gebhart/patrepeval huggingface dataset:
Quantification of antigen specific CD8+ T cells using an ELISPOT assay (1995)

An ELISPOT assay to detect and determine the number of antigen specific CD8+ T cells was standardized using cloned murine CD8+ T cells specific for the epitope SYVPSAEQI of a rodent malaria antigen. This assay is based on the detection of IFN-gamma secretion by single cells after their stimulation with antigen. The interferon secretion is visualized as spots revealed by using enzyme labeled anti-IFN-gamma monoclonal antibodies. Using known numbers of cloned murine CD8+ T cells it was determined that the assay detects 80-95% of these CD8+ T cells. The optimal culture conditions for the stimulation of the CD8+ T cells were determined and the antigen concentration, number of antigen presenting cells and supplement of growth factors required to perform the assay were defined. This ELISPOT assay can be performed with spleen cells from immunized mice, and provide the precise number of antigen specific CD8+ T cells present in mixed lymphocyte populations. This method is more sensitive than the chromium-51 release assay, and much simpler than the conventional precursor frequency analysis, providing the number of antigen specific CD8+ T cells in 36-48 h.
1,n-Alkanedithiol (n = 2, 4, 6, 8, 10) Self-Assembled Monolayers on Au(111): Electrochemical and Theoretical Approach (2009)

The structures of 1,n-alkanedithiol (n = 2, 4, 6, 8, 10) self-assembled monolayers (SAMs) on a Au(111) substrate were investigated by electrochemical measurements and theoretical calculations. The results of the experimental techniques indicated that the dithiols, except n = 2, showed an upright molecular structure in the SAMs, in which alkanedithiols were bound to the Au surface via only one thiol functionality and the other one faced up to the air. The results also suggested that the formed dithiol SAMs were densely packed and highly oriented. Except ethanedithiol, which was thought to form a bilayer, the reductive desorption peak potentials of 1,n-alkanedithiol (n = 4, 6, 8, 10) SAMs were more negative than those of the corresponding monothiol ones in 0.1 M KOH solutions. This illustrates that the dithiol SAMs had higher stability than the corresponding monothiol ones. The major part of the high stability may be attributed to the van der Waals interaction among the sulfur atoms on top of the dithiol SAMs. The molecular modeling calculation showed that the structures of dithiol SAMs were similar to those of the corresponding monothiol SAMs and that all the dithiol SAMs, except ethanedithiol, were more stable than the corresponding monothiol SAMs. The calculated energy differences between dithiol and monothiol SAMs decreased with the increment of alkyl-chain length.
Genome-Wide RNAi of C. elegans Using the Hypersensitive rrf-3 Strain Reveals Novel Gene Functions (2003)

RNA-mediated interference (RNAi) is a method to inhibit gene function by introduction of double-stranded RNA (dsRNA). Recently, an RNAi library was constructed that consists of bacterial clones expressing dsRNA, corresponding to nearly 90% of the 19,427 predicted genes of C. elegans. Feeding of this RNAi library to the standard wild-type laboratory strain Bristol N2 detected phenotypes for approximately 10% of the corresponding genes. To increase the number of genes for which a loss-of-function phenotype can be detected, we undertook a genome-wide RNAi screen using the rrf-3 mutant strain, which we found to be hypersensitive to RNAi. Feeding of the RNAi library to rrf-3 mutants resulted in additional loss-of-function phenotypes for 393 genes, increasing the number of genes with a phenotype by 23%. These additional phenotypes are distributed over different phenotypic classes. We also studied interexperimental variability in RNAi results and found persistent levels of false negatives. In addition, we used the RNAi phenotypes obtained with the genome-wide screens to systematically clone seven existing genetic mutants with visible phenotypes. The genome-wide RNAi screen using rrf-3 significantly increased the functional data on the C. elegans genome. The resulting dataset will be valuable in conjunction with other functional genomics approaches, as well as in other model organisms.
Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology (1995)

We report on the analysis of 214kb of the parasitic eubacterium Mycoplasma capricolum sequenced by genomic walking techniques. The 287 putative proteins detected to date represent about half of the estimated total number of 500 predicted for this organism. A large fraction of these (75%) can be assigned a likely function as a result of similarity searches. Several important features of the functional organization of this small genome are already apparent. Among these are (i) the expected relatively large number of enzymes involved in metabolic transport and activation, for efficient use of host cell nutrients; (ii) the presence of anabolic enzymes; (iii) the unexpected diversity of enzymes involved in DNA replication and repair; and (iv) a sizeable number of orthologues (82 so far) in Escherichia coli. This survey is beginning to provide a detailed view of how M. capricolum manages to maintain essential cellular processes with a genome much smaller than that of its bacterial relatives.
Characterization and Thermal Stability of SEI Between a Graphite Electrode and Methyl Difluoroacetate-Based Electrolyte (2006)

Abstract not Available.
c-myc products trans-activate the adenovirus E4 promoter in EC stem cells by using the same target sequence as E1A products (1988)

Using a short-term transfection assay, we show that the E4 early adenovirus promoter is expressed to a certain extent in undifferentiated F9 and PCC4 cells, which are known to possess cellular E1A-like activity. We have also observed that c-myc products trans-activate the E4 promoter in EC stem cells and HeLa cells. Using 5' deletion mutants of the E4 promoter, we show that the same target sequence is used by c-myc and E1A. This sequence is located between positions -179 and -158 upstream of the cap site and is known to contain an activating transcription factor (ATF)-binding site. Moreover, the basal of level of activity of the deletion mutants. is related to the number of ATF binding sites. We therefore suggest that c-myc is a functional cellular homolog of the viral E1A gene and that it might correspond to one of the cellular E1A-like activities previously described for EC stem cells. We have also observed that only a c-myc plasmid coding for both p67 and 64 proteins, in contrast to one coding for p64 only, is able to trans-activate the E4 and E2A adenovirus promoter, suggesting that the p67 protein plays an essential part in activation.
Targeting Costimulatory Pathways for Tumor Immunotherapy (2007)

Tumor immunotherapy harnesses the potential of the host immune system to recognize and eradicate neoplastic tissue. The efficiency of the immune system in mediating tumor regression depends on the induction of antigen-specific T-cell responses through physiologic immune surveillance, priming by vaccination, or following adoptive transfer of T-cells. Although a variety of tumor-associated antigens have been identified and many immunotherapeutic strategies have been tested, objective clinical responses are rare. The reasons for this include the inability of current immunotherapy approaches to generate efficient T-cell responses, the presence of regulatory cells that inhibit T-cell responses, and other tumor escape mechanisms. The activation of effector T-cells depends on interactions between the T-cell receptor (TCR) and cognate antigen presented as peptides within the major histocompatibility complex (MHC) and costimulatory signals delivered by CD28, which binds to B7.1 and B7.2. More recently, several new molecular receptors and ligands have been identified that integrate into stimulatory or inhibitory activity for T-cells. These signals have been loosely associated with the costimulatory molecules but actually represent a diverse group of molecular pathways that have unique and overlapping functions. This review will focus on these pathways and emphasize their role in mediating T-cell activation for the purpose of enhancing tumor immunotherapy. As we gain a better understanding of the molecular and cellular consequences of T-cell signaling through the costimulatory pathways, a more rational approach to the activation or inhibition of T-cell responses can be developed for the treatment of cancer and other immune-mediated diseases.
5 Adenovirus Vectors (1999)

From a historical perspective, the murine retroviruses were the first recombinant viruses that were used in human gene transfer studies. As to be expected with any developing system, there were significant positive and negative aspects. Transduction of the target cells was done in an ex vivo manner that accommodated both biological and safety issues. In the ex vivo setting, it was possible to control the target cell population being transduced by methods of selection such as fluorescence-activated cell sorting, and expanding the cells in culture assured the requisite dividing cells necessary for retrovirus-mediated gene transfer. The in vitro environment excluded the presence of human complement that was known to inactivate retroviruses. While retroviral vectors integrate into the chromosomes of the targeted cells, thus developing a potential for long-term gene expression, the pattern of strictly random insertion raises the issue of insertional mutagenesis with its predisposition to oncogenicity. To develop in vivo strategies for gene transfer that could target terminally differentiated cells, such as those in the respiratory tract or liver, it was necessary to consider the use of other viruses. It soon became obvious that adenoviruses had properties that were advantageous for in vivo gene delivery because they could transfer recombinant genes into a wide variety of dividing and nondividing cells. Because of their natural affinity for respiratory epithelium, adenoviral vectors were first used to study cystic fibrosis transmembrane conductance regulator (CFTR) gene transfer in patients with cystic fibrosis. Adenoviral vectors can be grown to much higher titers (10 11 pfu/ml)...
Dendritic Cell-Based Immunotherapy of Prostate Cancer (1998)

The immunotherapy of cancer, based on eliciting or enhancing the body's own capacity to mount an effective antitumor response, has produced encouraging early results in the areas of melanoma and renal-cell carcinoma. Such treatments utilizing dendritic cells (DC), immune cells that are excellent antigen presenters, are especially promising. We performed a phase I clinical trial assessing the administration of autologous DC pulsed with HLA-A0201-specific prostate-specific membrane antigen (PSMA) for the treatment of 51 men with hormone-refractory prostate cancer. Participants were divided into five groups receiving four or five infusions of peptides alone (PSM-P1 or PSM-P2; group 1 and 2, respectively), autologous DC (group 3), or DC pulsed with PSM-P1 or P2 (group 4 and 5, respectively). No significant toxicity was observed. Immune reactivity against PSM-P2 was detected in HLA-A2+ patients infused with DC pulsed with PSM-P1 or -P2 (group 4 and 5). An average decrease in PSA was observed only in group 5. Seven partial responders were identified based on NPCP criteria + PSA. The excellent tolerance of this treatment approach, as well as the enhanced cellular responses, decreased PSA levels, and partial clinical responses in some patients suggests that it holds great potential in prostate cancer therapy.
Overexpression of Myc suppresses CCAAT transcription factor/nuclear factor 1-dependent promoters in vivo. (1993)

Overexpression of Myc in cells can suppress the transcription of specific genes. Because several of these genes have common transcriptional regulatory elements, we investigated the possibility that this effect of Myc is mediated through a specific transcription factor. In vitro DNA-binding assays detect only one form of CCAAT transcription factor/nuclear factor 1 (CTF/NF-1) in quiescent 3T3-L1 cells. By contrast, quiescent 3T3-L1 cells that stably overexpress either c-Myc or N-Myc contain at least three forms of CTF/NF-1. Biochemical characterization of the various CTF/NF-1 forms showed that they have the same native molecular weight but differ in charge density. The more negatively charged CTF/NF-1 forms present in Myc-overexpressing cells are converted into that found in normal cells by treatment with acid phosphatase, suggesting that they represent a more phosphorylated form of the CTF/NF-1 protein. The various CTF/NF-1 forms have a similar DNA-binding affinity. Transfection experiments demonstrated that transcription from CTF/NF-1-dependent promoters is specifically suppressed in cells that stably overexpress c-Myc. This effect requires CTF/NF-1 binding. CTF/NF-1-dependent promoter activity is also suppressed in 3T3-L1 cells during active growth (relative to the quiescent state). Interestingly, actively growing 3T3-L1 cells contain forms of CTF/NF-1 similar to those in quiescent cells that stably overexpress c-Myc. Thus, the CTF/NF-1 forms present in cells that express high amounts of c-Myc correlate with a lower transcription rate of CTF/NF-1-dependent promoters in vivo. Our results provide a basis for the suppression of specific gene transcription by c-Myc.
Sleep and Stroke (2005)

More than 50% of stroke patients have sleep-disordered breathing (SDB), mostly in the form of obstructive sleep apnea (OSA). SDB represents both a risk factor and a consequence of stroke. The presence of SDB has been linked with poorer long-term outcome and increased long-term stroke mortality. Continuous positive airway presure is the treatment of choice for OSA. Oxygen and other forms of ventilation may be helpful in other (e.g., central) forms of SDB. SDB can improve spontaneously after stroke. About 20 to 40% of stroke patients have sleep-wake disorders (SWD), mostly in form of insomnia, excessive daytime sleepiness/fatigue, or hypersomnia (increased sleep needs). Depression, anxiety, SDB, stroke complications, and medications may contribute to SWD and should be addressed first therapeutically. Brain damage per se, often at thalamic or brainstem level, can be also a cause of persisting SWD. In these patients, hypnotics, dopeminergic agents, and stimulants (e.g., modafinil) can be attempted.
BIG-ALIGN: Fast Bipartite Graph Alignment (2013)

How can we find the virtual twin (i.e., the same or similar user) on Linked In for a user on Facebook? How can we effectively link an information network with a social network to support cross-network search? Graph alignment - the task of finding the node correspondences between two given graphs - is a fundamental building block in numerous application domains, such as social networks analysis, bioinformatics, chemistry, pattern recognition. In this work, we focus on aligning bipartite graphs, a problem which has been largely ignored by the extensive existing work on graph matching, despite the ubiquity of those graphs (e.g., users-groups network). We introduce a new optimization formulation and propose an effective and fast algorithm to solve it. We also propose a fast generalization of our approach to align unipartite graphs. The extensive experimental evaluations show that our method outperforms the state-of-art graph matching algorithms in both alignment accuracy and running time, being up to 10x more accurate or 174x faster on real graphs.
Bacterial Cytochrome P450 System Catabolizing the Fusarium Toxin Deoxynivalenol (2012)

Deoxynivalenol (DON) is a natural toxin of fungi that cause Fusarium head blight disease of wheat and other small-grain cereals. DON accumulates in infected grains and promotes the spread of the infection on wheat, posing serious problems to grain production. The elucidation of DON-catabolic genes and enzymes in DON-degrading microbes will provide new approaches to decrease DON contamination. Here, we report a cytochrome P450 system capable of catabolizing DON in Sphingomonas sp. strain KSM1, a DON-utilizing bacterium newly isolated from lake water. The P450 gene ddnA was cloned through an activity-based screening of a KSM1 genomic library. The genes of its redox partner candidates (flavin adenine dinucleotide [FAD]-dependent ferredoxin reductase and mitochondrial-type [2Fe-2S] ferredoxin) were not found adjacent to ddnA; the redox partner candidates were further cloned separately based on conserved motifs. The DON-catabolic activity was reconstituted in vitro in an electron transfer chain comprising the three enzymes and NADH, with a catalytic efficiency (k(cat)/K(m)) of 6.4 mM(-1) s(-1). The reaction product was identified as 16-hydroxy-deoxynivalenol. A bioassay using wheat seedlings revealed that the hydroxylation dramatically reduced the toxicity of DON to wheat. The enzyme system showed similar catalytic efficiencies toward nivalenol and 3-acetyl deoxynivalenol, toxins that frequently cooccur with DON. These findings identify an enzyme system that catabolizes DON, leading to reduced phytotoxicity to wheat.
Electric field recording on the sea floor with short span instruments. (1974)

Oceanic electric fields originate from (1) induction by magnetic pulsations in the ionosphere, (2) water motions across the earth's field and (3) electrochemical processes associated with sea floor materials and with tissues of marine organisms. Precise recording of these signals is difficult because of (1) their small size, and (2) a large and unavoidable noise occurs at the contact points between sea water and measuring devices.The spectrum P of average natural electric activity at the sea floor in the band 10-3 to 10+1 cph roughly follows the trend P=kf-1, f=frequency, k centered at 10-2 μV2 m-2. The noise spectrum of typical Ag-AgCl electrode pairs P′ on the sea floor environment approximates k′= 10-1 μV2 with tenfold variations in both directions. Thus, achieving a 101 signal to noise ratio requires an electrode separation of 10 meters. Even so, the unavoidable electrode voltage mismatch, typically 102 to 103 μV, fatally eradicates the signal datum unless considerably longer lines area used.Rejection of electrode bias and noise to allow short electrode separations can be done by physically inverting the electrodes positions, which is most practically achieved with rotating instruments, or (2) by switching back and forth the sea water connections between electrodes and the salt bridge pipes which perform electrical contact with the ocean. A method to achieve this “water chopping” is described.Examples of ionospheric and barotropic velocity signals recorded on the sea floor with 5m span instruments and presented.
A novel diffracted tubes technology based on the method of ray tracing (2011)

It is well known that the method of ray tracing tubes could be used to predict the propagation of radiowave in complex environment. Moreover, it is an important technology used to explore the characteristics of indoor radiowave propagation. But the traditional methods could not compute the path vector correspond to diffraction ray tube when ray which ray tube intersect with the obstacle such as furniture. In this paper, a novel diffracted tubes technology has been put forword, which can effectively overcome the shortcoming of traditional method and the diffracted tube path vector expression has been calculated. According to the novel method, none of the diffraction tubes which is contributed to the receiver is given up. As the result, the prediction efficiency can be improved.
Medical hyperspectral imaging to facilitate residual tumor identification during surgery (2007)

We conclude that MHSI may be useful in identifying small residual tumor in a tumor resection bed and for indicating areas requiring more extensive resection and more effective biopsy locations to the surgeon.
Measuring Gene Expression with Light (1985)

Light is produced by recombinant Escherichia coli that contain lux genes cloned from the marine bacterium Vibrio fischeri. The bioluminescence phenotype requires genes for regulatory and biochemical functions, the latter encoded by five lux genes contained in a single operon. These lux genes were disconnected from their native promoter and inserted into the transposon mini-Mu. The resulting transposon, mini-Mulux, could induce mutations by insertional inactivation of a target gene, and the lux DNA was oriented to align target gene transcription with that of the lux genes. Genes in Escherichia coli and Vibrio parahaemolyticus were mutagenized, and mutants containing transposon-generated lux gene fusions produced light as a function of target gene transcription. Light production offers a simple, sensitive, in vivo indicator of gene expression.
Molecular characterization of human trk proto-oncogene product monoclonal antibodies. (1991)

Monoclonal antibodies specific for the human trk protooncogene product, a tyrosine kinase receptor, have been produced from mice in which tumors were generated by injection of stably transfected NIH3T3 cells expressing the human trk proto-oncogene product. The panel of eleven antibodies are reactive in ELISA, immunostaining and immunoprecipitation. These antibodies bind to the extracellular domain of the human trk proto-oncogene product and demonstrate no cross-reactivity to the trk oncogene or murine trkB gene products. The antibodies are equally effective in recognizing human proto-trk when expressed by transfected human or mouse cell lines. These antibodies either bind to the carbohydrate moieties or are dependent upon the conformational structure created by the extensive glycosylations. The localization and nature of the epitopes recognized by these monoclonal antibodies were defined by immunoprecipitation analyses using several different trk oncoproteins. Potential applications of these antibodies are discussed.
Inhibition of Morphine Tolerance and Dependence by the NMDA Receptor Antagonist MK-801 (1991)

The N-methyl-D-aspartate (NMDA) subtype of the glutamate receptor is an important mediator of several forms of neural and behavioral plasticity. The present studies examined whether NMDA receptors might be involved in the development of opiate tolerance and dependence, two examples of behavioral plasticity. The noncompetitive NMDA receptor antagonist MK-801 attenuated the development of tolerance to the analgesic effect of morphine without affecting acute morphine analgesia. In addition, MK-801 attenuated the development of morphine dependence as assessed by naloxone-precipitated withdrawal. These results suggest that NMDA receptors may be important in the development of opiate tolerance and dependence.
48.1: Distinguished Student Paper : A Depth‐Fused Multi‐Focal‐Plane Display Prototype Enabling Focus Cues in Stereoscopic Displays (2011)

Abstract Lack of focus cues in stereoscopic displays may have significant effects on depth perception accuracy and visual fatigue. In this paper, we present a depth‐fused six‐focal plane display prototype, capable of rendering nearly‐accurate focus cues for a depth range of 3 diopters with high image quality at flicker‐free speed.