gebhart/patrepeval huggingface dataset:
MCP-1-induced protein-1, an immune regulator (2012)

MCP-1-induced protein-1 (MCPIP1) is a newly identified protein that is crucial to immune regulation. Mice lacking MCPIP1 gene suffer from severe immune disorders, and most of them cannot survive longer than 12 weeks. Considerable progress has been made in revealing the mechanism underlying the immune regulatory function of MCPIP1. MCPIP1 can act as an RNase to promote the mRNA degradation of some inflammatory cytokines, such as IL-6 and IL-1. Pre-microRNAs are also confirmed to be the substrate of MCPIP1 RNase. The structure of MCPIP1 N-terminal conserved domain shows a PilT N-terminus-like RNase structure, further supporting the notion that MCPIP1 has RNase activity. MCPIP1 can also deubiquitinate TNF receptor-associated factor family proteins, which are known to mediate immune and inflammatory responses. In this review, we summarize recent progress on the immune regulatory role of MCPIP1 and discuss the mechanisms underlying its function.
Single-Chain Antigen-Binding Proteins (1988)

Single-chain antigen-binding proteins are novel recombinant polypeptides, composed of an antibody variable light-chain amino acid sequence (VL) tethered to a variable heavy-chain sequence (VH) by a designed peptide that links the carboxyl terminus of the VL sequence to the amino terminus of the VH sequence. These proteins have the same specificities and affinities for their antigens as the monoclonal antibodies whose VL and VH sequences were used to construct the recombinant genes that were expressed in Escherichia coli. Three of these proteins, one derived from the sequence for a monoclonal antibody to growth hormone and two derived from the sequences of two different monoclonal antibodies to fluorescein, were designed, constructed, synthesized, purified, and assayed. These proteins are expected to have significant advantages over monoclonal antibodies in a number of applications.
CD26 Inhibition on CD34 + or Lineage − Human Umbilical Cord Blood Donor Hematopoietic Stem Cells/Hematopoietic Progenitor Cells Improves Long-Term Engraftment into NOD/SCID/Beta2 null Immunodeficient Mice (2007)

Given the tremendous need for and potential of umbilical cord blood (CB) to be utilized as a donor source for hematopoietic stem cell (HSC) transplantation in adults, there is a strong push to overcome the constraints created by the limited volumes and subsequent limited HSC and hematopoietic progenitor cell (HPC) numbers available for HSC transplantation from a single collection. We have previously described the use of CD26 inhibitor treatment of donor cells as a method to increase the transplant efficiency of mouse HSCs and HPCs into a mouse recipient. To study the use of CD26 inhibitors as a method of improving the transplantation of human CB HSCs and HPCs, we utilized the nonobese diabetic/severe combined immunodeficient/beta 2 microglobulin null (NOD/SCID/B2m(null)) immunodeficient mouse model of HSC transplantation. We report here significant improvements in the engraftment of long-term repopulating cells following the treatment of either CD34(+) or lineage negative (lin()) donor CB with the CD26 inhibitor, Diprotin A, prior to transplant. These results establish a basis on which to propose the use of CD26 inhibitor treatment of donor CB units prior to transplantation for the purpose of improving transplant efficiency and subsequently patient outcome.
Selection of aminoacyl-tRNAs at sense codons: the size of the tRNA variable loop determines whether the immediate 3′ nucleotide to the codon has a context effect (1995)

Codon context can affect translational efficiency by several molecular mechanisms. The base stacking interactions between a codon-anticodon complex and the neighboring nucleotide immediately 3' can facilitate translation by amber suppressors and the tRNA structure is also known to modulate the sensitivity to context. In this study the relative rates of aminoacyl-tRNA selection were measured at four sense codons (UGG, CUC, UUC and UCA), in all four 3' nucleotide contexts, through direct competition with a programmed frameshift at a site derived from the release factor 2 gene. Two codons (UGG and UUC) are read by tRNAs with small variable regions and their rates of aminoacyl-tRNA selection correlated with the potential base stacking strength of the 3' neighboring nucleotide. The other two codons (CUC and UCA) are read by tRNAs with large variable regions and the rate of selection of the aminoacyl-tRNAs in these cases varied little among the four contexts. Re-examination of published data on amber suppression also revealed an inverse correlation between context sensitivity and the size of the variable region. Collectively the data suggest that a large variable loop in a tRNA decreases the influence of the 3' context on tRNA selection, probably by strengthening tRNA-ribosomal interactions.
Pro-Leu-Ser/Thr-Pro is a consensus primary sequence for substrate protein phosphorylation. Characterization of the phosphorylation of c-myc and c-jun proteins by an epidermal growth factor receptor threonine 669 protein kinase (1991)

A growth factor-stimulated (MAP2-related) protein kinase, ERT, that phosphorylates the epidermal growth factor receptor at Thr669 has been purified from KB human tumor cells by Northwood and co-workers (Northwood, I. C., Gonzalez, F. A., Wartmann, M., Raden, D. L., and Davis, R. J. (1991) J. Biol. Chem. 266, 15266-15276). The ERT protein kinase has a restricted substrate specificity, and the structural determinants employed for substrate recognition by this enzyme have not been defined. As an approach toward understanding the specificity of substrate phosphorylation, we have used an in vitro assay to identify additional substrates for the ERT protein kinase. In this report we describe two novel substrates: (a) the human c-myc protein at Ser62 and (b) the rat c-jun protein at Ser246. Alignment of the primary sequences surrounding the phosphorylation sites located within the epidermal growth factor receptor (Thr669), Myc (Ser62), and Jun (Ser246) demonstrated a marked similarity. The observed consensus sequence was Pro-Leu-Ser/Thr-Pro. We propose that this sequence forms part of a substrate structure that is recognized by the ERT protein kinase.
Building wireless Internet services: state of the art (2004)

Summary form only given. Most Internet technologies have been designed for desktop and large computers running on reliable networks with relatively high bandwidth. Handheld wireless devices (or mobile devices), however, have a more constrained computing environment compared to desktop computers. Mobile devices tend to have less memory, less powerful CPUs, different input devices, and smaller displays. Further, wireless networks have less bandwidth and more latency compared to wired computer networks. Several solutions have been proposed to address these constraints, but as the wireless Internet market is moving at fast pace; new devices and technologies are always on the horizon and developers are faced with the challenge of learning about these devices, the technologies and development environments available that can be used to develop applications for these mobile devices. We present an overview of the three widely used technologies for building wireless Internet services, followed by a comparison of the different technologies.
Chlamydia pneumoniae Infection in a Breeding Colony of African Clawed Frogs (Xenopus tropicalis) (2000)

More than 90% of a breeding colony of clawed frogs (Xenopus tropicalis) imported to the United States from western Africa died in an epizootic of chlamydiosis. Chlamydial inclusions were observed by light and electron microscopy in the liver of an infected frog. Chlamydia pneumoniae was isolated in cell cultures from four frogs. A cutaneous infection by a chytridiomycete fungus observed in two frogs could have been a cofactor in the die-off.ous Diseases
Antibody-based assay discriminates Zika virus infection from other flaviviruses (2017)

Zika virus (ZIKV) is a mosquito-borne flavivirus that emerged recently as a global health threat, causing a pandemic in the Americas. ZIKV infection mostly causes mild disease, but is linked to devastating congenital birth defects and Guillain-Barré syndrome in adults. The high level of cross-reactivity among flaviviruses and their cocirculation has complicated serological approaches to differentially detect ZIKV and dengue virus (DENV) infections, accentuating the urgent need for a specific and sensitive serological test. We previously generated a ZIKV nonstructural protein 1 (NS1)-specific human monoclonal antibody, which we used to develop an NS1-based competition ELISA. Well-characterized samples from RT-PCR-confirmed patients with Zika and individuals exposed to other flavivirus infections or vaccination were used in a comprehensive analysis to determine the sensitivity and specificity of the NS1 blockade-of-binding (BOB) assay, which was established in laboratories in five countries (Nicaragua, Brazil, Italy, United Kingdom, and Switzerland). Of 158 sera/plasma from RT-PCR-confirmed ZIKV infections, 145 (91.8%) yielded greater than 50% inhibition. Of 171 patients with primary or secondary DENV infections, 152 (88.9%) scored negative. When the control group was extended to patients infected by other flaviviruses, other viruses, or healthy donors (<i>n</i> = 540), the specificity was 95.9%. We also analyzed longitudinal samples from DENV-immune and DENV-naive ZIKV infections and found inhibition was achieved within 10 d postonset of illness and maintained over time. Thus, the Zika NS1 BOB assay is sensitive, specific, robust, simple, low-cost, and accessible, and can detect recent and past ZIKV infections for surveillance, seroprevalence studies, and intervention trials.
Hydrogen configurations and stability in amorphous sputtered silicon (1997)

The effects of the deposition parameters on configurations and stability of hydrogen (deuterium) in amorphous sputtered silicon a-Si:H have been analyzed using Fourier transformed infrared absorption spectroscopy, deuterium effusion experiments, and x-ray diffractometry. The ratio of monohydride bonds Si–H was calculated from the infrared absorption stretching mode spectrum. This ratio was increased when the substrate temperature was increased. The effusion results in a-Si:D, when deposited with a simple cathode, have shown the presence of clustered deuterium weak bonds in microvoids (400 °C deuterium effusion peak), beside isolated Si–D bonds embedded in the more compact tissue (650 °C deuterium effusion peak). The deconvolutions of the stretching mode infrared absorption spectrum of the as-grown sample and after isothermal annealing at 510 °C have allowed one to conclude that it is not possible to identify the low temperature and high temperature effusion peaks, respectively, with the decomposition of Si–H2 and Si–H centers. The effusion of the less stable hydrogen improved the amorphous structural relaxation. The ratio of monohydride bonds was increased by introducing a magnetron cathode in the deposition chamber. At the same time, the deuterium effusion spectrum was modified, showing a continuous deuterium effusion from 350 °C, instead of two well-defined effusion peaks.
Delayed extraction matrix‐assisted laser desorption time‐of‐flight mass spectrometry (1995)

Abstract A new delayed extraction matrix‐assisted laser desorption/ionization (MALDI) time‐of‐flight (TOF) mass spectrometer system is described which provides dramatically improved performance over that obtained with identical TOF analyzers operated with constant electrical fields. In this system the ions formed by MALDI are produced in a weak electrical field, and subsequently extracted by application of a high voltage pulse after a predetermined time delay. Three parameters can be independently adjusted to optimize the performance. These include the field magnitude and direction during and immediately following ion production, the magnitude of the extraction field, and the time delay between the laser pulse and application of the extraction field. Theoretical equations are presented which guide the selection of these parameters to optimize the performance. Results are presented from three TOF analyzers of similar design, but ranging in size from a 1.3 m linear analyzer to a 6.4 m reflector. In all cases delayed extraction provides substantially improved resolution over that obtained from static operation. In the smallest linear analyzer resolution of M/ΔM (full width at half maximum) of 4000 is demonstrated for angiotensin I, and with the largest reflecting analyzer, the isotope peaks of bovine insulin are resolved nearly to baseline. With larger proteins, the isotopic peaks are not resolved, but resolution approaching the width of the isotopic envelope is obtained. Resolution improvement is demonstrated for proteins up to 30 kDa. In addition to improved resolution, delayed extraction is shown to improve the quality of MALDI mass spectra by suppressing matrix background, reducing chemical noise, and minimizing the effect of laser intensity on performance.
Translational genomics using Arabidopsis as a model enables the characterization of pennycress genes through forward and reverse genetics (2018)

Thlaspi arvense (pennycress) has the potential for domestication as a new oilseed crop. Information from an extensive body of research on the related plant species Arabidopsis can be used to greatly speed this process. Genome-scale comparisons in this paper documented that pennycress and Arabidopsis share similar gene duplication. This finding led to the hypothesis that it should be possible to isolate Arabidopsis-like mutants in pennycress. This proved to be true, as forward genetic screens identified floral and vegetative pennycress mutants that were similar to mutants found in Arabidopsis. Extending this approach, it was shown that most of the pennycress genes responsible for the formation of oxidized tannins could be rapidly identified. The causative mutations in the pennycress mutants could be identified either by PCR amplification of candidate genes or through whole-genome sequencing (WGS) analysis. In all, WGS was used to characterize 95 ethyl methane sulfonate mutants, which revealed a mutation rate of 4.09 mutations per megabase. A sufficient number of non-synonymous mutations were identified to create a mutant gene index that could be used for reverse genetic approaches to identify pennycress mutants of interest. As proof of concept, a Ta-max3-like dwarf mutant and Ta-kcs5/cer60-like wax mutants deficient in the biosynthesis of long chain fatty acids were identified. Overall, these studies demonstrate that translational genomics can be used to promote the domestication of pennycress. Furthermore, the ease with which important findings could be made in pennycress makes this species a new potential model plant.
Single-cell RNA-sequencing: The future of genome biology is now (2016)

Genome-wide single-cell analysis represents the ultimate frontier of genomics research. In particular, single-cell RNA-sequencing (scRNA-seq) studies have been boosted in the last few years by an explosion of new technologies enabling the study of the transcriptomic landscape of thousands of single cells in complex multicellular organisms. More sensitive and automated methods are being continuously developed and promise to deliver better data quality and higher throughput with less hands-on time. The outstanding amount of knowledge that is going to be gained from present and future studies will have a profound impact in many aspects of our society, from the introduction of truly tailored cancer treatments, to a better understanding of antibiotic resistance and host-pathogen interactions; from the discovery of the mechanisms regulating stem cell differentiation to the characterization of the early event of human embryogenesis.
Fabrication of GaN nanowire arrays by confined epitaxy (2006)

The authors report the fabrication of GaN nanowire arrays inside a thick SiNx, selective growth mask that was patterned by interferometric lithography and dry etching. The GaN nanowires are molded by the apertures in the selective growth mask and the growth is epitaxial with respect to the underlying GaN layer. The precise location and diameter of each nanowire in the array are controlled by the growth mask patterning, and the resulting array has a long-range order that is compatible with photonic crystal applications. This process uses conventional metal organic precursors and does not require any additional metal catalysts.
Prenatal identification of potential donors for umbilical cord blood transplantation for Fanconi anemia (1990)

Reported here are studies of Fanconi anemia fetal cells that led to the first use of umbilical cord blood for hematopoietic reconstitution in a clinical trial. Prenatal diagnosis and HLA typing were performed in fetuses at risk for Fanconi anemia (FA) to identify, prior to birth, those that were unaffected with the syndrome and were HLA-identical to affected siblings. Umbilical cord blood was harvested at the delivery of these infants; assays of progenitor cells indicated the presence of colony-forming units-granulocyte-macrophage (CFU-GM) in numbers similar to those of bone marrow CFU-GM that are associated with successful engraftment in HLA-matched allogeneic bone marrow transplantation. The possibility that umbilical cord blood from a single individual can be used as an alternative to bone marrow for hematopoietic reconstitution has now been demonstrated by the successful engraftment of two patients with FA. Progenitor cell assays of umbilical cord blood collected at the birth of a child affected with FA, who had been misdiagnosed on the basis of chorionic villus sampling (CVS) studies, indicated a profound deficiency in colony formation, consistent with previously reported abnormalities in the growth of FA cells in vitro. These results suggest that the hematopoietic disorder in FA is related to an underlying problem with cell proliferation.
Cellulase activities in biomass conversion: measurement methods and comparison (2010)

Cellulose, the major constituent of all plant materials and the most abundant organic molecule on the Earth, is a linear biopolymer of glucose molecules, connected by β-1,4-glycosidic bonds. Enzymatic hydrolysis of cellulose requires mixtures of hydrolytic enzymes including endoglucanases, exoglucanases (cellobiohydrolases), and β-glucosidases acting in a synergistic manner. In biopolymer hydrolysis studies, enzyme assay is an indispensable part. The most commonly used assays for the individual enzymes as well as total cellulase activity measurements, including their advantages and limitations, are summarized in this review article. In addition, some novel approaches recently used for enzyme assays are summarized.
Automatic TEM Sample Preparation (1999)

Abstract The rising demand in the semiconductor industry for higher spatial resolution in the analysis of device defects has focused attention on the use of transmission electron microscopy (TEM). However, conventional TEM sample preparation may be difficult and time-consuming, and depending on the operator may result in a low yield of quality specimens. One solution to this problem is the use of focused ion beam (FIB) milling for the final stage of TEM sample preparation. However, specimens have to be mechanically thinned prior to FIB processing, and the need to characterize specific devices requires a pre-FIB preparation method to isolate specific regions on the wafer. An innovative and automated solution that isolates specific devices and prepares TEM specimens for subsequent thinning by FIB has been developed. Based on controlled microcleaving technology, the system automatically performs the pre-FIB preparation in less than 30 minutes. An important added benefit is that the target area to be analyzed can be positioned at a specific distance from the sample edge, thereby facilitating the final FIB milling stage. The thinned specimen is automatically packaged for subsequent FIB processing and TEM. Details of the method and examples showing TEM results from tungsten filled vias are presented.
P-glycoprotein targeting: a unique strategy to selectively eliminate immunoreactive T cells (2002)

T lymphocytes have been found to harbor P-glycoprotein (Pgp) and to demonstrate modulation of its ion channel transporter function according to the state of activation of T lymphocytes. We hypothesized that cytotoxic chemicals that are extruded by Pgp could be used to specifically eliminate immunoreactive T-cell populations. In this study, we evaluated the capacity of 4,5-dibromorhodamine methyl ester (TH9402), a photosensitizer structurally similar to rhodamine, a dye transported by Pgp, and which becomes highly cytotoxic on activation with visible light to selectively deplete alloreactive T lymphocytes. Stimulation of T cells with mitogens or allogeneic major histocompatibility complex-mismatched cells resulted in the preferential retention of the TH9402 rhodamine-derivative in activated T cells, both CD4+ and CD8+. Photodynamic cell therapy of TH9402-exposed T cells led to the selective elimination of immunoreactive T-cell populations. In addition, this treatment preserved resting T cells and their capacity to respond to third-party cells. Inhibition of Pgp enhanced cellular trapping of the dye in nonactivated T cells and resulted in their depletion after exposure to light. Targeting of Pgp-deficient cells may therefore represent an appealing strategy for the prevention and treatment of graft-versus-host disease and other alloimmune or autoimmune disorders.
Pathogenesis and intervention strategies in diabetic retinopathy (2001)

Diabetic retinopathy is the leading cause of new blindness in the working-age population. If improved treatment regimens are to be developed it is crucial that the underlying pathophysiological mechanisms responsible for diabetic retinopathy are better understood. The multifactorial nature of the many pathways implicated in diabetic retinopathy requires a very detailed approach to elucidate the key mechanisms involved and their interactions in order to develop logical strategies aimed at therapeutic intervention. Fortunately, the streptozotocin rat model of diabetes displays many of the morphological and functional changes to the retinal vasculature that are evident in human diabetic retinopathy. This study reviews some of the recent experimental work by the authors in the streptozotocin rat, compares their findings to the human pathology and outlines potential new avenues for therapeutic intervention. In particular the improved understanding of which layers of the inner retina have the most stringent metabolic demands has helped identify which retinal layers are most susceptible to metabolic or hypoxic/ischaemic insult. It is concluded that improved treatment outcomes may ensue if the therapy is targeted at the appropriate tissue at specific stages of the disease.
The effects of ethanol methotrexate and diphenylhydantoin on [14C] leucine incorporation by human trophoblast cells cultured in vitro (1987)

The effects of alcohol, diphenylhydantoin and methotrexate on protein synthesis by human trophoblast have been studied in vitro using a cell culture technique. None of the drugs depressed protein synthesis at pharmacological levels and for diphenylhydantoin there was evidence that the cellular accumulation of this drug was negligible.