gebhart/patrepeval huggingface dataset:
Extracellular Matrix Proteoglycans Control the Fate of Bone Marrow Stromal Cells (2005)

Extracellular matrix glycoproteins and proteoglycans bind a variety of growth factors and cytokines thereby regulating matrix assembly as well as bone formation. However, little is known about the mechanisms by which extracellular matrix molecules modulate osteogenic stem cells and bone formation. Using mice deficient in two members of the small leucine-rich proteoglycans, biglycan and decorin, we uncovered a role for these two extracellular matrix proteoglycans in modulating bone formation from bone marrow stromal cells. Our studies showed that the absence of the critical transforming growth factor-beta (TGF-beta)-binding proteoglycans, biglycan and decorin, prevents TGF-beta from proper sequestration within the extracellular matrix. The excess TGF-beta directly binds to its receptors on bone marrow stromal cells and overactivates its signaling transduction pathway. Overall, the predominant effect of the increased TGF-beta signaling in bgn/dcn-deficient bone marrow stromal cells is a "switch in fate" from growth to apoptosis, leading to decreased numbers of osteoprogenitor cells and subsequently reduced bone formation. Thus, biglycan and decorin appear to be essential for maintaining an appropriate number of mature osteoblasts by modulating the proliferation and survival of bone marrow stromal cells. These findings underscore the importance of the micro-environment in controlling the fate of adult stem cells and reveal a novel cellular and molecular basis for the physiological and pathological control of bone mass.
Signal modeling for ion cyclotron resonance (1978)

A new signal model, called the rotating electric monopole signal model, is developed for ion cyclotron resonance (ICR) experiments. Unlike prior signal models, the model is applicable to all forms of ICR spectroscopy which use radio-frequency detection methods. The signal model consists of a rotating electric monopole which is shown to be equivalent for signal generation purposes to a rotating electric dipole and for a macroscopic number of ions to a rotating electric polarization. The rotating polarization induces an alternating charge in the plates of the ICR cell and an alternating current between and an alternating voltage across the plates of the ICR cell. A noise analysis is performed, and if amplifier noise is neglected, the ICR sensitivity according to the model is found to be inversely proportional to the ion mass. This is the same sensitivity dependence as is found with conventional ICR power absorption experiments. The ICR voltage signal strength is inversely proportional to ion mass if the monitoring circuit is predominantly resistive and is independent of ion mass if the circuit is predominantly capacitive. The model clearly illustrates the parallelism between signal generation in ICR spectroscopy and signal generation in other coherent radiation spectroscopies such as NMR and microwave spectroscopy.
Nucleosides and Nucleotides. 104. Radical and Palladium-Catalyzed Deoxygenation of the Allylic Alcohol Systems in the Sugar Moiety of Pyrimidine Nucleosides§,1 (1992)

Abstract New methods for the synthesis of 2′,3′-didehydro-2′,3′-dideoxy-2′ (and 3′)-methyl-5-methyluridines and 2′,3′-dideoxy-2′ (and 3′)-methylidene pyrimidine nucleosides have been developed from the corresponding 2′ (and 3′)-deoxy-2′ (and 3′)-methylidene pyrimidine nucleosides. Treatment of a 3′-deoxy-3′-methylidene-5-methyluridine derivative 8 with 1,1′-thiocarbonyldiimidazole gave the allylic rearranged 2′,3′-didehydro-2′,3′-dideoxy-3′-[(imidazol-1-yl)carbonylthiomethyl] derivative 24. On the other hand, reaction of 8 with methyloxalyl chloride afforded 2′-O-methyloxalyl ester 25. Radical deoxygenation of both 24 and 25 gave 26 exclusively. Palladium-catalyzed reduction of 2′,5′-di-O-acetyl-3′-deoxy-3′-methylidene-5-methyluridine (32) with triethylammonium formate as a hydride donor regioselectively afforded the 2′,3′-dideoxy-3′-methylidene derivative 35 and 2′,3′-didehydro-2′,3′-dideoxy-3′-methyl derivative 34 in a ratio of 95:5 in 78% yield. These reactions were used on the corresponding 2′-deoxy-2′-methylidene derivatives. An alternative synthesis of 2′,3′-dideoxy-2′-methylidene pyrimidine nucleosides (43, 52, and 54) was achieved from the corresponding 1-(3-deoxy-β-D-thero-pentofuranosyl)pyrimidines (44 and 45). The cytotoxicity against L1210 and KB cells and inhibitory activity of the pathogenicity of HIV-1 are also described
Comparative Analysis of Single-Species and Polybacterial Wound Biofilms Using a Quantitative, In Vivo, Rabbit Ear Model (2012)

This study reveals that mixed-species biofilms have a greater impact on wound healing dynamics than their monospecies counterparts. The increased virulence of polybacterial biofilm appears dependent on the combined pathogenicity of each species, verified using a mutant strain. These data suggest that individual bacterial species can interact synergistically within a single biofilm structure.
Cryptographic sealing for information secrecy and authentication (1982)

A new protection mechanism is described that provides general primitives for protection and authentication. The mechanism is based on the idea of sealing an object with a key. Sealed objects are self-authenticating, and in the absence of an appropriate set of keys, only provide information about the size of their contents. New keys can be freely created at any time, and keys can also be derived from existing keys with operators that include Key-And and Key-Or . This flexibility allows the protection mechanism to implement common protection mechanisms such as capabilities, access control lists, and information flow control. The mechanism is enforced with a synthesis of conventional cryptography, public-key cryptography, and a threshold scheme.
A systematic RNAi screen for longevity genes in C. elegans (2005)

We report here the first genome-wide functional genomic screen for longevity genes. We systematically surveyed Caenorhabditis elegans genes using large-scale RNA interference (RNAi), and found that RNAi inactivation of 89 genes extend C. elegans lifespan. Components of the daf-2/insulin-like signaling pathway are recovered, as well as genes that regulate metabolism, signal transduction, protein turnover, and gene expression. Many of these candidate longevity genes are conserved across animal phylogeny. Genetic interaction analyses with the new longevity genes indicate that some act upstream of the daf-16/FOXO transcription factor or the sir2.1 protein deacetylase, and others function independently of daf-16/FOXO and sir2.1, and might define new pathways to regulate lifespan.
Separation of active tubulin and microtubule-associated proteins by ultracentrifugation and isolation of a component causing the formation of microtubule bundles (1984)

A new method for separating microtubule-associated proteins (MAPs) and tubulin, appropriate for relatively large-scale preparations, was developed. Most of the active tubulin was separated from the MAPs by centrifugation after selective polymerization of the tubulin was induced with 1.6 M 2-(N-morpholino)ethanesulfonate (Mes) and GTP. The MAPs-enriched supernatant was concentrated and subsequently clarified by prolonged centrifugation. The supernatant (total soluble MAPs) contained almost no tubulin, most of the nucleosidediphosphate kinase activity of the microtubule protein, good activity in promoting microtubule assembly in 0.1 M Mes, and proteins with the electrophoretic mobility of MAP-1, MAP-2, and tau factor. The pellet, inactive in supporting microtubule assembly, contained denatured tubulin, most of the ATPase activity of the microtubule protein, and significant amounts of protein with the electrophoretic mobility of MAP-2. Insoluble material at this and all previous stages, including the preparation of the microtubule protein, could be heat extracted to yield soluble protein active in promoting microtubule assembly and containing MAP-2 as a major constituent. The total soluble MAPs were further purified by DEAE-cellulose chromatography into bound and unbound components, both of which induced microtubule assembly. The bound component (DEAE-MAPs) contained proteins with the electrophoretic mobility of MAP-1, MAP-2, and tau factor. The polymerization reaction induced by the unbound component (flow-through MAPs) produced very high turbidity readings. This was caused by the formation of bundles of microtubules. Although the flow-through MAPs contained significantly more ATPase, tubulin-independent GTPase, and, especially, nucleosidediphosphate kinase activity than the DEAE-MAPs, preparation of a MAPs fraction without these enzymes required heat treatment.
Examination of Mycobacterium tuberculosis sigma factor mutants using low-dose aerosol infection of guinea pigs suggests a role for SigC in pathogenesis (2006)

Secondary sigma factors in bacteria direct transcription of defence regulons in response to specific stresses. To identify which sigma factors in the human respiratory pathogen Mycobacterium tuberculosis are important for adaptive survival in vivo, defined null mutations were created in individual sigma factor genes. In this study, in vitro growth virulence and guinea pig pathology of M. tuberculosis mutants lacking functional sigma factors (SigC, SigF, or SigM) were compared to the parent strain, H37Rv. None of the mutant strains exhibited a growth deficiency in Middlebrook 7H9 broth, nor were any impaired for intracellular replication in the human monocytic macrophage cell-line THP-1. Following low-dose aerosol infection of guinea pigs, however, differences could be detected. While a SigM mutant resulted in lung and spleen granulomas of comparable composition to those found in H37Rv-infected animals, a SigF mutant was partially attenuated, exhibiting necrotic spleen granulomas and ill-defined lung granulomas. SigC mutants exhibited attenuation in the lung and spleen; notably, necrotic granulomas were absent. These data suggest that while SigF may be important for survival in the lung, SigC is likely a key regulator of pathogenesis and adaptive survival in the lung and spleen. Understanding how SigC mediates survival in the host should prove useful in the development of anti-tuberculosis therapies.
Distribution of transferrin, ferritin, and lactoferrin in human tissues. (1978)

An immunoperoxidase staining technique was used for detecting three major iron-binding proteins (transferrin, ferritin, and lactoferrin) in routine histological paraffin sections of human tissue. Transferrin was found mainly in hepatocytes, a variety of epithelial and myoepithelial cells, renal tubular cells, and histiocytes. Ferritin was most readily found in histiocytes and liver cells, with weaker reactions seen in epithelial cells. Lactoferrin was found in lactating breast tissue, bronchial glands, polymorphs, and gastric and duodenal epithelial cells. The technique is potentially valuable for investigating abnormal iron states.
Isolation and sequence of a human gene encoding a potent inhibitor of leukocyte proteases (1986)

We report the isolation of the human gene encoding an inhibitor of neutrophil elastase and cathepsin G. We have sequenced the gene and a cDNA clone isolated from human parotid tissue. The protein encoded by this gene appears to contain two functional domains, one having a trypsin inhibitory site and the other an elastase inhibitory site. The two-domain structure of the protein is reflected in the organization of the gene, with each domain represented by a separate exon. We have also noted that the intervening sequence separating the trypsin-inhibitor-exon and the elastase-inhibitor-exon is flanked by eleven base-pair direct repeats, suggesting that this intron may have been generated by a transposition-type event.
Development of Star Tracker System for Accurate Estimation of Spacecraft Attitude (2009)

This thesis researches different star pattern recognition and attitude determination algorithms for a three-axis rotational spacecraft. A simulated star field will be suspended above the experimental Three-Axis Spacecraft simulator to proved a reference for the star-pattern recognition algorithms. A star field inertial reference frame database of stars will be developed with the simulator at zero attitude. The angle, planar triangle and spherical triangle star patter recongition algorithms will then be used to identify which stars are within a camera's field of vision. The imaged stars will then be matched up to the corresponding stars within the test bed database. With the imaged stars identified and the corresponding inertial frame reference data, the test bed's attitude will be determined using the least-squares, TRIAD, and Quaternion Estimator (QUEST) attitude determination algorithms. On the three-axis simulator, an iterative algorithm is developed to demonstrate increasing star tracker accuracy with each update A matrix.
Low Free Energy Surfaces Using Blends of Fluorinated Acrylic Copolymer and Hydrocarbon Acrylic Copolymer Latexes (2000)

Blends of small particle size fluorinated acrylic copolymer latexes with a large particle size styrene/acrylic copolymer latex were examined with regard to formation of low free energy surfaces, amount of incorporated fluorinated copolymer, particle size, and particle size asymmetry. The styrene/acrylic latex was prepared by emulsion polymerization of n-butyl acrylate and styrene. Several varieties of fluorinated latexes were prepared. One was prepared by copolymerization of n-butyl acrylate and the fluorinated monomer, FMA, H2CC(CH3)CO2(CH2)2(CF2)nF (n̄ ≈ 7.7). Two types of copolymer core/fluorinated copolymer shell latex systems were prepared. One was comprised of a highly cross-linked core of poly(divinylbenzene) and a shell of poly(n-butyl acrylate-co-FMA). The other had a lightly cross-linked core of poly(n-butyl acrylate-co-divinylbenzene) and a shell of poly(n-butyl acrylate-co-FMA). Films cast from blends of styrene/acrylic and fluorinated copolymer latexes were examined by contact angle goniometry, X-ray photoelectron spectroscopy (XPS), time-of-flight static secondary ion mass spectroscopy (ToF-SIMS), and tapping mode atomic force microscopy (TMAFM). In some cases, low free energy surfaces were created at small mole fractions (∼10-4−10-2) of fluorinated monomer copolymerized with acrylic monomers in the mixture. AFM images were used to differentiate fluorinated, phase-segregated regions in the mixtures. Because of the disparity in particle size (asymmetry) between the styrene/acrylic and fluorine-containing latexes, the phenomena of percolation and excluded volume can be used to establish a substantial excess of fluorinated, low free energy material at the surface of an asymmetric blend of the two.
Interleukin-18 Regulates Both Th1 and Th2 Responses (2001)

Although interleukin-18 is structurally homologous to IL-1 and its receptor belongs to the IL-1R/Toll-like receptor (TLR) superfamily, its function is quite different from that of IL-1. IL-18 is produced not only by types of immune cells but also by non-immune cells. In collaboration with IL-12, IL-18 stimulates Th1-mediated immune responses, which play a critical role in the host defense against infection with intracellular microbes through the induction of IFN-gamma. However, the overproduction of IL-12 and IL-18 induces severe inflammatory disorders, suggesting that IL-18 is a potent proinflammatory cytokine that has pathophysiological roles in several inflammatory conditions. IL-18 mRNA is expressed in a wide range of cells including Kupffer cells, macrophages, T cells, B cells, dendritic cells, osteoblasts, keratinocytes, astrocytes, and microglia. Thus, the pathophysiological role of IL-18 has been extensively tested in the organs that contain these cells. Somewhat surprisingly, IL-18 alone can stimulate Th2 cytokine production as well as allergic inflammation. Therefore, the functions of IL-18 in vivo are very heterogeneous and complicated. In principle, IL-18 enhances the IL-12-driven Th1 immune responses, but it can also stimulate Th2 immune responses in the absence of IL-12.
Role of Echocardiography in Percutaneous Occlusion of the Left Atrial Appendage (2007)

Echocardiographic guidance of this procedure is essential. Which approach will be preferred will depend on the development of these two methods.
Thymidine Kinase Gene Therapy for Human Malignant Glioma, Using Replication-Deficient Retroviruses or Adenoviruses (2000)

Herpes simplex virus thymidine kinase (HSV tk) gene therapy combined with ganciclovir (GCV) medication is a potential new method for the treatment of malignant glioma. We have used both retrovirus-packaging cells (PA317/tk) and adenoviruses (Adv/tk) for gene therapy for malignant glioma. Retrovirus-packaging cells were used for eight tumors in seven patients and adenoviruses were used for seven tumors in seven patients. As a control group, seven tumors in seven patients were transduced with lacZ marker gene 4-5 days before tumor resection. Safety and efficacy of the gene therapy were studied with clinical evaluation, blood and urine samples, MRI follow-up, and survival of the patients. Four patients with adenovirus injections had a significant increase in anti-adenovirus antibodies and two of them had a short-term fever reaction. Frequency of epileptic seizures increased in two patients. No other adverse events possibly related to gene therapy were detected. In the retrovirus group, all treated gliomas showed progression by MRI at the 3-month time point, whereas three of the seven patients treated with Adv/tk remained stable (p < 0.05). Mean survival times for retrovirus, adenovirus, and control groups were 7.4, 15.0, and 8. 3 months, respectively. The difference in the survival times between the adenovirus and retrovirus groups was significant (p < 0.012). It is concluded that HSV tk gene therapy is safe and well tolerated. On the basis of these results further trials are justified, especially with adenovirus vectors.
Inhibition of Epidermal Growth Factor Receptor-associated Tyrosine Kinase Blocks Glioblastoma Invasion of the Brain (1997)

Our observations support the role of EGFR activation as a determinant by which glioblastoma invades normal brain tissue, and we show that invasion can be effectively inhibited at much lower concentrations of TK inhibitors than are necessary for growth suppression.
Differential Expression of the Vegetative and Spore‐Bound Hydrophobins of Trichoderma Reesei Cloning and Characterization of the Hfb2 Gene (1997)

The hfb2 gene encoding the hydrophobin HFBII of the filamentous fungus Trichoderma reesei was isolated by heterologous hybridization using the vegetative hydrophobin I, hfb1, gene of T. reesei as a probe. The hfb2 gene codes for a typical fungal secreted hydrophobin of 71 amino acids containing eight cysteine residues. The amino acid similarity towards HFBI is 69%. The HFBII protein was isolated from the fungal spores by extraction with trifluoroacetic acid/acetonitrile solution, and by bubbling from the lactose-based culture medium. Expression of the hfb1 and hfb2 genes is divergent. hfb1 expression was only observed in vegetative cultures on glucose-containing and sorbitol-containing media. It was not expressed on media containing complex plant polysaccharides, cellulose, xylan, cellobiose or lactose, whereas hfb2 was highly expressed in vegetative cultures on these media. Expression of hfb2 was also strongly induced by N and C starvation, by light and in conidiating cultures.
Self-Association of the Erythroid Transcription Factor GATA-1 Mediated by Its Zinc Finger Domains (1995)

GATA-1, the founding member of a distinctive family of transcription factors, is expressed predominantly in erythroid cells and participates in the expression of numerous erythroid cell-expressed genes. GATA-binding sites are found in the promoters and enhancers of globin and nonglobin erythroid genes as well as in the alpha- and beta-globin locus control regions. To elucidate how GATA-1 may function in a variety of regulatory contexts, we have examined its protein-protein interactions. Here we show that GATA-1 self-associates in solution and in whole-cell extracts and that the zinc finger region of the molecule is sufficient to mediate this interaction. This physical interaction can influence transcription, as GATA-1 self-association is able to recruit a transcriptionally active but DNA-binding-defective derivative of GATA-1 to promoter-bound GATA-1 and result in superactivation. Through in vitro studies with bacterially expressed glutathione S-transferase fusion proteins, we have localized the minimal domain required for GATA-1 self-association to 40 amino acid residues within the C-terminal zinc finger region. Finally, we have detected physical interaction of GATA-1 with other GATA family members (GATA-2 and GATA-3) also mediated through the zinc finger domain. These findings have broad implications for the involvement of GATA factors in transcriptional control. In particular, the interaction of GATA-1 with itself and with other transcription factors may facilitate its function at diverse promoters in erythroid cells and also serve to bring together, or stabilize, loops between distant regulatory elements, such as the globin locus control regions and downstream globin promoters. We suggest that the zinc finger region of GATA-1, and related proteins, is multifunctional and mediates not only DNA binding but also important protein-protein interactions.
Recent Advances in the Chemical Synthesis of RNA (2009)

As a consequence largely of recent developments in RNA interference (RNAi) research, the availability of rapid and efficient methods for the chemical synthesis of RNA sequences has become a matter of considerable urgency. This unit is concerned mainly with work that has been carried out, especially in the past decade, on the design of new and improved methods of RNA synthesis. The main criteria for the choice of protecting groups for the 2'-hydroxy functions of the ribonucleoside building blocks, which is arguably the most crucial strategic decision to be made, are discussed. A number of new ether-, acetal-, orthoester-, and ester-based 2'-protecting groups are described and their application, mainly in phosphoramidite-based solid-phase synthesis, is discussed in some detail. Brief consideration is also given to solution-phase RNA synthesis, which may well prove to be of great importance if a systemic drug is developed and multikilogram quantities of synthetic RNA sequences are required.