gebhart/patrepeval huggingface dataset:
Apical Sorting by Galectin‐3‐Dependent Glycoprotein Clustering (2007)

Epithelial cells are characterized by their polarized organization based on an apical membrane that is separated from the basolateral membrane domain by tight junctions. Maintenance of this morphology is guaranteed by highly specific sorting machinery that separates lipids and proteins into different carrier populations for the apical or basolateral cell surface. Lipid-raft-independent apical carrier vesicles harbour the beta-galactoside-binding lectin galectin-3, which interacts directly with apical cargo in a glycan-dependent manner. These glycoproteins are mistargeted to the basolateral membrane in galectin-3-depleted cells, dedicating a central role to this lectin in raft-independent sorting as apical receptor. Here, we demonstrate that high-molecular-weight clusters are exclusively formed in the presence of galectin-3. Their stability is sensitive to increased carbohydrate concentrations, and cluster formation as well as apical sorting are perturbed in glycosylation-deficient Madin-Darby canine kidney (MDCK) II cells. Together, our data suggest that glycoprotein cross-linking by galectin-3 is required for apical sorting of non-raft-associated cargo.
Enhanced genomic instabilities caused by deregulated microtubule dynamics and chromosome segregation: a perspective from genetic studies in mice (2009)

Aneuploidy is defined as numerical abnormalities of chromosomes and is frequently (>90%) present in solid tumors. In general, tumor cells become increasingly aneuploid with tumor progression. It has been proposed that enhanced genomic instability at least contributes significantly to, if not requires, tumor progression. Two major modes for genomic instability are microsatellite instability (MIN) and chromosome instability (CIN). MIN is associated with DNA-level defects (e.g. mismatch repair defects), and CIN is associated with mitotic errors such as chromosome mis-segregation. The mitotic spindle assembly checkpoint (SAC) ensures that cells with defective mitotic spindles or defective interaction between the spindles and kinetochores do not initiate chromosomal segregation during mitosis. Thus, the SAC functions to protect the cell from chromosome mis-segregation and anueploidy during cell division. A loss of the SAC function results in gross aneuploidy, a condition from which cells with an advantage for proliferation will be selected. During the past several years, a flurry of genetic studies in mice and humans strongly support the notion that an impaired SAC causes enhanced genomic instabilities and tumor development. This review article summarizes the roles of key spindle checkpoint proteins {i.e. Mad1/Mad1L1, Mad2/Mad2L1, BubR1/Bub1B, Bub3/Bub3 [conventional protein name (yeast or human)/mouse protein name]} and the modulators (i.e. Chfr/Chfr, Rae1/Rae1, Nup98/Nup98, Cenp-E/CenpE, Apc/Apc) in genomic stability and suppression of tumor development, with a focus on information from genetically engineered mouse model systems. Further elucidation of molecular mechanisms of the SAC signaling has the potential for identifying new targets for rational anticancer drug design.
High-Resolution EM of Colloidal Nanocrystal Growth Using Graphene Liquid Cells (2012)

We introduce a new type of liquid cell for in situ transmission electron microscopy (TEM) based on entrapment of a liquid film between layers of graphene. The graphene liquid cell facilitates atomic-level resolution imaging while sustaining the most realistic liquid conditions achievable under electron-beam radiation. We employ this cell to explore the mechanism of colloidal platinum nanocrystal growth. Direct atomic-resolution imaging allows us to visualize critical steps in the process, including site-selective coalescence, structural reshaping after coalescence, and surface faceting.
Spontaneous Assembly of Helical Cyanine Dye Aggregates on DNA Nanotemplates (1999)

3,3‘-Diethylthiadicarbocyanine (DiSC2(5)) is a symmetrical cationic cyanine dye consisting of two N-ethylated benzothiazole groups linked by a pentamethine bridge. Spectroscopic analysis indicates dimerization of the dye in the presence of duplex DNA sequences consisting of alternating adenine/thymine (A/T) or inosine/cytosine (I/C) residues, based on the following observations: (i) the absorption maximum shifts from 647 to 590 nm, (ii) exciton splitting is observed in the induced circular dichroism spectrum, and (iii) fluorescence from the dye is strongly quenched. Dimerization on I/C, but not G/C sequences indicates that the cyanine dimers insert into the minor groove, a conclusion that is supported by viscometric analysis. Spectroscopic studies with short synthetic oligonucleotide duplexes demonstrate that dimerization is highly cooperative: binding of one dimer greatly facilitates binding of a second dimer. For longer binding sites, this cooperativity leads to the formation of extended helical cyanine dye aggregates consisting of dimers aligned in an end-to-end fashion within the minor groove of the DNA. The DNA structure strictly controls the dimensions of the aggregate, permitting distinction between inter- and intradimer interactions.
SNaPP: Simplified Nanoproteomics Platform for Reproducible Global Proteomic Analysis of Nanogram Protein Quantities (2016)

Global proteomic analyses of complex protein samples in nanogram quantities require a fastidious approach to achieve in-depth protein coverage and quantitative reproducibility. Biological samples are often severely mass limited and can preclude the application of more robust bulk sample processing workflows. In this study, we present a system that minimizes sample handling by using online immobilized trypsin digestion and solid phase extraction to create a simple, sensitive, robust, and reproducible platform for the analysis of nanogram-size proteomic samples. To demonstrate the effectiveness of our simplified nanoproteomics platform, we used the system to analyze preimplantation blastocysts collected on day 4 of pregnancy by flushing the uterine horns with saline. For each of our three sample groups, blastocysts were pooled from three mice resulting in 22, 22, and 25 blastocysts, respectively. The resulting proteomic data provide novel insight into mouse blastocyst protein expression on day 4 of normal pregnancy because we characterized 348 proteins that were identified in at least two sample groups, including 59 enzymes and blastocyst specific proteins (eg, zona pellucida proteins). This technology represents an important advance in which future studies could perform global proteomic analyses of blastocysts obtained from an individual mouse, thereby enabling researchers to investigate interindividual variation as well as increase the statistical power without increasing animal numbers. This approach is also easily adaptable to other mass-limited sample types.
Beware: Armed and Dangerous—Acquired Non-Accommodative Esotropia (1996)

Acquired nonaccommodative esotropia is generally considered to be a benign phenomenon. However, numerous instances of posterior fossa tumors initially presenting as acute comitant esotropia have been reported. The presence of any of the following warrant further investigation when associated with acute onset, nonaccommodative esotropia: nystagmus, vertical strabismus, other cranial nerve involvement, parental concerns of poor motor control, headache or persistent diplopia.Other types of acquired nonaccommodative esotropia include decompensated esophoria/monofixation syndrome, VI N paresis, divergence paresis, myasthenia gravis and mechanical/restrictive strabismus resulting from Graves disease, trauma, iatrogenesis and orbital myositis are discussed. Clinical investigation and treatment are briefly reviewed.
Molecular cloning of Fyn-associated molecules in the mouse central nervous system (1997)

Fyn tyrosine kinase is expressed extensively in the central nervous system (CNS) of mammals, and its genetic disruption in mouse displays several behavioral abnormalities with morphological and electrophysiological defects in the brain. To understand the signaling pathways in which Fyn is involved in the CNS, we screened molecules that directly associate with Fyn in neonatal mouse brain by using a two-hybrid yeast system. We isolated five cDNA clones with strong and reproducible Fyn-binding activity. Sequence analyses revealed that three of them are previously reported molecules, SON, tctex-1, and hnRNP K, and that two clones encode novel sequences. The hnRNP K has been shown to associate with Fyn, so our yeast system is appropriate to isolate Fyn-binding molecules. Northern hybridization analyses indicated that all isolated clones are expressed in the mouse brain and that the mRNA levels of the two molecules (tctex-1 and clone 82) change during development in the brain. A full-length cDNA of clone 82 was obtained and its deduced amino acid sequence was homologous to the RNA-binding proteins. Isolation of many Fyn-binding molecules suggest that, in the mouse CNS, Fyn mediates multiple signaling pathways by binding to multiple molecules and that some of these pathways play critical roles in determining a certain type of behavior.
Biogenesis and germline functions of piRNAs (2007)

Small interfering RNAs and microRNAs are generated from double-stranded RNA precursors by the Dicer endonucleases, and function with Argonaute-family proteins to target transcript destruction or to silence translation. A distinct class of 24- to 30-nucleotide-long RNAs, produced by a Dicer-independent mechanism, associates with Piwi-class Argonaute proteins. Studies in flies, fish and mice implicate these Piwi-associated RNAs (piRNAs) in germline development, silencing of selfish DNA elements, and in maintaining germline DNA integrity. However, whether piRNAs primarily control chromatin organization, gene transcription, RNA stability or RNA translation is not well understood, neither is piRNA biogenesis. Here, we review recent studies of piRNA production and function, and discuss unanswered questions about this intriguing new class of small RNAs.
Mouse complement receptors type 1 (CR1;CD35) and type 2 (CR2;CD21): expression on normal B cell subpopulations and decreased levels during the development of autoimmunity in MRL/lpr mice (1997)

Human complement receptors type 1 (hCR1;CD35) and type 2 (hCR2;CD21) are expressed on B lymphocytes at specific stages during differentiation and activation. These receptors play critical roles in the immune response to T-dependent Ags in addition to germinal center formation. Expression of both hCR2 and hCR1 is decreased on B lymphocytes of patients with systemic lupus erythematosus (SLE). We have studied the expression of mouse CR2 and CR1 on normal populations of mouse B lymphocytes in BALB/c mice. Our results demonstrate that expression of these receptors in the normal state closely parallels that of hCR2. During bone marrow development, expression is first detected on low B220/high IgM cells, demonstrating that complement receptors appear after central tolerance mechanisms are completed. In the splenic microenvironment the highest levels of receptor expression are found on marginal zone B lymphocytes. Mouse CR2 and CR1 are also found on peritoneal B1a and B1b cells in addition to IgA+ Peyer's patch B cells. Activation of splenic B cells under Th2 conditions results in a marked decrease in receptor expression. To determine whether the patterns of receptor expression also parallel those found in human disease, we studied the MRL lpr/lpr (MRL/lpr) model of SLE. Interestingly, we found an early decrease in complement receptor expression that is progressive and first detectable before major clinical manifestations of nephritis. We hypothesize that the early decrease in complement receptor expression such as that demonstrated by MRL/lpr mice plays an important role in the pathogenesis of murine and perhaps human SLE.
Design and synthesis of ribonucleic guanidine: a polycationic analog of RNA. (1996)

Replacement of the phosphodiester linkages of the polyanion RNA with guanidinium linkers (represented by g) provides the polycation ribonucleic guanidine (RNG). An anticipated structure for the triple-helical hybrid [r(Up)9U.r(Ag)9A.r(Up)9U] is presented. A basic strategy for the synthesis of RNG oligomers is described. Synthetic procedures are provided for tetrameric adenosyl RNG [r(Ag)3A].
CD4+ but not CD8+ cells are essential for allorejection. (1996)

The generation of knockout mice with targeted gene disruption has provided a valuable tool for studying the immune response. Here we describe the use of CD4 and CD8 knockout mice to examine the role of CD4+ and CD8+ cells in initiating allotransplantation rejection. Pretreatment with a brief course of depletive anti-CD4 monoclonal antibody therapy allowed permanent survival of heart, but not skin, allografts transplanted across a major histocompatibility barrier. However, skin as well as heart grafts were permanently accepted in the CD4 knockout mice. Transfer of CD4+ cells into CD4 knockout recipient mice 1 d before skin engraftment reconstituted rejection, demonstrating that CD4+ cells are necessary for initiating rejection of allogeneic transplants. Major histocompatibility complex disparate heart and skin allografts transplanted into CD8 knockout recipients were rejected within 10 d. This study demonstrates that CD4+ but not CD8+ T cells are absolutely required to initiate allograft rejection.
Roles of tobacco cellulose, sugars, and chlorogenic acid as precursors to catechol in cigarette smoke (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRoles of tobacco cellulose, sugars, and chlorogenic acid as precursors to catechol in cigarette smokeSteven G. Carmella, Stephen S. Hecht, T. C. Tso, and Dietrich HoffmannCite this: J. Agric. Food Chem. 1984, 32, 2, 267–273Publication Date (Print):March 1, 1984Publication History Published online1 May 2002Published inissue 1 March 1984https://pubs.acs.org/doi/10.1021/jf00122a023https://doi.org/10.1021/jf00122a023research-articleACS PublicationsRequest reuse permissionsArticle Views245Altmetric-Citations32LEARN 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
The Physical Properties of Spider’s Silk and Their Role in the Design of Orb-Webs (1976)

ABSTRACT Determinations were made of several physical properties of the viscid and frame silks of the orb-webs built by the spider Araneus sericatus (Cl.). Both types of silk show a breaking stress of approximately 1 GN/m2 and an initial resilience of approximately 0·35. The breaking extension ratio of viscid silk (λ = 3·00) is much greater than that of frame silk (λ = 1·25), and the viscid silk relaxes to a relatively greater extent. These properties are correlated with the degree of crystallization of the protein from which the silk is made, this factor being controlled by the sequence of amino acids in the protein. The physical properties of the viscid and frame silks allow them to function effectively as shock absorbers and structural elements, respectively; and allow the orb-web to function as an aerial filter with a minimum expenditure of material and energy.
TCP and explicit congestion notification (1994)

This paper discusses the use of Explicit Congestion Notification (ECN) mechanisms in the TCP/IP protocol. The first part proposes new guidelines for TCP's response to ECN mechanisms (e.g., Source Quench packets, ECN fields in packet headers). Next, using simulations, we explore the benefits and drawbacks of ECN in TCP/IP networks. Our simulations use RED gateways modified to set an ECN bit in the IP packet header as an indication of congestion, with Reno-style TCP modified to respond to ECN as well as to packet drops as indications of congestion. The simulations show that one advantage of ECN mechanisms is in avoiding unnecessary packet drops, and therefore avoiding unnecessary delay for packets from low-bandwidth delay-sensitive TCP connections. A second advantage of ECN mechanisms is in networks (generally LANs) where the effectiveness of TCP retransmit timers is limited by the coarse granularity of the TCP clock. The paper also discusses some implementation issues concerning specific ECN mechanisms in TCP/IP networks.
Modulation of plasminogen activation and type IV collagenase activity by a synthetic peptide derived from the laminin A chain (1991)

Laminin is a large multidomain glycoprotein with diverse biological activities which include stimulation of neurite outgrowth, enhancement of tumor metastasis, and promotion of cell growth, adhesion, and differentiation. A 19 amino acid synthetic peptide derived from the E8 fragment of the laminin A chain (Cys-Ser-Arg-Ala-Arg-Lys-Gln-Ala-Ala-Ser-Ile-Lys-Val-Ala-Val-Ser-Ala-Asp -Arg- NH2) was identified which promotes metastasis and stimulates collagenase IV activity in the culture medium of B16 melanoma cells (Kanemoto et al., 1990). We report that this peptide, here designated LamA2091-2108, is also a potent stimulator of tissue plasminogen activator (t-PA)-catalyzed plasminogen activation, resulting in a 22-fold increase in the kcat/Km of the activation reaction. The activity of purified type I and type IV collagenase was inhibited by LamA2091-2108 with IC50 values of 3 and 43 microM, respectively. These data support an alternative mechanism for the appearance of collagenase activity in the culture media of melanoma cells, namely, that the peptide stimulates plasminogen activation, subsequently generating collagenase activity.
Patterns of pulmonary structural remodeling after experimental paraquat toxicity. The morphogenesis of intraalveolar fibrosis. (1985)

For a study of the evolution of interstitial and intraalveolar fibrosis, ultrastructural and immunohistochemical observations were made of the lungs of 16 cynomolgous monkeys given 1 or 2 injections of 10 mg/kg of paraquat and sacrificed 2 days to 8 weeks later. At 2-3 days, alveolar epithelial cells were denuded in many areas, and fibronectin was conspicuous in alveolar spaces. At 1 week, fibroblasts and inflammatory cells were migrating through gaps in the denuded epithelial basement membranes; Type II cells were regenerating in some areas. At 3-4 weeks, alveoli developing intraalveolar fibrosis contained many myofibroblasts, collagen fibrils, and small elastic fibers; fibrotic alveolar walls were lined by metaplastic squamous cells and bronchiolar epithelial cells. Spiraling collagen fibrils were found in interstitium but not in alveolar spaces, which suggests that they were formed from breakdown of collagen. Newly formed intraalveolar collagen was mainly Type I. At 8 weeks, intraalveolar fibrosis had led to extensive remodeling, with new glandlike alveoli lined by Type II cells; alveoli without intraalveolar fibrosis had more normal architecture. Thus, intraalveolar fibrosis in paraquattreated lung is mediated by intraalveolar migration of interstitial cells, through gaps in the epithelial basement membranes, after epithelial injury. This is followed by connective tissue synthesis on the luminal side of the epithelial basement membrane, by differentiation of interstitial cells into myofibroblasts and smooth-muscle cells, by incorporation of areas of intraalveolar fibrosis into the interstitium, and by coalescence of alveolar walls. Intraalveolar fibrosis is more important than interstitial fibrosis in the structural remodeling that occurs in paraquattreated lung, because it results in obliteration of alveoli, coalescence of alveolar walls, and loss of functional alveolar-capillary units.
Functional role of mucoid exopolysaccharide (alginate) in antibiotic-induced and polymorphonuclear leukocyte-mediated killing of Pseudomonas aeruginosa (1991)

We evaluated in vitro the functional role of mucoid exopolysaccharide (MEP) of Pseudomonas aeruginosa in blocking antibiotic-induced and polymorphonuclear leukocyte (PMN)-mediated pseudomonal killing. The serum-resistant P. aeruginosa isolates used were mucoid strain 144MR and its nonmucoid revertant, strain 144NM. By timed kill curves, early bacterial effects of amikacin against mucoid strain 144MR were substantially less than those observed with nonmucoid strain 144NM; this effect was reversible with enzymatic hydrolysis of MEP of strain 144MR by alginase. Also, early tobramycin uptake (15 to 30 min) by mucoid 144MR cells was less than that seen with nonmucoid strain 144NM; pretreatment of 144MR cells with alginase substantially enhanced early tobramycin uptake compared with untreated 144MR cells (P = 0.08). In strain 144NM (but not in strain 114MR) there was a notable postantibiotic leukocidal enhancement effect manifested by increased nonopsonic killing following brief exposure of these cells to supra-MIC amikacin; pretreatment of strain 144MR with alginase rendered these cells more susceptible to amikacin-induced postantibiotic leukocidal enhancement. Similarly, direct PMN-mediated nonopsonic killing of mucoid strain 144MR was significantly less than that observed with strain 144NM (P less than 0.05); pretreatment of 144MR cells with alginase rendered this strain equal to strain 144NM in susceptibility to nonopsonic killing. In addition, exogenous sodium alginate or extracted MEP of strain 144MR interfered with effective nonopsonic killing of strain 144NM by PMNs. Studies also indicated that mucoid strain 144MR was phagocytosed significantly less well than its nonmucoid mate (P less than 0.00001), an effect reversed by pretreatment of the mucoid cells with alginase. These data confirm that P. aeruginosa MEPs functionally decrease the uptake and early bactericidal effect of aminoglycosides in vitro and interfere with effective PMN-mediated nonopsonic phagocytosis and killing of mucoid strains.
A low-cost CD-ROM--based image archival system. (1995)

Many radiologists have large collections of original or copied radiographs, as well as 35-mm slides of radiographs that require conventional carousel-type projectors for display. These images cannot be digitally manipulated or displayed in other formats. The authors used compact disk, read-only memory (CD-ROM) technology as a low-cost method of digitally storing these images. The CD-ROM disks were created from slide images optically scanned and digitally transferred to a disk. The images may be incorporated into any type of computer application, used on multiple computer platforms, and are easily transportable. The process is a low-cost, high-quality method of transferring images to digital media and is currently available to anyone with a conventional 35-mm camera, a CD-ROM reader, and a computer.