gebhart/patrepeval huggingface dataset:
Oligonudeotide-targeted degradation of U1 and U2 snRNAs reveals differential interactions of simian virus 40 pre-mRNAs with snRNPs (1989)

We have investigated the roles of U1 and U2 snRNP particles in SV40 pre-mRNA splicing by oligonucleotide-targeted degradation of U1 or U2 snRNAs in Xenopus laevis oocytes. Microinjection of oligonucleotides complementary to regions of U1 or U2 RNAs either in the presence or absence of SV40 DNA resulted in specific cleavage of the corresponding snRNA. Unexpectedly, degradation of U1 or U2 snRNA was far more extensive when the oligonucleotide was injected without, or prior to, introduction of viral DNA. In either co-injected or pre-injected oocytes, these oligonucleotides caused a dramatic reduction in the accumulation of spliced SV40 mRNA expressed from the viral late region, and a commensurate increase in unspliced late RNA. When pre-injected, two different U2 specific oligonucleotides also inhibited the formation of both large and small tumor antigen spliced early mRNAs. However, even when, by pre-injection of a U1 5' end-specific oligonucleotide, greater than 95% degradation of the U1 snRNA 5' ends occurred in oocytes, no reduction in early pre-mRNA splicing was observed. In contrast, the same U1 5' end oligonucleotide, when added to HeLa splicing extracts, substantially inhibited the splicing of SV40 early pre-mRNA, indicating that U1 mRNP is not totally dispensable for early splicing. These findings confirm and extend our earlier observations which suggested that different pre-mRNAs vary in their requirements for snRNPs.
Welcome to the International Polar Year (2007)

On 1 March 2007 the Australian Antarctic Division (AAD) joined others around the world to celebrate the start of the International Polar Year (IPY). The Australian Antarctic Division is leading four IPY projects, co-leading three, and participating in more than 40 other international projects. This issue of the Australian Antarctic Magazine features some of these projects, including the first marine research voyage for the AAD-coordinated Census of Antarctic Marine Life.
Requirement of Mip-1α for an Inflammatory Response to Viral Infection (1995)

Macrophage inflammatory protein-1 alpha (MIP-1 alpha) is a chemokine that has pro-inflammatory and stem cell inhibitory activities in vitro. Its biologic role in vivo was examined in mice in which the gene encoding MIP-1 alpha had been disrupted. Homozygous MIP-1 alpha mutant (-/-) mice were resistant to Coxsackievirus-induced myocarditis seen in infected wild-type (+/+) mice. Influenza virus-infected -/- mice had reduced pneumonitis and delayed clearance of the virus compared with infected +/+ mice. The -/- mice had no overt hematopoietic abnormalities. These results demonstrate that MIP-1 alpha is an important mediator of virus-induced inflammation in vivo.
Collection of small subunit (16S- and 16S-like) ribosomal RNA structures (1993)

Journal Article Collection of small subunit (16S- and 16S-like) ribosomal RNA structures Get access Robin Ray Gutell Robin Ray Gutell MCB Biology, Campus Box 347, University of ColoradoBoulder, CO 80309-0347, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 21, Issue 13, 1 July 1993, Pages 3051–3054, https://doi.org/10.1093/nar/21.13.3051 Published: 01 July 1993
Understanding Activities and Intentions for Human-Robot Interaction (2010)

As robots move from the factory and into the daily lives of men, women, and children around the world, it is becoming increasingly clear that the skills they will require are vastly different from the majority of skills with which they were programmed in the 20 th century. In fact, it would appear that many of these skills will center on the challenge of interacting with humans, rather than with machine parts or other robots. To this end, modern-day roboticists are actively studying the problem of human-robot interaction -how best to create robots that can interact with humans, usually in a social setting. Among the many problems of human robot interaction, one of the most interesting is the problem of intent recognition: the problem of predicting the intentions of a person, usually just by observing that person. If we understand intentions to be non-observable goal-directed mental activities, then we may (quite understandably) view the intent recognition problem for robots as one of reading peoples' minds. As grandiose as this claim may sound, we believe that this understanding of intent recognition is quite reasonable; it is this interpretation that we seek to justify in the following pages. Every day, humans observe one another and on the basis of their observations "read people's minds," correctly inferring the intentions of others. Moreover, this ability is regarded not as remarkable, but as entirely ordinary and effortless. If we hope to build robots that are similarly capable of successfully interacting with people in a social setting, we must endow our robots with an ability to understand humans' intentions. In this paper, we review the intent recognition problem, and provide as an example a system we have been developing to recognize human intentions. Our approach is ultimately based on psychological and neuroscientific evidence for a theory of mind The mechanism relies on taking the perspective of others Although this process is innate to humans, it does not take place in a vacuum. Intuitively, it would seem that our understanding of others' intentions depend heavily on the contexts in which we find ourselves and those we observe. This intuition is supported
Mixed Allogeneic Chimerism And Renal Allograft Tolerance In Cynomolgus Monkeys (1995)

We have developed a nonmyeloablative preparative regimen that can produce mixed chimerism and renal allograft tolerance between MHC-disparate nonhuman primates. The basic regimen includes ATG, nonmyeloablative total-body irradiation (TBI, 300 rads), thymic irradiation (TI, 700 rads), and donor bone marrow infusion. Kidney allografts from MHC-mismatched donors were transplanted with various manipulations of the preparative regimen. Monkeys treated with the basic regimen alone (n = 2) rejected allografts by day 15. With the addition of cyclosporine (CsA) for one month (n = 3), one monkey developed multilineage mixed chimerism and renal allograft tolerance thereafter (> 430 days). To reduce the toxicity of the preparative regimen, TBI was fractionated to 150 rads on two successive days in subsequent studies. All monkeys receiving this modified regimen (n = 4) developed multilineage chimerism with fewer side effects and accepted renal allografts long-term with no further immunosuppression (196 days, 198 days, > 150 days, and > 40 days). In long-term survivors, donor-specific nonreactivity was confirmed by MLR and skin transplantation. Three monkeys treated with the basic regimen plus CsA but with only 150 rads of TBI (n = 1) or no TBI (n = 2) did not develop multilineage chimerism and grafts were rejected (day 40-50) soon after the CsA discontinuation. Monkeys treated with the same regimen, but without DBM (n = 2), rejected kidney allografts by day 52. Therefore, at least transient engraftment of DBM appears to be essential for induction of donor specific tolerance in this monkey model.
Dazl Promotes Germ Cell Differentiation from Embryonic Stem Cells (2009)

It has been demonstrated that through the formation of embryoid bodies (EBs) germ cells can be derived from embryonic stem (ES) cells. Here, we describe a transgene expression approach to derive germ cells directly from ES cells in vitro without EB formation. Through the ectopic expression of Deleted in Azoospermia-Like (Dazl), a germ cell-specific RNA-binding protein, both motile tailed-sperm and oocytes were induced from mouse ES (mES) cells in culture. Furthermore, transient overexpression of Dazl led to suppression of Nanog but induced germ cell nuclear antigen in mES cells. Dazl knockdown resulted in reduction in the expression of germ cell markers including Stella, MVH and Prdm1. Our study indicates that Dazl is a master gene controlling germ cell differentiation and that ectopic expression of Dazl promotes the dynamic differentiation of mouse ES cells into gametes in vitro.
Magnetic-field-induced DNA strand breaks in brain cells of the rat. (2004)

In previous research, we found that rats acutely (2 hr) exposed to a 60-Hz sinusoidal magnetic field at intensities of 0.1-0.5 millitesla (mT) showed increases in DNA single- and double-strand breaks in their brain cells. Further research showed that these effects could be blocked by pretreating the rats with the free radical scavengers melatonin and N-tert-butyl-alpha-phenylnitrone, suggesting the involvement of free radicals. In the present study, effects of magnetic field exposure on brain cell DNA in the rat were further investigated. Exposure to a 60-Hz magnetic field at 0.01 mT for 24 hr caused a significant increase in DNA single- and double-strand breaks. Prolonging the exposure to 48 hr caused a larger increase. This indicates that the effect is cumulative. In addition, treatment with Trolox (a vitamin E analog) or 7-nitroindazole (a nitric oxide synthase inhibitor) blocked magnetic-field-induced DNA strand breaks. These data further support a role of free radicals on the effects of magnetic fields. Treatment with the iron chelator deferiprone also blocked the effects of magnetic fields on brain cell DNA, suggesting the involvement of iron. Acute magnetic field exposure increased apoptosis and necrosis of brain cells in the rat. We hypothesize that exposure to a 60-Hz magnetic field initiates an iron-mediated process (e.g., the Fenton reaction) that increases free radical formation in brain cells, leading to DNA strand breaks and cell death. This hypothesis could have an important implication for the possible health effects associated with exposure to extremely low-frequency magnetic fields in the public and occupational environments.
Conjugation of Transferrin to Azide‐Modified CdSe/ZnS Core–Shell Quantum Dots using Cyclooctyne Click Chemistry (2012)

Twinkle twinkle quantum dot: Conjugation of biomolecules to azide-modified quantum dots (QDs) through a bifunctional linker, using strain-promoted azide-alkyne cycloaddition with the QD and a squaramide linkage to the biomolecule (see scheme). Transferrin-conjugated QDs were internalized by transferrin-receptor expressing HeLa cells.
Method Development, Validation and Forced Degradation Studies For the Determination of Moxifloxacin in Bulk and Pharmaceutical Dosage Forms Using UV Spectroscopy (2021)

The objective of this work was to develop and validate spectrophotometric method for moxifloxacin for analysis. A very simple, unique, novel, reliable and easy method of spectrophotometric estimation in UV-region has been developed for the assay of moxifloxacin tablet formulation and also to perform forced degradation studies.&#x0D; Method: water was used as diluents to perform all the validation parameters and stress studies.&#x0D; Results: ICH guidelines were adopted during the method development and the method was validated statistically by calculating RSD and %RSD. The drug obeys Beer’s lamberts law at 1-10 mcg/ml concentration. Accuracy, Linearity, precision and robustness LOD at 3.3 ppb levels, LOQ at 11.2 ppb levels was performed. % of drug Degradations at different parameters were determined.&#x0D; Conclusion: - This method can be used for the routine laboratory analysis and can extend the studies to chromatographic techniques.&#x0D;
A Study on the Standard Cell and Its Enclosure (1992)

Acid type saturated Weston cells that can be used as the standard of electromotive force unit were constructed and their characteristics in a specially designed enclosure were evaluated. Cadmium sulfate was purified by recrystallization under vaccum. Mercurous sulfate with dispersed mercury and the exact composition of cadmium amalgam were obtained by means of electrolysis. The enclosure was constructed using a commercial circulator. Temperature of the enclosure was only drifted in the range of 5 mK in the case of extreme change of room temperature. The electromotive force of standard cells was measured over the temperature range of 5∼. The standard deviation of the electromotive forces was about 1 ppm.
Taverna: a tool for building and running workflows of services (2006)

Taverna is an application that eases the use and integration of the growing number of molecular biology tools and databases available on the web, especially web services. It allows bioinformaticians to construct workflows or pipelines of services to perform a range of different analyses, such as sequence analysis and genome annotation. These high-level workflows can integrate many different resources into a single analysis. Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL) from http://taverna.sourceforge.net/.
Frequent hypermethylation of MST1 and MST2 in soft tissue sarcoma (2007)

The RASSF1A tumor suppressor is involved in regulation of apoptosis and cell cycle progression. RASSF1A is localized to microtubules and binds the apoptotic kinases MST1 and MST2. It has been shown that this interaction is mediated by the Sav-RASSF-Hpo domain, which is an interaction domain characterized for the Drosophila proteins Sav (human WW45), Hpo (human MST1 and MST2) and Warts/LATS (large tumor suppressor). Previously, we have reported that RASSF1A hypermethylation occurs frequently in soft tissue sarcoma and is associated with an unfavorable prognosis for cancer patients. In our study, we performed methylation analysis of the CpG island promoter of MST1, MST2, WW45, LATS1 and LATS2 in soft tissue sarcomas by methylation-specific PCR. No or a very low methylation frequency was detected for WW45, LATS1 and LATS2 (<7%). In 19 out of 52 (37%) sarcomas, a methylated promoter of MST1 was detected and 12 out of 60 (20%) samples showed methylation of the MST2 promoter. Methylation status of MST1 was confirmed by bisulfite sequencing. In tumors harboring a methylated promoter of MST1, a reduction of MST1 expression was observed by RT-PCR. In leiomyosarcomas, MST1 and MST2 or RASSF1A methylation were mutually exclusive (P = 0.007 and P = 0.025, respectively). Surprisingly, a significantly increased risk for tumor-related death was found for patients with an unmethylated MST1 promoter (P = 0.036). In summary, our results suggest that alteration of the Sav-RASSF1-Hpo tumor suppressor pathway may occur through hypermethylation of the CpG island promoter of MST1, MST2 and/or RASSF1A in human sarcomas.
Energetic Determinants of Internal Motif Recognition by PDZ Domains (2001)

PDZ domains are protein-protein interaction modules that organize intracellular signaling complexes. Most PDZ domains recognize specific peptide motifs followed by a required COOH-terminus. However, several PDZ domains have been found which recognize specific internal peptide motifs. The best characterized example is the syntrophin PDZ domain which, in addition to binding peptide ligands with the consensus sequence -E-S/T-X-V-COOH, also binds the neuronal nitric oxide synthase (nNOS) PDZ domain in a manner that does not depend on its precise COOH-terminal sequence. In the structure of the syntrophin-nNOS PDZ heterodimer complex, the two PDZ domains interact in a head-to-tail fashion, with an internal sequence from the nNOS PDZ domain binding precisely at the peptide binding groove of the syntrophin PDZ domain. To understand the energetic basis of this alternative mode of PDZ recognition, we have undertaken an extensive mutagenic and biophysical analysis of the nNOS PDZ domain and its interaction with the syntrophin PDZ domain. Our data indicate that the presentation of the nNOS internal motif within the context of a rigid beta-hairpin conformation is absolutely essential to binding; amino acids crucial to the structural integrity of the hairpin are as important or more important than residues that make direct contacts. The results reveal the general rules of PDZ recognition of diverse ligand types.
In vivo and in vitro transcription of the Clostridium pasteurianum ferredoxin gene. Evidence for "extended" promoter elements in gram-positive organisms. (1986)

Analysis of Clostridium pasteurianum genomic DNA indicates that the ferredoxin (Fd) gene is present in a single copy. The cloned Fd gene previously described (Graves, M.C., Mullenbach, G. T., and Rabinowitz, J. C. (1985) Proc. Natl. Acad. Sci. U. S. A. 82, 1653-1657) was used to map in vivo and in vitro synthesized Fd transcripts. The in vivo mRNA was sized in two ways: by Northern hybridization analysis, and more directly from the known DNA sequence after the 5'- and 3'-termini were identified. The 5'-end was determined by primer extension-dideoxy sequencing and the 3'-end by S1 nuclease mapping. The monocistronic Fd mRNA contains about 255 nucleotides and, thus, is one of the shortest bacterial mRNAs yet described. We also examined the Fd transcripts produced by Escherichia coli transformed with the plasmid containing the Fd gene. E. coli RNA polymerase most likely recognizes the same promoter (P1) as the clostridial polymerase, and furthermore, efficiently uses an additional promoter (P2) that is poorly recognized by the normal host enzyme. For comparison, in vitro transcripts were generated by E. coli and Bacillus subtilis RNA polymerases. In vitro, only promoter P1 is used by either E. coli or B. subtilis RNA polymerase. The 3'-end of each of the four types of transcripts occurs essentially at the same location and maps to within a large dyad symmetry element. Comparison of the Fd promoter with other Gram-positive promoters reveals that some sequences outside of the traditional Pribnow and -35 regions are conserved. This analysis indicates that an "extended" promoter recognition site may be required in these organisms.
Identification of potential protective antigens of Ostertagia ostertagi with local antibody probes (2002)

The identification of protective helminth antigens remains the most important challenge in the development of parasitic vaccines. To identify protective antigens of Ostertagia ostertagi, an important abomasal parasite of cattle, parasite-specific local antibodies from the abomasal mucus and from the draining lymph nodes were collected from calves immunized with multiple infections and from 'primary infected' animals. With these probes, Western blots of extracts and excretion/ secretion (E/S) material from L3, L4 and adult life-stages as well as cDNA expression libraries were screened to identify antigens that were exclusively recognized by antibodies from 'immunized' calves. In the adult stage, a protein of 32 kDa was specifically detected on Western blot by mucus antibodies from 'immunized' animals. In the L3 and L4 larval stages, proteins situated in the regions of 28-29 kDa were recognized by mucus antibodies and a 59 kDa antigen was specifically recognized by lymph node antibodies from 'immunized' animals. Screening E/S material revealed no specific difference in recognition pattern between 'immunized' and 'primary infected' animals. Screening of the cDNA libraries revealed 26 relevant clones, coding for 15 proteins, among these several with potential protective capacity, immunodominant properties or functional and physiological importance e.g. metalloproteases, an aspartyl protease inhibitor and collagen.
Reversal of regiochemistry of Wacker-type reactions oriented by heteroatoms (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReversal of regiochemistry of Wacker-type reactions oriented by heteroatomsJinyu Lai, Xiaoxin Shi, and Lixin DaiCite this: J. Org. Chem. 1992, 57, 12, 3485–3487Publication Date (Print):June 1, 1992Publication History Published online1 May 2002Published inissue 1 June 1992https://pubs.acs.org/doi/10.1021/jo00038a045https://doi.org/10.1021/jo00038a045research-articleACS PublicationsRequest reuse permissionsArticle Views517Altmetric-Citations42LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Multistep Carcinogenesis: a 1992 Perspective (1992)

Cancer is the leading cause of death in Japan. Recent changes in cancer incidence patterns may reflect the trend toward a more Western diet and life-style. Among the dietary factors that contribute to carcinogenesis are the heterocyclic amines, a group of mutagenic compounds present in cooked meat and fish. Carcinogenesis is a multistep process in which cells accumulate multiple genetic alterations as they progress to a more malignant phenotype. Recognition of the growing number of interacting factors that contribute to carcinogenesis may force reconsideration of current methods of risk assessment.
An Adaptive Issue Queue for Reduced Power at High Performance (2000)

Increasing power dissipation has become a major constraint for future performance gains in the design of microprocessors. In this paper, we present the circuit design of an issue queue for a superscalar processor that leverages transmission gate insertion to provide dynamic low-cost configurability of size and speed. A novel circuit structure dynamically gathers statistics of issue queue activity over intervals of instruction execution. These statistics are then used to change the size of an issue queue organization onthe-fly to improve issue queue energy and performance. When applied to a fixed, full-size issue queue structure, the result is up to a 70 % reduction in energy dissipation. The complexity of the additional circuitry to achieve this result is almost negligible. Furthermore, self-timed techniques embedded in the adaptive scheme can provide a 56 % decrease in cycle time of the issue queue when we change the adaptive issue queue size from 32 entries (largest possible) to 8 entries (smallest possible in our design). 1
Purification of DNA-binding transcription factors by their selective adsorption on the affinity latex particles (1989)

A simple method with the use of affinity latex particles has been developed for the fast and efficient purification of sequence-specific DNA-binding proteins on the basis of their ability to selectively bind to their target sequences. Complementary oligodeoxynucleotides that contained a recognition site for a sequence-specific DNA-binding protein were chemically synthesized, annealed and ligated to give oligomers. The oligomers were coupled to latex particles, composed of polyglycidyl methacrylate, using cyanogen bromide to yield affinity latex particles. The concentration of covalently bound DNA on the affinity latex particles was 6 times as much DNA per ml as that in the Sepharose resin conventionally used. By sequential batch-wise procedures with the affinity particles, one of the sequence-specific DNA binding transcription factors, ATF or E4TF3, was quickly and efficiently purified to homogeneity from either a protein fraction in which the factor was enriched or a crude cell extract.