gebhart/patrepeval huggingface dataset:
Isolation and characterization of a cloned DNA sequence associated with the murine Ah locus and a 3-methylcholanthrene-induced form of cytochrome P -450 (1981)

Using partially purified mouse liver 23S mRNA known to be associated with the Ah locus and 3-methylcholanthrene-induced cytochrome P(1)-450, we synthesized double-stranded cDNA by the successive action of reverse transcriptase (RNA-directed DNA nucleotidyltransferase) and the Klenow A fragment of Escherichia coli DNA polymerase I. The double-stranded cDNA was inserted into pBR322 plasmid DNA by Pst I cleavage and homopolymeric "tailing" and cloned in E. coli LE392. Clone 46 hybridized with [(32)P]cDNA made from 23S mRNA from "Ah-responsive" C57BL/6N mice but did not hybridize with similarly prepared [(32)P]cDNA from "Ah-nonresponsive" DBA/2N mice. Clone 30 was positive, and clone 7 was negative, with both C57BL/6N and DBA/2N [(32)P]cDNA probes; these two clones were therefore used as "positive" and "negative" control clones, respectively. By translation-arrest experiments, clone 46 DNA and clone 30 DNA were shown to be associated with anti-P(1)-450- and anti-albumin-precipitable material, respectively. By agarose gel electrophoresis of Pst I digests, the clone 46 DNA insert was shown to be 1100 base pairs in total length and to contain one internal Pst I site. The cDNA made from total mRNA isolated from 3-methylcholanthrene-treated C57BL/6N mice hybridized to the two fragments of Pst I-digested DNA from clone 46, whereas similarly prepared cDNA from 3-methylcholanthrene-treated DBA/2N and control C57BL/6N and DBA/2N mice did not. Of 11 restriction endonucleases used, two (Pst I and Xba I) had sites within the clone 46 DNA insert. After hybridization of clone 46 (32)P-labeled nick-translated DNA to EcoRI fragments from A/HeJ mouse genomic DNA and fractionation by RPC-5 chromatography and gel electrophoresis, only one positive band (3-4 kilobase pairs appeared. These data demonstrate conclusively that pBR322 clone 46 DNA is associated with mRNA controlled by the murine Ah locus, presumably the structural gene encoding 3-methylcholanthrene-induced P(1)-450.
Should Tables Be Sorted? (1981)

Optmaahty questions are examined m the following information retrieval problem. Given a set S of n keys, store them so that queries of the form, "Is x E S?" can be answered quickly It is shown that m a rather general model including all the commonly used schemes, [lg(n + I)] probes to the table are needed m the worst case, prowded the key space is sufficiently large The effects of smaller key space and arbitrary encoding are also explored
Silicon carbide-free graphene growth on silicon for lithium-ion battery with high volumetric energy density (2015)

Silicon is receiving discernable attention as an active material for next generation lithium-ion battery anodes because of its unparalleled gravimetric capacity. However, the large volume change of silicon over charge-discharge cycles weakens its competitiveness in the volumetric energy density and cycle life. Here we report direct graphene growth over silicon nanoparticles without silicon carbide formation. The graphene layers anchored onto the silicon surface accommodate the volume expansion of silicon via a sliding process between adjacent graphene layers. When paired with a commercial lithium cobalt oxide cathode, the silicon carbide-free graphene coating allows the full cell to reach volumetric energy densities of 972 and 700 Wh l(-1) at first and 200th cycle, respectively, 1.8 and 1.5 times higher than those of current commercial lithium-ion batteries. This observation suggests that two-dimensional layered structure of graphene and its silicon carbide-free integration with silicon can serve as a prototype in advancing silicon anodes to commercially viable technology.
The role of autolysins during vegetative growth of Bacillus subtilis 168 (1998)

A set of isogenic mutants of Bacillus subtilis 168, insertionally inactivated in the genes encoding a number of lytic enzymes and a sigma factor (sigma D, which controls the expression of a number of autolysins) was constructed. Phenotypic analysis of the mutants determined the individual and combined roles of the autolysins in vegetative growth. The major vegetative autolysins of B. subtilis, LytC (50 kDa amidase) and LytD (90 kDa glucosaminidase), were shown to have roles in cell separation, cell wall turnover, antibiotic-induced lysis and motility. LytC was also shown to have a role in general cell lysis induced by sodium azide. Renaturing SDS-PAGE of cell-wall-binding protein extracts of the mutant strains revealed the presence of a novel autolysin that was previously masked by LytC. This 49 kDa enzyme was shown to be sigma D-controlled and was identified as a candidate cell separation and cell wall turnover enzyme. A multiple mutant strain, lacking LytC, LytD and the 49 kDa enzyme, retained at least ten bands of autolytic activity. These may correspond to individual or proteolytically processed novel autolysins, the functions of which are unknown. The multiple mutant strains facilitate the study of these, and other lytic enzymes, to determine their cellular functions.
The phylogenetic position and phenotypic changes of a Chlorella-like alga during 5-year microcosm culture (2013)

Recent phylogenetic studies of Chlorella-like algae revealed that this group has diversified into free-living and endosymbiotic niches, the latter within protists and invertebrate organisms. Our previous studies using a long-term culture composed of an alga (Chlorella vulgaris, rDNA sequence unknown), a bacterium (Escherichia coli) and a ciliate (Tetrahymena thermophila), suggested that some clones in the algal population developed an endosymbiotic ability with T. thermophila while others developed an ectosymbiotic ability with E. coli from a non-associated stage. In this paper, an rDNA (18S, ITS1, 5.8S, ITS2)-based phylogeny of the ancestral strain and derived clones isolated from 5-year microcosm cultures was constructed and revealed that the alga belongs to the genus Micractinium. This result was supported by analysis of the secondary structure of the rRNA gene. No difference was observed in the sequence between the ancestral and derived clones. On the other hand, some morphological and physiological traits of the ancestral strain and the derived clones were analysed and revealed that several phenotypic changes had occurred among the algal clones. In particular, the derived clones obtained from long-term cultures had increased in cell size, changed in their ability to grow at pH 4.0, and developed a tendency for cell-aggregation or sedimentation.
The Interleukin-12–Mediated Pathway of Immune Events Is Dysfunctional in Human Immunodeficiency Virus–Infected Individuals (1999)

Interleukin-12 (IL-12) is a potentially critical factor in the immune response against human immunodeficiency virus (HIV) because it is important for regulating proliferation and interferon-gamma (IFN-gamma) production by T cells and natural killer (NK) cells, antigen presentation and accessory cell function by macrophages and dendritic cells, and cytolytic activities of cytotoxic T-lymphocyte cells and NK cells, which are all functions known to be dysfunctional in patients with acquired immune deficiency syndrome. Peripheral blood mononuclear cells (PBMC) from HIV-infected patients have been previously shown to be deficient in the ability to produce IL-12 in response to the bacterial pathogen Staphylococcus aureus Cowan. In this study, impaired IL-12 production in cells from PBMC of HIV-infected patients compared with healthy donors was observed across a broad panel of stimuli derived from infectious pathogens with or without priming with cytokines such as IFN-gamma and IL-4, which amplify the IL-12 induction signal. Analysis of p40 and p35 mRNA accumulation showed that reductions in both subunits contribute to the lower IL-12 secretion of cells from HIV-infected individuals. PBMC from HIV-infected donors also failed to upregulate the IL-12 receptor beta2 chain (IL-12Rbeta2) in response to mitogenic stimuli. The expression of the IL-12Rbeta2 gene could, however, be restored by in vitro exposure to rIL-12. Thus, it is possible that a primary IL-12 defect may lead to secondary deficiencies in expression of the genes for IL-12Rbeta2 and IFN-gamma, thus amplifying immune deficiency during HIV infection.
Enhanced Photocatalytic CO2-Reduction Activity of Anatase TiO2 by Coexposed {001} and {101} Facets (2014)

Control of TiO2 crystal facets has attracted enormous interest due to the fascinating shape-dependent photocatalytic activity of this material. In this work, the effect of the ratio of {001} and {101} facets on the photocatalytic CO2-reduction performance of anatase TiO2 is reported. A new "surface heterojunction" concept is proposed on the basis of the density functional theory (DFT) calculations to explain the difference in the photocatalytic activity of TiO2 with coexposed {001} and {101} facets.
Dynamic range of nanotube- and nanowire-based electromechanical systems (2005)

Nanomechanical resonators with high aspect ratio, such as nanotubes and nanowires are of interest due to their expected high sensitivity. However, a strongly nonlinear response combined with a high thermomechanical noise level limits the useful linear dynamic range of this type of device. We derive the equations governing this behavior and find a strong dependence [∝d(d∕L)5] of the dynamic range on aspect ratio.
Templated Self‐Assembly: Formation of Folded Structures by Relaxation of Pre‐stressed, Planar Tapes (2005)

A strategy for the formation of three-dimensional (3D) structures based on the spontaneous folding of elastomeric tapes is described. These tapes are fabricated in crimped, quasi-3D forms, and carry metal features supporting liquid solder. Self-assembly based on capillary interactions between drops of liquid solder results in folding of the tapes into structures that have quasi- and true 3D topology (see Figure).
Effects of Varying Levels of Subatmospheric Pressure on the Rate of Granulation Tissue Formation in Experimental Wounds in Swine (2001)

The use of subatmospheric pressure to promote wound healing has increased in popularity during the last several years. The original studies on granulation tissue formation used a 125-mmHg vacuum. The use of alternative sources of subatmospheric pressure has led to many questions regarding efficacy or risk. In this report a swine model is used to quantify and compare the effects of low vacuum suction (25 mmHg) and high vacuum suction (500 mmHg) produced by various vacuum pumps and wall suction systems with the standard 125-mmHg vacuum. Additionally, the effects of an unregulated air leak in the sealing system were examined. All four wound treatments were examined on each of 4 pigs. Wounds were treated until one of the wounds had granulated to a level flush with the surrounding tissue. Wounds treated with the standard 125-mmHg vacuum had filled with granulation tissue by day 8. At this time wounds treated with 25 mmHg had filled 21.2% with new granulation tissue, and wounds treated with 500 mmHg had filled 5.9% with new tissue. Wounds treated with 125 mmHg with a hole in the sealing drape had increased in size 197% because of the debridement of necrotic tissue. In conclusion, wounds treated with a 125-mmHg vacuum exhibited a significant (p < 0.0001) increase in the rate of granulation tissue formation compared with treatment at 25 mmHg or 500 mmHg. The presence of an unregulated air leak in the sealing drape results in significant progression (p < 0.0001) of the wound secondary to dehydration and progressive necrosis.
Electrochemical Evaluation of the Interfacial Capacitance upon Phosphorylation of Amino Acid Analogue Molecular Films (2001)

An approach based on electrochemistry to differentiate between phosphorylated and nonphosphorylated amino acid analogues adsorbed on gold is presented. Analogues of serine, threonine, and tyrosine, containing thiohexadecyl headgroups, were synthesized and assembled on gold, and the surface capacitance was evaluated using electrochemical impedance spectroscopy. A procedure for deprotection of tert-butyl phosphate protecting groups, on the monolayer, is also described. Characterizations of the assembled analogues by cyclic voltammetry, infrared spectroscopy, and ellipsometry are used to confirm the insulating properties of the monolayers and the outcome of surface modifications. The results from cyclic voltammetry show good insulating properties for the monolayers even after phosphate deprotection. The infrared measurements reveal well-ordered monolayers, and the thickness from ellipsometry is in good agreement with expectations from molecular modeling. The impedance experiments show a capacitance increase up to 0.6 microF/cm2 as phosphate groups are introduced. The results in this study indicate the possibility of using a surface chemical and impedance spectroscopy approach to detect the kinase/phosphatase activity and kinetics involved in phosphorylation reactions.
Surface modification for mitigation of corrosion/localised corrosion of magnesium alloys (2007)

(2007). Surface modification for mitigation of corrosion/localised corrosion of magnesium alloys. Surface Engineering: Vol. 23, No. 5, pp. 319-323.
The Wilms' Tumor Antigen Is a Novel Target for Human CD4+ Regulatory T Cells: Implications for Immunotherapy (2008)

Compelling evidences indicate a key role for regulatory T cells (T(reg)) on the host response to cancer. The Wilms' tumor antigen (WT1) is overexpressed in several human leukemias and thus considered as promising target for development of leukemia vaccine. However, recent studies indicated that the generation of effective WT1-specific cytotoxic T cells can be largely affected by the presence of T(regs). We have generated T-cell lines and clones that specifically recognized a WT1-84 (RYFKLSHLQMHSRKH) peptide in an HLA-DRB1*0402-restricted manner. Importantly, they recognized HLA-DRB1*04-matched fresh leukemic cells expressing the WT1 antigen. These clones exerted a T helper 2 cytokine profile, had a CD4(+)CD25(+)Foxp3(+)GITR(+)CD127(-) T(reg) phenotype, and significantly inhibited the proliferative activity of allogeneic T cells independently of cell contact. Priming of alloreactive T cells in the presence of T(regs) strongly inhibited the expansion of natural killer (NK), NK T, and CD8(+) T cells and had an inhibitory effect on NK/NK T cytotoxic activity but not on CD8(+) T cells. Furthermore, priming of T cells with the WT1-126 HLA-A0201-restricted peptide in the presence of T(regs) strongly inhibited the induction of anti-WT1-126 CD8(+) CTL responses as evidenced by both very low cytotoxic activity and IFN-gamma production. Moreover, these T(reg) clones specifically produced granzyme B and selectively induced apoptosis in WT1-84-pulsed autologous antigen-presenting cells but not in apoptotic-resistant DR4-matched leukemic cells. Importantly, we have also detected anti-WT1-84 interleukin-5(+)/granzyme B(+)/Foxp3(+) CD4(+) T(regs) in five of eight HLA-DR4(+) acute myeloid leukemia patients. Collectively, our in vitro and in vivo findings strongly suggest important implications for the clinical manipulation of T(regs) in cancer patients.
Identification of an autologous insulin B chain peptide as a target antigen for H-2Kb-restricted cytotoxic T lymphocytes. (1992)

We have examined the CD8+ peripheral T cell repertoire of C57BL/6 (H-2b) mice for cytotoxic T lymphocyte (CTL) reactivities to insulin, using in vitro immunization with a chymotryptic digest of reduced bovine insulin. The results presented in this study demonstrate that potentially autoreactive H-2Kb-restricted cytotoxic T cells specific for an autologous insulin B chain peptide are present in the preimmune splenic T cell repertoire. The immunogenic peptide comprises residues 7-15 from the insulin B chain and has features in common with naturally processed Kb-restricted peptides identified by others. The minimal peptide sequence recognized by these cytotoxic T cells is 10-15, which is highly conserved in mammalian species and constitutes a self-peptide in mice. The presence of class I major histocompatibility complex-restricted CTLs with potentially autoreactive specificities in preimmune animals raises the possibility of a role for such cells in autoimmune disease states. Possible mechanisms for the in vivo expansion of insulin peptide-specific CTLs are discussed.
NMDA Receptor Currents Suppress Synapse Formation on Sprouting AxonsIn Vivo (2005)

NMDA receptors (NMDARs) play an important role in the structural maintenance and functional strength of synapses. The causal relationship between these anatomical and functional roles is poorly defined. Using quantitative confocal microscopy, synaptic vesicle immunoreactivity, and differential label of retinal projections, we measured axon volume and synapse density along ipsilateral retinal axons (ipsi axons) sprouting into the superficial visual layers of the superior colliculus (sSC) deafferented by a contralateral retinal lesion (a scotoma) 8 d earlier. When retinal lesions were made at postnatal day 6 (P6), glutamatergic synaptic currents on neurons within the scotoma were significantly reduced. Both ipsi axon sprouting and synapse density were increased by chronic d-AP-5 antagonism of NMDARs. Conversely, ipsi axon sprouting and synapse density were reduced by chronic exposure to the agonist, NMDA, known to functionally depress glutamate transmission in this system. After P11 lesions, however, NMDAR blockade had no effect on sprouting or synapse density. Developmental changes in NMDAR current kinetics could not account for this difference in the structural effects of NMDAR function. Also, synaptic current frequencies within the scotoma were not affected after the P11 lesions. The corticocollicular projection matures during the P11 survival interval and, as indicated by previous work, it is a source of competition for synaptic space and probably of maintained activity in the older sSC. Thus, our results suggest that during early development, NMDAR currents predominantly destabilize nascent synapses. As the neuropil matures, however, competition for synaptic space suppresses axon sprouting and synapse formation regardless of NMDAR function.
The EUROpean and Chinese cardiac and renal Remote Ischemic Preconditioning Study (EURO-CRIPS) (2014)

The EURO-CRIPS Study will be the first large-scale, multicentre clinical trial to test the role of RIPC in current clinical practice. The results of this randomized trial will provide important insights to optimize management strategy of patients undergoing PCI and to improve their outcome.
A quantitative atlas of mitotic phosphorylation (2008)

The eukaryotic cell division cycle is characterized by a sequence of orderly and highly regulated events resulting in the duplication and separation of all cellular material into two newly formed daughter cells. Protein phosphorylation by cyclin-dependent kinases (CDKs) drives this cycle. To gain further insight into how phosphorylation regulates the cell cycle, we sought to identify proteins whose phosphorylation is cell cycle regulated. Using stable isotope labeling along with a two-step strategy for phosphopeptide enrichment and high mass accuracy mass spectrometry, we examined protein phosphorylation in a human cell line arrested in the G(1) and mitotic phases of the cell cycle. We report the identification of >14,000 different phosphorylation events, more than half of which, to our knowledge, have not been described in the literature, along with relative quantitative data for the majority of these sites. We observed >1,000 proteins with increased phosphorylation in mitosis including many known cell cycle regulators. The majority of sites on regulated phosphopeptides lie in [S/T]P motifs, the minimum required sequence for CDKs, suggesting that many of the proteins may be CDK substrates. Analysis of non-proline site-containing phosphopeptides identified two unique motifs that suggest there are at least two undiscovered mitotic kinases.
Surgical Adhesives in Ophthalmology (1970)

Abstract Cyanoacrylate adhesives were tested for tissue tolerance in rabbit eyes. The monomers were applied on deepithelialized corneas, and the polymers were implanted intracorneally and in the anterior chamber. The following classification is made based on clinical and histological observations. Best tolerated: n-decyl, n-octyl, n-heptyl, n-hexyl, n-butyl, and isobutyl 2-cyanoacrylate; less well tolerated: β,β,β-trifluoroisopropyl 2-cyanoacrylate; and least tolerated: methyl 2-cyanoacrylate. The clinical applications of cyanoacrylate adhesives in corneal and retinal surgery are reviewed, including, 1) sealing of traumatic perforations and ulcers in the cornea, 2) attaching artificial membranes to the anterior surface of the cornea (artificial epithelium) and to the posterior surface (artificial endothelium), 3) adhesives with penetrating corneal prostheses, 4) sealing choroidal perforations, and 5) sutureless scleral buckles.
[Sacral nerve stimulation in the treatment of the lower urinary tract function disorders]. (2011)

Functional disorders of the female lower urinary tract like urge incontinence, idiopathic urinary retention and symptoms of urgency-frequency occasionally do not respond properly to classical behavioral and pharmacological therapy Therefore, additional alternative therapies are needed to alleviate these bothersome symptoms. Sacral neuromodulation (SNS) utilize mild electrical pulses which activate or suppress neural reflexes responsible for voiding by stimulating the sacral nerves that innervate the bladder, external urethral sphincter and pelvic floor muscles. The exact mechanism of SNS action is not yet fully understood but it is assumed that it influences the neuroaxis at different levels of the central nervous system and restores the balance between inhibitory and activatory control over the voiding reflex. There is numerous evidence on the success of SNS not only in the treatment of refractory urge incontinence in adult and children but also in idiopathic urinary retention and symptoms of urgency-frequency
Chemically Functionalized Carbon Nanotubes (2004)

Since their discovery, carbon nanotubes have attracted the attention of many a scientist around the world. This extraordinary interest stems from their outstanding structural, mechanical, and electronic properties. In fact, apart from being the best and most easily available one-dimensional (1D) model system, carbon nanotubes show strong application potential in electronics, scanning probe microscopy, chemical and biological sensing, reinforced composite materials, and in many more areas. While some of the proposed applications remain still a far-off dream, others are close to technical realization. Recent advances in the development of reliable methods for the chemical functionalization of the nanotubes provide an additional impetus towards extending the scope of their application spectrum. In particular, covalent modification schemes allow persistent alteration of the electronic properties of the tubes, as well as to chemically tailor their surface properties, whereby new functions can be implemented that cannot otherwise be acquired by pristine nanotubes.