gebhart/patrepeval huggingface dataset:
Iris: A Directional MAC Protocol With Applications to Millimeter-Wave Mobile Ad-Hoc Networks (2019)

The scarcity of spectrum in sub-6 GHz frequency bands to meet projected wireless traffic demands has led to the wireless industry incorporating millimeter-wave technology in the design of next-generation wireless systems. The high path loss of millimeter-wave signals necessitates radios that operate in these frequencies to employ highly directional beams for transmission and reception. The transition from traditional omni-directional transmission and reception to highly directional links has drastic implications on the Medium Access Control (MAC) design, since it shifts the objective of the MAC layer from proactive interference avoidance to transmitter-receiver coordination to achieve beam alignment. In this paper, we present IRIS, a directional MAC protocol for mm-wave ad-hoc mobile networks that achieves this objective. Specifically, the Iris protocol is designed to distributedly coordinate the nodes so that transmitters and their intended receivers align their antenna boresights to establish a physical link between them when required. We establish certain performance guarantees that the Iris protocol provides, and illustrate the design process of a mm-wave ad-hoc MAC based on the Iris protocol.
The role of human ribosomal proteins in the maturation of rRNA and ribosome production (2008)

Production of ribosomes is a fundamental process that occurs in all dividing cells. It is a complex process consisting of the coordinated synthesis and assembly of four ribosomal RNAs (rRNA) with about 80 ribosomal proteins (r-proteins) involving more than 150 nonribosomal proteins and other factors. Diamond Blackfan anemia (DBA) is an inherited red cell aplasia caused by mutations in one of several r-proteins. How defects in r-proteins, essential for proliferation in all cells, lead to a human disease with a specific defect in red cell development is unknown. Here, we investigated the role of r-proteins in ribosome biogenesis in order to find out whether those mutated in DBA have any similarities. We depleted HeLa cells using siRNA for several individual r-proteins of the small (RPS6, RPS7, RPS15, RPS16, RPS17, RPS19, RPS24, RPS25, RPS28) or large subunit (RPL5, RPL7, RPL11, RPL14, RPL26, RPL35a) and studied the effect on rRNA processing and ribosome production. Depleting r-proteins in one of the subunits caused, with a few exceptions, a decrease in all r-proteins of the same subunit and a decrease in the corresponding subunit, fully assembled ribosomes, and polysomes. R-protein depletion, with a few exceptions, led to the accumulation of specific rRNA precursors, highlighting their individual roles in rRNA processing. Depletion of r-proteins mutated in DBA always compromised ribosome biogenesis while affecting either subunit and disturbing rRNA processing at different levels, indicating that the rate of ribosome production rather than a specific step in ribosome biogenesis is critical in patients with DBA.
α-Tocopheryl Succinate Inhibits Malignant Mesothelioma byDisrupting the Fibroblast Growth Factor Autocrine Loop (2005)

We have studied the potential effect against human malignant mesotheliomas (MM) of alpha-tocopheryl succinate (alpha-TOS), a redox-silent vitamin E analog with strong pro-apoptotic and anti-cancer activity. alpha-TOS at sub-apoptotic levels inhibited proliferation of MM cell lines, while being nontoxic to nonmalignant mesothelial cells. Because MM cells are typified by a highly metastatic phenotype, we investigated the effect of alpha-TOS on genes playing a major role in MM progression. Of these, alpha-TOS down regulated fibroblast growth factor (FGF)-1 and, in particular, FGF-2 on the transcriptional level in MM cells, and this was not observed in their nonmalignant counterparts. FGF-2 short interfering RNA suppressed proliferation of MM cells. Down-regulation of FGF-2 was likely because of inhibition of the egr-1 transcription activity that was decreased in MM cells via oxidative stress induced by alpha-TOS, as evidenced by EPR spectroscopy, whereas nonmalignant cells did not show this response. Treatment of MM cells with egr-1 short interfering RNA suppressed proliferation, which was overridden by exogenously added recombinant FGF-1 and, in particular, FGF-2. An analog of coenzyme Q targeted to mitochondria and superoxide dismutase overrode inhibition of MM cell proliferation by alpha-TOS as well as alpha-TOS-induced inhibition of egr-1-dependent transactivation. Finally, alpha-TOS significantly suppressed experimental MM in immunocompromised mice. Our data suggest that alpha-TOS suppresses MM cell proliferation by disrupting the FGF-FGF receptor autocrine signaling loop by generating oxidative stress and point to the agent as a selective drug against thus far fatal mesotheliomas.
Transcription elongation past O6-methylguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase (2008)

O(6)-Methylguanine (O(6)-meG) is a major mutagenic, carcinogenic and cytotoxic DNA adduct produced by various endogenous and exogenous methylating agents. We report the results of transcription past a site-specifically modified O(6)-meG DNA template by bacteriophage T7 RNA polymerase and human RNA polymerase II. These data show that O(6)-meG partially blocks T7 RNA polymerase and human RNA polymerase II elongation. In both cases, the sequences of the truncated transcripts indicate that both polymerases stop precisely at the damaged site without nucleotide incorporation opposite the lesion, while extensive misincorporation of uracil is observed in the full-length RNA. For both polymerases, computer models suggest that bypass occurs only when O(6)-meG adopts an anti conformation around its glycosidic bond, with the methyl group in the proximal orientation; in contrast, blockage requires the methyl group to adopt a distal conformation. Furthermore, the selection of cytosine and uracil partners opposite O(6)-meG is rationalized with modeled hydrogen-bonding patterns that agree with experimentally observed O(6)-meG:C and O(6)-meG:U pairing schemes. Thus, in vitro, O(6)-meG contributes substantially to transcriptional mutagenesis. In addition, the partial blockage of RNA polymerase II suggests that transcription-coupled DNA repair could play an auxiliary role in the clearance of this lesion.
Association of the IL12RB1 promoter polymorphisms with increased risk of atopic dermatitis and other allergic phenotypes (2005)

Atopic dermatitis (AD) is frequently associated with eosinophilia, highly elevated immunoglobulin E (IgE) levels and increased levels of T-helper 2-type (Th2) cytokines in skin lesions due to infiltrating T cells. Interleukin-12 (IL-12), in combination with interferon-gamma (IFN-gamma), inhibits IgE synthesis and Th2 cell function. As the IFN-gamma-inducing cytokines IL-12 and IL-23 utilize IL-12Rbeta1 as part of their receptors, it is possible that polymorphic variants of the IL-12Rbeta1 (IL12RB1) gene might determine an individual's susceptibility to AD. Here, we carried out a systemic search for genetic variants of the human IL12RB1 in Japanese subjects and identified 48 genetic variants. In a case-control association study, we found that promoter polymorphisms -111A/T and -2C/T were significantly associated with an increased risk of AD under a recessive model. The -111T-allele frequency in the independent population of child asthmatics was also much higher than that in the control group. In addition, the -111T/T genotype was progressively more common in AD with high total serum IgE levels in an IgE-level-dependent manner. Deletion analysis of the IL12RB1 promoter suggested that the -265 to -104 region that contained the -111A/T polymorphic site harbored an important regulatory element. Furthermore, we showed that the -111A/T substitution appeared to cause decreased gene transcriptional activity such that cells from -111A/A individuals exhibited higher IL12RB1 mRNA levels than those from -111T allele carriers. Our results suggested that in individuals with the -111T/T genotype, reduced IL-12Rbeta1 expression may lead to increased Th2 cytokine production in the skin and contribute to the development of AD and other subsequent allergic diseases.
Gene recombination in postmitotic cells. Targeted expression of Cre recombinase provokes cardiac-restricted, site-specific rearrangement in adult ventricular muscle in vivo. (1997)

Mouse models of human disease can be generated by homologous recombination for germline loss-of-function mutations. However, embryonic-lethal phenotypes and systemic, indirect dysfunction can confound the use of knock-outs to elucidate adult pathophysiology. Site-specific recombination using Cre recombinase can circumvent these pitfalls, in principle, enabling temporal and spatial control of gene recombination. However, direct evidence is lacking for the feasibility of Cre-mediated recombination in postmitotic cells. Here, we exploited transgenic mouse technology plus adenoviral gene transfer to achieve Cre-mediated recombination in cardiac muscle. In vitro, Cre driven by cardiac-specific alpha-myosin heavy chain (alphaMyHC) sequences elicited recombination selectively at loxP sites in purified cardiac myocytes, but not cardiac fibroblasts. In vivo, this alphaMyHC-Cre transgene elicited recombination in cardiac muscle, but not other organs, as ascertained by PCR analysis and localization of a recombination-dependent reporter protein. Adenoviral delivery of Cre in vivo provoked recombination in postmitotic, adult ventricular myocytes. Recombination between loxP sites was not detected in the absence of Cre. These studies demonstrate the feasibility of using Cre-mediated recombination to regulate gene expression in myocardium, with efficient induction of recombination even in terminally differentiated, postmitotic muscle cells. Moreover, delivery of Cre by viral infection provides a simple strategy to control the timing of recombination in myocardium.
Hypoplasia of pancreatic islets in transgenic mice expressing activin receptor mutants. (1998)

Activin, a member of the TGF-beta superfamily, regulates the growth and differentiation of a variety of cell types. Based on the expression of activin in pancreatic rudiments of rat embryos and stimulation of insulin secretion from adult rat pancreatic islets by activin, activin is implicated in the development and function of islets. To examine the significance of activin signaling in the fetal and postnatal development of islets, transgenic mice expressing a dominant negative form of activin receptor (dn-ActR) or a constitutively active form of activin receptor (ActR-T206D) in islets were generated together with the transgenic mice expressing intact activin receptor (intact ActR) as a negative control. Transgenic mice with both dn-ActR and ActR-T206D showed lower survival rates, smaller islet area, and lower insulin content in the whole pancreas with impaired glucose tolerance when compared with transgenic mice with intact ActR or littermates, but they showed the same alpha cell/beta cell ratios as their littermates. In addition to islet hypoplasia, the insulin response to glucose was severely impaired in dn-ActR transgenic mice. It is suggested that a precisely regulated intensity of activin signaling is necessary for the normal development of islets at the stage before differentiation into alpha and beta cells, and that activin plays a role in the postnatal functional maturation of islet beta cells.
Quality Control in Self/Nonself Discrimination (2006)

Unicellular eukaryotes primarily employ self/nonself discrimination to avoid self-mating, whereas multicellular organisms also use self/nonself discrimination in immune defense. Recent advances in understanding self/nonself discrimination in eukaryotes shed new light on the emergence of the most sophisticated self/nonself discrimination system known, the antigen receptors employed in the adaptive immune system.
A comparative analysis of SIFT, SURF, KAZE, AKAZE, ORB, and BRISK (2018)

Image registration is the process of matching, aligning and overlaying two or more images of a scene, which are captured from different viewpoints. It is extensively used in numerous vision based applications. Image registration has five main stages: Feature Detection and Description; Feature Matching; Outlier Rejection; Derivation of Transformation Function; and Image Reconstruction. Timing and accuracy of feature-based Image Registration mainly depend on computational efficiency and robustness of the selected feature-detector-descriptor, respectively. Therefore, choice of feature-detector-descriptor is a critical decision in feature-matching applications. This article presents a comprehensive comparison of SIFT, SURF, KAZE, AKAZE, ORB, and BRISK algorithms. It also elucidates a critical dilemma: Which algorithm is more invariant to scale, rotation and viewpoint changes? To investigate this problem, image matching has been performed with these features to match the scaled versions (5% to 500%), rotated versions (0° to 360°), and perspective-transformed versions of standard images with the original ones. Experiments have been conducted on diverse images taken from benchmark datasets: University of OXFORD, MATLAB, VLFeat, and OpenCV. Nearest-Neighbor-Distance-Ratio has been used as the feature-matching strategy while RANSAC has been applied for rejecting outliers and fitting the transformation models. Results are presented in terms of quantitative comparison, feature-detection-description time, feature-matching time, time of outlier-rejection and model fitting, repeatability, and error in recovered results as compared to the ground-truths. SIFT and BRISK are found to be the most accurate algorithms while ORB and BRISK are most efficient. The article comprises rich information that will be very useful for making important decisions in vision based applications and main aim of this work is to set a benchmark for researchers, regardless of any particular area.
Diketopiperazines as a new class of platelet-activating factor inhibitors (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiketopiperazines as a new class of platelet-activating factor inhibitorsNorihiko Shimazaki, Ichiro Shima, Keiji Hemmi, and Masashi HashimotoCite this: J. Med. Chem. 1987, 30, 10, 1706–1709Publication Date (Print):October 1, 1987Publication History Published online1 May 2002Published inissue 1 October 1987https://doi.org/10.1021/jm00393a002RIGHTS & PERMISSIONSArticle Views172Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (582 KB) Get e-Alerts Get e-Alerts
Novel Human Homologues of p47 and p67 Participate in Activation of Superoxide-producing NADPH Oxidases (2003)

The catalytic core of a superoxide-producing NADPH oxidase (Nox) in phagocytes is gp91phox/Nox2, a membrane-integrated protein that forms a heterodimer with p22phox to constitute flavocytochrome b558. The cytochrome becomes activated by interacting with the adaptor proteins p47phox and p67phox as well as the small GTPase Rac. Here we describe the cloning of human cDNAs for novel proteins homologous to p47phox and p67phox, designated p41nox and p51nox, respectively; the former is encoded by NOXO1 (Nox organizer 1), and the latter is encoded by NOXA1 (Nox activator 1). The novel homologue p41nox interacts with p22phox via the two tandem SH3 domains, as does p47phox. The protein p51nox as well as p67phox can form a complex with p47phox and with p41nox via the C-terminal SH3 domain and binds to GTP-bound Rac via the N-terminal domain containing four tetratricopeptide repeat motifs. These bindings seem to play important roles, since p47phox and p67phox activate the phagocyte oxidase via the same interactions. Indeed, p41nox and p51nox are capable of replacing the corresponding classical homologue in activation of gp91phox. Nox1, a homologue of gp91phox, also can be activated in cells, when it is coexpressed with p41nox and p51nox, with p41nox and p67phox, or with p47phox and p51nox; in the former two cases, Nox1 is partially activated without any stimulants added, suggesting that p41nox is normally in an active state. Thus, the novel homologues p41nox and p51nox likely function together or in combination with a classical one, thereby activating the two Nox family oxidases.
Investigation on the role of the molecular weight of polyvinyl pyrrolidone in the shape control of high-yield silver nanospheres and nanowires (2014)

Serving as shape control agent, polyvinyl pyrrolidone (PVP) has been widely used in chemical synthesis of metal nanoparticles. However, the role of molecular weight (MW) of PVP has been rarely concerned. In this study, we show a facile method to control the shapes of silver nanocrystals using PVP with different MWs. PVPMW=8,000, PVPMW=29,000, PVPMW=40,000, and PVPMW=1,300,000 are compared in the present study. Surprisingly, high-yield silver rodlike nanostructures, nanospheres, and nanowires can be obtained under the same growth environment and reactant concentrations by simply changing the MW of PVP. The mechanism studies of the role of PVP with different MWs in the growth process were carried out systemically using the morphology and spectroscopic measurement, FT-IR spectrum analysis, and seed crystallization monitoring. The results indicate that the MW of PVP plays a determinant role in the morphology and optical property control of the silver nanocrystals. Meantime, the concentration of PVP was found to be an assistant factor to further improve the shape and the yield of the synthesized nanocrystals.
Early fertilization events in the sexual and aposporous egg apparatus of Pennisetum ciliare (L.) Link (1995)

While detailed descriptions exist on the fine structural characteristics of double fertilization in sexual angiosperms, few studies have described fertilization in apomictic species. The results of this study with buffelgrass ( Pennisetum ciliare (L.) Link syn= Cenchrus ciliaris L.) show that differences exist between the early fertilization events in sexual and apomictic (aposporous) female gametophytes. In unpollinated sexual female gametophytes, the egg cell did not show signs of parthenogenetic activity. In contrast, autonomous egg embryony was observed in unpollinated aposporous female gametophytes. Compared with the sexual genotype, degeneration of the synergids in the aposporous female gametophyte was precocious and rapid. During the first 4 h after pollination, the chalazal end of the sexually functional egg cell remained covered by the plasma membrane. In the aposporous embryo sac, a cell wall covered the plasma membrane of the egg cell several hours before penetration of the pollen tube into the female gametophyte.
Immunoglobulin light chain variable region gene sequences for human antibodies to Haemophilus influenzae type b capsular polysaccharide are dominated by a limited number of V kappa and V lambda segments and VJ combinations. (1992)

The immune repertoire to Haemophilus influenzae type b capsular polysaccharide (Hib PS) appears to be dominated by certain light chain variable region genes (IgVL). In order to examine the molecular basis underlying light chain bias, IgVL genes have been cloned from a panel of heterohybridomas secreting human anti-Hib PS (antibody) (anti-Hib PS Ab). One hybridoma, representative of the predominant serum clonotype of anti-Hib PS Ab in older children and adults following immunization or Hib infection, uses a V kappa II segment identical to the germline gene A2, and a JK3 segment. A second kappa hybridoma uses a member of the V kappa I family and a JK4 segment. Four lambda antibodies, all cross-reactive with the structurally related antigen Escherichia coli K100 PS, use V lambda VII segments which are 96-98% homologous to one another, and may originate from a single germline gene. Two additional lambda antibodies, not K100-cross-reactive, are encoded by members of the V lambda II family. All lambda antibodies use highly homologous J lambda 2 or J lambda 3 segments. The VJ joints of all lambda antibodies and the V kappa II-encoded antibody are notable for the presence of an arginine codon, suggesting an important role in antigen binding. Although more complex than heavy chain variable region gene usage, a significant portion of serum anti-Hib PS Ab is likely to be encoded by a limited number of V kappa and V lambda segments and VJ combinations, which may be selectively expressed during development, or following antigen exposure.
Parallel Optics in Waveguide Displays: A Flat Panel Autostereoscopic Display (2010)

In order to demonstrate the Wedge as a parallel optic we have built a flat panel multi-projector autostereoscopic 3D display. The bulk, otherwise inherent in such displays, has been eliminated by use of a wedge-shaped light-guide. Two 280-mm (11") diagonal VGA resolution views were formed on a 406-mm (16") diagonal screen by pointing a pair of LED-illuminated pico-projectors measuring 115 X 50 X 22 mm into the 20-mm thick input face of a 710-mm long acrylic wedge. Distortions introduced by the Wedge were reduced to less than 2% by predistortion algorithms and distortion between views was less than 0.4%. Between the projectors was placed an infrared camera which imaged objects placed directly in front of the 3D screen.
Evaluation and treatment of patients with suicidal ideation. (1999)

Suicidal ideation is more common than completed suicide. Most persons who commit suicide have a psychiatric disorder at the time of death. Because many patients with psychiatric disorders are seen by family physicians and other primary care practitioners rather than by psychiatrists, it is important that these practitioners recognize the signs and symptoms of the psychiatric disorders (particularly alcohol abuse and major depression) that are associated with suicide. Although most patients with suicidal ideation do not ultimately commit suicide, the extent of suicidal ideation must be determined, including the presence of a suicide plan and the patient's means to commit suicide.
Strong Resistance of a Thin Crystalline Layer of Balanced Charged Groups to Protein Adsorption (2006)

Resistance of mixed self-assembled monolayers (SAMs) with various counter-charged terminal groups of different valence and protonation/deprotonation states to nonspecific protein adsorption is investigated. It is demonstrated that excellent nonfouling surfaces can be readily constructed from mixed positively and negatively charged components of equal valence in a wide range of thiol solution compositions. Furthermore, the lattice structure of one of the mixed SAM systems studied is revealed by atomic force microscopy (AFM) to be (5.2 +/- 0.2 A x 5.2 +/- 0.2 A)60 degrees . Results indicate that the packing structure of mixed charged SAMs is determined by strong charge-charge interactions of the terminal groups rather than S-Au and chain-chain interactions. This work provides direct evidence that conformational flexibility is not required for protein resistance of a surface and even a single compact layer of charged groups of balanced charge with a crystalline structure can resist nonspecific protein adsorption, suggesting that tightly bound water molecules on the topmost part of the mixed SAMs play a dominant role in surface resistance to nonspecific protein adsorption.