gebhart/patrepeval huggingface dataset:
Histological Features of Anthers from Normal and ms3 Mutant Soybean1 (1984)

Anthers of male‐sterile mutant ( ms 3 ) and normal soybean [ Glycine max (L.) Merr.] were compared by using a triple‐staining procedure for DNA, polysaccharides and proteins, and a single‐staining procedure for sporopollenin in conjunction with brightfield and fluorescent microscopy. The purpose of this study was to determine at what stage of anther development histological differences were detectable between male‐sterile ( ms 3 ) and normal soybean. At the tetrad stage, a prominent greenish‐blue material, visible with the triple‐staining procedure, filled some of the enlarged tapetal cells of anthers of ms 3 plants. This material was also autofluorescent and had an affinity for the fluorochrome primuline which identified sporopollenin. By the early microspore stage, microspores of ms 3 plants were unusually enlarged and the tapetum surrounding them prematurely degenerated. This abnormality of tapetal behavior seems to be associated with microspore abortion and serves as an early marker for sterility. Other differences noted between the anthers of ms 3 and normal plants with the staining procedures used, were variations in the endothecium and the thickness and degree of staining of the microspore and pollen walls. All of these differences suggest that the effect of the ms 3 gene in the homozygous condition is expressed during early anther development, probably beginning at meiosis and directly influences the malfunctioning of the tapetum. The results of this study support numerous other published reports on both genetic and cytoplasmic male sterility implicating the tapetum as the primary tissue responsible for male sterility.
Gene Splicing by Overlap Extension: Tailor-Made Genes Using the Polymerase Chain Reaction (2013)

Gene Splicing by Overlap Extension or "gene SOEing" is a PCR-based method of recombining DNA sequences without reliance on restriction sites and of directly generating mutated DNA fragments in vitro. By modifying the sequences incorporated into the 5'-ends of the primers, any pair of polymerase chain reaction products can be made to share a common sequence at one end. Under polymerase chain reaction conditions, the common sequence allows strands from two different fragments to hybridize to one another, forming an overlap. Extension of this overlap by DNA polymerase yields a recombinant molecule. This powerful and technically simple approach offers many advantages over conventional approaches for manipulating gene sequences.
Nozaki−Hiyama−Kishi Reactions Catalytic in Chromium (1996)

A procedure is described which allows for the first time to perform chromium-catalyzed additions of organic halides to aldehydes (“Nozaki−Hiyama−Kishi reactions”). The reactions are mediated by trimethylchlorosilane, and the active Cr2+ species is constantly recycled by means of nontoxic, commercial manganese powder as the stoichiometric reductant. This method nicely applies to different substituted aryl, heteroaryl, alkynyl, alkenyl, and allyl halides as well as to alkenyl triflates as the starting materials and rivals its stoichiometric precedent in terms of efficiency, practicability, and chemo- and diastereoselectivity. Specifically, it has been demonstrated that the addition of crotyl bromide to various aldehydes is highly stereoconvergent, i.e. the respective anti-configurated homoallyl alcohols are obtained with excellent diastereomeric excess independent of whether the starting halide is (E)- or (Z)-configurated. In accordance with the likely catalytic cycle, both CrCl2(cat.) or CrCl3(cat) turned out to efficiently mediate reactions of this type, with the latter being preferred for practical reasons. Finally, attempts were made to optimize the number of turnovers in chromium. In this context the use of either chromocene (Cp2Cr) or CpCrCl2·THF as “pre-catalysts” were found to significantly upgrade the efficiency of such C−C bond formations, with ≤1 mol % of chromium being required in these cases for quantitative conversions.
Enantioselective Synthesis of (S)-3-Hydroxy-3-phenyl-3,4-dihydroquinolin-2(1H)-one Ring System (2006)

A series of new enantiomerically pure (S)-3-hydroxy-3-phenyl-3,4-dihydroquinolin-2(1H)-ones was prepared in good yields according to a two-step synthesis using a benzylation of the sodium enolate of the (2S,5S)-cis-2-tert-butyl-5-phenyl-1,3-dioxolan-4-one with substituted o-nitrobenzyl bromides followed by reduction of the nitro group to amine with concomitant intramolecular aminolysis of the dioxolanone ring.
C-Type Natriuretic Peptide and the Guanylyl Cyclase Receptors in the Rat Ovary are Modulated by the Estrous Cycle1 (1997)

We have previously shown that rat ovaries synthesize atrial natriuretic peptide (ANP) and express the cognate guanylyl cyclase (GC-A and GC-B) receptors for ANP. Since another natriuretic peptide, termed the C-type natriuretic peptide (CNP), can also interact with these receptors, we have investigated whether rat ovaries express CNP and if so, whether the concentration of this natriuretic peptide and the guanylyl-cyclase receptors are influenced by the estrous cycle. CNP mRNA was detected in rat ovaries using a reverse transcription (RT) polymerase chain reaction (PCR) strategy. RIA of ovarian extracts, obtained at the individual days of the estrous cycle, revealed the presence of immunoreactive CNP. The highest levels of CNP were detected at proestrus and were approximately 4-fold higher than the levels seen at any other stage of the cycle. GC-A and GC-B receptors were detected using quantitative autoradiography after application of either [125I]ANP or [125I]-tyr0CNP to sections of frozen ovaries. The highest specific binding of each radiolabeled ligand was seen in ovaries from proestrous animals. The GC-B receptors were localized to the membrana granulosa of developing ovarian follicles. Using quantitative PCR, we determined that levels of GC-A and GC-B mRNAs were highest in the ovaries of proestrous animals and were approximately 2- to 3-fold higher than the levels seen at diestrus. These findings demonstrate that a natriuretic peptide system, consisting of ligands and receptors, is present in the rat ovary. Since CNP and the GC receptors show coordinate estrous cycle-dependent variation with maximal expression at proestrus, we speculate that the natriuretic peptides may play an important role in either the development of ovulatory follicles or in the ovulatory process.
(−)‐Epigallocatechin‐3‐gallate induces Du145 prostate cancer cell death via downregulation of inhibitor of DNA binding 2, a dominant negative helix‐loop‐helix protein (2009)

(-)-Epigallocatechin-3-gallate (EGCG) is one of the major polyphenol components in green tea. It effectively induces apoptosis in prostate cancer cells. The anticancer effect of this reagent is appealing because it is a natural component of a popular daily beverage that has proven harmless for thousands of years, making it a good candidate chemopreventive agent. EGCG suppresses cell growth and causes cell death, but the mechanisms are not well characterized, especially in androgen-independent prostate cancer cells. In the present study, using Affymetrix genechip Hu133 2.0, we analyzed the gene expression patterns of the androgen-independent prostate cancer cell line Du145, treated with or without EGCG, and found 40 genes whose expression levels were altered (>twofold, either upregulated or downregulated, P < 0.01) upon treatment with EGCG. These gene products are involved in the functions of transcription, RNA processing, protein folding, phosphorylation, protein degradation, cell motility, and ion transport. Among them, inhibitor of DNA binding 2 (ID2), known as a dominant anti-retinoblastoma (Rb) helix-loop-helix protein, was found to be downregulated fourfold by EGCG treatment. Forced expression of ID2 in Du145 cells reduced apoptosis and increased cell survival in the presence of EGCG, and knockdown ID2 expression in Du145 cells using a morpholino oligonucleotide specific for ID2 mimicked the apoptosis effect generated by EGCG treatment, although it was milder. To our knowledge, this is the first report indicating that ID2 is one of the critical factors in the signaling pathway of Du145 cell death induced by EGCG.
Efficiency, error and yield in light-directed maskless synthesis of DNA microarrays (2011)

Maskless array synthesis is an efficient and versatile method for synthesizing high density arrays of long oligonucleotides for hybridization- and other molecular binding-based experiments. For applications requiring high sequence purity, such as gene assembly, diffraction and flare remain significant obstacles, but can be significantly reduced with straightforward experimental strategies.
Measles virus blind to its epithelial cell receptor remains virulent in rhesus monkeys but cannot cross the airway epithelium and is not shed (2008)

The current model of measles virus (MV) pathogenesis implies that apical infection of airway epithelial cells precedes systemic spread. An alternative model suggests that primarily infected lymphatic cells carry MV to the basolateral surface of epithelial cells, supporting MV shedding into the airway lumen and contagion. This model predicts that a mutant MV, unable to enter cells through the unidentified epithelial cell receptor (EpR), would remain virulent but not be shed. To test this model, we identified residues of the MV attachment protein sustaining EpR-mediated cell fusion. These nonpolar or uncharged polar residues defined an area located near the binding site of the signaling lymphocytic activation molecule (SLAM), the receptor for MV on lymphatic cells. We then generated an EpR-blind virus maintaining SLAM-dependent cell entry and inoculated rhesus monkeys intranasally. Hosts infected with the selectively EpR-blind MV developed rash and anorexia while averaging slightly lower viremia than hosts infected with wild-type MV but did not shed virus in the airways. The mechanism restricting shedding was characterized using primary well-differentiated human airway epithelial cells. Wild-type MV infected columnar epithelial cells bearing tight junctions only when applied basolaterally, while the EpR-blind virus did not infect these cells. Thus, EpR is probably a basolateral protein, and infection of the airway epithelium is not essential for systemic spread and virulence of MV.
Detection of cardiac allograft rejection by real‐time PCR analysis of circulating mononuclear cells (2004)

Quantitative analysis of gene expression in PBMC may be a valuable tool for non-invasive diagnosis of allograft rejection and may allow further insight in the biological process of graft rejection.
Cell line models for differentiation: preadipocytes and adipocytes (2010)

In vitro models have been invaluable in determining the mechanisms involved in adipocyte proliferation, differentiation, adipokine secretion and gene/protein expression. The cells presently available for research purposes all have unique advantages and disadvantages that one should be aware of when selecting cells. Established cell lines, such as 3T3-L1 cells, are easier and less costly to use than freshly isolated cells, even though freshly isolated cells allow for various comparisons such as the in vitro evaluation of different in vivo conditions that may not be possible using cell lines. Moreover, stem cells, transdifferentiated cells or dedifferentiated cells are relatively new cell models being evaluated for the study of adipocyte regulation and physiology. The focus of this brief review is to highlight similarities and differences in adipocyte models to aid in appropriate model selection and data interpretation for successful advancement of our understanding of adipocyte biology.
Ibalizumab: an anti-CD4 monoclonal antibody for the treatment of HIV-1 infection (2010)

The majority of currently available agents for the treatment of HIV-1 infection act by targeting one of several intracellular steps in the viral life cycle. Despite improvements in efficacy and tolerability, the development of viral resistance to these agents is common and significant toxicity and adherence issues still occur. For this reason the development of safe, well tolerated antiviral agents that target a novel step in the viral life cycle remains important. Viral entry into host cells affords several potential extracellular targets for antiretroviral therapy. Ibalizumab, a humanized monoclonal antibody to CD4, the primary host cellular receptor for HIV-1 entry, has been shown to block HIV-1 entry in vitro. Early clinical trials have demonstrated significant antiviral efficacy with a >1 log(10) reduction in viral load when given as monotherapy. Its long half-life, which allows weekly dosing, and its administration as an intravenous infusion differentiate it from other currently available antiretroviral agents. These properties may prove useful in allowing improved drug delivery to patients who have had difficulty adhering to daily oral regimens. Its unique mode of action reduces the risk of cross-resistance with currently available antiretroviral agents, with the potential to expand the choices available to treat drug-resistant HIV-1.
Rational design of artificial riboswitches based on ligand-dependent modulation of internal ribosome entry in wheat germ extract and their applications as label-free biosensors (2011)

Riboswitches are RNA elements in mRNA that control gene expression in cis in response to their specific ligands. Because artificial riboswitches make it possible to regulate any gene with an arbitrary molecule, they are expected to function as biosensors, in which the output is easily detectable protein expression. I report herein a fully rational design strategy for artificially constructing novel riboswitches that work in a eukaryotic cell-free translation system (wheat germ extract). In these riboswitches, translation mediated by an internal ribosome entry site (IRES) is promoted only in the presence of a specific ligand (ON), while it is inhibited in the absence of the ligand (OFF). The first rationally designed riboswitch, which is regulated by theophylline, showed a high switching efficiency and dependency on theophylline. In addition, based on the design of the theophylline-dependent riboswitch, other three kinds of riboswitches controlled by FMN, tetracycline, and sulforhodamine B, were constructed only by calculating the ΔG value of one stem-loop structure. The rational design strategy described herein is therefore useful for easily producing various ligand-dependent riboswitches, which are available as biosensors for detecting their ligands.
Performance Analysis of IEEE 802.11 DCF Based on OFDM (2015)

In order to evaluate the throughput performance of DCF about both ultra-rate and longtime delay wireless local area network (WLAN) based on Orthogonal Frequency Division Multiplexing (OFDM) modulation channel, this paper analyzes the operating principle of DCF and the throughput of system on the basis of two-dimensional Markov Model. Through theoretical analysis of the relationship among 802.11a/g throughput, the number of node and the length of data packet are acquired. Analysis, calculation and simulation are done on the influences of bit number of information carried by OFDM, free aslottime and time span of OFDM symbol on system throughput. Results of theoretical calculation and simulation testing explain that under the environment of high speed and high delay, throughput of DCF would decrease in which throughput of basic schema is generally higher than that of RTS/CTS. Furthermore, our results indicate that the longer aslotime and OFDM symbol have and the higher wireless physical channel rate is, the lower throughput of DCF is. Index Terms—OFDM, throughput, stability, CSMA/CA, DCF, Ultra Rate WLAN
Angiogenesis: new aspects relating to its initiation and control (1997)

Angiogenesis, the formation of new microvessels from parent microvessels, involves remodeling the basement membrane and interstitial extracellular matrix (ECM) using degrading proteases produced by the endothelial cells (ECs) and other adjacent cells, and the synthesis of ECM molecules by these cells. Degraded ECM releases previously bound heparin-binding cytokines (and growth factors) which are able to act as ligands to high-affinity receptors on various target cells, including ECs. The EC carries receptors for a number of cytokines which are produced by neighboring cells or released from the ECM and which can either induce or suppress the angiogenic phenotype of the EC. ECs are able to synthesize and secrete cytokines with auto- and paracrine effects. Angiogenesis, which virtually never occurs physiologically in adult tissues (except in the ovary, the endometrium and the placenta), is essential in wound healing and inflammation. Angiogenesis is, in fact, strictly controlled by a redundancy of pro- and anti-angiogenic paracrine peptide molecules, some of which have recently been described. The expression and synthesis of two distinct anti-angiogenic factors is, for example, controlled by the p53 tumor suppressor gene. In certain hypoxic conditions, chronic inflammatory diseases and syndromes, angiogenesis is of pathogenic and prognostic significance. Angiogenesis is, moreover, essential for the growth and metastatic spread of solid tumors. This indicates the potential for developing new therapeutic strategies not only for tumors but also in diseases such as rheumatoid arthritis, psoriasis, liver cirrhosis and diabetic retinopathy. Moreover, the therapeutic induction of angiogenesis in ischemic tissues using recombinant cytokines is also promising for clinical application. In fact, the first successful human gene therapy for stimulating angiogenesis has recently been reported.
Complexity-based consistent-quality encoding in the cloud (2016)

A cloud-based encoding pipeline which generates streams for video-on-demand distribution typically processes a wide diversity of content that exhibit varying signal characteristics. To produce the best quality video streams, the system needs to adapt the encoding to each piece of content, in an automated and scalable way. In this paper, we describe two algorithm optimizations for a distributed cloud-based encoding pipeline: (i) per-title complexity analysis for bitrate-resolution selection; and (ii) per-chunk bitrate control for consistent-quality encoding. These improvements result in a number of advantages over a simple “one-size-fits-all” encoding system, including more efficient bandwidth usage and more consistent video quality.
Branched BBB-shuttle peptides: chemoselective modification of proteins to enhance blood–brain barrier transport (2018)

The blood-brain barrier (BBB) hampers the delivery of therapeutic proteins into the brain. BBB-shuttle peptides have been conjugated to therapeutic payloads to increase the permeability of these molecules. However, most BBB-shuttles have several limitations, such as a lack of resistance to proteases and low effectiveness in transporting large biomolecules. We have previously reported on the THRre peptide as a protease-resistant BBB-shuttle that is able to increase the transport of fluorophores and quantum dots <i>in vivo</i>. In this work, we have evaluated the capacity of linear and branched THRre to increase the permeability of proteins in cellular models of the BBB. With this purpose, we have covalently attached peptides with one or two copies of the BBB-shuttle to proteins in order to develop chemically well-defined peptide-protein conjugates. While THRre does not enhance the uptake and transport of a model protein in BBB cellular models, branched THRre peptides displaying two copies of the BBB-shuttle result in a 2.6-fold increase.
Feed-forward echo state networks (2006)

New method for modeling nonlinear systems called the echo state networks (ESNs) has been proposed recently by H. Jaeger and H. Haas (2004). ESNs make use of the dynamics created by huge randomly created layer of recurrent units. Dynamical behavior of untrained recurrent networks was already explained in the literature and models using this behavior were studied by J.F. Kolen (1994) and by P. Tino et al. (1998). They are based on the fact that the activities of the recurrent layer of the recurrent network randomly initialized with small weights reflect history of the inputs presented to the network. Knowing how the recurrent layer stores the information and understanding the state dynamics of recurrent neural networks we propose modified ESN architecture. The only "true" recurrent connections are backward connection from output to recurrent units and the reservoir is built only by "forwardly" connected recurrent units. We show that this simplified version of the ESNs can also be successful in modeling nonlinear systems.
Effects of Lipid Peroxidation-Related Protein Modifications on RPE Lysosomal Functions and POS Phagocytosis (2007)

The results indicate that lipid peroxidation-derived protein modifications are involved in lipofuscinogenesis and may contribute to cell damaging effects of lipofuscin in retinal diseases such as AMD.
Eradication of intraperitoneal and distant tumor by adenovirus-mediated interferon-beta gene therapy is attributable to induction of systemic immunity. (2001)

Malignant mesothelioma remains an incurable disease for which immune-modulatory therapies, such as exogenous cytokines, have shown some promise. One such cytokine, IFN-beta, has potent antiproliferative and immunostimulatory activity in vitro, but its in vivo use has been limited by toxicity. We thus conducted studies evaluating intracavitary delivery of a replication-deficient adenoviral (Ad) vector encoding for the murine IFN-beta gene (Ad.muIFN-beta) in mouse models of malignant mesothelioma. In contrast to multiple injections of recombinant protein, a single i.p. injection of Ad.muIFN-beta into animals with established tumors elicited remarkable antitumor activity leading to long-term survival in >90% of animals bearing either AB12 or AC29 i.p. mesotheliomas. A control adenovirus vector had minimal antitumor effect in vivo. Significant therapeutic effects were also seen in animals treated with large tumor burdens. Importantly, treatment of i.p. tumor also led to reduction of growth in tumors established at a distant site (flank). A number of experiments suggested that these effects were attributable to an acquired CD8(+) T-cell-mediated response including: (a) the induction of long-lasting antitumor immunity; (b) loss of efficacy of Ad.muIFN-beta in tumor-bearing, immune-deficient (SCID, SCID/beige) mice; (c) detection of high levels of specific antitumor cytolytic activity from unstimulated splenocytes harvested from Ad.muIFN-beta-treated animals that was abolished by CD8(+) T-cell depletion; and (d) abrogation of antitumor effects of Ad.muIFN-beta in tumor-bearing CD8(+) T-cell-depleted animals. These data show that intracavitary IFN-beta gene therapy using an adenoviral vector provides strong CD8(+) T-cell-mediated antitumor effects in murine models of mesothelioma and suggest that this may be a promising strategy for the treatment of localized tumors such as mesothelioma or ovarian cancer in humans.
Structure of mouse ADP-ribosylhydrolase 3 (mARH3) (2008)

ADP-ribosylation is a reversible and covalent post-translational modification in which the attachment of ADP-ribose is catalyzed by ADP-ribosyltransferases and the removal of ADP-ribose is catalyzed by ADP-ribosylhydrolases. ADP-ribosylhydrolase 3 from mouse, consisting of 347 amino-acid residues, has been cloned, purified and crystallized. The three-dimensional structure has been resolved at a resolution of 1.8 A. The structure constitutes a compact all-alpha-helical protein with two Mg(2+) ions located in the active-site crevice. A structural comparison of mouse ADP-ribosylhydrolase 3 with its human orthologue shows a high degree of structural similarity. Furthermore, four prokaryotic proteins deposited in the PDB could be identified as being structurally related.