gebhart/patrepeval huggingface dataset:
Transformation of Plants and Soil Microorganisms (1995)

Over the past fifty years plant breeders have achieved impressive improvements in yield, quality and disease resistance. These gains suggest that many more modifications might be introduced if appropriate genes can be identified. Current DNA techniques allow the construction of transgenic plants and this important new book reviews the current state of knowledge. A team of leading researchers provide in-depth reviews at the cutting edge of technology for laboratory techniques for the transformation of important soil microorganisms and recalcitrant plants of economic value. The book is divided into three sections: soil microorganisms; cereal crops; and industrially important plants. The most effective methods used to date are compared, and their merits and limitations discussed. Some chapters emphasise case studies and applications. In cases where obstacles remain to be overcome, an overview of progress to date is given. The book will serve as a general guide and reference tool for those working on transformation in microbiology and plant science.
Imaging of Endogenous Messenger RNA Splice Variants in Living Cells Reveals Nuclear Retention of Transcripts Inaccessible to Nonsense-Mediated Decay in Arabidopsis (2014)

Alternative splicing (AS) is an important regulatory process that leads to the creation of multiple RNA transcripts from a single gene. Alternative transcripts often carry premature termination codons (PTCs), which trigger nonsense-mediated decay (NMD), a cytoplasmic RNA degradation pathway. However, intron retention, the most prevalent AS event in plants, often leads to PTC-carrying splice variants that are insensitive to NMD; this led us to question the fate of these special RNA variants. Here, we present an innovative approach to monitor and characterize endogenous mRNA splice variants within living plant cells. This method combines standard confocal laser scanning microscopy for molecular beacon detection with a robust statistical pipeline for sample comparison. We demonstrate this technique on the localization of NMD-insensitive splice variants of two Arabidopsis thaliana genes, RS2Z33 and the SEF factor. The experiments reveal that these intron-containing splice variants remain within the nucleus, which allows them to escape the NMD machinery. Moreover, fluorescence recovery after photobleaching experiments in the nucleoplasm show a decreased mobility of intron-retained mRNAs compared with fully spliced RNAs. In addition, differences in mobility were observed for an mRNA dependent on its origin from an intron-free or an intron-containing gene.
Organic Optical Limiter with a Strong Nonlinear Absorptive Response (1996)

Molecules with weak ground-state absorption that form strongly absorbing excited states can be used in optical limiters, which can protect sensors or human eyes from optical damage. Phthalocyanine complexes bearing heavy atoms or paramagnetic groups or in solvents containing heavy atoms show optical limiting enhanced by excited triplet-state absorption. A nonhomogeneous distribution of indium tetra( tert -butyl)phthalocyanine chloride along the beam path substantially enhances the excited-state absorption, yielding an optical limiter with a linear transmittance of 0.70 that can attenuate 8-nanosecond, 532-nanometer laser pulses by factors of up to 540.
A common mutation in the methylenetetrahydrofolate reductase gene is associated with an accumulation of formylated tetrahydrofolates in red blood cells (1998)

A common mutation (C677T) in the gene encoding for methylenetetrahydrofolate reductase (MTHFR) (5-methyltetrahydrofolate:(acceptor) oxidoreductase, EC 1.7.99.5), a key regulatory enzyme in one-carbon metabolism, results in a thermolabile variant of the MTHFR enzyme with reduced activity in vitro. In the present study we used a chromatographic method for folate analysis to test the hypothesis that this mutation would be associated with altered distribution of red blood cell (RBC) folates. An alteration was found as manifested by the presence of formylated tetrahydrofolate polyglutamates in addition to methylated derivatives in the RBCs from homozygous mutant individuals. 5-Methyltetrahydrofolate polyglutamates were the only folate form found in RBCs from individuals with the wild-type genotype. Existence of formylated folates in RBCs only from individuals with the thermolabile MTHFR is consistent with the hypothesis that there is in vivo impairment in the activity of the thermolabile variant of MTHFR and that this impairment results in an altered distribution of RBC folates.
Current status and new developments in the treatment of psoriasis and psoriatic arthritis with biological agents (2010)

Psoriasis is a chronic inflammatory disease affecting 1-3% of the general population. Among psoriatic patients, 5-40% are affected by psoriatic arthritis. Due to the chronic nature of the disease, patients suffer from substantial psychological and financial burdens, thus adding to a significantly impaired quality of life. Traditional systemic therapies for psoriasis, such as methotrexate, cyclosporin A, retinoids or PUVA therapy, have a potential for long-term toxicity and may not always provide sufficient improvement of the disease. The development of novel therapies targeting key steps in the pathogenesis of psoriasis and psoriatic arthritis now provide new and efficient treatment options. Biological therapies for the treatment of psoriasis and/or psoriatic arthritis are defined by their mode of action and can be classified into three categories: the T-cell modulating agents (alefacept and efalizumab), the inhibitors of tumour necrosis factor-alpha (TNFalpha blockers, e.g. adalimumab, certolizumab, etanercept, golimumab and infliximab) and the inhibitors of interleukin (IL) 12 and IL-23 (e.g. ustekinumab and briakinumab). This article provides a brief overview of the currently approved biological agents in the European Union and of some newer agents, such as briakinumab, certolizumab and golimumab.
Integrated Microfluidic Systems for DNA Analysis (2005)

This study reports the integration of an electrokinetically-driven micro-mixer with a on-chip temperature control system, and applies the integrated microfluidic chip to the DNA amplification process. Using the integrated chip, the cultured cells are initially broken down in a micro lysis reactor. Extracted DNA, primers and reagents are then driven electroosmotically into a mixing region where they are mixed by an electrokinetically-driven micro-mixer. The mixture is then cycled in a micro-PCR (polymerase chain reaction) chamber to perform DNA amplification. Experimental results show that the proposed device can automate the sample pretreatment operation for DNA amplification, thereby achieving significant time and effort savings. This novel integrated microfluidic device, which facilitates cell lysis, sample driving/mixing, and DNA amplification, could make a promising contribution to the continuing efforts aimed at miniaturizing bio-analysis systems.
Identification and characterization of differentially methylated CpG islands in pancreatic carcinoma. (2001)

To identify CpG islands differentially methylated in pancreatic adenocarcinoma, we used methylated CpG island amplification (MCA) coupled with representational difference analysis. Of 42 CpG islands identified by MCA/representational difference analysis, 7 CpG islands [methylated in carcinoma of the pancreas (MICP)] were differentially methylated in a panel of eight pancreatic cancer cell lines compared with normal pancreas. In a larger panel of 75 pancreatic adenocarcinomas, these 7 MICPs (ppENK, Cyclin G, ZBP, MICP25, 27, 36, and 38) were methylated in 93, 3, 9, 15, 48, 19, and 41% of cancers, respectively, by methylation-specific PCR but not in any of 15 normal pancreata. In pancreatic cancer cell lines, methylation of ppENK, a gene with known growth suppressive properties, was associated with transcriptional silencing that was reversible with 5-aza-2'-deoxycytidine treatment. Relationships between the methylation patterns of pancreatic adenocarcinomas and their clinicopathological features were also determined. Larger pancreatic cancers and those from older patients (P = 0.017) harbored more methylated loci than smaller tumors and those from younger patients (P = 0.017). ppENK, MICP25, and 27 were variably methylated in normal gastric, duodenal, and colonic mucosae. These data indicate that aberrant methylation of ppENK and its transcriptional repression is a common event in pancreatic carcinogenesis.
Conserved Methylation Patterns of Human Papillomavirus Type 16 DNA in Asymptomatic Infection and Cervical Neoplasia (2004)

DNA methylation contributes to the chromatin conformation that represses transcription of human papillomavirus type16 (HPV-16), which is prevalent in the etiology of cervical carcinoma. In an effort to clarify the role of this phenomenon in the regulation and carcinogenicity of HPV-16, 115 clinical samples were studied to establish the methylation patterns of the 19 CpG dinucleotides within the long control region and part of the L1 gene by bisulfite modification, PCR amplification, DNA cloning, and sequencing. We observed major heterogeneities between clones from different samples as well as between clones from individual samples. The methylation frequency of CpGs was measured at 14.5%. In addition, 0.21 and 0.23%, respectively, of the CpA and CpT sites, indicators of de novo methylation, were methylated. Methylation frequencies exceeded 30% in the CpGs overlapping with the L1 gene and were about 10% for most other positions. A CpG site located in the linker between two nucleosomes positioned over the enhancer and promoter of HPV-16 had minimal methylation. This region forms part of the HPV replication origin and is close to binding sites of master-regulators of transcription during epithelial differentiation. Methylation of most sites was highest in carcinomas, possibly due to tandem repetition and chromosomal integration of HPV-16 DNA. Methylation was lowest in dysplasia, likely reflecting the transcriptional activity in these infections. Our data document the efficient targeting of HPV genomes by the epithelial methylation machinery, possibly as a cellular defense mechanism, and suggest involvement of methylation in HPV oncogene expression and the early-late switch.
Plague as a Biological Weapon (2000)

The Working Group on Civilian Biodefense has developed consensus-based recommendations for measures to be taken by medical and public health professionals following the use of plague as a biological weapon against a civilian population.The working group included 25 representatives from major academic medical centers and research, government, military, public health, and emergency management institutions and agencies.MEDLINE databases were searched from January 1966 to June 1998 for the Medical Subject Headings plague, Yersinia pestis, biological weapon, biological terrorism, biological warfare, and biowarfare. Review of the bibliographies of the references identified by this search led to subsequent identification of relevant references published prior to 1966. In addition, participants identified other unpublished references and sources. Additional MEDLINE searches were conducted through January 2000.The first draft of the consensus statement was a synthesis of information obtained in the formal evidence-gathering process. The working group was convened to review drafts of the document in October 1998 and May 1999. The final statement incorporates all relevant evidence obtained by the literature search in conjunction with final consensus recommendations supported by all working group members.An aerosolized plague weapon could cause fever, cough, chest pain, and hemoptysis with signs consistent with severe pneumonia 1 to 6 days after exposure. Rapid evolution of disease would occur in the 2 to 4 days after symptom onset and would lead to septic shock with high mortality without early treatment. Early treatment and prophylaxis with streptomycin or gentamicin or the tetracycline or fluoroquinolone classes of antimicrobials would be advised.
Toll-like receptor agonists influence the magnitude and quality of memory T cell responses after prime-boost immunization in nonhuman primates (2006)

There is a remarkable heterogeneity in the functional profile (quality) of T cell responses. Importantly, the magnitude and/or quality of a response required for protection may be different depending on the infection. Here, we assessed the capacity of different Toll like receptor (TLR)-binding compounds to influence T helper cell (Th)1 and CD8+ T cell responses when used as adjuvants in nonhuman primates (NHP) with HIV Gag as a model antigen. NHP were immunized with HIV Gag protein emulsified in Montanide ISA 51, an oil-based adjuvant, with or without a TLR7/8 agonist, a TLR8 agonist, or the TLR9 ligand cytosine phosphate guanosine oligodeoxynucleotides (CpG ODN), and boosted 12 wk later with a replication-defective adenovirus-expressing HIV-Gag (rAD-Gag). Animals vaccinated with HIV Gag protein/Montanide and CpG ODN or the TLR7/8 agonist had higher frequencies of Th1 responses after primary immunization compared to all other vaccine groups. Although the rAD-Gag boost did not elevate the frequency of Th1 memory cytokine responses, there was a striking increase in HIV Gag-specific CD8+ T cell responses after the boost in all animals that had received a primary immunization with any of the TLR adjuvants. Importantly, the presence and type of TLR adjuvant used during primary immunization conferred stability and dramatically influenced the magnitude and quality of the Th1 and CD8+ T cell responses after the rAD-Gag boost. These data provide insights for designing prime-boost immunization regimens to optimize Th1 and CD8+ T cell responses.
Antisense phosphorodiamidate morpholino oligomer inhibits viability of Escherichia coli in pure culture and in mouse peritonitis (2005)

An 11 base antisense PMO targeted to acpP significantly inhibited viability of a strain of E. coli with a normal, intact outer membrane both in pure culture and in infected mice. Inhibition by PMOs was sequence-specific.
Processing of Proinsulin by Furin, PC2, and PC3 in (Co) Transfected COS (Monkey Kidney) Cells (1995)

The enzymology of proinsulin conversion was studied in COS cells by cotransfection of three species of proinsulin and each of three conversion endoproteases (furin, PC2, and PC3). In addition to the pairs of basic residues linking the B-chain to C-peptide (Arg31-Arg32) and C-peptide to the A-chain (Lys64-Arg65), which were present in all three proinsulins studied, human proinsulin presents a P4 basic residue (four residues NH2-terminal to the point of cleavage) only at the former junction (Lys29) and rat proinsulin II only at the latter (Arg62). Human proinsulin Arg62 (prepared by site-directed mutagenesis of human proinsulin) contains a P4 basic residue at both junctions. Transfected cells were incubated for four successive 2-h periods. The media were pooled, and proinsulin, conversion intermediates, and insulin were separated by reverse-phase high-performance liquid chromatography to monitor conversion activity. There was little conversion of any proinsulin in COS cells without cotransfection of an exogenous endoprotease. When furin or PC3 was cotransfected with any of the three proinsulins, there was extensive processing, with insulin as the major conversion product. PC2, by contrast, failed to cleave human proinsulin but was able to cleave both human proinsulin Arg62 and rat proinsulin II. Cleavage by PC2 of these proinsulins was predominantly at the C-peptide–A-chain junction, generating the conversion intermediate des-64,65-split proinsulin as the major product and only very small amounts of insulin itself.
CdSe/CdS/ZnS Double Shell Nanorods with High Photoluminescence Efficiency and Their Exploitation As Biolabeling Probes (2009)

We report the synthesis, the structural and optical characterization of CdSe/CdS/ZnS "double shell" nanorods and their exploitation in cell labeling experiments. To synthesize such nanorods, first "dot-in-a-rod" CdSe(dot)/CdS(rod) core/shell nanocrystals were prepared. Then a ZnS shell was grown epitaxially over these CdSe/CdS nanorods, which led to a fluorescence quantum yield of the final core-shell-shell nanorods that could be as high as 75%. The quantum efficiency was correlated with the aspect ratio of the nanorods and with the thickness of the ZnS shell around the starting CdSe/CdS rods, which varied from 1 to 4 monolayers (as supported by a combination of X-ray diffraction, elemental analysis with inductively coupled plasma atomic emission spectroscopy and high resolution transmission electron microscopy analysis). Pump-probe and time-resolved photoluminescence measurements confirmed the reduction of trapping at CdS surface due to the presence of the ZnS shell, which resulted in more efficient photoluminescence. These double shell nanorods have potential applications as fluorescent biological labels, as we found that they are brighter in cell imaging as compared to the starting CdSe/CdS nanorods and to the CdSe/ZnS quantum dots, therefore a lower amount of material is required to label the cells. Concerning their cytotoxicity, according to the MTT assay, the double shell nanorods were less toxic than the starting core/shell nanorods and than the CdSe/ZnS quantum dots, although the latter still exhibited a lower intracellular toxicity than both nanorod samples.
Porcine Small Intestine Submucosa As A Treatment for Enterocutaneous Fistulas (2002)

Schultz, David J MD; Brasel, Karen J MD, MPH; Spinelli, Kristine S MD; Rasmussen, Jason BS; Weigelt, John A MD Author Information
The Dynamics of Capillary Flow (1921)

Penetration of Liquids into Cylindrical Capillaries.---The rate of penetration into a small capillary of radius $r$ is shown to be: $\frac{\mathrm{dl}}{\mathrm{dt}}=\frac{P({r}^{2}+4\ensuremath{\epsilon}r)}{8\ensuremath{\eta}l}$, where $P$ is the driving pressure, $\ensuremath{\epsilon}$ the coefficient of slip and $\ensuremath{\eta}$ the viscosity. By integrating this expression, the distance penetrated by a liquid flowing under capillary pressure alone into a horizontal capillary or one with small internal surface is found to be the square root of ($\frac{\ensuremath{\gamma}\mathrm{rt}\ifmmode\cdot\else\textperiodcentered\fi{}cos\ensuremath{\theta}}{2\ensuremath{\eta}}$), where $\ensuremath{\gamma}$ is the surface tension and $\ensuremath{\theta}$ the angle of contact. The quantity ($\frac{\ensuremath{\gamma}cos\ensuremath{\theta}}{2\ensuremath{\eta}}$) is called the coefficient of penetrance or the penetrativity of the liquid.Penetration of Liquids into a Porous Body.---(1) Theory. If a porous body behaves as an assemblage of very small cylindrical capillaries, the volume which penetrates in a time $t$ would be proportional to the square root of ($\frac{\ensuremath{\gamma}t}{\ensuremath{\eta}}$). (2) Experiments with mercury, water and other liquids completely verify the theoretical deductions.Dynamic capillary method of measuring surface tension is described. It possesses certain advantages on the static method of capillary rise.
Generation and Characterization of Anti-Idiotypic Antibodies Recognizing the Interferon-α Receptor: Implications for Ligand–Receptor Interactions (1993)

Monoclonal antibodies LI-1 and LI-8 against interferon-alpha A (IFN-alpha A) block IFN-alpha A activity and binding to its receptor, but they recognize distinct epitopes. Surprisingly, anti-idiotypic antibodies to both LI-1 and LI-8 have properties consistent with recognition of the receptor: anti-LI-1 and anti-LI-8 antibodies inhibit the binding of IFN-alpha A to its receptor. However, anti-LI-1 is an antagonist of IFN-alpha A, while anti-LI-8 is an agonist. Thus, at least some part of the epitopes on IFN-alpha A recognized by LI-1 and LI-8 are directly involved in receptor binding. Because these epitopes are spatially distinct, the implication is that the receptor binding site on IFN-alpha A must be extensive, or there are minimally two regions of IFN-alpha A involved in receptor interactions.
Differential characterization of neural sources with the bimodal truncated SVD pseudo-inverse for EEG and MEG measurements (1998)

A method for obtaining a practical inverse for the distribution of neural activity in the human cerebral cortex is developed for electric, magnetic, and bimodal data to exploit their complementary aspects. Intracellular current is represented by current dipoles uniformly distributed on two parallel sulci joined by a gyrus. Linear systems of equations relate electric, magnetic, and bimodal data to unknown dipole moments. The corresponding lead-field matrices are characterized by singular value decomposition (SVD). The optimal reference electrode location for electric data is chosen on the basis of the decay behavior of the singular values. The singular values of these matrices show better decay behavior with increasing number of measurements, however, that property is useful depending on the noise in the measurements. The truncated SVD pseudo-inverse is used to control noise artifacts in the reconstructed images. Simulations for single-dipole sources at different depths reveal the relative contributions of electric and magnetic measures. For realistic noise levels the performance of both unimodal and bimodal systems do not improve with an increase in the number of measurements beyond approximately 100. Bimodal image reconstructions are generally superior to unimodal ones in finding the center of activity.
High performance and highly uniform gate-all-around silicon nanowire MOSFETs with wire size dependent scaling (2009)

We demonstrate undoped-body, gate-all-around (GAA) Si nanowire (NW) MOSFETs with excellent electrostatic scaling. These NW devices, with a TaN/Hf-based gate stack, have high drive-current performance with NFET/PFET I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DSAT</sub> = 825/950 ¿A/¿m (circumference-normalized) or 2592/2985 ¿A/¿m (diameter-normalized) at supply voltage V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DD</sub> = 1 V and off-current I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OFF</sub> = 15 nA/¿m. Superior NW uniformity is obtained through the use of a combined hydrogen annealing and oxidation process. Clear scaling of short-channel effects versus NW size is observed.
New evidence claimed for nuclear process in "cold fusion" (1991)

RETURN TO ISSUEPREVNewsNEXTNew evidence claimed for nuclear process in "cold fusion"RON DAGANIView Author Information C&EN WashingtonCite this: Chem. Eng. News 1991, 69, 13, 31–33Publication Date (Print):April 1, 1991Publication History Published online12 November 2010Published inissue 1 April 1991https://pubs.acs.org/doi/10.1021/cen-v069n013.p031https://doi.org/10.1021/cen-v069n013.p031newsACS PublicationsCopyright © 1991 American Chemical SocietyArticle Views10Altmetric-Citations1LEARN 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 options SUBJECTS:Electrical energy,Electrolytic cells,Helium,Nuclear reactions Get e-Alerts