gebhart/patrepeval huggingface dataset:
The Large Subunit of Replication Factor C Interacts with the Histone Deacetylase, HDAC1 (2002)

Replication factor C (RFC) is a pentameric complex of five distinct subunits that functions as a clamp loader, facilitating the loading of proliferating cell nuclear antigen (PCNA) onto DNA during replication and repair. More recently the large subunit of RFC, RFC (p140), has been found to interact with the retinoblastoma (Rb) tumor suppressor and the CCAAT/enhancer-binding protein alpha (C/EBP alpha) transcription factor. We now report that RFC (p140) associates with histone deacetylase activity and interacts with histone deacetylase 1 (HDAC1). This complex is functional and when targeted to promoters as a Gal4 fusion, RFC (p140) is a strong, deacetylase-dependent repressor of transcription. Further analysis revealed that RFC (p140) contains two distinct transcriptional repression domains. Moreover, both of these domains interact separately with HDAC1.
Modeling and Analysis of a Permanently Magnetized Sphere's Motion Facilitated by Field Manipulation (2006)

A model describing the motion of a magnetized sphere in a fluid medium subject to an applied field is developed. The inspiration for this system is rooted in technologies and procedures being explored in the biomedical community. In these systems, the accepted approximation of Stokes' flow about the sphere is discussed and limitations to this are identified with drag force relations accounting for wall effects presented. For this system, the sphere is approximated as a point dipole and the resulting electromagnetic force model is presented. For motion of the sphere using static electromagnets, a reduced coil set technique is proposed. The technique consists of utilizing the minimum number of coils for generation of the desired force on the sphere. This approach is in contrast to the existing solutions which use the full coil set for parallel and anti-parallel motion and single out a solution for the under determined system. A technique for determining the proper coil combination is developed from examining the definiteness of the geometric field functions. A coil array configuration consisting of a four coil assembly is investigated to facilitate planar motion of a magnetized spherical particle in a fluid medium. For this configuration, the reduced coil set consists of only two adjacent coils being active at any given time. The exact inverse current solution for the minimized coil set is derived and presented. The system dynamic model is formulated and represented in a nonlinear state space system
A study of an SCI switch fabric (2002)

The scalable coherent interface (SCI) defines a high-speed interconnect system that provides a coherent memory system. It specifies a topology-independent communication protocol with the possibility of connecting up to 64 K nodes. SCI switches are the key components in building large SCI systems effectively. An SCI switch which uses several internal buses is studied as well as more complex systems composed of several switches. Computer simulations are used to compare the different models and to determine system parameters.
Detection of p53 in primary lung tumors and nonsmall cell lung carcinoma cell lines. (1991)

Immunohistochemical analysis of p53, a nuclear protein involved in the development of numerous human tumors, was performed in a series of 50 primary nonsmall cell lung carcinomas and in a group of eight lung carcinoma cell lines. Using two mouse monoclonal antibodies, PAb1801 and PAb421, sixteen of thirty-five (45.7%) lung adenocarcinomas and seven of fifteen (46.6%) squamous cell carcinomas showed marked-to-moderate immunoreactivity. In fifty-six percent of the positive tumors more than 40% of all cells were p53 positive, and in only 17% of positive tumors the percentage of immunostained cells was less than ten. Although the number of p53 negative adenocarcinomas without metastasis was larger than the number of p53 positive tumors without metastasis, there were not clear differences between p53 positive and negative tumors with metastasis. Furthermore, six adenocarcinomas that infiltrated the pleura and/or the thoracic wall were p53 positive, whereas only two of these invasive tumors were p53 negative. From eight cell lines studied, six were positive for p53. A good correlation between immunocytochemistry and immunoprecipitation was observed. Two tumorigenic and metastatic cell lines, Calu 1 and Calu 6, that were not immunoreactive also showed lack of protein by immunoprecipitation, as well as absence of mRNA in Northern analysis. In addition, Calu 1 showed an important gene deletion. These observations point to the fact that deletions and alterations in transcription of the p53 gene could coincide with or eventuate in an advanced malignant phenotype that nevertheless results in a p53 negative immunostain. Although this type of change cannot be detected immunohistochemically in primary tumors without further molecular analysis, the results presented herein indicate that p53 can be detected immunohistochemically in a majority of lung tumors and that there is a tendency for more advanced adenocarcinoma stages to exhibit positive p53 immunostain.
Blue-Green Algal (Cyanophyta) Toxins (1979)

In the past toxin production by blue-green algae has been demonstrated by feeding large quantities of algae to vertebrates and observing symptoms leading to animal death. It was the purpose of this investigation to develop a more convenient way to test for the presence of an alga toxin using instead of vertebrates, other algae and those organisms with which it lives and competes in fresh water habitats. Using axenic algae cultures and three different agar media MBL, DAA and NA, the latter to check for bacterial contamination, algae were streaked on the agar surface in petri dishes to form a cross. The alga being tested for toxin production was streaked in a vertical line from top to bottom on the surface of the agar. The second alga formed the horizontal part of the cross and was streaked from left to right. The passing of the second alga across the vertical or first alga provided many close associations of the two algae in the right part of the horizontal streak, supplementing the overall growth and interactions occurring on the agar surface. In this way many combinations of seven species of blue-greens, four species of green algae, Euglena gracilis, and Tetrahymena pyriformis were made. From macroscopic and microscopic examinations it was found that three algae Scytonema hofmanni, Anabaena cylindrica and Anabaena 7119 inhibited the growth of other microorganisms. As a result of this study toxin production by axenic blue-green algae can now be detected qualitatively using microorganisms.
Controlling Congestion in Safety-Message Transmissions: A Philosophy for Vehicular DSRC Systems (2013)

Dedicated short-range communication (DSRC) is a powerful new technology that allows vehicles to communicate with each other. [DSRC is the U.S. vehicle communication technology operating in the 5.9-GHz Intelligent Transportation Systems (ITS) band; the analogous technology in Europe is called Cooperative ITS, and the band is referred to as ITS G5.] In particular, they exchange safety messages that allow collision threats to be identified and avoided. Channel congestion is a significant challenge because it causes safety messages to be lost and introduces latency in threat modeling at the application layer. This article describes a philosophy of DSRC congestion control, based on maximizing channel throughput via distributed control of the rate at which each vehicle transmits safety messages. It then defines a specific adaptive control algorithm, a weighted version of the LInear MEssage Rate Integrated Control (LIMERIC) algorithm. Weighted-LIMERIC has provable stability, convergence, and weighted fairness attributes. NS-2 simulation results that demonstrate these attributes are also presented.
An ECN-based end-to-end congestion-control framework: experiments and evaluation (2000)

In this paper we describe a study of an end-to-end architecture in a packet network where congestion is signalled to all contributing users, who then react accordingly. We assume a generic form of packet marking, where congested nodes set a single bit in the packets flowing through them using ECN (Explicit Congestion Notification). We briefly describe how allowing greater freedom to the end-systems lays the foundation for a differential QoS framework as a possible future extension to ECN. Not surprisingly, this QoS is a function of the user-network interaction. Focussing on a specific class of user behaviors, related to streaming applications, we decompose this interaction at the relevant timescales, relying both on simulations and dynamical system models. Results indicate that within the framework, single-bit notification achieves end-to-end QoS differentiation, approaching proportionally fair sharing of bandwidth.
Real-Time Spectrofluorometric Assays for the Lumenal Environment of the Maturing Phagosome (2008)

The ultimate goal of phagosomal maturation is the delivery of internalized, particulate cargo to acidic, hydrolytically competent compartments capable of mediating its degradation. Here we outline in detail three fluorometric techniques that allow the study of phagosomal maturation in macrophages by quantifying functionally important features of the lumenal environment of the developing phagosome in real time. The first assay utilizes a particle-restricted, pH-sensitive fluorochrome to measure the acidification of the phagosome. The second reports on the development of the proteolytic capacity of the phagosome by following the hydrolysis of a fluorogenic, generic proteinase substrate. The third quantifies the accumulation of lysosomal constituents within the phagosome by measuring the fluorescence resonance energy transfer (FRET) efficiency between a particle-restricted, donor fluor and a fluid phase acceptor fluor that had been chased previously into lysosomes. The assays are described as population-based methodologies utilizing a spectrofluorometer but, alternatively, can be adapted readily to confocal-based technologies for single phagosomal measurements.
Improved Sound Radiation of Flat Panel Loudspeakers Using the Local Air Spring Effect (2020)

The low-frequency performance of exciter-driven flat-panel loudspeakers is technically challenging. The lower modal density results in high deviations in the frequency response, and dips of more than 20 dB are possible. This paper presents an alternative approach for optimizing the modal behavior through the additional air spring effect of an irregular shaped enclosure. The additional mode-dependent air compliance suppresses the panel’s anti-phase components, which minimizes dips in the frequency response and improves the response without adding mass to the system. The approach is analyzed with the measured and simulated results of a prototype. Furthermore, additional enclosure changes were made to visualize the influence of the air spring improved system.
Identification of a regulatory transposon that controls the Mutator transposable element system in maize. (1991)

The Mutator system of maize consists of more than eight different classes of transposable elements each of which can be found in multiple copies. All Mu elements share the approximately 220-bp terminal inverted repeats, whereas each distinct element class is defined by its unique internal sequences. The regulation of instability of this system has been difficult to elucidate due to its multigenic inheritance. Here we present genetic experiments which demonstrate that there is a single locus, MuR1, which can regulate the transposition of Mu1 elements. We describe the cloning of members of a novel class of Mu elements, MuR, and demonstrate that a member of the class is the regulator of Mutator activity, MuR1. This conclusion is based on several criteria: MuR1 activity and a MuR-homologous restriction fragment cosegregate; when MuR1 undergoes a duplicative transposition, an additional MuR restriction fragment is observed, and MuR1 activity and the cosegregating MuR fragment are simultaneously lost within clonal somatic sectors. In addition, the MuR element hybridizes to transcripts in plants with Mutator activity. Our genetic experiments demonstrate that the MuR1 transposon is necessary to specify Mutator activity in our lines.
Aqueous MADIX/RAFT polymerization of diallyldimethylammonium chloride: Extension to the synthesis of poly(DADMAC)‐based double hydrophilic block copolymers (2010)

Abstract Macromolecular design by interchange of xanthates/reversible addition fragmentation chain transfer polymerization (MADIX/RAFT) of diallyldimethylammonium chloride (DADMAC) using the hydrophobic O ‐ethyl‐ S ‐(1‐methoxycarbonyl) ethyl dithiocarbonate MADIX/RAFT mediating agent, Rhodixan A1, was investigated. Attempts to obtain an efficient control of DADMAC polymerization in a water/ethanol mixture failed because of significant chain transfer to ethanol. The use of a water‐soluble Rhodixan A1‐terminated acrylamide oligomer as the MADIX/RAFT agent enabled the controlled polymerization of DADMAC in water at 50 °C using the cationic azo initiator V‐50. An excellent agreement was found between experimental and theoretical M n values throughout polymerization and over a broad range of initial concentration of xanthate. Polydispersity indexes (PDIs) at the end of the polymerization were abnormally high for a process showing a linear increase of M n with monomer conversion (1.8 < PDI < 2.0). This feature was explained by the measurement of a high transfer constant to xanthate ( C x = 18.8 ± 1.6) but a low interchange transfer constant ( C ex = 1.5). Nevertheless, poly(acrylamide)–poly(DADMAC) double hydrophilic block copolymers (DHBCs) of controlled M n and composition could be successfully synthesized for the first time. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010
The Influence of Dietary Lutein and Zeaxanthin on Visual Performance (2009)

The idea that normal constituents of the diet can influence visual function is not new. As early as 1782, Buzzi identified the yellow of the macula and Schulze (1866) specifically postulated that the yellow pigments led to improvements in human vision. These pigments were later found to be derived from dietary lutein and zeaxanthin that are known to be oxygenated carotenoids (xanthophylls). Walls and Judd (1933) postulated that these yellow intraocular pigments could improve visual performance by absorbing light scattered both within (for example, glare) and outside of the eye (increasing visual range by absorbing blue light scattered in the atmosphere), and by improving spatial vision through enhancing contrast and reducing chromatic blur. In this article, evidence for these ideas is reviewed with particular emphasis towards more recent data on glare effects.
Polymers for Second-Order Nonlinear Optics (1995)

The science and technology of second-order nonlinear optical polymers (NLOP) are briefly reviewed in an attempt to explain: (1) why these materials are important; (2) the origin of optical nonlinearity; (3) the strengths and weaknesses of various polymer topologies; (4) thin film processing techniques; (5) how to create and measure polar order (noncentrosymmetry); (6) stability issues; (7) fabrication of waveguides; and (8) useful devices that can be made from NLOP.
How to Quantify and Interpret Treatment Effects in Comparative Clinical Studies of COVID-19 (2020)

Clinical trials of treatments for coronavirus disease 2019 (COVID-19) draw intense public attention. More than ever, valid, transparent, and intuitive summaries of the treatment effects, including efficacy and harm, are needed. In recently published and ongoing randomized comparative trials evaluating treatments for COVID-19, time to a positive outcome, such as recovery or improvement, has repeatedly been used as either the primary or key secondary end point. Because patients may die before recovery or improvement, data analysis of this end point faces a competing risk problem. Commonly used survival analysis techniques, such as the Kaplan-Meier method, often are not appropriate for such situations. Moreover, almost all trials have quantified treatment effects by using the hazard ratio, which is difficult to interpret for a positive event, especially in the presence of competing risks. Using 2 recent trials evaluating treatments (remdesivir and convalescent plasma) for COVID-19 as examples, a valid, well-established yet underused procedure is presented for estimating the cumulative recovery or improvement rate curve across the study period. Furthermore, an intuitive and clinically interpretable summary of treatment efficacy based on this curve is also proposed. Clinical investigators are encouraged to consider applying these methods for quantifying treatment effects in future studies of COVID-19.
The Saccharomyces cerevisiae DNA repair gene RAD23 encodes a nuclear protein containing a ubiquitin-like domain required for biological function. (1993)

In eukaryotes, the posttranslational conjugation of ubiquitin to various cellular proteins marks them for degradation. Interestingly, several proteins have been reported to contain ubiquitin-like (ub-like) domains that are in fact specified by the DNA coding sequences of the proteins. The biological role of the ub-like domain in these proteins is not known; however, it has been proposed that this domain functions as a degradation signal rendering the proteins unstable. Here, we report that the product of the Saccharomyces cerevisiae RAD23 gene, which is involved in excision repair of UV-damaged DNA, bears a ub-like domain at its amino terminus. This finding has presented an opportunity to define the functional significance of this domain. We show that deletion of the ub-like domain impairs the DNA repair function of RAD23 and that this domain can be functionally substituted by the authentic ubiquitin sequence. Surprisingly, RAD23 is highly stable, and the studies reported herein indicate that its ub-like domain does not mediate protein degradation. Thus, in RAD23 at least, the ub-like domain affects protein function in a nonproteolytic manner.
Competing autocrine pathways involving alternative neuropilin-1 ligands regulate chemotaxis of carcinoma cells. (2003)

Neuropilin-1 (NP1), in conjunction with plexins, promotes axon repulsion by binding to semaphorin 3A (SEMA3A). Although NP1 is expressed in carcinoma cells, its functions have remained elusive, and neither SEMA3A nor plexin expression has been explored in cancer. Here we provide evidence that breast carcinoma cells support an autocrine pathway involving SEMA3A, plexin-A1, and NP1 that impedes their ability to chemotax. Reducing SEMA3A or NP1 expression by RNA interference or inhibiting plexin-A1 signaling enhanced migration. Conversely, expression of constitutively active plexin-A1 impaired chemotaxis. The paradox of how breast carcinoma cells expressing these endogenous chemotaxis inhibitors are able to migrate is explained by their expression of vascular endothelial growth factor (VEGF), a NP1 ligand that competes with SEMA3A for receptor binding. Finally, we establish that the ratio of endogenous VEGF and SEMA3A concentrations in carcinoma cells determines their chemotactic rate. Our findings lead to the surprising conclusion that opposing autocrine loops involving NP1 regulate the chemotaxis of breast carcinoma cells. Moreover, our data indicate a novel autocrine function for VEGF in chemotaxis.
White light on-axis digital holographic microscopy based on spectral phase shifting (2006)

A white light on-axis digital holographic microscopy based on spectral phase shifting is described. We show experimentally that the spectral phase shifting based on-axis digital holographic microscopy can be used as an alternative to the PZT based phase shifting digital holographic microscopy. The proposed spectral phase shifting approach can provide a speckle-free capability since it employs the partial coherent source produced by combining a white light source and a spectral tunable filter. Another benefit of the proposed white light on-axis digital holographic microscopic system stemmed from spectral phase shifting approach is in the capability of providing a full color 3-D spectral section imaging.
Folate synthesis in plants: The <i>p</i> -aminobenzoate branch is initiated by a bifunctional PabA-PabB protein that is targeted to plastids (2004)

It is not known how plants synthesize the p-aminobenzoate (PABA) moiety of folates. In Escherichia coli, PABA is made from chorismate in two steps. First, the PabA and PabB proteins interact to catalyze transfer of the amide nitrogen of glutamine to chorismate, forming 4-amino-4-deoxychorismate (ADC). The PabC protein then mediates elimination of pyruvate and aromatization to give PABA. Fungi, actinomycetes, and Plasmodium spp. also synthesize PABA but have proteins comprising fused domains homologous to PabA and PabB. These bipartite proteins are commonly called "PABA synthases," although it is unclear whether they produce PABA or ADC. Genomic approaches identified Arabidopsis and tomato cDNAs encoding bipartite proteins containing fused PabA and PabB domains, plus a putative chloroplast targeting peptide. These cDNAs encode functional enzymes, as demonstrated by complementation of an E. coli pabA pabB double mutant and a yeast PABA-synthase deletant. The partially purified recombinant Arabidopsis protein did not produce PABA unless the E. coli PabC enzyme was added, indicating that it forms ADC, not PABA. The enzyme behaved as a monomer in size-exclusion chromatography and was not inhibited by physiological concentrations of PABA, its glucose ester, or folates. When the putative targeting peptide was fused to GFP and expressed in protoplasts, the fusion protein appeared only in chloroplasts, indicating that PABA synthesis is plastidial. In the pericarp of tomato fruit, the PabA-PabB mRNA level fell drastically as ripening advanced, but there was no fall in total PABA content, which stayed between 0.7 and 2.3 nmol.g(-1) fresh weight.
Constitutive NF-kappa B activity in neurons. (1994)

NF-kappa B is inducible transcription factor present in many cell types in a latent cytoplasmic form. So far, only immune cells including mature B cells, thymocytes, and adherent macrophages have been reported to contain constitutively active forms of NF-kappa B in the nucleus. A recent study showed that the human immunodeficiency virus type 1 (HIV-1) promoter is highly active in several brain regions of transgenic mice (J. R. Corboy, J. M. Buzy, M. C. Zink, and J. E. Clements, Science 258:1804-1807, 1992). Since the activity of this viral enhancer is governed mainly by two binding sites for NF-kappa B, we were prompted to investigate the state of NF-kappa B activity in neurons. Primary neuronal cultures derived from rat hippocampus and cerebral cortex showed a high constitutive expression of an HIV-1 long terminal repeat-driven luciferase reporter gene, which was primarily dependent on intact NF-kappa B binding sites and was abolished upon coexpression of the NF-kappa B-specific inhibitor I kappa B-alpha. Indirect immunofluorescence and confocal laser microscopy showed that the activity of NF-kappa B correlated with the presence of the NF-kappa B subunits p50 and RelA (p65) in nuclei of cultured neurons. NF-kappa B was also constitutively active in neurons in vivo. As investigated by electrophoretic mobility shift assays, constitutive NF-kappa B DNA-binding activity was highly enriched in fractions containing neuronal nuclei prepared from rat cerebral cortex. Nuclear NF-kappa B-specific immunostaining was also seen in cryosections from mouse cerebral cortex and hippocampus. Only a subset of neurons was stained. Activated NF-kappa B in the brain is likely to participate in normal brain function and to reflect a distinct state of neuronal activity or differentiation. Furthermore, it may explain the high level of activity of the HIV-1 enhancer in neurons, an observation potentially relevant for the etiology of the AIDS dementia complex caused by HIV infection of the central nervous system.