gebhart/patrepeval huggingface dataset:
Sho1 and Msb2-Related Proteins Regulate Appressorium Development in the Smut Fungus Ustilago maydis (2010)

The dimorphic fungus Ustilago maydis switches from budding to hyphal growth on the plant surface. In response to hydrophobicity and hydroxy fatty acids, U. maydis develops infection structures called appressoria. Here, we report that, unlike in Saccharomyces cerevisiae and other fungi where Sho1 (synthetic high osmolarity sensitive) and Msb2 (multicopy suppressor of a budding defect) regulate stress responses and pseudohyphal growth, Sho1 and Msb2-like proteins play a key role during appressorium differentiation in U. maydis. Sho1 was identified through a two-hybrid screen as an interaction partner of the mitogen-activated protein (MAP) kinase Kpp6. Epistasis analysis revealed that sho1 and msb2 act upstream of the MAP kinases kpp2 and kpp6. Furthermore, Sho1 was shown to destabilize Kpp6 through direct interaction with the unique N-terminal domain in Kpp6, indicating a role of Sho1 in fine-tuning Kpp6 activity. Morphological differentiation in response to a hydrophobic surface was strongly attenuated in sho1 msb2 mutants, while hydroxy fatty acid-induced differentiation was unaffected. These data suggest that Sho1 and the transmembrane mucin Msb2 are involved in plant surface sensing in U. maydis.
Molecule counting made easy (2009)

ADVERTISEMENT RETURN TO ISSUEPREVResearch ProfileNEXTMolecule counting made easyErika GebelCite this: Anal. Chem. 2009, 81, 17, 7130–7131Publication Date (Web):August 11, 2009Publication History Published online11 August 2009Published inissue 1 September 2009https://pubs.acs.org/doi/10.1021/ac901633nhttps://doi.org/10.1021/ac901633nnewsACS PublicationsCopyright © 2009 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views1266Altmetric-Citations-LEARN 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 PDF (453 KB) Get e-AlertscloseSUBJECTS:Biopolymers,Immunology,Ligands,Molecules,Peptides and proteins Get e-Alerts
Longitudinally Profiling Neutralizing Antibody Response to SARS Coronavirus with Pseudotypes (2005)

The severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike protein (S) is a major target for neutralizing antibodies. Retroviral SARS-CoV S pseudotypes have been constructed and used to develop an in vitro microneutralization assay that is both sensitive and specific for SARS-CoV neutralizing antibodies. Neutralization titers measured by this assay are highly correlated to those measured by an assay using replication-competent SARS-CoV. No cross-neutralization occurred with human sera known to contain antibodies to coronavirus strains OC43 and 229E. The pseudotype assay was used to profile neutralizing antibody responses against SARS-CoV S in sequential serum samples taken from 41 confirmed SARS patients during the 2003 outbreak in Hong Kong and shows long-lasting immunity in most recovered patients. The pseudotype assay does not require handling live SARS virus; it is a useful tool to determine neutralizing titers during natural infection and the preclinical evaluation of candidate vaccines.
Multiple transcription-factor genes are early targets of phytochrome A signaling (2001)

The phytochrome family of sensory photoreceptors directs adaptational changes in gene expression in response to environmental light signals. Using oligonucleotide microarrays to measure expression profiles in wild-type and phytochrome A (phyA) null-mutant Arabidopsis seedlings, we have shown that 10% of the genes represented on the array are regulated by phyA in response to a continuous far-red light signal. Strikingly, 44% of the genes responding to the signal within 1 h are predicted to encode multiple classes of transcriptional regulators. Together with previous data, this observation suggests that phyA may regulate seedling photomorphogenesis by direct targeting of light signals to the promoters of genes encoding a master set of diverse transcriptional regulators, responsible in turn for orchestrating the expression of multiple downstream target genes in various branches of a phyA-regulated transcriptional network.
The determination of foil thickness by scanning transmission electron microscopy (1975)

A simple and accurate method of determining foil thickness is described. The method makes use of measurements of the spacing of intensity oscillations in convergent beam diffraction patterns obtained with commercial scanning transmission electron microscopes. Extension of the technique to determination of extinction distances and anomalous absorption parameters required for the two-beam dynamical theory is outlined briefly. Une méthode simple et exacte pour déterminer l′épaisseur des échantillons minces est décrite. Cette méthode se sert des mesures d′espacement aux oscillations d′intensité qui se trouvent sur les figures de diffraction obtenues au moyen d′un microscope électronique industriel à balayage par transmission. L′extension de cette méthode pour déterminer les distances d′extinction et des paramètres d′absorption anomalaux nécessaires pour la théorie dynamique à deux rayons est briévement discutée.
Rapid Detection of West Nile Virus from Human Clinical Specimens, Field-Collected Mosquitoes, and Avian Samples by a TaqMan Reverse Transcriptase-PCR Assay (2000)

The authors report on the development and application of a rapid TaqMan assay for the detection of West Nile (WN) virus in a variety of human clinical specimens and field-collected specimens. Oligonucleotide primers and FAM- and TAMRA-labeled WN virus-specific probes were designed by using the nucleotide sequence of the New York 1999 WN virus isolate. The TaqMan assay was compared to a traditional reverse transcriptase (RT)-PCR assay and to virus isolation in Vero cells with a large number ( approximately 500) of specimens obtained from humans (serum, cerebrospinal fluid, and brain tissue), field-collected mosquitoes, and avian tissue samples. The TaqMan assay was specific for WN virus and demonstrated a greater sensitivity than the traditional RT-PCR method and correctly identified WN virus in 100% of the culture-positive mosquito pools and 98% of the culture-positive avian tissue samples. The assay should be of utility in the diagnostic laboratory to complement existing human diagnostic testing and as a tool to conduct WN virus surveillance in the United States.
Absence of Diurnal Variation of C-Reactive Protein Concentrations in Healthy Human Subjects (2001)

Our data show that baseline CRP concentrations are not subject to time-of-day variation and thus help to explain why CRP concentrations are a better predictor of vascular risk than interleukin-6. Determination of CRP for cardiovascular risk prediction may be performed without concern for diurnal variation.
6-O-Sulfotransferase-1 Represents a Critical Enzyme in the Anticoagulant Heparan Sulfate Biosynthetic Pathway (2001)

Using recombinant retroviral transduction, we have introduced the heparin/heparan sulfate (HS) 3-O-sulfotransferase 1 (3-OST-1) gene into Chinese hamster ovary (CHO) cells. Expression of 3-OST-1 confers upon CHO cells the ability to produce anticoagulantly active HS (HS(act)). To understand how 6-OST and other proteins regulate HS(act) biosynthesis, a CHO cell clone with three copies of 3-OST-1 was chemically mutagenized. Resulting mutants that make HS but are defective in generating HS(act) were single-cell-cloned. One cell mutant makes fewer 6-O-sulfated residues. Modification of HS chains from the mutant with pure 6-OST-1 and 3'-phosphoadenosine 5'-phosphosulfate increased HS(act) from 7% to 51%. Transfection of this mutant with 6-OST-1 created a CHO cell line that makes HS, 50% of which is HS(act). We discovered in this study that (i) 6-OST-1 is a limiting enzyme in the HS(act) biosynthetic pathway in vivo when the limiting nature of 3-OST-1 is removed; (ii) HS chains from the mutant cells serve as an excellent substrate for demonstrating that 6-OST-1 is the limiting factor for HS(act) generation in vitro; (iii) in contradiction to the literature, 6-OST-1 can add 6-O-sulfate to GlcNAc residues, especially the critical 6-O-sulfate in the antithrombin binding motif; (iv) both 3-O- and 6-O-sulfation can be the final step in HS(act) biosynthesis in contrast to prior publications that concluded 3-O-sulfation is the final step in HS(act) biosynthesis; (v), in the presence of HS interacting protein peptide, 3-O-sulfate-containing sugars can be degraded into disaccharides by heparitinase digestion as demonstrated by capillary high performance liquid chromatography coupled with mass spectrometry.
Spatial Resolution and Sensitivity of the Inveon Small-Animal PET Scanner (2009)

The Inveon showed high spatial resolution and high sensitivity, both of which can be maintained using OSEM3D/MAP reconstruction instead of rebinning and 2D algorithms.
Introduction to Hardware Security (2015)

Hardware security has become a hot topic recently with more and more researchers from related research domains joining this area. However, the understanding of hardware security is often mixed with cybersecurity and cryptography, especially cryptographic hardware. For the same reason, the research scope of hardware security has never been clearly defined. To help researchers who have recently joined in this area better understand the challenges and tasks within the hardware security domain and to help both academia and industry investigate countermeasures and solutions to solve hardware security problems, we will introduce the key concepts of hardware security as well as its relations to related research topics in this survey paper. Emerging hardware security topics will also be clearly depicted through which the future trend will be elaborated, making this survey paper a good reference for the continuing research efforts in this area.
Tunable-focus flat liquid crystal spherical lens (2004)

A tunable-focus spherical lens using two flat substrates and inhomogeneous electric field over a homogeneous liquid crystal (LC) layer is demonstrated. The top flat substrate has an imbedded spherical indium–tin–oxide (ITO) electrode and the bottom has a planar ITO electrode on its inner surface. The inhomogeneous electric field generates a centrosymmetric gradient refractive index profile within the LC layer which causes the focusing behavior. The focal length of the LC lens can be tuned continuously from infinity to 0.6 m by the applied voltage.
A graduated assignment algorithm for graph matching (1996)

A graduated assignment algorithm for graph matching is presented which is fast and accurate even in the presence of high noise. By combining graduated nonconvexity, two-way (assignment) constraints, and sparsity, large improvements in accuracy and speed are achieved. Its low order computational complexity [O(lm), where l and m are the number of links in the two graphs] and robustness in the presence of noise offer advantages over traditional combinatorial approaches. The algorithm, not restricted to any special class of graph, is applied to subgraph isomorphism, weighted graph matching, and attributed relational graph matching. To illustrate the performance of the algorithm, attributed relational graphs derived from objects are matched. Then, results from twenty-five thousand experiments conducted on 100 mode random graphs of varying types (graphs with only zero-one links, weighted graphs, and graphs with node attributes and multiple link types) are reported. No comparable results have been reported by any other graph matching algorithm before in the research literature. Twenty-five hundred control experiments are conducted using a relaxation labeling algorithm and large improvements in accuracy are demonstrated.
Determination of the viability of crushed cartilage grafts: clinical implications for wound healing in nasal surgery. (1994)

Transplantation of uncrushed and crushed cartilage has assumed a role of great importance in reconstructive surgery of the nose. There are many divergent and contradictory opinions with regard to the outcome of cartilage, so we formulated this study to assess the functional state of chondrocytes in severely and mildly crushed as well as uncrushed and cut cartilage. Crushing and cutting leads to necrosis of a part of the graft. More of the cartilage cells are irreversibly damaged by crushing. The proportion of surviving cells, depending on the severity of crushing, is between 10 and 30%. In contrast to this, after cutting most of the cells remained viable and were able to proliferate. It is concluded that crushed cartilage not only remains unviable but is also not able to produce new cartilage; therefore, it will be subjected to resorption processes and not be useful for the reconstruction of parts of the nasal skeleton that support mechanical stress.
Split-superpositive GFP reassembly is a fast, efficient, and robust method for detecting protein–protein interactions in vivo (2012)

Split-GFP reassembly is an operationally simple in vivo technique used to identify and study interactions involving proteins and/or peptides. However, the instability of split-GFP fragments and their susceptibility to aggregation place limitations on the broader use of split-GFP reassembly. Supercharged proteins, including supercharged GFP, are variants with high theoretical negative or positive charge that are resistant to aggregation. We show that a split-superpositive GFP (split-spGFP) variant reassembles faster and more efficiently than previously reported split-sg100 GFP and split-folding-reporter GFP (split-frGFP) systems. In addition, interaction-dependent split-spGFP reassembly is efficient at physiological temperature. The increased efficiency and robustness of split-spGFP reassembly make this reporter system ideal for identifying and studying interactions involving proteins and/or peptides in vivo, and may be particularly useful for identifying or studying interactions involving proteins or peptides that are themselves susceptible to aggregation.
Suppression of the progression phenotype in somatic cell hybrids occurs in the absence of altered adenovirus type 5 gene expression. (1990)

In the present study we have analyzed the genetic regulation of increased expression of transformation-associated traits, a process termed progression, in adenovirus type 5 (Ad5)-transformed secondary rat embryo cells. Somatic cell hybrids were formed between a highly progressed neomycin-resistant Ad5-transformed cloned cell line (E11-NMTneo) and an untransformed chloramphenicol-resistant rat embryo fibroblast cell line (CREFcap). Parental E11-NMTneo cells grew with high efficiency in agar, exhibited reduced 125I-epidermal growth factor (EGF) binding, and were tumorigenic in nude mice. Parental CREFcap cells exhibited phenotypes opposite to those of E11-NMTneo cells. A high proportion (84%) of the presumptive hybrid cell types obtained after fusion and genetic selection (G418 and chloramphenicol) displayed a flat morphological phenotype intermediate between CREFcap and E11-NMTneo cells, suggesting that a trans-dominant extinction phenomenon had occurred. Two hybrids with a round morphology (R), which still exhibited the progressed phenotype, and two hybrids with a flat morphology (F), which had lost the progressed phenotype, were chosen for detailed analysis. Both R hybrids grew efficiently in agar, exhibited low 125I-EGF binding, and were tumorigenic in nude mice, whereas both F hybrids grew poorly in agar, displayed increased 125I-EGF binding in comparison with E11-NMTneo and R hybrids, and were nontumorigenic in nude mice. An analysis of the viral DNA integration patterns and the rates of transcription, steady-state mRNA accumulation, and relative levels of the Ad5 E1A and E1B gene products revealed no differences among the parental and hybrid cells. These studies indicate that normal CREF cells may contain a suppressor gene(s) which can inhibit the expression of specific traits of the progression phenotype in Ad5-transformed cells and that this suppression is not associated with changes in the expression of Ad5 transforming genes.
TREATMENT OF BASAL CELL CARCINOMA WITH INTRALESIONAL INTERFERON ALPHA: A CASE REPORT AND LITERATURE REVIEW (1992)

We report the case of a 76 year old man with three ulcerated basal cell carcinomas on his lower limbs. He was considered unsuitable for surgical therapy and was treated by intralesional interferon alpha-2b (Intron A) injections. Twenty months post therapy two of the three treatment sites remain clinically cured. Recurrence occurred at the site which received the smallest total dose of interferon. A review of the therapeutic trials of interferon alpha for basal cell carcinoma is presented. We conclude that interferon alpha-2b is a useful agent for treatment of basal cell carcinoma in selected patients.
Design, Synthesis And Evaluation Of Constrained Methoxyethyl (cMOE) and Constrained Ethyl (cEt) Nucleoside Analogs (2008)

Antisense drug discovery technology is a powerful method to modulate gene expression in animals and represents a novel therapeutic platform.(1) We have previously demonstrated that replacing 2'O-methoxyethyl (MOE, 2) residues in second generation antisense oligonucleotides (ASOs) with LNA (3) nucleosides improves the potency of some ASOs in animals. However, this was accompanied with a significant increase in the risk for hepatotoxicity.(2) We hypothesized that replacing LNA with novel nucleoside monomers that combine the structural elements of MOE and LNA might mitigate the toxicity of LNA while maintaining potency. To this end we designed and prepared novel nucleoside analogs 4 (S-constrained MOE, S-cMOE) and 5 (R-constrained MOE, R-cMOE) where the ethyl chain of the 2'O-MOE moiety is constrained back to the 4' position of the furanose ring. As part of the SAR series, we also prepared nucleoside analogs 7 (S-constrained ethyl, S-cEt) and 8 (R-constrained Ethyl, R-cEt) where the methoxymethyl group in the cMOE nucleosides was replaced with a methyl substituent. A highly efficient synthesis of the nucleoside phosphoramidites with minimal chromatography purifications was developed starting from cheap commercially available starting materials. Biophysical evaluation revealed that the cMOE and cEt modifications hybridize complementary nucleic acids with the same affinity as LNA while greatly increasing nuclease stability. Biological evaluation of oligonucleotides containing the cMOE and cEt modification in animals indicated that all of them possessed superior potency as compared to second generation MOE ASOs and a greatly improved toxicity profile as compared to LNA.
Increasing cloning possibilities using artificial zinc finger nucleases (2008)

The ability to accurately digest and ligate DNA molecules of different origins is fundamental to modern recombinant DNA research. Only a handful of enzymes are capable of recognizing and cleaving novel and long DNA sequences, however. The slow evolution and engineering of new restriction enzymes calls for alternative strategies to design novel and unique restriction enzymes capable of binding and digesting specific long DNA sequences. Here we report on the use of zinc finger nucleases (ZFNs)—hybrid synthetic restriction enzymes that can be specifically designed to bind and cleave long DNA sequences—for the purpose of DNA recombination. We show that novel ZFNs can be designed for the digestion of specific sequences and can be expressed and used for cloning purposes. We also demonstrate the power of ZFNs in DNA cloning by custom-cloning a target DNA sequence and assembling dual-expression cassettes on a single target plasmid, a task that rarely can be achieved using type-II restriction enzymes. We demonstrate the flexibility of ZFN design and the ability to shuffle monomers of different ZFNs for the digestion of compatible recognition sites through ligation of compatible ends and their cleavage by heterodimer ZFNs. Of no less importance, we show that ZFNs can be designed to recognize and cleave existing DNA sequences for the custom-cloning of native target DNA molecules.
Integrated Planar Multiband Antennas for Personal Communication Handsets (2006)

The advent of new, multistandard mobile phone devices is an important challenge for antenna designers, as they have to implement integrated antennas with multiband operation within a volume that is rapidly shrinking. In the paper, research results concerning the input return loss, radiation characteristics and efficiency of novel internal, planar, multiband patch antennas are presented.
3D FOCUSING IN PARALLEL MICROCHANNELS FOR HIGH-THROUGHPUT SYNTHESIS OF POLYMERIC NANOPARTICLES (2012)

We have developed a multilayer microfluidic device for the parallelization of nanoparticles synthesis by microfluidic rapid nanoprecipitation in 3D hydrodynamic flow focusing geometry.Since the shape and position of interconnecting holes between upper and lower poly(dimethylsiloxane) (PDMS) channels could be optimized, stable vertical focusing could be achieved.The poly(lactide-co-glycolide)-b-polyethyleneglycol (PLGA-PEG) nanoparticles with various sizes could be synthesized with polymers of different molecular weights and concentrations.In addition, the size of nanoparticles could be precisely tuned simply by changing the flow ratio of organic stream to the total flow rate of water when the molecular weights and concentrations of polymer were fixed.
Deaths: final data for 2009. (2011)

The decline of the age-adjusted death rate to a record low value for the United States and the increase in life expectancy to a record high value of 78.5 years are consistent with long-term trends in mortality.
A series of systematic reviews to inform a decision analysis for sampling and treating infected diabetic foot ulcers (2006)

The available evidence is too weak to be able to draw reliable implications for practice. This means that, in terms of diagnosis, infection in DFUs cannot be reliably identified using clinical assessment. This has implications for determining which patients need formal diagnostic testing for infection, on whether empirical treatment with antibiotics (before the results of diagnostic tests are available) leads to better outcomes, and on identifying the optimal methods of diagnostic testing. With respect to treatment, it is not known whether treatment with systemic or local antibiotics leads to better outcomes or whether any particular agent is more effective. Limited evidence suggests that both G-CSF and cadexomer iodine dressings may be less expensive than 'standard' care, that ampicillin/sulbactam may be less costly than imipenem/cilastatin, and that an unlicensed cream (pexiganan) may be as effective as oral ofloxacin. Further research is needed to ascertain the characteristics of infection in people with DFUs that influence healing and amputation outcomes, to determine whether detecting infection prior to treatment offers any benefit over empirical therapy, and to establish the most effective and cost-effective methods for detecting infection, as well as the relative effectiveness and cost-effectiveness of antimicrobial interventions for DFU infection.