gebhart/patrepeval huggingface dataset:
Imaging Surface Immobilization Chemistry: Correlation with Cell Patterning on Non‐Adhesive Hydrogel Thin Films (2008)

High-fidelity surface functional group (e.g., N-hydroxysuccinimide (NHS) reactive ester) patterning is readily and reliably achieved on commercial poly(ethylene glycol) (PEG)-based polymer films already known to exhibit high performance non-fouling properties in full serum and in cell culture conditions. NHS coupling chemistry co-patterned with methoxy-capped PEG using photolithographic methods is directly spatially imaged using imaging time-of-flight secondary ion mass spectrometry (ToF-SIMS) and principal components statistical analysis. Patterned NHS surface reactive zones are clearly resolved at high sensitivity despite the complexity of the polymer matrix chemistry. ToF-SIMS imaging also reveals the presence of photo-resist residue remaining from typical photolithography processing methods. High cross-correlation between various ion-derived ToF-SIMS images is observed, providing sensitive chemical corroboration of pattern chemistry and biological reactivity in complex milieu. Surface-specific protein coupling is observed first by site-selective reaction of streptavidin with NHS patterns, followed by identical patterns of biotinylated Alexa-labeled albumin coupling. This suggests that streptavidin immobilized on the patterns remains bioactive. Fluorescently labeled full serum is shown to react selectively with NHS-reactive regions, with minimal signal from methoxy-capped regions. Insufficient serum is adsorbed under any conditions to these surfaces to support cell attachment in serum-containing media. This reflects the high intrinsic non-adsorptive nature of this chemistry. Fibroblasts attach and proliferate in serum culture only when a cell adhesion peptide (RGD) is first grafted to NHS regions on the PEG-based surfaces. Longer-term serum-based cell culture retains high cell-pattern fidelity that correlates with chemical imaging of both the NHS and RGD patterns and also lack of cell adhesion to methoxy-capped regions. Cell staining shows orientation of adherent cells within the narrow patterned areas. Cell patterns are consistently retained beyond 15 days in serum media.
Inhibition of bone resorption in vitro by antisense RNA and DNA molecules targeted against carbonic anhydrase II or two subunits of vacuolar H(+)-ATPase. (1994)

The bone resorbing cells, osteoclasts, express high levels of carbonic anhydrase II (CA II) and vacuolar H(+)-ATPase (V-ATPase) during bone resorption. We have used antisense RNA and DNA molecules targeted against CA II, and against 16- and 60-kD subunits of vacuolar H(+)-ATPase (V-ATPase), to block the expression of these proteins in vitro. Osteoclastic bone resorption was studied in two in vitro culture systems: release of 45Calcium from prelabeled newborn mouse calvaria cultures, and resorption pit assays performed with rat osteoclasts cultured on bovine bone slices. Both antisense RNA and DNA against CA II and the V-ATPase were used to compare their specificities as regards inhibiting bone resorption in vitro. The antisense molecules inhibited the synthesis of these proteins by decreasing the amounts of mRNA in the cells in a highly specific manner. In osteoclast cultures treated with the 16-kD V-ATPase antisense RNA, acidification of an unknown population of intracellular vesicles was highly stimulated. The acidification of these vesicles was not sensitive to amiloride or bafilomycin A1. This suggests the existence of a back-up system for acidification of intracellular vesicles, when the expression of the V-ATPase is blocked. Our results further indicate that blocking the expression of CA II and V-ATPase with antisense RNA or DNA leads to decreased bone resorption.
Synthesis of 1,3,4,6,11,11a-Hexahydro-2H-pyrazino[1,2-b]isoquinoline and Perhydro-1H-pyrazino[1,2-a]quinoline (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of 1,3,4,6,11,11a-Hexahydro-2H-pyrazino[1,2-b]isoquinoline and Perhydro-1H-pyrazino[1,2-a]quinolineHobart B. Sullivan and Allan R. DayCite this: J. Org. Chem. 1964, 29, 2, 326–328Publication Date (Print):February 1, 1964Publication History Published online1 May 2002Published inissue 1 February 1964https://pubs.acs.org/doi/10.1021/jo01025a018https://doi.org/10.1021/jo01025a018research-articleACS PublicationsRequest reuse permissionsArticle Views110Altmetric-Citations9LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Expression, distribution, and biochemistry of human CD39. Role in activation-associated homotypic adhesion of lymphocytes (1991)

The distribution, biochemical properties, and function of CD39 were characterized with the use of a new mAb termed 400. CD39 is an acidic (isoelectric point, approximately 4.2) glycoprotein of Mr approximately 78,000, containing approximately 24 kDa of N-linked oligosaccharide but no detectable O-linked sugars. CD39 was not expressed by resting blood T, B, or NK cells, neutrophils, or monocytes, but was expressed on activated NK cells, B cells, subsets of T cells, and T cell clones. Furthermore, the pattern of expression of CD39 was distinct from the "classic" activation Ag CD25 and CD71, inasmuch as it was expressed long after expression of CD25 and CD71 had returned to basal levels. CD39 was easily detectable on EBV-transformed B cell lines but was absent from pre-B and non-EBV-transformed B cell lines, most myeloid cell lines, and leukemic T cell lines. In lymphoid tissues, germinal center cells expressed little or no CD39, whereas some paracortical lymphocytes and most macrophages and dendritic cells were positive. CD39 was strongly expressed by endothelium in all tissues examined, including skin, and was present on some, but not all, endothelial cell lines propagated in vitro. Interestingly, mAb binding to certain epitopes on CD39 induced rapid homotypic adhesion that appeared to involve LFA-1 (CD11a/CD18), but was morphologically and kinetically distinct from that induced by PMA. Anti-CD39 mAb also induced homotypic adhesion in an CD11/CD18-EBV-transformed B cell line derived from a patient with severe leukocyte adhesion deficiency. This adhesion was unaffected by EDTA, suggesting that this pathway of anti-CD39-induced homotypic adhesion was not mediated by any of the known integrins. These studies suggest that CD39 is involved in the cellular signaling that regulates adhesion.
The Chemical Composition of Wool (1964)

A study is made of the disruption of wool by ultrasonic disintegration and the separation and identification by microscopy of the major components of the fibre. The ultrasonic disintegration process is investigated empirically in order to establish the conditions under which maximum rates of disruption occur. Of a large number of liquids examined it is found, in confirmation of earlier work, that the rate of disintegration of wool is very slow in water but usually increases in amount as the swelling of the fibre increases. The several exceptions to this rule show that there are other factors of secondary importance in determining the rate of disruption. The amount of disruption is sufficient for preparative purposes and increases in amount in the series dimethyl sulphoxide, formic acid, and dichloroacetic acid.
Lessons from T cell responses to virus induced tumours for cancer eradication in general. (1992)

Immunotherapy of virus induced tumours by adoptive transfer of virus specific cytotoxic T cells (CTL) is now feasible in experimental murine systems. These CTL recognize viral peptide sequences of defined length presented in the groove of MHC class I molecules. Effective eradication of large tumour masses requires coadministration of IL-2. In essence, T cell immunity against virus induced tumours does not differ from anti-viral T cell immunity in general. Tumour escape strategies are numerous but, in various instances, can be counteracted by defined measures. Initiation of CTL responses against poorly immunogenic non-virus induced tumours (the majority of human cancer) requires novel strategies to overcome T cell inertia. Rather than waiting to see whether tumour specific CTL (against unknown antigens) can be cultured from TIL, we propose an alternative strategy in which CTL are raised against target molecules of choice, including differentiation antigens of restricted tissue distribution (autoantigens) or mutated/overexpressed oncogene products. The various steps proposed include: (a) identification of target molecules of choice; (b) identification in these target molecules of MHC allele specific peptide motifs involved in peptide binding to MHC molecules; (c) evaluation of actual binding of such peptides to specific MHC class I molecules; (d) in vitro CTL response induction by such peptides, presented either by highly efficient antigen presenting cells (such as processing defective cells, which carry empty MHC class I molecules) loaded with a single peptide or by dendritic cells, both cell types being capable of primary CTL response induction in vitro and (e) adoptive transfer of tumour specific CTL generated in vivo or, more conveniently, vaccination with immunodominant peptides. The latter possibility seems to be feasible because peptide vaccination with a single immunodominant viral peptide can install CTL memory and confer protection against lethal virus infection.
Nanocomposite materials from latex and cellulose whiskers (1995)

Abstract Composite materials were processed by casting a mixture of aqueous suspensions of latex and microfibrils. These microfibrils, or whiskers, are extracted from a sea animal and are monocrystals of cellulose, with an aspect ratio around 100 and an average diameter of 20 nm. It has been found that the mechanical properties (shear modulus) are increased by more than two orders of magnitude in the rubbery state of the polymeric matrix, when the whisker content was 6% (w/w). This very large effect is discussed on the basis of different types of mechanical models and it is concluded that these whiskers form a rigid network, probably linked by hydrogen bonds. The formation of this network is assumed to be governed by a percolation mechanism.
Thermocapillary valve for droplet production and sorting (2007)

Droplets are natural candidates for use as microfluidic reactors, if active control of their formation and transport can be achieved. We show here that localized heating from a laser can block the motion of a water-oil interface, acting as a microfluidic valve for two-phase flows. A theoretical model is developed to explain the forces acting on a drop due to thermocapillary flow, predicting a scaling law that favors miniaturization. Finally, we show how the laser forcing can be applied to sorting drops, thus demonstrating how it may be integrated in complex droplet microfluidic systems.
Role of microRNAs in skeletal muscle hypertrophy (2014)

Skeletal muscle comprises approximately 40% of body weight, and is important for locomotion, as well as for metabolic homeostasis. Adult skeletal muscle mass is maintained by a fine balance between muscle protein synthesis and degradation. In response to cytokines, nutrients, and mechanical stimuli, skeletal muscle mass is increased (hypertrophy), whereas skeletal muscle mass is decreased (atrophy) in a variety of conditions, including cancer cachexia, starvation, immobilization, aging, and neuromuscular disorders. Recent studies have determined two important signaling pathways involved in skeletal muscle mass. The insulin-like growth factor-1 (IGF-1)/Akt pathway increases skeletal muscle mass via stimulation of protein synthesis and inhibition of protein degradation. By contrast, myostatin signaling negatively regulates skeletal muscle mass by reducing protein synthesis. In addition, the discovery of microRNAs as novel regulators of gene expression has provided new insights into a multitude of biological processes, especially in skeletal muscle physiology. We summarize here the current knowledge of microRNAs in the regulation of skeletal muscle hypertrophy, focusing on the IGF-1/Akt pathway and myostatin signaling.
Bone Microdamage and Skeletal Fragility in Osteoporotic and Stress Fractures (1997)

The accumulation of bone microdamage has been proposed as one factor that contributes to increased skeletal fragility with age and that may increase the risk for fracture in older women. This paper reviews the current status and understanding of microdamage physiology and its importance to skeletal fragility. Several questions are addressed: Does microdamage exist in vivo in bone? If it does, does it impair bone quality? Does microdamage accumulate with age, and is the accumulation of damage with age sufficient to cause a fracture? The nature of the damage repair mechanism is reviewed, and it is proposed that osteoporotic fracture may be a consequence of a positive feedback between damage accumulation and the increased remodeling space associated with repair.
Is adenomyosis an immune disease? (1998)

Adenomyosis is characterized as ectopic endometrial tissues within the myometrium in the uterus. The only difference between adenomyosis and endometriosis is the site of endometriotic tissues: inside or outside of the uterus. It is well known that endometriosis is frequently associated with various autoimmune phenomena. This short review covers various aspects of the immune cascade found in adenomyosis. In adenomyosis, a series of immune responses is activated, including changes in both cellular and humoral immunity, i.e. a strong expression of cell surface antigens or adhesion molecules, an increased number of macrophages or immune cells, and deposition of immunoglobulins and complement components. Furthermore, the disease exhibited high frequency of autoantibodies in peripheral blood. Thus, an immunological 'vicious circle' is formed in the endometrium in adenomyosis. Endometrial cells seem to be under immunological stress, protecting themselves by exposing heat shock proteins. It is concluded that the endometrial environment in adenomyosis differs widely from that in normal fertile women. These abnormal immune responses might be involved in poor reproductive performance in adenomyosis.
TIMP-3, collagen, and elastin immunohistochemistry and histopathology of Sorsby's fundus dystrophy. (2000)

Sub-RPE TIMP-3 immunoreactivity appears more extensive in SFD than in control subjects. There is also a correspondence between TIMP-3 and elastin immunoreactivies, which invites speculation as to a link between the SFD TIMP-3 mutation and altered elastin processing. The accumulation of abnormal material in SFD is more widespread than previously reported. In view of this, SFD might be better termed Sorsby's ocular epitheliopathy.
D4-GDI, a Substrate of CPP32, Is Proteolyzed during Fas-induced Apoptosis (1996)

Apoptosis (programmed cell death) is a fundamental process for normal development of multicellular organisms, and is involved in the regulation of the immune system, normal morphogenesis, and maintenance of homeostasis, ICE/CED-3 family cysteine proteases have been implicated directly in apoptosis, but relatively few of the substrates through which their action is mediated have been identified. Here we report that D4-GDI, an abundant hematopoietic cell GDP dissociation inhibitor for the Ras-related Rho family GTPases, is a substrate of the apoptosis protease CPP32/Yama/Apopain. D4-GDI was rapidly truncated to a 23-kDa fragment in Jurkat cells with kinetics that parallel the onset of apoptosis following Fas cross-linking with agonistic antibody or treatment with staurosporine. Fas- and staurosporine-induced apoptosis as well as cleavage of D4-GDI were inhibited by the ICE inhibitor, YVAD-cmk. D4-GDI was cleaved in vitro by recombinant CPP32 expressed in Escherichia coli to form a 23-kDa fragment. The CPP32-mediated cleavage of D4-GDI was completely inhibited by 1 microM DEVD-CHO, a reported selective inhibitor of CPP32. In contrast, the ICE-selective inhibitors, YVAD-CHO or YVAD-cmk, did not inhibit CPP32-mediated D4-GDI cleavage at concentrations up to 50 microM. N-terminal sequencing of the 23-kDa D4-GDI fragment demonstrated that D4-GDI was cleaved between Asp19 and Ser20 of the poly(ADP-ribose) polymerase-like cleavage sequence DELD19S. These data suggest that regulation by D4-GDI of Rho family GTPases may be disrupted during apoptosis by CPP32-mediated cleavage of the GDI protein.
Ballistic transport-reaction prediction of film conformality in tetraethoxysilane O2 plasma enhanced deposition of silicon dioxide (1992)

EVOLVE, a low pressure deposition process simulator based on a fundamental model for free molecular transport and heterogeneous surface reactions in features, is used to predict the evolution of silicon dioxide film profiles during plasma enhanced chemical vapor deposition from mixtures of tetraethoxysilane (TEOS) and oxygen. The constitutive relationships required by EVOLVE are supplied by simple models for the plasma, the plasma sheath and the surface chemistry. The intrinsic kinetic model used in the simulations involves film growth by oxidative attack on adsorbed TEOS and/or TEOS fragments by both oxygen ions and oxygen atoms. Recombination of oxygen atoms on the surface of the growing film competes with TEOS oxidation by atoms. The plasma models are used to predict the fluxes of oxygen ions and oxygen atoms to the surface. The fluxes of all neutral species from the source and from all surfaces are assumed to obey cosine distribution functions. Oxygen ions are assumed to follow an exponential distribution; the standard deviation of the distribution is adjusted to match predicted film profiles with experimentally determined profiles. This combination of an almost directional component and an almost isotropic component allows the prediction of the experimental trends in deposition rate and film conformality with operating conditions. The constitutive models are used by EVOLVE to predict film profiles as a function of temperature, within their window of validity, for deposition in ideal rectangular trenches with an aspect ratio of 2. Film conformality decreases as temperature increases, even though deposition rate actually decreases. Film conformality decreases with increasing pressure and increases with increasing power. All of these predicted trends in conformality agree with our experimental results.
The drift of Fennoscandia during the Proterozoic with special reference to the Bergslagen province, south-central Sweden; a discussion (1991)

(1991). The drift of Fennoscandia during the Proterozoic with special reference to the Bergslagen province, south-central Sweden; a discussion. Geologiska Föreningen i Stockholm Förhandlingar: Vol. 113, No. 2-3, pp. 249-250.
Role for the Related Poly(ADP-Ribose) Polymerases Tankyrase 1 and 2 at Human Telomeres (2002)

Telomere maintenance is essential for the continuous growth of tumor cells. In most human tumors telomeres are maintained by telomerase, a specialized reverse transcriptase. Tankyrase 1, a human telomeric poly(ADP-ribose) polymerase (PARP), positively regulates telomere length through its interaction with TRF1, a telomeric DNA-binding protein. Tankyrase 1 ADP-ribosylates TRF1, inhibiting its binding to telomeric DNA. Overexpression of tankyrase 1 in the nucleus promotes telomere elongation, suggesting that tankyrase 1 regulates access of telomerase to the telomeric complex. The recent identification of a closely related homolog of tankyrase 1, tankyrase 2, opens the possibility for a second PARP at telomeres. We therefore sought to establish the role of tankyrase 1 at telomeres and to determine if tankyrase 2 might have a telomeric function. We show that endogenous tankyrase 1 is a component of the human telomeric complex. We demonstrate that telomere elongation by tankyrase 1 requires the catalytic activity of the PARP domain and does not occur in telomerase-negative primary human cells. To investigate a potential role for tankyrase 2 at telomeres, recombinant tankyrase 2 was subjected to an in vitro PARP assay. Tankyrase 2 poly(ADP-ribosyl)ated itself and TRF1. Overexpression of tankyrase 2 in the nucleus released endogenous TRF1 from telomeres. These findings establish tankyrase 2 as a bona fide PARP, with itself and TRF1 as acceptors of ADP-ribosylation, and suggest the possibility of a role for tankyrase 2 at telomeres.
Rab8b GTPase, a protein transport regulator, is an interacting partner of otoferlin, defective in a human autosomal recessive deafness form (2008)

Mutations within OTOF encoding otoferlin lead to a recessive disorder called DFNB9. Several studies have indicated otoferlin's association with ribbon synapses of cochlear sensory hair cells, as well as data showing the protein's presence in neurons, nerve fibers and hair cells, suggesting a more ubiquitous function. Otoferlin's co-localization not only with ribbon synaptic proteins, but also with additional endosomal (EEA1) or Golgi proteins (GM130) were motivation for a search for further binding partners of otoferlin by a yeast two-hybrid screen in a rodent cochlear cDNA library (P3-P15). This screen identified Rab8b GTPase as a novel interacting partner, substantiated by transient co-expression and co-localization in HEK 293 cells and co-immunoprecipitation of the complex using tagged proteins in vitro and native proteins from cochlea. This finding implies that otoferlin could be a part of components contributing to trans-Golgi trafficking.
A regularization approach to joint blur identification and image restoration (1996)

The primary difficulty with blind image restoration, or joint blur identification and image restoration, is insufficient information. This calls for proper incorporation of a priori knowledge about the image and the point-spread function (PSF). A well-known space-adaptive regularization method for image restoration is extended to address this problem. This new method effectively utilizes, among others, the piecewise smoothness of both the image and the PSF. It attempts to minimize a cost function consisting of a restoration error measure and two regularization terms (one for the image and the other for the blur) subject to other hard constraints. A scale problem inherent to the cost function is identified, which, if not properly treated, may hinder the minimization/blind restoration process. Alternating minimization is proposed to solve this problem so that algorithmic efficiency as well as simplicity is significantly increased. Two implementations of alternating minimization based on steepest descent and conjugate gradient methods are presented. Good performance is observed with numerically and photographically blurred images, even though no stringent assumptions about the structure of the underlying blur operator is made.