gebhart/patrepeval huggingface dataset:
The Telomerase/Vault-Associated Protein Tep1 Is Required for Vault RNA Stability and Its Association with the Vault Particle (2001)

Vaults and telomerase are ribonucleoprotein (RNP) particles that share a common protein subunit, TEP1. Although its role in either complex has not yet been defined, TEP1 has been shown to interact with the mouse telomerase RNA and with several of the human vault RNAs in a yeast three-hybrid assay. An mTep1(-/-) mouse was previously generated which resulted in no apparent change in telomere length or telomerase activity in six generations of mTep1-deficient mice. Here we show that the levels of the telomerase RNA and its association with the telomerase RNP are also unaffected in mTep1(-/-) mice. Although vaults purified from the livers of mTep1(-/-) mice appear structurally intact by both negative stain and cryoelectron microscopy, three-dimensional reconstruction of the mTep1(-/-) vault revealed less density in the cap than previously observed for the intact rat vault. Furthermore, the absence of TEP1 completely disrupted the stable association of the vault RNA with the purified vault particle and also resulted in a decrease in the levels and stability of the vault RNA. Therefore, we have uncovered a novel role for TEP1 in vivo as an integral vault protein important for the stabilization and recruitment of the vault RNA to the vault particle.
The clinical significance of human leukocyte antigen (HLA) allele compatibility in patients receiving a marrow transplant from serologically HLA-A, HLA-B, and HLA-DR matched unrelated donors (2002)

To improve the clinical outcome of allogeneic hematopoietic stem cell transplantation from an unrelated donor, the identification of human leukocyte antigen (HLA) alleles responsible for immunologic events such as graft-versus-host disease (GVHD), engraftment failure, and graft-versus-leukemia effect is essential. Genomic typing of HLA-A, -B, -C, -DRB1, and -DQB1 was retrospectively performed in 1298 donor-patient pairs in cases where marrow was donated from serologically HLA-A, -B, and -DR compatible donors. Single disparities of the HLA-A, -B, -C, or -DRB1 allele were independent risk factors for acute GVHD, and the synergistic effect of the HLA-C allele mismatch with other HLA allele mismatches on acute GVHD was remarkable. HLA-A and/or HLA-B allele mismatch was found to be a significant factor for the occurrence of chronic GVHD. HLA class I (A, B, and/or C) allele mismatch caused a significantly higher incidence of engraftment failure than HLA match. Significant association of HLA-C allele mismatch with leukemia relapse was not observed. As the result of these events, HLA-A and/or HLA-B allele mismatch reduced overall survival remarkably in both standard-risk and high-risk leukemia cases, whereas the HLA-C mismatch or HLA-class II (DRB1 and/or DQB1) mismatch did not. Furthermore, multiple mismatch of the HLA locus was found to reduce survival in leukemia cases. Thus, the role of the HLA class I allele in unrelated bone marrow transplantation was elucidated. Notably, HLA-C alleles had a different mode from HLA-A or -B alleles for acute GVHD and survival.
Boundary of pRNA functional domains and minimum pRNA sequence requirement for specific connector binding and DNA packaging of phage phi29. (1997)

Bacteriophage phi29 utilizes a viral-encoded 120-base RNA (pRNA) to accomplish dsDNA packaging into a preformed procapsid. Six pRNAs bind to the procapsid and work sequentially. The pRNA contains two functional domains, one for binding to the DNA translocating connector, and the other for interacting with another component of the DNA packaging machinery during DNA translocation. By UV crosslinking, the pRNA was found to bind to the connector specifically and not to the capsid or scaffolding proteins. When purified connectors were incubated with pRNA, rosette-like connector oligomers were observed. These oligomers were found to contain pRNA. A series of deletion mutants of the pRNA were constructed and their ability to perform various tasks involved in phi29 assembly were assayed. The minimum sizes of the pRNA needed for the following activities have been determined: (1) specific binding to procapsid or to connectors; (2) connector or procapsid binding with full efficiency compared with wild-type pRNA; and (3) genomic DNA packaging. In summary, bases 37-91 (55 nt) comprised the minimum sequence required for specific connector binding, although with lower efficiency; bases 6-113 (105 nt with the additional deletion of two nonessential bases, C109 and A106) comprised the minimum sequence required for full connector binding activity; and bases 1-117 comprised the minimum sequence needed for full DNA packaging activity. These data indicate clearly that the helical region composed of bases 1-6 and 113-117 plays a crucial role in DNA translocation, but is dispensable for connector binding. A model for the role of the pRNA in DNA packaging was also presented.
Castanospermine, a Potent Inhibitor of Dengue Virus Infection In Vitro and In Vivo (2005)

Previous studies have suggested that alpha-glucosidase inhibitors such as castanospermine and deoxynojirimycin inhibit dengue virus type 1 infection by disrupting the folding of the structural proteins prM and E, a step crucial to viral secretion. We extend these studies by evaluating the inhibitory activity of castanospermine against a panel of clinically important flaviviruses including all four serotypes of dengue virus, yellow fever virus, and West Nile virus. Using in vitro assays we demonstrated that infections by all serotypes of dengue virus were inhibited by castanospermine. In contrast, yellow fever virus and West Nile virus were partially and almost completely resistant to the effects of the drug, respectively. Castanospermine inhibited dengue virus infection at the level of secretion and infectivity of viral particles. Importantly, castanospermine prevented mortality in a mouse model of dengue virus infection, with doses of 10, 50, and 250 mg/kg of body weight per day being highly effective at promoting survival (P < or = 0.0001). Correspondingly, castanospermine had no adverse or protective effect on West Nile virus mortality in an analogous mouse model. Overall, our data suggest that castanospermine has a strong antiviral effect on dengue virus infection and warrants further development as a possible treatment in humans.
Escherichia coli DnaA Protein (1998)

Initiation of DNA replication at the Escherichia coli chromosomal origin occurs through an ordered series of events that depends first on the binding of DnaA protein, the replication initiator, to DnaA box sequences followed by unwinding of an AT-rich region. A step that follows is the binding of DnaB helicase at oriC so that it is properly positioned at each replication fork. We show that DnaA protein actively mediates the entry of DnaB at oriC. One region (amino acids 111-148) transiently binds to DnaB as determined by surface plasmon resonance. A second functional domain, possibly involving formation of a unique nucleoprotein structure, promotes the stable binding of DnaB during the initiation process and is inactivated in forming an intermediate termed the prepriming complex by removal of the N-terminal 62 residues. Based on similarities in the replication process between prokaryotes and eukaryotes, these results suggest that a similar mechanism may load the eukaryotic replicative helicase.
Polyamine levels and pigment contents in rapeseed regenerated in vitro in the presence of zinc (2011)

The present work was designed to select hyperaccumulator plants by in vitro breeding from transversal thin cell layers. The thin layer explants of Brassica napus cv. Jumbo were cultivated directly in the presence of ZnSO4 at different concentrations (0.1 to 1 mM). Regenerated shoots were transferred into pots, acclimatized, and cultured in the greenhouse. After 3 weeks, the regenerants were treated with 2 mM of ZnSO4 during 7 days. Growth parameters, guaiacol peroxidase activity (GPOX), malondialdehyde (MDA), polyamines (PAs) and pigment contents were evaluated. ZnSO4 applied during the regeneration process influenced significantly both physiological and biochemical characteristics of regenerated plants. Particularly, an increase of Zn level in the tissue culture induced an increase in MDA content and GPOX activity in the leaves and a decrease in pigment contents. Exposure to 2 mM Zn induced 112% increase in free polyamines in the leaves and roots, while this increase was as high as 399% for plants regenerated in the presence of the metal.

	 

	Key words: Phytoremediation, hyperaccumulator, in vitro, polyamines, malondialdehyde, guaiacol peroxidase, zinc stress.
Effect of platelet activating factor-acetylhydrolase on the formation and action of minimally oxidized low density lipoprotein. (1995)

Mildly oxidized low density lipoprotein (MM-LDL) produced by oxidative enzymes or cocultures of human artery wall cells induces endothelial cells to produce monocyte chemotactic protein-1 and to bind monocytes. HDL prevents the formation of MM-LDL by cocultures of artery wall cells. Using albumin treatment and HPLC we have isolated and partially characterized bioactive oxidized phospholipids in MM-LDL. Platelet activating factor-acetylhydrolase (PAF-AH), a serine esterase, hydrolyzes short chain acyl groups esterified to the sn-2 position of phospholipids such as PAF and particular oxidatively fragmented phospholipids. Treatment of MM-LDL with PAF-AH (2-4 x 10(-2) U/ml) eliminated the ability of MM-LDL to induce endothelial cells to bind monocytes. When HDL protected against the formation of MM-LDL by cocultures, lysophosphatidylcholine was detected in HDL; whereas when HDL was pretreated with diisopropyl fluorophosphate, HDL was no longer protective and lysophosphatidylcholine was undetectable. HPLC analysis also revealed that the active oxidized phospholipid species in MM-LDL had been destroyed after PAF-AH treatment. In addition, treatment of MM-LDL with albumin removed polar phospholipids that, when reisolated, induced monocyte binding to endothelial cells. These polar phospholipids, when treated with PAF-AH, lost biological activity and were no longer detected by HPLC. These results suggest that PAF-AH in HDL protects against the production and activity of MM-LDL by facilitating hydrolysis of active oxidized phospholipids to lysolipids, thereby destroying the biologically active lipids in MM-LDL.
Rapid-Thermal Nitridation of SiO2 for Radiation-Hardened MOS Gate Dielectrics (1986)

Nitridation of thin SiO2 layers has been achieved by a rapid thermal process in the presence of ammonia. The pre-and post-radiation performances of transistors with nitridated gate insulators have been presented. Nitridation causes a lowering of threshold voltage and channel mobility. Total dose testing indicates that nitridated gate oxides, under certain conditions, produce lower threshold voltage shift as well as less interface state generation than control (oxide) samples.
The Effects of Arterial Blood Gas Values on Lesion Volumes in a Graded Rat Spinal Cord Contusion Model (1994)

The detrimental effects of extreme blood gas values are well documented. However, the range of normal values has not been rigorously defined. There is an ongoing debate concerning the need for ventilation and tight control of blood gas values in spinal cord injury models. Consequently, we performed a retrospective study of 84 rats using a graded rat spinal cord contusion model. Spinal cord ionic lesion volumes were calculated from Na and K shifts at 24 h after injury. Blood gas measurements were obtained 5 min before contusion. For pH values of 7.31-7.46, systemic acidosis was associated with a small but significant decrease in ionic lesion volumes in the 12.5 and 25 g.cm contusion groups (p < 0.05 and p < 0.03, respectively). pH had no effect on ionic lesion volumes in the 50 g.cm contusion group (p > 0.5). PaCO2 values from 23 to 53 mm Hg showed an effect only at 25 g.cm (p < 0.05). PaO2 values of 46-138 mm Hg and calculated HCO3 values of 13-28 mEq/L had no effect on ionic lesion volumes. Two conclusions may be derived from these data. First, mild systemic acidosis is associated with a small reduction in ionic lesion volumes after mild and moderate injury but not after severe injury. This suggests that secondary mechanisms play a greater role in mild injuries. Second, variations in arterial blood gases within clinically normal ranges do not strongly influence 24-h ionic lesion volumes in a graded spinal cord injury model. The effects of blood gas values on ionic lesion volumes are not statistically significant unless the data are adjusted for injury severity. Although blood gas values must be carefully monitored, ventilation may not be needed routinely in rat spinal cord injury models. We recommend maintaining pH values between 7.35 and 7.40, PaCO2 between 35 and 41 mm Hg, and PaO2 greater than 71 mm Hg.
Plasmid reorganization during integrative transformation in Hansenula polymorpha (1995)

During studies of integrative transformation in Hansenula polymorpha, it was found that transformants with plasmids possessing the LEU2 gene of H. polymorpha were frequently unstable and lost plasmids while growing on non-selective medium. These transformants possessed reorganized plasmids capable of replication in H. polymorpha. Two such plasmids were isolated and characterized. It was shown that they contain additional DNA segments which were not present in the original plasmid used for transformation. Southern hybridization analysis carried out with labeled DNA probes derived from these segments showed that they consisted of H. polymorpha DNA. The hybridization patterns indicated that corresponding sequences were homologous to several chromosomal regions. These chromosomal DNA segments apparently carried H. polymorpha autonomous replicating sequences (HARS), since plasmids bearing them could transform H. polymorpha with high efficiency and were maintained in transformants in an autonomous state. Sequence analysis of one such captured chromosomal fragment revealed several eight- to ten-base AT-rich blocks similar to the presumed HARS sequence defined by Roggenkamp et al. (1986). Analogous reorganization was also observed with respect to integrative plasmids carrying the TRP3 and HIS3 genes of H. polymorpha and the ADE2 gene of Saccharomyces cerevisiae as selectable markers.
Latent Space Approaches to Social Network Analysis (2002)

Network models are widely used to represent relational information among interacting units. In studies of social networks, recent emphasis has been placed on random graph models where the nodes usually represent individual social actors and the edges represent the presence of a specified relation between actors. We develop a class of models where the probability of a relation between actors depends on the positions of individuals in an unobserved “social space.” We make inference for the social space within maximum likelihood and Bayesian frameworks, and propose Markov chain Monte Carlo procedures for making inference on latent positions and the effects of observed covariates. We present analyses of three standard datasets from the social networks literature, and compare the method to an alternative stochastic blockmodeling approach. In addition to improving on model fit for these datasets, our method provides a visual and interpretable model-based spatial representation of social relationships and improves on existing methods by allowing the statistical uncertainty in the social space to be quantified and graphically represented.
Texture features for browsing and retrieval of image data (1996)

Image content based retrieval is emerging as an important research area with application to digital libraries and multimedia databases. The focus of this paper is on the image processing aspects and in particular using texture information for browsing and retrieval of large image data. We propose the use of Gabor wavelet features for texture analysis and provide a comprehensive experimental evaluation. Comparisons with other multiresolution texture features using the Brodatz texture database indicate that the Gabor features provide the best pattern retrieval accuracy. An application to browsing large air photos is illustrated.
Spreadsheet Conditional Formatting: An Untapped Resource for Mathematics Education (2005)

Electronic spreadsheets have been with us for almost 25 years. In that period, innovative educators have found many ways in which this ubiquitous class of software may be leveraged in support of learning, especially in mathematics and the physical sciences. Conditional formatting is a relatively recent feature of the modern graphical spreadsheet, and may be viewed as a generalization of the accounting procedure of indicating debits by red ink and other amounts in black. The paper discusses advances in technology-enabled pedagogy made possible by this seemingly trivial feature of the modern spreadsheet program.
Inhibitors of Angiotensin-Converting Enzyme Prevent Myointimal Proliferation After Vascular Injury (1989)

The role of a local angiotensin system in the vascular response to arterial injury was investigated by administering the angiotensin-converting enzyme (CE) inhibitor cilazapril to normotensive rats in which the left carotid artery was subjected to endothelial denudation and injury by balloon catheterization. In control animals, by 14 days after balloon injury, the processes of smooth muscle cell (SMC) proliferation, migration of SMCs from the media to the intima, and synthesis of extracellular matrix produced marked thickening of the intima, with reduction of the cross-sectional area of the lumen. However, in animals that received continuous treatment with the CE inhibitor, neointima formation was decreased (by about 80 percent), and lumen integrity was preserved. Thus, the angiotensin-converting enzyme may participate in modulating the proliferative response of the vascular wall after arterial injury, and inhibition of this enzyme may have therapeutic applications to prevent the proliferative lesions that occur after coronary angioplasty and vascular surgery.
Split−Pool Synthesis of 1,3-Dioxanes Leading to Arrayed Stock Solutions of Single Compounds Sufficient for Multiple Phenotypic and Protein-Binding Assays (2001)

Diversity-oriented organic synthesis offers the promise of advancing chemical genetics, where small molecules are used to explore biology. While the split--pool synthetic method is theoretically the most effective approach for the production of large collections of small molecules, it has not been widely adopted due to numerous technical and analytical hurdles. We have developed a split--pool synthesis leading to an array of stock solutions of single 1,3-dioxanes. The quantities of compounds are sufficient for hundreds of phenotypic and protein-binding assays. The average concentration of these stock solutions derived from a single synthesis bead was determined to be 5.4 mM in 5 microL of DMSO. A mass spectrometric strategy to identify the structure of molecules from a split--pool synthesis was shown to be highly accurate. Individual members of the 1,3-dioxane library have activity in a variety of phenotypic and protein-binding assays. The procedure developed in this study allows many assays to be performed with compounds derived from individual synthesis beads. The synthetic compounds identified in these assays should serve as useful probes of cellular and organismal processes.
Neutral- and Multi-Colored Semitransparent Perovskite Solar Cells (2016)

In this review, we summarize recent works on perovskite solar cells with neutral- and multi-colored semitransparency for building-integrated photovoltaics and tandem solar cells. The perovskite solar cells exploiting microstructured arrays of perovskite "islands" and transparent electrodes-the latter of which include thin metallic films, metal nanowires, carbon nanotubes, graphenes, and transparent conductive oxides for achieving optical transparency-are investigated. Moreover, the perovskite solar cells with distinctive color generation, which are enabled by engineering the band gap of the perovskite light-harvesting semiconductors with chemical management and integrating with photonic nanostructures, including microcavity, are discussed. We conclude by providing future research directions toward further performance improvements of the semitransparent perovskite solar cells.
10-Qubit Entanglement and Parallel Logic Operations with a Superconducting Circuit (2017)

Here we report on the production and tomography of genuinely entangled Greenberger-Horne-Zeilinger states with up to ten qubits connecting to a bus resonator in a superconducting circuit, where the resonator-mediated qubit-qubit interactions are used to controllably entangle multiple qubits and to operate on different pairs of qubits in parallel. The resulting 10-qubit density matrix is probed by quantum state tomography, with a fidelity of 0.668±0.025. Our results demonstrate the largest entanglement created so far in solid-state architectures and pave the way to large-scale quantum computation.
VH sequence of a human anti-Sm autoantibody. Evidence that autoantibodies can be unmutated copies of germline genes. (1989)

The utilization of germline genes for the synthesis of autoantibodies has been suspected for many years based on the presence of cross-reactive idiotypes among patients as well as in some healthy first-degree relatives of patients with several autoimmune diseases including SLE. One such system of idiotypes involves anti-Sm antibodies, which are highly specific for SLE. To definitively establish the utilization of germline genes in the Sm system, we produced human-human B cell hybridomas from a patient with SLE who had circulating anti-Sm antibodies. One stable hybridoma designated 4B4 secretes an IgM-kappa mAb that binds Sm and shares idiotypic determinants with other anti-Sm antibodies. A second anti-Sm antibody (3C3), isolated from the same patient was also studied. Oligo(dT) priming was used to produce cDNA corresponding to full length IgM. Sequence analysis revealed that the VH gene segment (1-96) of 4B4 is identical to a VH sequence previously detected in a fetal liver cDNA library by Schroeder and his co-workers as well as a germline VH recently described by Berman and his associates. The identity of a lupus mAb and sequences derived from unrelated individuals provides strong evidence that this autoantibody is a direct copy of a germline gene.
Fluorescence studies of hematoporphyrin derivative in normal and malignant rat tissue. (1986)

Laser-induced fluorescence in rat tissue was studied during the uptake and clearing period of i.v.-injected hematoporphyrin derivative. A malignant rat tumor and normal tissue of 20 different kinds from the tumor-bearing animals were investigated. A pulsed nitrogen laser (337 nm) was used in conjunction with an optical multichannel analyzer system, in which the whole fluorescence light distribution was captured for each laser pulse. Several of the organs exhibited an initial and a delayed intensity peak in the characteristic hematoporphyrin derivative laser-induced fluorescence intensity (630 nm) that might be interpreted as due to intracellular transformations of different chemical components of the hematoporphyrin derivative preparation. By dividing the background-free 630-nm signal by the blue fluorescence intensity, a dimensionless quantity is obtained that could have many advantages in practical endoscopic laser-induced fluorescence work. This ratio was also shown to exhibit a larger contrast between tumor and surrounding tissue. The ratio between the two red fluorescence peaks was also found to be useful for discriminating tumor from normal tissue. A combination of the two ratios was shown to be particularly valuable for tumor discrimination.