gebhart/patrepeval huggingface dataset:
Development of a Gene Knockout System for the Halophilic ArchaeonHaloferax volcaniiby Use of thepyrEGene (2003)

ABSTRACT So far, the extremely halophilic archaeon Haloferax volcanii has the best genetic tools among the archaea. However, the lack of an efficient gene knockout system for this organism has hampered further genetic studies. In this paper we describe the development of pyrE -based positive selection and counterselection systems to generate an efficient gene knockout system. The H. volacanii pyrE1 and pyrE2 genes were isolated, and the pyrE2 gene was shown to code for the physiological enzyme orotate phosphoribosyl transferase. A Δ pyrE2 strain was constructed and used to isolate deletion mutants by the following two steps: (i) integration of a nonreplicative plasmid carrying both the pyrE2 wild-type gene, as a selectable marker, and a cloned chromosomal DNA fragment containing a deletion in the desired gene; and (ii) excision of the integrated plasmid after selection with 5-fluoroorotic acid. Application of this gene knockout system is described.
Discharge Performance of All-Solid-State Battery Using a Lithium Superionic Conductor Li10GeP2S12 (2012)

A solid electrolyte, Li10GeP2S12, exhibits a high lithium ionic conductivity of 12 mS/cm at room temperature. Because of its high ionic conductivity, high charge-discharge performance would be expected for the all-solid-state batteries using the Li10GeP2S12 electrolytes. In this study, all-solid-state batteries using Li10GeP2S12, were constructed and their battery performances were examined. The batteries using the Li10GeP2S12 electrolyte showed higher discharge capacities than those with glass electrolyte, 75Li2S·25P2S5, particularly under the high-rate current discharge.
Portable real-time optical coherence tomography system for intraoperative imaging and staging of breast cancer (2007)

Breast cancer continues to be one of the most widely diagnosed forms of cancer amongst women and the second leading type of cancer deaths amongst women. The recurrence rate of breast cancer is highly dependent on several factors including the complete removal of the primary tumor and the presence of cancer cells in involved lymph nodes. The metastatic spread and staging of breast cancer is also evaluated through the nodal assessment of the regional lymphatic system. A portable real-time spectral domain optical coherence tomography system is being presented as a clinical diagnostic tool in the intraoperative delineation of tumor margins as well as for real time lymph node assessment. The system employs a super luminescent diode centered at 1310 nm with a bandwidth of 92 nm. Using a spectral domain detection system, the data is acquired at a rate of 5 KHz / axial scan. The sample arm is a galvanometer scanning telecentric probe with an objective lens (f = 60 mm, confocal parameter = 1.5 mm) yielding an axial resolution of 8.3 &mgr;m and a transverse resolution of 35.0 &mgr;m. Images of tumor margins are acquired in the operating room ex vivo on freshly excised human tissue specimen. This data shows the potential of the use of OCT in defining the structural tumor margins in breast cancer. Images taken from ex-vivo samples on the bench system clearly delineate the differences between clusters of tumor cells and nearby adipose cells. In addition, the data shows the potential for OCT as a diagnostic tool in the staging of cancer metastasis through locoregional lymph node assessment.
DIP: a member of the MIP family of membrane proteins that is expressed in mature seeds and dark‐grown seedlings of Antirrhinum majus (1993)

DiP, a gene from Antirrhinum majus, which encodes a protein with striking homology to other integral membrane proteins, was cloned. The gene was specifically expressed in mature seeds and during seedling germination, particularly in cotyledons of seedlings grown in the dark. The deduced product, called DiP, for dark intrinsic protein, shows strong homology with the MIP family of channel transporters which include; the bovine major intrinsic protein (MIP), the Escherichia coli glycerol facilitator (GIpF), the peribacteroid nodulin-26 (Nod26), and the tonoplast protein from kidney bean (TIP). DiP is most similar to other plant members of this family, and in particular to the tobacco protein TobRB7 which is expressed specifically in roots. However, the expression pattern of diP suggests that its product is functionally more similar to the tonoplast intrinsic protein from kidney bean since it is most highly expressed in the cotyledons of germinating seedlings, before the cells undergo expansion growth and become photosynthetic.
Ectopic induction of cartilage and bone by water-soluble proteins from bovine bone using a collagenous delivery vehicle (1989)

A controlled-release delivery vehicle for water-soluble osteogenic proteins from demineralized bone matrix was constructed using purified type I collagen. The water-soluble proteins were isolated from a 4 M GdnHCl extract of bone matrix. Although the water-soluble proteins were capable of inducing cartilage formation in vitro, they were incapable of inducing cartilage or bone in vivo when implanted intramuscularly into mice in the absence of an appropriate delivery vehicle. The collagen-based delivery vehicle alone was also incapable of inducing osteogenesis in vivo. However, when the water-soluble proteins were incorporated into the delivery vehicle, the combination was capable of inducing cartilage and bone 76% of the time. These results demonstrate that it is possible to formulate a controlled-release delivery vehicles for soluble bioactive factors which upon release interact with local responsive cells.
Quorum sensing: the many languages of bacteria (2005)

In the conventional view of prokaryotic existence, bacteria live unicellularly, with responses to external stimuli limited to the detection of chemical and physical signals of environmental origin. This view of bacteriology is now recognized to be overly simplistic, because bacteria communicate with each other through small 'hormone-like' organic compounds referred to as autoinducers. These bacterial cell-to-cell signaling systems were initially described as mechanisms through which bacteria regulate gene expression via cell density and, therefore, they have been collectively termed quorum sensing. The functions controlled by quorum sensing are varied and reflect the needs of a particular species of bacteria to inhabit a given niche. Three major quorum-sensing circuits have been described: one used primarily by Gram-negative bacteria, one used primarily by Gram-positive bacteria, and one that has been proposed to be universal.
Zinc-modified cyanoborohydride as a selective reducing agent (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTZinc-modified cyanoborohydride as a selective reducing agentSunggak Kim, Chang Ho Oh, Jae Suk Ko, Kyo Han Ahn, and Yong Jin KimCite this: J. Org. Chem. 1985, 50, 11, 1927–1932Publication Date (Print):May 1, 1985Publication History Published online1 May 2002Published inissue 1 May 1985https://pubs.acs.org/doi/10.1021/jo00211a028https://doi.org/10.1021/jo00211a028research-articleACS PublicationsRequest reuse permissionsArticle Views4024Altmetric-Citations154LEARN 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
Evolutionary Comparisons of the S Segments in the Genomes of Herpes Simplex Virus Type 1 and Varicella-Zoster Virus (1986)

The genomes of herpes simplex virus type 1 (HSV-1) and varicella-zoster virus (VZV) consist of two covalently joined segments, L and S. Each segment comprises an unique sequence flanked by inverted repeats. We have reported previously the DNA sequences of the S segments in these two genomes, and have identified protein-coding regions therein. In HSV-1, the unique sequence of S contains ten entire genes plus the major parts of two more, and each inverted repeat contains one entire gene; in VZV, the unique sequence of S contains two entire genes plus the major parts of two more, and each inverted repeat contains three entire genes. In this report, an examination of polypeptide sequence homology has shown that each VZV gene has an HSV-1 counterpart, but that six of the HSV-1 genes have no VZV homologues. Thus, although these regions of the two genomes differ in gene layout, they are related to a significant degree. The analysis indicates that the inverted repeats are evidently capable of large-scale expansion or contraction during evolution. The differences in gene layout can be understood as resulting from a small number of recombinational events during the descent of HSV-1 and VZV from a common ancestor.
Mutant Trp Repressors with New DNA-Binding Specificities (1988)

Oligonucleotide-directed mutagenesis of the codons for glutamine-68 (Gln68), lysine-72 (Lys72), isoleucine-79 (Ile79), alanine-80 (Ala80), and threonine-81 (Thr81) of the Escherichia coli trpR (tryptophan aporepressor) gene was used to make mutant repressors with each of 36 different amino acid changes. Mutant repressors were tested for binding to each member of a set of 28 different operators closely related to the consensus trp operator. Of the 36 mutant repressors, 11 bind a subset of the 28 operators; 5 of these have new binding specificities. These new specificities indicate that the hydroxyl group of Thr81 makes a specific contact with one of the four critical base pairs in a trp operator half-site, and the methyl group of Thr81 determines specificity at a second, critical base pair. The Trp repressor does not use the first two amino acids of its "recognition alpha-helix," Ile79 and Ala80, to make sequence-specific DNA contacts, and interacts with its operator in vivo in a way fundamentally different from the way that phage lambda repressor, lambda Cro protein, and coliphage 434 repressor contact their respective binding sites.
Common path optical coherence tomography with fibre bundle probe (2009)

A simple common path optical coherence tomography using a fibre optic bundle as a probe is demonstrated experimentally. The mechanical lateral scans are accomplished outside the specimen, proximal entrance of the fibre bundle, which eliminated the need for moving parts in the distal end of the probe. This feature allows the probe to be made submillimetre in size and easily integrated into surgical tools for intraoperative imaging. The axial and lateral resolutions of the system, and preliminary images of phantom samples, are reported.
Synthesis of self-immolative glucuronide-based prodrugs of a phenol mustard. (1998)

The design and synthesis of the mustard pro-prodrugs which can be used in ADEPT is reported. Prodrugs 1 and 2 include a glucuronide group which is connected to the drug via an aromatic and/or aliphatic bis-carbamate spacer. The design of these new prodrugs takes advantage of a spontaneous 1,6-elimination and/or an intramolecular cyclization reaction after enzymatic cleavage. Thus, enzymatic-catalyzed hydrolysis of the glucuronyl moiety of 1 by Escherichia coli beta-glucuronidase results in the liberation of the parent mustard drug 20 with formation of CO2, 2-nitro-4-hydroxymethylphenol 19 and dimethylimidazolidinone 21. Surprisingly, prodrug 2 was not cleaved under the same conditions. According to in vitro experiments, prodrugs 1 and 2 were approximately 50- and 80-fold less cytotoxic than the parent drug and, when treated with beta-glucuronidase, the level of cytotoxic activity of 1 became comparable to that of the drug. Stability of 1 in phosphate buffer was satisfactory. These results demonstrate that 1 is a prodrug that can be specifically activated to release the cytotoxic agent.
Cell Death Caused by Selenium Deficiency and Protective Effect of Antioxidants (2003)

Selenium is an essential trace element and it is well known that selenium is necessary for cell culture. However, the mechanism underlying the role of selenium in cellular proliferation and survival is still unknown. The present study using Jurkat cells showed that selenium deficiency in a serum-free medium decreased the selenium-dependent enzyme activity (glutathione peroxidases and thioredoxin reductase) within cells and cell viability. To understand the mechanism of this effect of selenium, we examined the effect of other antioxidants, which act by different mechanisms. Vitamin E, a lipid-soluble radical-scavenging antioxidant, completely blocked selenium deficiency-induced cell death, although alpha-tocopherol (biologically the most active form of vitamin E) could not preserve selenium-dependent enzyme activity. Other antioxidants, such as different isoforms and derivatives of vitamin E, BO-653 and deferoxamine mesylate, also exerted an inhibitory effect. However, the water-soluble antioxidants, such as ascorbic acid, N-acetyl cysteine, and glutathione, displayed no such effect. Dichlorodihydrofluorescein (DCF) assay revealed that cellular reactive oxygen species (ROS) increased before cell death, and sodium selenite and alpha-tocopherol inhibited ROS increase in a dose-dependent manner. The generation of lipid hydroperoxides was observed by fluorescence probe diphenyl-1-pyrenylphosphine (DPPP) and HPLC chemiluminescence only in selenium-deficient cells. These results suggest that the ROS, especially lipid hydroperoxides, are involved in the cell death caused by selenium deficiency and that selenium and vitamin E cooperate in the defense against oxidative stress upon cells by detoxifying and inhibiting the formation of lipid hydroperoxides.
Synthesis, enzymatic stability and base-pairing properties of oligothymidylates containing thymidine dimers with different N-substituted guanidine linkages (1993)

Reaction of 5′-amino-5′-deoxythymidine 1 with different S,S-dimethyl-N-substituted dithiocarbonimidates 2a–j afforded the N-substituted isothioureas 3a–j which, on further reaction with 3′-amino-3′-deoxythymidine 4 in the presence of AgNO3, led to thymidine dimers 5a–j with different N-substituted guanidine linkages. The dimer with a thiourea linkage (compound 9) was also prepared. Dimers 5a–h were incorporated at different positions in oligothymidylates by using phosphoramidite chemistry. Attempts to incorporate compounds 5i,j and 9 led to complex mixtures. 3′-Protected oligonucleotides showed somewhat higher stability to snake venom phosphodiesterase. Melting experiments revealed that the N-methylsulfonyl-substituted guanidine linkage best mimics the natural phosphodiester bridge. The fluorescence properties of oligonucleotides with dimer 5f were studied in view of its potential use as a non-radioactive label for DNA.
Catalytic Hydrogenation of Esters. Development of an Efficient Catalyst and Processes for Synthesising (R)-1,2-Propanediol and 2-(l-Menthoxy)ethanol (2011)

A ruthenium catalyst for the reduction of esters by hydrogenation has been developed. Processes for the hydrogenation of esters have also been developed for (R)-1,2-propanediol and 2-(l-menthoxy)ethanol. The catalyst shows good catalytic activity for the hydrogenation of esters in methanol. Methyl lactate was reduced at 30 °C and gave turnover numbers (TON) up to 4000. The optical purity of the (R)-1,2-propanediol made by the hydrogenation of methyl (R)-lactate was higher than that via the asymmetric hydrogenation of hydroxyacetone. A hydrogenation process to replace the lithium aluminum hydride (LAH) reduction used in the production of 2-(l-menthoxy)ethanol was developed.
Azacytidine Inhibits RNA Methylation at DNMT2 Target Sites in Human Cancer Cell Lines (2009)

The cytosine analogues azacytidine and decitabine are currently being developed as drugs for epigenetic cancer therapy. Although various studies have shown that both drugs are effective in inhibiting DNA methylation, it has also become clear that their mode of action is not limited to DNA demethylation. Because azacytidine is a ribonucleoside, the primary target of this drug may be cellular RNA rather than DNA. We have now analyzed the possibility that azacytidine inhibits the RNA methyltransferase DNMT2. We found that DNMT2 is variably expressed in human cancer cell lines. RNA bisulfite sequencing showed that azacytidine, but not decitabine, inhibits cytosine 38 methylation of tRNA(Asp), a major substrate of DNMT2. Azacytidine caused a substantially stronger effect than decitabine on the metabolic rate of all the cancer cell lines tested, consistent with an effect of this drug on RNA metabolism. Of note, drug-induced loss of RNA methylation seemed specific for DNMT2 target sites because we did not observe any significant demethylation at sites known to be methylated by other RNA methyltransferases. Our results uncover a novel and quantifiable drug activity of azacytidine and raise the possibility that tRNA hypomethylation might contribute to patient responses.
A Wavelet Transform Based Method to Determine Depth of Anesthesia to Prevent Awareness during General Anesthesia (2014)

Awareness during general anesthesia for its serious psychological effects on patients and some juristically problems for anesthetists has been an important challenge during past decades. Monitoring depth of anesthesia is a fundamental solution to this problem. The induction of anesthesia alters frequency and mean of amplitudes of the electroencephalogram (EEG), and its phase couplings. We analyzed EEG changes for phase coupling between delta and alpha subbands using a new algorithm for depth of general anesthesia measurement based on complex wavelet transform (CWT) in patients anesthetized by Propofol. Entropy and histogram of modulated signals were calculated by taking bispectral index (BIS) values as reference. Entropies corresponding to different BIS intervals using Mann-Whitney U test showed that they had different continuous distributions. The results demonstrated that there is a phase coupling between 3 and 4 Hz in delta and 8-9 Hz in alpha subbands and these changes are shown better at the channel T 7 of EEG. Moreover, when BIS values increase, the entropy value of modulated signal also increases and vice versa. In addition, measuring phase coupling between delta and alpha subbands of EEG signals through continuous CWT analysis reveals the depth of anesthesia level. As a result, awareness during anesthesia can be prevented.
Code scheduling and register allocation in large basic blocks (2014)

We discuss the issues about the interdependency between code scheduling and register allocation. We present two methods as solutions: (1) an integrated code scheduling technique; and (2) a DAG-driven register allocator. The integrated code scheduling method combines two scheduling techniques—one to reduce pipeline delays and the other to minimize register usage—into a single phase. By keeping track of the number of available registers, the scheduler can choose the appropriate scheduling technique to schedule a better code sequence. The DAG-driven register allocator uses a dependency graph to assist in assigning registers; it introduces much less extra dependency than does an ordinary register allocator. For large basic blocks, both approaches were shown to generate more efficient code sequences than conventional techniques in the simulations.
Nitrogen analogs of crown ethers (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNitrogen analogs of crown ethersJack E. Richman and Thomas J. AtkinsCite this: J. Am. Chem. Soc. 1974, 96, 7, 2268–2270Publication Date (Print):April 1, 1974Publication History Published online1 May 2002Published inissue 1 April 1974https://pubs.acs.org/doi/10.1021/ja00814a056https://doi.org/10.1021/ja00814a056research-articleACS PublicationsRequest reuse permissionsArticle Views4319Altmetric-Citations537LEARN 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
Effect of codeine and loperamide on upper intestinal transit and absorption in normal subjects and patients with postvagotomy diarrhoea. (1988)

Patients with chronic severe diarrhoea after truncal vagotomy and pyloroplasty are often difficult to treat using conventional antidiarrhoeal drugs and remain severely disabled. We examined the effect of two drugs, codeine phosphate and loperamide, on upper intestinal transit and carbohydrate absorption, measured non-invasively by serial exhaled breath hydrogen monitoring, in patients with postvagotomy diarrhoea who had previously failed to gain relief from drug therapy. Orocaecal transit was consistently faster in these patients than a group of controls and was associated with malabsorption of glucose. Codeine phosphate 60 mg significantly delayed transit in patients and controls and was associated with a reduction in glucose malabsorption and improvement in symptoms. Loperamide also delayed transit and improved symptoms, but the doses required for this effect (12-24 mg) were higher than usually considered necessary in secretory diarrhoea. These studies indicate that rapid intestinal nutrient transit and associated malabsorption is a factor in the development of diarrhoea postvagotomy and that symptomatic relief can be achieved in most patients by more rational use of existing drugs.
Targeted Expression of Human MYCN Selectively Causes Pancreatic Neuroendocrine Tumors in Transgenic Zebrafish (2004)

The zebrafish model organism has been used extensively for studies of genetic pathways in development, indicating its potential applicability to cancer. Here we show that targeted expression of MYCN in cells of the pancreatic islet induces neuroendocrine carcinoma. Four transgenic fish developed abdominal tumors between 4 and 6 months of age, and histologic analysis revealed lobulated arrangements of neoplastic cells with expression of the MYCN transgene. The tumors also expressed insulin mRNA, and pancreatic exocrine cells and ducts were identified within the neoplasms, indicating a pancreatic origin for the tumor. Transmission electron microscopy revealed cytoplasmic, endocrine-dense core granules, analogous to those found in human neuroendocrine tumors. Our studies establish a zebrafish transgenic model of pancreatic neuroendocrine carcinoma, setting the stage to evaluate molecular pathways downstream of MYCN in this vertebrate forward genetic model system.