gebhart/patrepeval huggingface dataset:
Physical mapping of the 5S ribosomal RNA genes in Arabidopsis thaliana by multi‐color fluorescence in situ hybridization with cosmid clones (1997)

The 5S ribosomal RNA genes were mapped to mitotic chromosomes of Arabidopsis thaliana by fluorescence in situ hybridization (FISH). In the ecotype Landsberg erecta, hybridization signals appeared on three pairs of chromosomes, two of which were metacentric and the other acrocentric. Hybridization signals on one pair of metacentric chromosomes were much stronger than those on the acrocentric and the other pair of metacentric chromosomes, probably reflecting the number of copies of the genes on the chromosomes. Other ecotypes, Columbia and Wassilewskija, had similar chromosomal distribution of the genes, but the hybridization signals on one pair of metacentric chromosomes were very weak, and detectable only in chromosomes prepared from young flower buds. The chromosomes and arms carrying the 5S rDNA were identified by multi-color FISH with cosmid clones and a centromeric 180 bp repeat as co-probes. The metacentric chromosome 5 and its L arm carries the largest cluster of the genes, and the short arm of acrocentric chromosome 4 carries a small cluster in all three ecotypes. Chromosome 3 had another small cluster of 5S rRNA genes on its L arm. Chromosome 1 and 2 had no 5S rDNA cluster, but they are morphologically distinguishable; chromosome 1 is metacentric and 2 acrocentric. Using the 5S rDNA as a probe, therefore, all chromosomes of A. thaliana could be identified by FISH. Chromosome 1 is large and metacentric; chromosome 2 is acrocentric carrying 18S-5.8S-25S rDNA clusters on its short arm; chromosome 3 is metacentric carrying a small cluster of 5S rDNA genes on its L arm; chromosome 4 is acrocentric carrying both 18S-5.8S-25S and 5S rDNAs on its short (L) arm; and/chromosome 5 is metacentric carrying a large cluster of 5S rDNA on its L arm.
A First Generation DPGA implementation (1995)

Dynamically Programmable Gate Arrays (DPGAs) represent a hybrid architecture lying between traditional FPGAs and SIMD arrays. Notably, these arrays can efficiently support computations where the function of the array elements needs to vary both among array elements during any single cycle and within any single array element over time. We describe our minimal, first generation DPGA. This DPGA uses traditional 4-LUTs for the basic array element, but backs LUT and interconnect programming cells with a 4-context memory implemented using dynamic RAM. Additionally, this DPGA supports non-intrusive background loads of non-active contexts and automatic refresh for the dynamic memory cells. We draw several lessons from this design experience which may be relevant to future DPGA and FPGA designs. 1 Introduction Traditional Field-Programmable Gate Arrays (FPGAs) have a set of programmable elements which can be configured to personalize the FPGA to imAcknowledgments: This research is supported b...
Comparison of the bioavailability of oral, rectal and intramuscular promethazine (1984)

The bioavailabilities of generic and reference promethazine 50 mg rectal suppositories were compared with that of 50 mg reference oral solution (24 subjects), and all three treatments were compared with a 50 mg reference i.m. injection (six subjects). Plasma samples were assayed by an HPLC method with triflupromazine as the internal standard. Both suppositories produced lower peak plasma concentrations (Cmax) and longer times to peak concentration (Tmax) than did the oral solution. There were no significant differences in the mean area under the plasma concentration-time curves (AUC) from 0 to 24 h among the three treatments. The Cmax of the i.m. injection was significantly higher than the other three treatments, while the Tmax of the injection was significantly shorter than the reference suppository only. The mean AUC of the injection was significantly greater than the AUCs of the other three treatments. Rectal suppositories of promethazine are more slowly absorbed than oral solutions or i.m. injections; rectal suppositories and oral solutions are less bioavailable than i.m. injections. Diminished systemic bioavailability may result from extensive first-pass hepatic metabolism that occurs after both oral and rectal dosing. There is a high degree of intersubject variation in the bioavailability of promethazine rectal suppositories and oral solutions.
Transcriptional Activation of Fibroblast Growth Factor 1.B Promoter Is Mediated through an 18-Base Pair cis-Acting Element (1997)

Four different transcripts encoding fibroblast growth factor 1 (FGF-1, also known as aFGF) have been previously identified in our laboratory. Among them, FGF-1.B is the major transcript expressed specifically in the neuronal cells in brain tissue. Using the transient transfection experiment in a glioblastoma cell line, U1240MG, that expresses 1.B, we previously identified two regulatory regions (RR1 and RR2) in the brain-specific promoter, FGF-1.B. In the present study, we showed that the minimal region required for the DNA-protein interaction in RR2 resides in an 18-base pair (-484 to -467) sequence, by using DNase I footprinting and methylation interference studies and electrophoretic mobility shift assays. This minimal cis-acting element was found to be sufficient in enhancing the reporter activity driven by the heterologous herpes simplex virus thymidine kinase promoter in the 1.B-positive U1240MG cell line. This enhancing effect, however, was not detected in a glioblastoma cell line, U1242MG, which is negative for 1.B expression. By electrophoretic mobility shift assays, we also identified a specific DNA-protein complex, namely complex I, which is specific for 1.B-positive cell lines and human brain tissue. By in situ UV cross-linking experiment, we further showed that complex I contains two major DNA-binding proteins of apparent molecular masses of 37 and 98 kDa. Our results suggest that the formation of complex I, resulting from the heterodimerization of a 37-kDa protein (1.B-specific) and a 98-kDa protein (ubiquitous) may likely be a prerequisite for the enhanced expression of 1.B transcript in neuronal cells.
Peripheral T Cells Are the Therapeutic Targets of Glucocorticoids in Experimental Autoimmune Encephalomyelitis (2008)

High-dose glucocorticoid (GC) therapy is widely used to treat multiple sclerosis (MS), but the underlying mechanisms remain debatable. In this study, we investigated the impact of GC administration on experimental autoimmune encephalomyelitis using different GC receptor (GR)-deficient mutants. Heterozygous GR knockout mice were less sensitive to dexamethasone therapy, indicating that the expression level of the receptor determines therapeutic efficacy. Mice reconstituted with homozygous GR knockout fetal liver cells showed an earlier onset of the disease and were largely refractory to GC treatment, indicating that the GR in hematopoietic cells is essential for the beneficial effects of endogenous GCs and dexamethasone. Using cell-type specific GR-deficient mice, we could demonstrate that GCs mainly act on T cells, while modulation of macrophage function was largely dispensable in this context. The therapeutic effects were achieved through induction of apoptosis and down-regulation of cell adhesion molecules in peripheral T(H)17 and bystander T cells, while similar effects were not observed within the spinal cord. In addition, dexamethasone inhibited T cell migration into the CNS, confirming that peripheral but not CNS-residing T lymphocytes are the essential targets of GCs. Collectively, our findings reveal a highly selective mechanism of GC action in experimental autoimmune encephalomyelitis and presumably multiple sclerosis.
Estergruppenhaltige Polyalkenylene durch Olefin‐Metathese (1976)

Abstract Die ringöffnende Polymerisation von Estergruppen‐substituierten Cycloolefinen in Gegenwart geeigneter Metathese‐Katalysatoren wie WCl 6 /(CH 3 ) 4 Sn führt zu linearen Polyalkenylenen mit seitenständigen Estergruppen. Die Ausgangsmonomeren 9‐Äthoxycarbonyl‐bicyclo[6.1.0]non‐ cis ‐4‐en ( 3 ), 13‐Äthoxycarbonyl‐bicyclo[10.1.0]trideca‐ trans ‐4, trans ‐8‐dien ( 5 ) und 3‐Äthoxycarbonyl‐tricyclo[3.2.1.0 2,4 ]oct‐6‐en ( 7 ) werden über eine Carbenreaktion mit Diazoessigsäureäthylester aus den Cycloolefinen cis ‐1, cis ‐5‐Cyclooctadien ( 2 ), cis ‐1, trans ‐5, trans ‐9‐Cyclododecatrien ( 4 ) und Norbornadien ( 6 ) erhalten. Die entsprechenden Polyalkenylene ( 3a, 5a sowie 7a ) besitzen relativ hohe Molekularge‐wichte. Ihre Konstitution wird spektroskopisch und durch gaschromatographische Analyse der Abbauprodukte nach Olefin‐Metathese mit einem niedermolekularen Olefin (4‐Octen) bestimmt.
Reverse immunology approach for the identification of CD8 T‐cell‐defined antigens: Advantages and hurdles (2006)

One of the challenges of tumour immunology remains the identification of strongly immunogenic tumour antigens for vaccination. Reverse immunology, that is, the procedure to predict and identify immunogenic peptides from the sequence of a gene product of interest, has been postulated to be a particularly efficient, high-throughput approach for tumour antigen discovery. Over one decade after this concept was born, we discuss the reverse immunology approach in terms of costs and efficacy: data mining with bioinformatic algorithms, molecular methods to identify tumour-specific transcripts, prediction and determination of proteasomal cleavage sites, peptide-binding prediction to HLA molecules and experimental validation, assessment of the in vitro and in vivo immunogenic potential of selected peptide antigens, isolation of specific cytolytic T lymphocyte clones and final validation in functional assays of tumour cell recognition. We conclude that the overall low sensitivity and yield of every prediction step often requires a compensatory up-scaling of the initial number of candidate sequences to be screened, rendering reverse immunology an unexpectedly complex approach.
Heterogeneous Immunosensing Using Antigen and Antibody Monolayers on Gold Surfaces with Electrochemical and Scanning Probe Detection (2000)

We report the use of antibody and antigen monolayer immunosurfaces as detection elements in a competitive heterogeneous immunoassay employing either electrochemical or scanning probe detection. Antibody or antigen monolayers were prepared by covalent attachment of the desired immunoreagent to a two-component self-assembled monolayer via amide linkages. More specifically, mixed monolayers of a carboxylic acid-terminated thiol (thioctic acid) and a methyl-terminated thiol (butanethiol) were used to control the surface epitope density. The microscopic structure of the resulting antibody and antigen arrays was characterized by AFM (atomic force microscopy). Individual, surface-confined rabbit IgG antibodies could be directly imaged in contact mode. The average height of the capture antibodies was found to be 7.1 nm; the average antibody diameter, after correcting for tip convolution effects, was determined to be between 7 and 10 nm. The surface epitope density could be varied over approximately 2 orders of magnitude by changing the composition of the mixed monolayer. AFM was also used to characterize the antibody-antigen binding characteristics of these immunosurfaces, and an average binding efficiency of 22.8% was measured for rabbit IgG antibody arrays. In the second part of this study, the electrochemical detection scheme originally developed by Heineman and co-workers was adapted to our system. A calibration data set was measured, and the linear least-squares correlation coefficient (R2) was found to be 0.993. Finally, the electrochemical and scanning probe detection modes were directly compared. We find an excellent correlation between the surface density of antibody-antigen complexes measured by AFM and the electrochemical response of the same immunosurfaces.
Vault Nanocapsules as Adjuvants Favor Cell-Mediated over Antibody-Mediated Immune Responses following Immunization of Mice (2012)

These experiments show that vault nanocapsules induced strong anti-OVA CD8(+) and CD4(+) T cell memory responses and modest antibody production, which markedly differed from the immune response induced by liposomes. We also found that the vault nanocapsule could be modified to change antibody isotypes in vivo. Thus it is possible to create a vault nanocapsule vaccine that can result in the unique combination of immunogen-responsive CD8(+) and CD4(+) T cell immunity coupled with an IgG1 response for future development of vault nanocapsule-based vaccines against antigens for human pathogens and cancer.
Applying LIDAR datasets and GIS based model to evaluate solar potential over roofs: a review (2015)

The precise knowledge of the capacity to produce energy from renewable resources requires an adequate study to determine the spatial dimension of the territory. The aim of this paper is to present diverse procedures for the solar potential analysis in urban environments. Models and tools, based on the implementation of geo-information technologies and airborne remote sensing data, have been developed considering a certain level of complexity, where urban structure is composed of different areas characterized by their morphology and function. Before any analysis, establish the available information and define the three-dimensional modeling of the urban environment are the first actions. In addition, techniques for the treatment of data and assess the parameters needed to define the optimal location of solar systems for energy generation, are taken into account. Besides, there is a description of some web services developed to show the results and finally, the advances which may improve the precision and increase the detail degree in these studies.
A substrate‐selective co‐fermentation strategy with Escherichia coli produces lactate by simultaneously consuming xylose and glucose (2008)

We describe a new approach for the simultaneous conversion of xylose and glucose sugar mixtures which potentially could be used for lignocellulosic biomass hydrolysate. In this study we used this approach to demonstrate the production of lactic acid. This process uses two substrate-selective strains of Escherichia coli, one which is unable to consume glucose and one which is unable to consume xylose. In addition to knockouts in pflB encoding for pyruvate formate lyase, the xylose-selective (glucose deficient) strain E. coli ALS1073 has deletions of the glk, ptsG, and manZ genes while the glucose-selective (xylose deficient) strain E. coli ALS1074 has a xylA deletion. By combining these two strains in a single process the xylose and glucose in a mixed sugar solution are simultaneously converted to lactate. Furthermore, the biomass concentrations of each strain can readily be adjusted in order to optimize the overall product formation. This approach to the utilization of mixed sugars eliminates the problem of diauxic growth, and provides great operational flexibility.
HER2 Testing in Breast Cancer: NCCN Task Force Report and Recommendations (2006)

The NCCN HER2 Testing in Breast Cancer Task Force was convened to critically evaluate the ability of the level of HER2 expression or gene amplification in breast cancer tumors to serve as a prognostic and a predictive factor in the metastatic and adjuvant settings, to assess the reliability of the methods of measuring HER2 expression or gene amplification in the laboratory, and to make recommendations regarding the interpretation of test results. The Task Force is a multidisciplinary panel of 24 experts in breast cancer representing the disciplines of medical oncology, pathology, radiation oncology, surgical oncology, epidemiology, and patient advocacy. Invited members included members of the NCCN Breast Cancer Panel and other needed experts selected solely by the NCCN. During a 2-day meeting, individual task force members provided didactic presentations critically evaluating important aspects of HER2 biology and epidemiology: HER2 as a prognostic and predictive factor; results from clinical trials in which trastuzumab was used as a targeted therapy against HER2 in the adjuvant and metastatic settings; the available testing methodologies for HER2, including sensitivity, specificity, and ability to provide prognostic and predictive information; and the principles on which HER2 testing should be based. Each task force member was charged with identifying evidence relevant to their specific expertise and presentation. Following the presentations, an evidence-based consensus approach was used to formulate recommendations relating to the pathologic and clinical application of the evidence to breast cancer patient evaluation and care. In areas of controversy, this process extended beyond the meeting to achieve consensus. The Task Force concluded that accurate assignment of the HER2 status of invasive breast cancer is essential to clinical decision making in the treatment of breast cancer in both adjuvant and metastatic settings. Formal validation and concordance testing should be performed and reported by laboratories performing HER2 testing for clinical purposes. If appropriate quality control/assurance procedures are in place, either immunohistochemistry (IHC) or fluorescence in situ hybridization (FISH) methods may be used. A tumor with an IHC score of 0 or 1+, an average HER2 gene/chromosome 17 ratio of less than 1.8, or an average number of HER2 gene copies/cell of 4 or less as determined by FISH is considered to be HER2 negative. A tumor with an IHC score of 3+, an average HER2 gene/chromosome 17 ratio of greater than 2.2 by FISH, or an average number of HER2 gene copies/cell of 6 or greater is considered HER2 positive. A tumor with an IHC score of 2+ should be further tested using FISH, with HER2 status determined by the FISH result. Tumor samples with an average HER2 gene/chromosome ratio of 1.8 to 2.2 or average number of HER2 gene copies/cell in the range of greater than 4 to less than 6 are considered to be borderline, and strategies to assign the HER2 status of such samples are proposed.
Ectopic Activation of Germline and Placental Genes Identifies Aggressive Metastasis-Prone Lung Cancers (2013)

Activation of normally silent tissue-specific genes and the resulting cell "identity crisis" are the unexplored consequences of malignant epigenetic reprogramming. We designed a strategy for investigating this reprogramming, which consisted of identifying a large number of tissue-restricted genes that are epigenetically silenced in normal somatic cells and then detecting their expression in cancer. This approach led to the demonstration that large-scale "off-context" gene activations systematically occur in a variety of cancer types. In our series of 293 lung tumors, we identified an ectopic gene expression signature associated with a subset of highly aggressive tumors, which predicted poor prognosis independently of the TNM (tumor size, node positivity, and metastasis) stage or histological subtype. The ability to isolate these tumors allowed us to reveal their common molecular features characterized by the acquisition of embryonic stem cell/germ cell gene expression profiles and the down-regulation of immune response genes. The methodical recognition of ectopic gene activations in cancer cells could serve as a basis for gene signature-guided tumor stratification, as well as for the discovery of oncogenic mechanisms, and expand the understanding of the biology of very aggressive tumors.
Operations standards for global ATM networks: network element view (1996)

The International Telecommunication Union (ITU) has completed work on a series of standards on asynchronous transfer mode (ATM) equipment functional operations and network element management. The objective of these standards is to enable flexible design and interoperability of network elements for use in a global ATM network, independent of any specific implementation. This article discusses these standards with respect to their development and application in planning ATM networks. Specifically, it addresses the following: the modeling approach taken in the development of the ITU standards, key operational features specified in the ATM network element functional model, and the capabilities of the ATM network element management interface. Examples of ATM equipment are provided to illustrate how the functional models specified in the ITU standards may be used by network planners and equipment manufacturers to specify and develop ATM equipment tailored to specific needs, while ensuring network interoperability. The article concludes with some points on the future enhancement of these and related ATM equipment operations standards.
Teflon™-coated silicon apertures for supported lipid bilayer membranes (2004)

We present a method for microfabricating apertures in a silicon substrate using well-known cleanroom technologies resulting in highly reproducible giga-seal resistance bilayer formations. Using a plasma etcher, 150μm apertures have been etched through a silicon wafer. Teflon™ has been chemically vapor deposited so that the surface resembles bulk Teflon and is hydrophobic. After fabrication, reproducible high resistance bilayers were formed and characteristic measurements of a self-inserted single OmpF porin ion channel protein were made.
Covert Wireless Communication With a Poisson Field of Interferers (2018)

In this paper, we study covert communication in wireless networks consisting of a transmitter, Alice, an intended receiver, Bob, a warden, Willie, and a Poisson field of interferers. Bob and Willie are subject to uncertain shot noise due to the ambient signals from interferers in the network. With the aid of stochastic geometry, we analyze the throughput of the covert communication between Alice and Bob subject to given requirements on the covertness against Willie and the reliability of decoding at Bob. We consider non-fading and fading channels. We analytically obtain interesting findings on the impacts of the density and the transmit power of the concurrent interferers on the covert throughput. That is, the density and the transmit power of the interferers have no impact on the covert throughput as long as the network stays in the interference-limited regime, for both the non-fading and the fading cases. When the interference is sufficiently small and comparable with the receiver noise, the covert throughput increases as the density or the transmit power of the concurrent interferers increases.
Kinin metabolism in the perfused ventilated rat lung. I: Bradykinin metabolism in a system modeling the normal, uninjured lung. (1991)

Bradykinin (BK) in an asanguinous salt solution was perfused through intact rat lung. BK concentration varied from 0.0015 to 89 microM. Below 17 microM, the amount degraded was greater than or equal to 90% of the dose. The BK fragment distributions expressed as a percentage of the BK dose degraded were constant. The BK fragments formed and percentage yields were Pro-Pro (2-3) 49%, Arg-Pro-Pro-Gly-Phe (1-5) 32%, Pro-Pro-Gly-Phe-Ser-Pro (2-7) 6%, Arg-Pro-Pro-Gly-Phe-Ser-Pro (1-7) 6%, Arg-Pro-Pro (1-3) 3% and residual BK 4%. Above 17 microM, the amount of BK degraded was not proportional to the dose. Captopril and enalaprilat inhibited BK degradation, and their maximum inhibitions were about 50% and 30%, respectively. The percentage yield of the 1-5 fragment was greatly reduced by both inhibitors, but the percentage yields of the 2-3 and 1-8 fragments were moderately increased. It was concluded that (1) the intact rat lung itself has a very large capacity to degrade BK in the range of 2 mumoles/min/kg body weight; (2) two major and several minor enzyme pathways exist to degrade BK; (3) the relative contributions of these pathways to overall BK degradation remain essentially constant over a bradykinin concentration range from 0.0015 to 17 microM; (4) ACE/kininase-II catalyzed hydrolysis is one of the major pathways but is not the single major route for BK degradation; and (5) the other major BK degradation pathway involves enzymes cleaving the Arg1-Pro2 and Pro3-Gly4 bonds of BK.