect of adiponectin on NK cell activity was investigated. Adiponectin was found to suppress the IL-2-enhanced cytotoxic activity of NK cells without affecting basal NK cell cytotoxicity and to inhibit IL-2-induced NF-kappaB activation via activation of the AMP-activated protein kinase, indicating that it suppresses IL-2-enhanced NK cell cytotoxicity through the AMP-activated protein kinase-mediated inhibition of NF-kappaB activation. IFN-gamma enhances NK cell cytotoxicity by causing an increase in the levels of expression of TRAIL and Fas ligand. The production of IFN-gamma, one of the NF-kappaB target genes in NK cells, was also found to be suppressed by adiponectin, accompanied by the subsequent down-regulation of IFN-gamma-inducible TRAIL and Fas ligand expression. These results clearly demonstrate that adiponectin is a potent negative regulator of IL-2-induced NK cell activation and thus may act as an in vivo regulator of anti-inflammatory functions.
Sodium Channels in Normal and Pathological Pain (2010)

Nociception is essential for survival whereas pathological pain is maladaptive and often unresponsive to pharmacotherapy. Voltage-gated sodium channels, Na(v)1.1-Na(v)1.9, are essential for generation and conduction of electrical impulses in excitable cells. Human and animal studies have identified several channels as pivotal for signal transmission along the pain axis, including Na(v)1.3, Na(v)1.7, Na(v)1.8, and Na(v)1.9, with the latter three preferentially expressed in peripheral sensory neurons and Na(v)1.3 being upregulated along pain-signaling pathways after nervous system injuries. Na(v)1.7 is of special interest because it has been linked to a spectrum of inherited human pain disorders. Here we review the contribution of these sodium channel isoforms to pain.