gebhart/patrepeval huggingface dataset:
A general strategy toward graphene@metal oxide core–shell nanostructures for high-performance lithium storage (2011)

We demonstrate a simple, efficient, yet versatile method for the realization of core–shell assembly of graphene around various metal oxide (MO) nanostructures, including nanowires (NWs) and nanoparticles (NPs). The process is driven by (i) the ring-opening reaction between the epoxy groups and amine groups in graphene oxide (GO) platelets and amine-modified MO nanostructures, respectively, and (ii) electrostatic interaction between these two components. Nearly every single NW or NP is observed to be wrapped by graphene. To the best of our knowledge, this is the first report that substrate-supported MO NWs are fully coated with a graphene shell. As an example of the functional properties of these compound materials, the graphene@α-Fe2O3 core–shell NPs are investigated as the lithium-ion battery (LIB) electrode, which show a high reversible capacity, improved cycling stability, and excellent rate capability with respect to the pristine α-Fe2O3. The superior performance of the composite electrode is presumably attributed to the effectiveness of the graphene shell in preventing the aggregation, buffering the volume change, maintaining the integrity of NPs, as well as improving the conductivity of the electrode.
High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides (2001)

Homologous DNA recombination is a fundamental, regenerative process within living organisms. However, in most organisms, homologous recombination is a rare event, requiring a complex set of reactions and extensive homology. We demonstrate in this paper that Beta protein of phage lambda generates recombinants in chromosomal DNA by using synthetic single-stranded DNAs (ssDNA) as short as 30 bases long. This ssDNA recombination can be used to mutagenize or repair the chromosome with efficiencies that generate up to 6% recombinants among treated cells. Mechanistically, it appears that Beta protein, a Rad52-like protein, binds and anneals the ssDNA donor to a complementary single-strand near the DNA replication fork to generate the recombinant. This type of homologous recombination with ssDNA provides new avenues for studying and modifying genomes ranging from bacterial pathogens to eukaryotes. Beta protein and ssDNA may prove generally applicable for repairing DNA in many organisms.
Itching after epidural and spinal opiates (1988)

When opiates are administered by the epidural and spinal routes, itching occurs as a side effect. We reviewed 52 reports in the literature of the use of epidural and spinal opiates to assess the incidence of itching and found an overall incidence of 8.5% in patients receiving epidural opiates, and 46% in patients receiving spinal opiates. The symptom is a recognised, though rare, side effect of systemically administered opiates, and in the case of systemic administration the itching is generalised. In the case of epidural and spinal administration, the itching may be generalised. But often a segmental distribution is demonstrable, centred on the level of injection, or the itching is localised to a particular area such as the nose and face. It is likely therefore, in the latter case, that there is an effect upon the spinal cord itself. Although occasionally spinal opiate-induced itching is extremely troublesome and lessens the value of spinal opiate pain relief, in the majority of cases, the itching is not severe and is treatable with naloxone. However, the frequent occurrence of the symptom and the likelihood of a spinal cord mechanism do provide valuable information about opioid actions, and benefit may be derived from better understanding the phenomenon. This paper states a hypothesis to explain spinal opiate-induced itch and explores the possible mechanisms of the effect.
Enhancement by stable butyrate derivatives of antitumor and antiviral actions of interferon (1992)

The use of n-butyric acid has been associated with induction of cell differentiation and bypassing of genetic defects in the suppression of malignancy. This biological response modifier satisfies the requirements for specificity and low toxicity, and its use can be considered as an alternative approach to conventional cancer chemotherapy. However, a lack of clinical efficacy has been observed with butyrate and attributed mainly to the rapid metabolism of the compound. Butyric acid pro-drugs derived from monosaccharides such as 3-O-butanoyl-1,2-O-isopropylidene-alpha-D-glucofuranose (MAG = 3but) have consequently been devised. Pharmacokinetic and biological advantages of MAG = 3but have been previously described. In the present report, we have studied the effect of MAG = 3but on murine interferon-alpha, beta (IFN) anticellular, antitumor and antiviral activities. In vitro, it appears that MAG = 3but predisposes malignant MSV cells to a later, complete establishment of the antiproliferative and the cell-differentiating effects of IFN, and the antiviral action of the latter in the same line of cells infected with encephalomyocarditis (EMC) virus. In vivo, combined treatment with MAG = 3but and IFN protects mice effectively against the fatal development of ascitic sarcoma 180 TG and the lethal effect of EMC virus infection.
Sequence-Specific Capture of Protein-DNA Complexes for Mass Spectrometric Protein Identification (2011)

The regulation of gene transcription is fundamental to the existence of complex multicellular organisms such as humans. Although it is widely recognized that much of gene regulation is controlled by gene-specific protein-DNA interactions, there presently exists little in the way of tools to identify proteins that interact with the genome at locations of interest. We have developed a novel strategy to address this problem, which we refer to as GENECAPP, for Global ExoNuclease-based Enrichment of Chromatin-Associated Proteins for Proteomics. In this approach, formaldehyde cross-linking is employed to covalently link DNA to its associated proteins; subsequent fragmentation of the DNA, followed by exonuclease digestion, produces a single-stranded region of the DNA that enables sequence-specific hybridization capture of the protein-DNA complex on a solid support. Mass spectrometric (MS) analysis of the captured proteins is then used for their identification and/or quantification. We show here the development and optimization of GENECAPP for an in vitro model system, comprised of the murine insulin-like growth factor-binding protein 1 (IGFBP1) promoter region and FoxO1, a member of the forkhead rhabdomyosarcoma (FoxO) subfamily of transcription factors, which binds specifically to the IGFBP1 promoter. This novel strategy provides a powerful tool for studies of protein-DNA and protein-protein interactions.
The expression of leucine-rich repeat gene family members in colorectal cancer (2012)

This study was conducted to evaluate the association of the leucine-rich repeat (LRR) gene family with colorectal cancer (CRC). The expression of members of the LRR gene family were analyzed in 17 CRC specimens and in 59 healthy colorectal tissues by using Human Exon1.0ST microarray, and in 25 CRC specimens and 32 healthy colorectal tissues by U133Plus2.0 microarray. An association was found for 25 genes belonging to the plant-specific (PS) class of LRR genes (P = 0.05 for Exon1.0 ST and P = 0.04 for U133Plus2.0). In both data-sets, in CRC, we found down-regulation of SHOC2 (P < 0.00003) and LRRC28 (P < 0.01) and up-regulation of LRSAM1 (P < 0.000001), while up-regulation of MFHAS1 (P = 0.0005) and down-regulation of WDFY3 (P = 0.026) were found only in the Exon1.0 ST data-set. The PS LLR gene class encodes proteins that activate immune cells and might play a key role in programmed cell death and autophagy. SHOC2 and LRRC28 genes involved in RAS-mediated signaling, which hinders nutrient deprivation-induced autophagy, might be a possible link between the negative control of autophagy and tumorigenesis.
An Official ATS/IDSA Statement: Diagnosis, Treatment, and Prevention of Nontuberculous Mycobacterial Diseases (2007)

Diagnostic Criteria of Nontuberculous Mycobacterial Lung Disease Key Laboratory Features of NTM Health Careand Hygiene-associated Disease Prevention Prophylaxis and Treatment of NTM Disease Introduction Methods Taxonomy Epidemiology Pathogenesis Host Defense and Immune Defects Pulmonary Disease Body Morphotype Tumor Necrosis Factor Inhibition Laboratory Procedures Collection, Digestion, Decontamination, and Staining of Specimens Respiratory Specimens Body Fluids, Abscesses, and Tissues Blood Specimen Processing Smear Microscopy Culture Techniques Incubation of NTM Cultures NTM Identification Antimicrobial Susceptibility Testing for NTM Molecular Typing Methods of NTM Clinical Presentations and Diagnostic Criteria Pulmonary Disease Cystic Fibrosis Hypersensitivity-like Disease Transplant Recipients Disseminated Disease Lymphatic Disease Skin, Soft Tissue, and Bone Disease
Biochemical pharmacology of (+)- and (-)-2',3'-dideoxy-3'-thiacytidine as anti-hepatitis B virus agents. (1992)

2',3'-Dideoxy-3'-thiacytidine (cis-(+/-)-SddC) was found to have potent activity against hepatitis B virus and human immunodeficiency viruses in culture. Recent studies by us identified (-)-SddC as the stereoisomer responsible for the antiviral effect and showed that the cytotoxicity was mainly caused by (+)-SddC. Metabolism studies showed that these drugs were converted to their monophosphates, diphosphates, and triphosphates. The enzyme responsible for the formation of monophosphates was identified to be cytoplasmic deoxycytidine kinase in CEM cells. Uptake studies showed that the intracellular concentration of (-)-SddC and its metabolites was approximately 5-fold higher than that of (+)-SddC metabolites. (-)-SddCTP was more potent than (+)-SddCTP in inhibiting hepatitis B virus replication; (+)- and (-)-SddCTP exhibited minimal inhibition on polymerases alpha and delta, more inhibition on beta, and strong inhibition on gamma. In all cases, (+)-SddCTP was found to be more inhibitory than (-)-SddCTP to all four polymerases. (+)-SddCMP competed with dCTP for incorporation into DNA by DNA polymerase gamma and beta and served as a chain terminator; however, similar incorporation was not detected using other polymerases. The selective inhibition of DNA synthesis in isolated mitochondria by (+)- and (-)-SddCTP suggests a stereospecificity on the mitochondrial uptake of deoxynucleoside triphosphates.
Drive Smartly as a Taxi Driver (2010)

GPS-equipped taxis are mobile sensors probing the traffic flow on road surfaces, and taxi drivers are experienced drivers who can usually find out the fastest path to a destination based on their knowledge. In this demo, we provide a user with the practically fastest path to a destination at a given departure time in terms of taxi drivers' intelligence mined from historical GPS trajectories of taxis. We build our system, called T-Drive, by using a real trajectory dataset generated by over 33,000 taxis in a period of 3 months, and conduct both synthetic experiments and in-the-field evaluations. As a result, our method outperforms the real-time-traffic-based (RT) and the speed-constraint-based (SC) approaches in both efficiency and effectiveness.
Enhancing the Thermostability of β-Glucuronidase by Rationally Redesigning the Catalytic Domain Based on Sequence Alignment Strategy (2016)

β-Glucuronidase has been widely used in improving the efficacy of the natural glucuronides, but the poor thermostability largely impedes its industrial application. In this study, the thermostability of β-glucuronidase from Penicillium purpurogenum Li-3 (PGUS-E) was enhanced by rationally mutating key residues within the catalytic domain based on in-depth structure analysis and sequence alignment. Three mutants F292L/T293K, S35P, R304L were obtained that showed significantly improved thermostability. PGUS-E showed a two-phase thermal deactivation process, and the thermal deactivation constants k1 and k2 were solved separately in each phase. The mutation of F292L/T293K and S35P contributed more to the maintenance of the enzyme stability in the first deactivation phase, with k1 decreased by 1 magnitude compared to that of wild-type. Meanwhile, the mutation R304L mainly took effect in the second deactivation phase with the lowest k2 of 0.0021 min–1. In addition, mutant F292L/T293K showed 6.4 times higher kcat/Km than wild-type. The MD simulation indicated that the improved thermostability of the three mutants was due to a unique C-terminal fixing effect (F292L/T293K), proline effect (S35P) and hydrophobic interaction (R304L). This study not only promotes the industrial application of β-glucuronidase but also provides new insight into the interplay between structure and stability of β-glucuronidase.
Molecular requirements for epigenetic modulators. Synthesis of active fragments of teleocidins and lyngbyatoxin. (1982)

A synthesis of 3, 4, 5, 6, 7, 8-hexahydro-6-oxo [1, 4] diazonino [7, 6, 5-cd] indoles (3 and 18) which have active fragments of teleocidins (1) and lyngbyatoxin (2) is described.
Transcription Factor Decoys: A New Model for Disease Intervention (2005)

Transcription factor proteins regulate gene expression via binding to specific DNA sequences found in the promoter/enhancer regions of the genes they control. Although most transcription factor binding has been associated with an increase in gene expression, gene suppression has also been described. Transcription factor decoys are molecules that mimic the binding sites for transcription factor proteins, and compete with promoter regions to absorb this binding activity in the cell nucleus. By blocking transcription factor-chromosomal DNA interaction, these molecules provide a powerful means to manipulate the regulation of gene expression, particularly as transcription factors are increasingly understood to alter gene activation during the course of normal and pathologic processes in cell biology. As methods for cellular and nuclear delivery of these agents improve, the increasing use of transcription factor decoys, both as investigative and therapeutic tools, promises to have a significant impact on our understanding of and ability to treat human disease.
Mobility enhancement in conjugated polymer field-effect transistors through chain alignment in a liquid-crystalline phase (2000)

A method is demonstrated by which liquid-crystalline self-organization in rigid-rod nematic conjugated polymers can be used to control the microstructure of the active semiconducting layer in solution-processed polymer thin-film transistors (TFTs). Enhanced charge carrier mobilities of 0.01–0.02 cm2/V s and good operating stability have been achieved in polyfluorene copolymer TFTs by preparing the polymer in a nematic glassy state and by aligning the polymer chains parallel to the transport direction with the help of an alignment layer. Mobility anisotropies of 5–8 for current flow parallel and perpendicular to the alignment direction have been observed that are of the same order of magnitude as optical dichroic ratios.
Structural Basis of Light Harvesting by Carotenoids: Peridinin-Chlorophyll-Protein from Amphidinium carterae (1996)

Peridinin-chlorophyll-protein, a water-soluble light-harvesting complex that has a blue-green absorbing carotenoid as its main pigment, is present in most photosynthetic dinoflagellates. Its high-resolution (2.0 angstrom) x-ray structure reveals a noncrystallographic trimer in which each polypeptide contains an unusual jellyroll fold of the alpha-helical amino- and carboxyl-terminal domains. These domains constitute a scaffold with pseudo-twofold symmetry surrounding a hydrophobic cavity filled by two lipid, eight peridinin, and two chlorophyll a molecules. The structural basis for efficient excitonic energy transfer from peridinin to chlorophyll is found in the clustering of peridinins around the chlorophylls at van der Waals distances.
Abstract 1128: The Leukocyte Integrin Mac-1 Promotes Acute Cardiac Allograft Rejection (2007)

Background: In allograft rejection, donor endothelial cells (EC) are the principal early targets of host leukocytes and alloantibodies. Although the leukocyte integrin Mac-1(αmβ2, CD11b/ CD18) facilitates leukocyte-leukocyte as well as leukocyte-EC interactions, its roles in allograft survival and vasculopathy remains unclear. This study used murine cardiac transplantation to test the hypothesis that Mac-1 deficiency in the recipient reduces accumulation of graft infiltrating cells and attenuates cardiac allograft rejection. Results: In total-allomismatched murine cardiac allografts (BALB/c donor hearts and C57BL/6 recipients), survival averaged 13.8 ± 2.3 days (n=6) for allografts in Mac-1-deficient (Mac-1−/−) recipients compared to 8.3 ± 1.3 days (n = 18, p&lt;0.0001) in wild-type (WT) recipients. At 7 d post-transplantation, allografts in Mac-1−/− recipients had significantly lower parenchymal rejection (PR) scores (2.3 ± 0.4) than WT recipients (3.0 ± 0.4, p&lt;0.01). Allograft accumulation of neutrophils, T cells, and macrophages (Mϕ) significantly diminished in Mac-1−/− compared to WT recipients. To determine the cell type involved in acute graft dysfunction, we performed adoptive transfer experiments. Adoptive transfer of WT, but not Mac-1−/−, Mϕ exacerbated parenchymal rejection of 7-day allografts placed into Mac-1−/− recipients (PR score: 2.3 ± 0.4 for WT vs. 1.5 ± 0.5 for Mac1−/− Mϕ; p &lt; 0.05), and significantly reduced graft survival (8.0 ± 1.4 vs. 13.5 ± 2.6 days, p&lt;0.01). Neither WT nor Mac-1−/− neutrophil adoptive transfer affected graft survival in Mac-1−/− recipients. Mac-1−/− Mϕ co-cultured with allo-EC (BALB/c) expressed significantly lower levels of the co-stimulatory molecules CD40 and CD80, and mixed leukocyte reaction using allo-EC-primed Mac-1−/− Mϕ showed significantly lower antigen-presenting function than WT Mϕ. Despite attenuating acute rejection, recipient Mac-1-deficiency did not prevent graft arterial disease. Conclusion: These studies demonstrate that Mac-1 contributes to acute allograft rejection by modulating macrophage recruitment, antigen presentation, and T cell priming. These observations establish a molecular target for modulating recipient responses to prolong graft survival.
Performance analysis of a color CMOS photogate image sensor (2000)

The performance of a color CMOS photogate image sensor is reported. It is shown that by using two levels of correlated-double sampling it is possible to effectively cancel all fixed-pattern noise due to read-out circuit mismatch. Instead the fixed-pattern noise performance of the sensor is limited by dark current nonuniformity at low signal levels, and conversion gain nonuniformity at high signal levels. It is further shown that the imaging performance of the sensor is comparable to low-end CCD sensors but inferior to that reported for high-end CCD sensors due to low quantum efficiency, high dark current, and pixel cross-talk. As such the performance of CMOS sensors is limited at the device level rather than at the architectural level. If the imaging performance issues can be addressed at the fabrication process level without increasing cost or degrading transistor performance, CMOS has the potential to seriously challenge CCD as the solid-state imaging technology of choice due to low power dissipation and compatibility with camera system integration.
Bispecific monoclonal antibodies directed to CD16 and to a tumor‐associated antigen induce target‐cell lysis by resting NK cells and by a subset of NK clones (1991)

CD16 surface antigens represent activatory molecules in CD3-16+ NK cells. In order to target NK cells against relatively NK-resistant ovarian carcinomas, we used an anti-CD16 monoclonal antibody (MAb) (VD4), together with an anti-ovarian carcinoma-associated antigen (MOV19), to construct biMAbs. To this end, hybrid hybridomas were generated by fusing a TK-deficient VD4 hybridoma mutant with a HGPRT-deficient MOV19 hybrid. Supernatants from hybrid hybridomas that had been selected in HAT medium were screened for their ability to induce a CD3-16+ NK clone to lyse an MOV19+ ovarian carcinoma cell line in a 4-hr 51Cr-release assay. The NMB.45 hybrid hybridoma secreted a biMAb which triggered lysis of MOV19+ but not of MOV19- target cells. Some degree of target cell lysis was also observed with MOV19 MAb (due to ADCC mechanisms), while the VD4 MAb was ineffective. HPLC fractionation of MAbs secreted by the hybrid hybridoma made it possible to identify 4 different peaks, one of which appeared to contain functional biMAb molecules. HPLC-purified biMAb (100 ng/ml) induced resting PBL to lyse the "NK-resistant" IGROVI ovarian carcinoma cell line. Fresh MOV19+ tumor cells were also lysed, although with lower efficiency. When IL-2-activated lymphocytes were used as a source of effectors, biMAb caused only minor increases in the IL-2-induced cytolytic activity. Further analyses of the effect of biMAb were performed at the clonal level. Among CD3-16+ NK cell clones, a clear enhancing effect could be observed only in GL183+ but not in GL183- clones. In CD3+ cytotoxic clones a triggering effect could be detected in one out of 4 TCR gamma/delta+ clones but not in TCR alpha/beta+ clones.
Inhibition of growth of HT-29 human colon cancer xenografts in nude mice by treatment with bombesin/gastrin releasing peptide antagonist (RC-3095). (1991)

Nude mice bearing xenografts of HT-29 human colon cancer cell line were treated for 4 weeks with a [D-Trp6] agonist of luteinizing hormone releasing hormone (LH-RH), somatostatin analogue (RC-160), and bombesin/gastrin releasing peptide antagonist (RC-3095). Some inhibitory effect of [D-Trp6] LH-RH microcapsules releasing 25 micrograms/day on tumor growth was observed that could be due to sex steroid deprivation, but the inhibition was not statistically significant. Microcapsules of RC-160, releasing 50 micrograms/day, significantly reduced tumor volume after 21 and 24 days of treatment, but at the end of the experiment the inhibition in tumor volume and weight was not significant. Bombesin/gastrin releasing peptide antagonist RC-3095, at a dose of 20 micrograms/day administered by daily s.c. injections or by continuous infusion using Alzet osmotic minipumps, had the greatest inhibitory effect on tumor growth. Tumor volume, percentage change in tumor volume, and tumor weights were significantly decreased in both groups treated with RC-3095. This is the first report on inhibition of human colon cancer growth in vivo by bombesin antagonists.
Pertactin, an Arg-Gly-Asp-containing Bordetella pertussis surface protein that promotes adherence of mammalian cells. (1991)

A 69-kDa protein has been identified on the surface of the Gram-negative pathogen Bordetella pertussis that can elicit a protective immune response in animal models. This protein is associated with virulent strains of B. pertussis but its function has remained unclear. In this report we demonstrate that purified preparations of the 69-kDa outer membrane protein can promote the attachment of Chinese hamster ovary (CHO) cells. The interaction between the mammalian cells and this protein can be specifically inhibited by an Arg-Gly-Asp (RGD)-containing synthetic peptide that is homologous with a region found in the 69-kDa protein sequence. These studies indicate that a specific cell binding site containing an Arg-Gly-Asp sequence may be involved in the interaction of this bacterial protein with mammalian cell surfaces. To further investigate the role of this protein as a bacterial adhesin, a mutant of B. pertussis W28 that does not express the 69-kDa protein was constructed using the plasmid vector pRTP1. This mutant was 30-40% less efficient at adhering to CHO cells and to human HeLa cells than was the parent strain. These data support a role for this 69-kDa outer membrane protein in the attachment of B. pertussis to mammalian cells. We propose the name "pertactin" for this protein.