gebhart/patrepeval huggingface dataset:
Efficient gene targeting in Drosophila by direct embryo injection with zinc-finger nucleases (2008)

We report very high gene targeting frequencies in Drosophila by direct embryo injection of mRNAs encoding specific zinc-finger nucleases (ZFNs). Both local mutagenesis via nonhomologous end joining (NHEJ) and targeted gene replacement via homologous recombination (HR) have been achieved in up to 10% of all targets at a given locus. In embryos that are wild type for DNA repair, the products are dominated by NHEJ mutations. In recipients deficient in the NHEJ component, DNA ligase IV, the majority of products arise by HR with a coinjected donor DNA, with no loss of overall efficiency in target modification. We describe the application of the ZFN injection procedure to mutagenesis by NHEJ of 2 new genes in Drosophila melanogaster: coil and pask. Pairs of novel ZFNs designed for targets within those genes led to the production of null mutations at each locus. The injection procedure is much more rapid than earlier approaches and makes possible the generation and recovery of targeted gene alterations at essentially any locus within 2 fly generations.
Phosphatidylserine Receptors: Role of CD36 in Binding of Anionic Phospholipid Vesicles to Monocytic Cells (1999)

Exposure of phosphatidylserine (PtdSer) has been implicated in the recognition and phagocytosis of senescent and apoptotic cells, and CD36 has been proposed as one receptor protein that recognizes PtdSer and other anionic phospholipids. We investigated the binding of phospholipid vesicles to the monocytic leukemia cell lines THP-1 and J774A.1 with a flow cytometric assay; vesicles contained 50 mol% PtdSer, phosphatidylinositol (PtdIns), or phosphatidylglycerol (PtdGro), with the balance being phosphatidylcholine. Specific, high affinity binding was observed for vesicles containing PtdSer, PtdIns, or PtdGro. Specificity of the assay was confirmed by control experiments with erythrocytes, which showed minimal vesicle binding, and with annexin V, which blocked the binding of PtdSer, PtdGro, and PtdIns vesicles to the THP-1 cells. However, O-phospho-L-serine (to 1 mM) had no effect on the binding of PtdSer vesicles, indicating that high affinity binding requires a surface containing multiple phosphoserine groups rather than a single molecule. A monoclonal antibody to CD36 blocked up to 60% of the specific binding of PtdSer vesicles but had minimal to no effect on the binding of PtdGro or PtdIns vesicles. This antibody also selectively inhibited the phagocytosis of PtdSer-containing vesicles as measured by fluorescence microscopy, indicating that CD36 is functionally significant for phagocytosis of this vesicle type. In addition, collagen and thrombospondin, two other putative ligands of CD36, were unable to inhibit the binding of PtdSer vesicles. We conclude that CD36 is the primary protein responsible for the high affinity binding of PtdSer vesicles to these monocyte-like cells. In addition, CD36 appears to be specific for PtdSer among anionic phospholipids, and non-phospholipid ligands of CD36 do not share binding sites with PtdSer on CD36.
Compartment Pressures During Nonreamed Tibial Nailing without Traction (1997)

When extrinsic factors that increase intramedullary pressures are avoided, then intramedullary nailing raises the intramedullary pressure only momentarily. The pressure peaks during manual reduction and nail passage, and then returns to normal before the patient is awakened. Intramedullary nailing performed without reaming or traction is safe with respect to compartment syndromes and continuous pressure is not required.
Effect of Intracarotid Etoposide on Opening the Blood-Brain Barrier (1984)

The effect of an intracarotid artery infusion of etoposide on blood-brain barrier (BBS) integrity was investigated in a rat model system. The external carotid arteries of Sprague-Dawley rats were catheterized in a retrograde manner. Etoposide in a dose range from 3.0 mg/kg to 22.5 mg/kg was infused into the internal carotid artery by this technique. BBB disruption was evaluated qualitatively by the appearance in the infused hemisphere of the systemically administered dye Evans blue and quantitatively by the ratio of counts of the technetium-labeled chetate of diethylenetriaminepentaacetic acid (99mTc-DTPA) in the infused to the noninfused hemisphere. Evidence of increased BBB permeability was seen at all doses of etoposide. Degree of BBB disruption increased with increasing doses of etoposide. The intracarotid infusion and subsequent BBB disruption were well tolerated. Further clinical trials employing the intracarotid administration of etoposide should be cognizant of the potential for BBB disruption.
Accurate position control of a pneumatic actuator using on/off solenoid valves (1997)

The development of a fast, accurate, and inexpensive position-controlled pneumatic actuator that may be applied to a variety of practical positioning applications is described. A novel pulse width modulation (PWM) valve pulsing algorithm allows on/off solenoid valves to be used in place of costly servo valves. The open-loop characteristic is shown both theoretically and experimentally to be near symmetrical. A comparison of the open- and closed-loop responses of standard PWM techniques and that of the novel PWM technique shows that there has been a significant improvement in the control. A linear process model is obtained from experimental data using system identification. A proportional integral derivative controller with added friction compensation and position feedforward has been successfully implemented. A worst case steady-state accuracy of 0.21 mm was achieved with a rise time of 180 ms for step inputs from 0.11 to 64 mm. Following errors to 64-mm S-curve profiles were less than 2.0 mm. The controller is robust to a sixfold increase in the system mass. The actuator's overall performance is comparable to that achieved by other researchers using servo valves.
Virus-Mediated Transduction of Murine Retina with Adeno-Associated Virus: Effects of Viral Capsid and Genome Size (2002)

Gene therapy vectors based on adeno-associated viruses (AAVs) show promise for the treatment of retinal degenerative diseases. In prior work, subretinal injections of AAV2, AAV5, and AAV2 pseudotyped with AAV5 capsids (AAV2/5) showed variable retinal pigmented epithelium (RPE) and photoreceptor cell transduction, while AAV2/1 predominantly transduced the RPE. To more thoroughly compare the efficiencies of gene transfer of AAV2, AAV3, AAV5, and AAV6, we quantified, using stereological methods, the kinetics and efficiency of AAV transduction to mouse photoreceptor cells. We observed persistent photoreceptor and RPE transduction by AAV5 and AAV2 up to 31 weeks and found that AAV5 transduced a greater volume than AAV2. AAV5 containing full-length or half-length genomes and AAV2/5 transduced comparable numbers of photoreceptor cells with similar rates of onset of expression. Compared to AAV2, AAV5 transduced significantly greater numbers of photoreceptor cells at 5 and 15 weeks after surgery (greater than 1,000 times and up to 400 times more, respectively). Also, there were 30 times more genome copies in eyes injected with AAV2/5 than in eyes injected with AAV2. Comparing AAVs with half-length genomes, AAV5 transduced only four times more photoreceptor cells than AAV2 at 5 weeks and nearly equivalent numbers at 15 weeks. The enhancement of transduction was seen at the DNA level, with 50 times more viral genome copies in retinas injected with AAV having short genomes than in retinas injected with AAV containing full-length ones. Subretinal injection of AAV2/6 showed only RPE transduction at 5 and 15 weeks, while AAV2/3 did not transduce retinal cells. We conclude that varying genome length and AAV capsids may allow for improved expression and/or gene transfer to specific cell types in the retina.
Clonal selection, attenuation and differentiation in an in vitro model of hyperplasia. (1974)

Observations of the growth kinetics and morphologies of clones and subclones of diploid human skin fibroblast cultures lead to the working hypothesis that these cells, presumably like their counterparts in healing wounds, constitute a differentiating system. There is attenuation of the growth of serial clones, with continual selection for more vigorous stem cells. The latter segregate daughter cells of varying growth potential, including a class of cells which may be regarded as terminally differentiating; we propose that such cells may be histiocytes or macrophages. These studies a) demonstrate extensive epigenetic heterogeneity in fibroblast cultures, b) suggest that hyperplastic foci may be monoclonal or oligoclonal, c) rule out a simple biologic clock mechanism as an explanation of clonal senescence, d) suggest a new approach to the analysis of various inborn errors of metabolism, such as Werner's Syndrome.
The Human Dopamine Transporter Forms a Tetramer in the Plasma Membrane (2003)

Using cysteine cross-linking, we demonstrated previously that the dopamine transporter (DAT) is at least a homodimer, with the extracellular end of transmembrane segment (TM) 6 at a symmetrical dimer interface. We have now explored the possibility that DAT exists as a higher order oligomer in the plasma membrane. Cysteine cross-linking of wild type DAT resulted in bands on SDS-PAGE consistent with dimer, trimer, and tetramer, suggesting that DAT forms a tetramer in the plasma membrane. A cysteine-depleted DAT (CD-DAT) into which only Cys243 or Cys306 was reintroduced was cross-linked to dimer, suggesting that these endogenous cysteines in TM4 and TM6, respectively, were cross-linked at a symmetrical dimer interface. Reintroduction of both Cys243 and Cys306 into CD-DAT led to a pattern of cross-linking indistinguishable from that of wild type, with dimer, trimer, and tetramer bands. This indicated that the TM4 interface and the TM6 interface are distinct and further suggested that DAT may exist in the plasma membrane as a dimer of dimers, with two symmetrical homodimer interfaces. The cocaine analog MFZ 2-12 and other DAT inhibitors, including benztropine and mazindol, protected Cys243 against cross-linking. In contrast, two substrates of DAT, dopamine and tyramine, did not significantly impact cross-linking. We propose that the impairment of cross-linking produced by the inhibitors results from a conformational change at the TM4 interface, further demonstrating that these compounds are not neutral blockers but by themselves have effects on the structure of the transporter.
Structural Biology and Chemistry of the Terpenoid Cyclases (2006)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructural Biology and Chemistry of the Terpenoid CyclasesDavid W. ChristiansonView Author Information Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323 Cite this: Chem. Rev. 2006, 106, 8, 3412–3442Publication Date (Web):June 1, 2006Publication History Received21 October 2005Published online1 June 2006Published inissue 1 August 2006https://pubs.acs.org/doi/10.1021/cr050286whttps://doi.org/10.1021/cr050286wresearch-articleACS PublicationsCopyright © 2006 American Chemical SocietyRequest reuse permissionsArticle Views8640Altmetric-Citations645LEARN 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 SUBJECTS:Anions,Cyclization,Hydrocarbons,Monomers,Peptides and proteins Get e-Alerts
China ranks second in scientific publications since 2006 (2008)

With the fast development of its economy, China plays an increasingly important role in the world. China's performance in science is also impressive. The exponential growth of Chinese scientific publications provides evidence. However, statistical results about China's world share of scientific publications provided by different institutions and researchers have been in disagreement. With the data for 2007 being now available, we provide an update on this issue and conclude that China has become the second largest producer of scientific publications since 2006.
A β-1,3- N -acetylglucosaminyltransferase with poly- N -acetyllactosamine synthase activity is structurally related to β-1,3-galactosyltransferases (1999)

Human and mouse cDNAs encoding a new beta-1, 3-N-acetylglucosaminyltransferase (beta3GnT) have been isolated from fetal and newborn brain libraries. The human and mouse cDNAs included ORFs coding for predicted type II transmembrane polypeptides of 329 and 325 aa, respectively. The human and mouse beta3GnT homologues shared 90% similarity. The beta3GnT gene was widely expressed in human and mouse tissues, although differences in the transcript levels were visible, thus indicating possible tissue-specific regulation mechanisms. The beta3GnT enzyme showed a marked preference for Gal(beta1-4)Glc(NAc)-based acceptors, whereas no activity was detected on type 1 Gal(beta1-3)GlcNAc and O-glycan core 1 Gal(beta1-3)GalNAc acceptors. The new beta3GnT enzyme was capable of both initiating and elongating poly-N-acetyllactosamine chains, which demonstrated its identity with the poly-N-acetyllactosamine synthase enzyme (E.C. 2.4.1.149), showed no similarity with the i antigen beta3GnT enzyme described recently, and, strikingly, included several amino acid motifs in its protein that have been recently identified in beta-1,3-galactosyltransferase enzymes. The comparison between the new UDP-GlcNAc:betaGal beta3GnT and the three UDP-Gal:betaGlcNAc beta-1,3-galactosyltransferases-I, -II, and -III reveals glycosyltransferases that share conserved sequence motifs though exhibiting inverted donor and acceptor specificities. This suggests that the conserved amino acid motifs likely represent residues required for the catalysis of the glycosidic (beta1-3) linkage.
Printing Meets Lithography: Soft Approaches to High-Resolution Patterning (2002)

We are developing a high-resolution printing technique based on transferring a pattern from an elastomeric stamp to a solid substrate by conformal contact. This is an attempt to enhance the accuracy of classical printing to a precision comparable with optical lithography, creating a low-cost, large-area, high-resolution patterning process. First, we introduce the components of this technique, called soft lithography, and review its evolution. Topics described in detail are the stamp material, stamp architecture, pattern design rules, and printing tools. The accuracy of the prints made by thin patterned elastomeric layers supported on a stiff and flexible backplane is then assessed, and defects are characterized using a new electrical metrology approach. This is followed by a discussion of various printing processes used in our laboratory: (1) thiol printing for high-resolution patterns of noble metals that may also be used as sacrificial masks; (2) confined contact processing with liquids in cavities or channels to chemically convert a substrate or deposit layers of materials or biomolecules; (3) printing of catalysts to mediate patterned deposition of metals; and (4) structured, light-guiding stamps for transferring high-resolution patterns into photoresists. Finally, we compare classical and high-resolution printing approaches, and describe their potential for emerging micro- and nanoscale patterning technologies.
Bromate Oxidation of Ammonium Salts: In Situ Acid Formation for Reservoir Stimulation (2019)

A redox chemistry approach has been employed to synthesize an assortment of acids in the subterranean environment for the purpose of enhancing productivity from hydrocarbon-bearing rock formations. Experimental studies revealed that bromate selectively oxidizes a series of ammonium salts NH<sub>4</sub>X where X = F<sup>-</sup>, Cl<sup>-</sup>, Br<sup>-</sup>, SO<sub>4</sub><sup>2-</sup>, and CF<sub>3</sub>CO<sub>2</sub><sup>-</sup> to produce 5-17 wt % HX. Importantly, the in situ method allows strategic placement of the acid in the zone of interest where the fluid is heated, and the reaction is triggered. Ammonium counteranions are shown to influence the kinetics of the bromate-ammonium reaction, and the conditions are tailored to promote oxidation of ammonium at reservoir temperatures. The reaction is observed to be acid-catalyzed, where the formation of bromous acid (HBrO<sub>2</sub>) is involved in the rate-limiting step. As a result, an induction period that scales with the p K<sub>a</sub> of the acid being formed is followed by rapid formation of the reaction products.
Evidence that the packaging signal of Moloney murine leukemia virus extends into the gag region (1987)

Replication-competent retroviruses can be modified to carry nonviral genes. Such gene transfer vectors help define regions of the retroviral genome that are required in cis for retroviral replication. Moloney murine leukemia virus has been used extensively in vector construction, and all of the internal protein-encoding regions can be removed and replaced with other genes while still allowing production of virions containing and transmitting the altered retroviral genome. However, inclusion of a portion of the gag region from Moloney murine leukemia virus markedly increases the titer of virus derived from these vectors. We determined that this effect was due to more efficient packaging of the vector RNA into particles and did not depend on protein synthesis from the gag region. We conclude that the retrovirus packaging signal extends into the gag region. We have found that retroviral vectors containing the complete packaging signal allow more efficient gene transfer into a variety of cell types. In addition, these results may help explain why many oncogenic retroviruses have retained gag sequences and often express transforming proteins that are gag-onc hybrids.
A pentahalogenated monoterpene from the red alga Portieria hornemannii produces a novel cytotoxicity profile against a diverse panel of human tumor cell lines (1992)

A polyhalogenated acyclic monoterpene, 6(R)-bromo-3(S)-(bromomethyl)-7- methyl-2,3,7-trichloro-1-octene (1) was obtained as a major component of the organic extract of the red alga Portieria hornemannii. X-ray diffraction analysis provided the complete structure, including correct placement of the different halogen atoms and determination of the absolute stereochemistry. Detailed NMR analyses provided complete 1H and 13C assignments. Compound 1 exhibited highly differential cytotoxicity against the U.S. National Cancer Institute's new in vitro human tumor cell line screening panel; brain tumor, renal, and colon tumor cell lines were most sensitive to 1, while leukemia and melanoma lines were relatively less sensitive. A second collection of P. hornemanni yielded the novel, monocyclic 2, considerably less cytotoxic and devoid of differential activity. On the basis of its unprecedented cytotoxicity profile in the NCI primary screen, compound 1 has been selected by the NCI Decision Network Committee for preclinical drug development.
Crystallization and Preliminary X-Ray Crystallographic Studies of SMU.134 Protein from Caries Pathogen Streptococcus mutans (2007)

The smu.134 gene encodes a putative transcriptional regulator of 217 residues in Streptococcus mutans, a major pathogen for human dental caries. The gene was cloned into expression vector pET28?? and expressed in soluble form in E. coli strain BL21 (DE3) with a His tag at its N-terminus. The recombinant protein SMU.134 was purified to homogeneity in a two step procedure of Ni2+ chelating and size exclusion chromatography. Crystals suitable for X-ray diffraction were obtained by hanging-drop vapor diffusion method and diffracted to 2.6 Å. The crystal belonged to space group P212121, with unit-cell parameters a=55.03 Å, b=80.84 Å, c=107.96 Å. Keywords: polymerase chain reaction, open reading frames, clostridium beijerincki, sds-page, luria-bertani
Impaired Macrophage Phagocytosis of Apoptotic Neutrophils in Patients with Human Immunodeficiency Virus Type 1 Infection (2002)

Dysfunction of neutrophils (polymorphonuclear leukocytes [PMNL]) and macrophagic cells occurs as a consequence of human immunodeficiency virus type 1 (HIV-1) infection. Macrophages contribute to the resolution of early inflammation ingesting PMNL apoptotic bodies. This study investigated macrophage ability to phagocytose PMNL apoptotic bodies in patients with HIV-1 infection in comparison with uninfected individuals and the effect of HIV Nef protein on apoptotic body phagocytosis to determine if phagocytic activity is impaired by HIV infection. Monocytes/macrophages were isolated from 10 HIV-1-infected patients and from five healthy volunteers, whereas PMNL were isolated from healthy volunteers. Macrophage phagocytosis of apoptotic PMNL was determined by staining of apoptotic bodies with fluorescein-conjugated concanavalin A or with fluorescein-labeled phalloidin. Our data show significant impairment of PMNL apoptotic body macrophage phagocytosis in subjects with HIV-1 infection presenting a concentration of CD4(+) T lymphocytes of >200/mm(3) and in particular in those with <200 CD4(+) T lymphocyte cells/mm(3). In addition, HIV-1 recombinant Nef protein is able to decrease phagocytosis of apoptotic PMNL from normal human macrophages in a dose-dependent manner. The results of our study suggest that impaired macrophage phagocytosis of PMNL apoptotic bodies may contribute to the persistence of the inflammatory state in HIV-infected subjects, especially during opportunistic infections that are often favored by defective phagocytic activity.
Anti-HER2 IgY antibody-functionalized single-walled carbon nanotubes for detection and selective destruction of breast cancer cells (2009)

We have demonstrated that the HER2 IgY-SWNT complex specifically targeted HER2-expressing SK-BR-3 cells but not receptor-negative MCF-7 cells. The complex can be potentially used for both detection and selective photothermal ablation of receptor-positive breast cancer cells without the need of internalization by the cells. Thus, the unique intrinsic properties of SWNTs combined with high specificity and sensitivity of IgY antibodies can lead to new strategies for cancer detection and therapy.