julilili42/papers huggingface dataset:
Para‐phenylenediamine‐specific lymphocyte activation test: a sensitive in vitro assay to detect para‐phenylenediamine sensitization in patients with severe allergic reactions
2010-01-25

Please cite this paper as: Para‐ phenylenediamine‐specific lymphocyte activation test: a sensitive in vitro assay to detect para‐ phenylenediamine sensitization in patients with severe allergic reactions. Experimental Dermatology 2010; 19: 435–441. Abstract: Patients sensitized to para ‐phenylenediamine (PPD) by semi‐permanent tattoos increasingly develop threatening allergic reactions in response to black hair dye. The gold standard to diagnose allergic contact dermatitis is to perform epicutaneous patch tests, however, iatrogenic sensitizations and severe patch test reactions to PPD have been described, the latter especially in patients with severe allergic reactions. We examined nine patients with severe allergic reactions in response to permanent hair dyes. Patch tests using the standard concentration of 1% or 0.5% PPD resulted in severe and sometimes even bullous reactions in all patients responsive to PPD. Titration revealed that at 1% of the standard concentration (0.01% PPD), patch test sensitivity decreased and only 50% of patients responded. Consequently, we established an in vitro assay to diagnose PPD allergy. Freshly isolated peripheral blood mononuclear cells (PBMC) were cultured with titrated concentrations of PPD with or without IL‐2 supplementation, and cell proliferation was determined by [3H]‐thymidine incorporation. Lymphocyte activation test (LAT ) detected PBMC cell proliferation specific to PPD, with at least 3.5‐fold increase in [3H]‐thymidine uptake in all PPD allergic patients. Most importantly, PPD – LAT without IL‐2 supplementation remained negative in three out of eight PPD allergic patients. Thus, PPD‐LAT with IL‐2 supplementation demonstrated a sensitivity of 100%, remained unresponsive in controls not sensitized to PPD, and in one patient sensitive to other p ‐amino compounds. These data demonstrate that LAT with PPD can be used to detect PPD sensitization as a possible alternative to patch testing at least in patients with severe allergic reactions to PPD.
Right Hemihepatectomy by Suprahilar Intrahepatic Transection of the Right Hemipedicle using a Vascular Stapler
2010-01-25

Successful hepatic resection requires profound anatomical knowledge and delicate surgical technique. Hemihepatectomies are mostly performed after preparing the extrahepatic hilar structures within the hepatoduodenal ligament, even in benign tumours or liver metastasis.(1-5). Regional extrahepatic lymphadenectomy is an oncological standard in hilar cholangiocarcinoma, intrahepatic cholangio-cellular carcinoma and hepatocellular carcinoma, whereas lymph node metastases in the hepatic hilus in patients with liver metastasis are rarely occult. Major disadvantages of these procedures are the complex preparation of the hilus with the risk of injuring contralateral structures and the possibility of bleeding from portal vein side-branches or impaired perfusion of bile ducts. We developed a technique of right hemihepatectomy or resection of the left lateral segments with intrahepatic transection of the pedicle that leaves the hepatoduodenal ligament completely untouched. (6) However, if intraoperative visualization or palpation of the ligament is suspicious for tumor infiltration or lymph node metastasis, the hilus should be explored and a lymphadenectomy performed.
Drug Treatment for Chronic Systolic Heart Failure
2010-01-25

Drug treatment of chronic systolic heart failure usually includes angiotensin-converting enzyme inhibitor, or an angiotensin II receptor blocker, and a beta blocker, as prognostic benefit of these agents has been demonstrated in a large body of clinical trials. Depending on the stage of the disease and concomitant factors, an aldosterone antagonist and/or a digitalis glycoside may provide additional benefit. Most patients also receive a diuretic for symptomatic relief. Conversely, some drugs may precipitate or aggravate chronic systolic heart failure.
Right Hemihepatectomy by Suprahilar Intrahepatic Transection of the Right Hemipedicle using a Vascular Stapler
2010-01-25

Successful hepatic resection requires profound anatomical knowledge and delicate surgical technique. Hemihepatectomies are mostly performed after preparing the extrahepatic hilar structures within the hepatoduodenal ligament, even in benign tumours or liver metastasis.1-5. Regional extrahepatic lymphadenectomy is an oncological standard in hilar cholangiocarcinoma, intrahepatic cholangio-cellular carcinoma and hepatocellular carcinoma, whereas lymph node metastases in the hepatic hilus in patients with liver metastasis are rarely occult. Major disadvantages of these procedures are the complex preparation of the hilus with the risk of injuring contralateral structures and the possibility of bleeding from portal vein side-branches or impaired perfusion of bile ducts. We developed a technique of right hemihepatectomy or resection of the left lateral segments with intrahepatic transection of the pedicle that leaves the hepatoduodenal ligament completely untouched. 6 However, if intraoperative visualization or palpation of the ligament is suspicious for tumor infiltration or lymph node metastasis, the hilus should be explored and a lymphadenectomy performed.
Arabidopsis V-ATPase activity at the tonoplast is required for efficient nutrient storage but not for sodium accumulation
2010-01-26

The productivity of higher plants as a major source of food and energy is linked to their ability to buffer changes in the concentrations of essential and toxic ions. Transport across the tonoplast is energized by two proton pumps, the vacuolar H + -ATPase (V-ATPase) and the vacuolar H + -pyrophosphatase (V-PPase); however, their functional relation and relative contributions to ion storage and detoxification are unclear. We have identified an Arabidopsis mutant in which energization of vacuolar transport solely relies on the activity of the V-PPase. The vha-a2 vha-a3 double mutant, which lacks the two tonoplast-localized isoforms of the membrane-integral V-ATPase subunit VHA-a, is viable but shows day-length-dependent growth retardation. Nitrate content is reduced whereas nitrate assimilation is increased in the vha-a2 vha-a3 mutant, indicating that vacuolar nitrate storage represents a major growth-limiting factor. Zinc is an essential micronutrient that is toxic at excess concentrations and is detoxified via a vacuolar Zn 2+ /H + -antiport system. Accordingly, the double mutant shows reduced zinc tolerance. In the same way the vacuolar Na + /H + -antiport system is assumed to be an important component of the system that removes sodium from the cytosol. Unexpectedly, salt tolerance and accumulation are not affected in the vha-a2 vha-a3 double mutant. In contrast, reduction of V-ATPase activity in the trans-Golgi network/early endosome (TGN/EE) leads to increased salt sensitivity. Taken together, our results show that during gametophyte and embryo development V-PPase activity at the tonoplast is sufficient whereas tonoplast V-ATPase activity is limiting for nutrient storage but not for sodium tolerance during vegetative and reproductive growth.
Role of staphylococcal wall teichoic acid in targeting the major autolysin Atl
2010-01-26

Summary Staphylococcal cell separation depends largely on the bifunctional autolysin Atl that is processed to amidase‐R 1,2 and R 3 ‐glucosaminidase. These murein hydrolases are targeted via repeat domains (R) to the septal region of the cell surface, thereby allowing localized peptidoglycan hydrolysis and separation of the dividing cells. Here we show that targeting of the amidase repeats is based on an exclusion strategy mediated by wall teichoic acid (WTA). In Staphylococcus aureus wild‐type, externally applied repeats (R 1,2 ) or endogenously expressed amidase were localized exclusively at the cross‐wall region, while in Δ tag O mutant that lacks WTA binding was evenly distributed on the cell surface, which explains the increased fragility and autolysis susceptibility of the mutant. WTA prevented binding of Atl to the old cell wall but not to the cross‐wall region suggesting a lower WTA content. In binding studies with ConcanavalinA‐fluorescein (ConA‐FITC) conjugate that binds preferentially to teichoic acids, ConA‐FITC was bound throughout the cell surface with the exception of the cross wall. ConA binding suggest that either content or polymerization of WTA gradually increases with distance from the cross‐wall. By preventing binding of Atl, WTA directs Atl to the cross‐wall to perform the last step of cell division, namely separation of the daughter cells.
Stem cells in aged mammalian ovaries
2010-01-26

The ovary undergoes several changes after the menopause.The main characteristics of the postmenopausal ovary are a loss of follicles and several changes as a consequence of apoptotic processes.Signs of atrophy and fibrosis are evident.Primordial follicles are usually absent in postmenopause, whereas corpora atretica, hemorrhagica and albicantia, scar tissue, and simple follicular cysts are common.
Identification of full length bovine TLR1 and functional characterization of lipopeptide recognition by bovine TLR2/1 heterodimer
2010-01-26

Toll-like receptors (TLR) are highly conserved pattern recognition receptors of the innate immune system. Toll-like receptor 2 (TLR2) recognizes bacterial lipopeptides in a heterodimeric complex with TLR6 or TLR1, thereby discriminating between di- or triacylated lipopeptides, respectively. Previously, we found that HEK293 cells transfected with bovine TLR2 (boTLR2) were able to respond to diacylated lipopeptides but did not recognize triacylated lipopeptides, even after cotransfection with the so far published sequence of boTLR1. In this study we now could show that primary bovine cells were in general able to detect triacylated lipopetides. A closer investigation of the boTLR1 gene locus revealed an additional ATG 195 base pairs upstream from the published start codon. Its transcription would result in an N-terminus with high identity to human and murine TLR1 (huTLR1, muTLR1). Cloning and cotransfection of this longer boTLR1 with boTLR2 now resulted in the recognition of triacylated lipopeptides by HEK293 cells, thereby resembling the ex vivo observation. Analysis of the structure-activity relationship showed that the ester-bound acid chains of these lipopeptides need to consist of at least 12 carbon atoms to activate the bovine heterodimer showing similarity to the recognition by huTLR2/huTLR1. In contrast, HEK293 cell cotransfected with muTLR2 and muTLR1 could already be activated by lipopeptides with shorter fatty acids of only 6 carbon atoms. Thus, our data indicate that the additional N-terminal nucleotides belong to the full length and functionally active boTLR1 (boTLR1-fl) which participates in a species-specific recognition of bacterial lipopeptides.
Changing importance of environmental factors driving secondary succession on molehills
2010-01-26

Question: Species composition during secondary succession is influenced by a number of factors, such as soil moisture, disturbance timing and surrounding vegetation. How does the importance of these factors change over the course of succession? Methods: We set up a full-factorial block design using molehills differing in (a) disturbance timing, (b) soil moisture and (c) composition of surrounding vegetation, and recorded the cover of all species present on the molehills over 3 years. M1ultiple regression analyses on the dissimilarity matrices of community composition and of environmental factors were applied for each of five age classes of molehills to estimate the effect of the single factors at different stages of succession. Results: The timing of disturbance did not significantly affect community composition at any stage of succession. In contrast, the effects of soil moisture and surrounding vegetation changed significantly over time, with moisture being more important at earlier stages of succession and surrounding vegetation at later stages. Conclusion: The importance of environmental factors for species composition change significantly over the course of secondary succession. Instead of aggregating the effects of environmental factors over time, future studies should consider underlying dynamics of recolonization more comprehensively.
Powerful narrow-line source of blue light for laser cooling Yb/Er and Dysprosium atoms
2010-01-26

This report for the first time presents the results of parameter optimisation of ultra-narrow-linewidth frequency-doubled CW Ti:Sapphire lasers pumped with 12.5-18.5 W of 532-nm light. Proposed laser systems are designed for atom cooling and provide output radiation power of more than 1.5 W at 399/401 nm (Ytterbium/Erbium) and more than 1 W at 421 nm (Dysprosium) pumped at 18.5 W. The output power of single-frequency radiation at 421 nm achieved during the present work is the highest published to-date for a commercially available system achieving a 10 kHz linewidth.
7-[4-(4-Fluorophenyl)-2-methylsulfanyl-1H-imidazol-5-yl]tetrazolo[1,5-a]pyridine
2010-01-26

The crystal structure of the title compound, C(15)H(11)FN(6)S, forms a three-dimensional network stabilized by π-π inter-actions between the imidazole core and the tetra-zole ring of the tetra-zolopyridine-unit; the centroid-centroid distance is 3.627 (1) Å. The crystal structure also displays bifurcated N-H⋯(N,N) hydrogen bonding and C-H⋯F inter-actions. The former involve the NH H atom of the imidazole core and the tetra-zolopyridine N atoms, while the latter involve a methyl H atom, of the methyl-sulfanyl group, and the 4-fluoro-phenyl F atom. In the mol-ecule, the imidazole ring makes dihedral angles of 40.45 (9) and 17.09 (8)°, respectively, with the 4-fluoro-phenyl ring and the tetra-zolopyridine ring mean plane.
Rapid Heteromerization and Phosphorylation of Ligand-activated Plant Transmembrane Receptors and Their Associated Kinase BAK1
2010-01-27

In plants leucine-rich repeat receptor kinases (LRR-RKs) located at the plasma membrane play a pivotal role in the perception of extracellular signals. For two of these LRR-RKs, the brassinosteroid receptor BRI1 and the flagellin receptor FLS2, interaction with the LRR receptor-like kinase BAK1 (BRI1-associated receptor kinase 1) was shown to be required for signal transduction. Here we report that FLS2.BAK1 heteromerization occurs almost instantaneously after perception of the ligand, the flagellin-derived peptide flg22. Flg22 can induce formation of a stable FLS2.BAK1 complex in microsomal membrane preparations in vitro, and the kinase inhibitor K-252a does not prevent complex formation. A kinase dead version of BAK1 associates with FLS2 in a flg22-dependent manner but does not restore responsiveness to flg22 in cells of bak1 plants, demonstrating that kinase activity of BAK1 is essential for FLS2 signaling. Furthermore, using in vivo phospholabeling, we are able to detect de novo phosphorylation of both FLS2 and BAK1 within 15 s of stimulation with flg22. Similarly, brassinolide induces BAK1 phosphorylation within seconds. Other triggers of plant defense, such as bacterial EF-Tu and the endogenous AtPep1 likewise induce rapid formation of heterocomplexes consisting of de novo phosphorylated BAK1 and proteins representing the ligand-specific binding receptors EF-Tu receptor and Pep1 receptor 1, respectively. Thus, we propose that several LRR-RKs form tight complexes with BAK1 almost instantaneously after ligand binding and that the subsequent phosphorylation events are key initial steps in signal transduction.
Analysis of Arabidopsis with Highly Reduced Levels of Malate and Fumarate Sheds Light on the Role of These Organic Acids as Storage Carbon Molecules
2010-01-27

Abstract While malate and fumarate participate in a multiplicity of pathways in plant metabolism, the function of these organic acids as carbon stores in C3 plants has not been deeply addressed. Here, Arabidopsis (Arabidopsis thaliana) plants overexpressing a maize (Zea mays) plastidic NADP-malic enzyme (MEm plants) were used to analyze the consequences of sustained low malate and fumarate levels on the physiology of this C3 plant. When grown in short days (sd), MEm plants developed a pale-green phenotype with decreased biomass and increased specific leaf area, with thin leaves having lower photosynthetic performance. These features were absent in plants growing in long days. The analysis of metabolite levels of rosettes from transgenic plants indicated similar disturbances in both sd and long days, with very low levels of malate and fumarate. Determinations of the respiratory quotient by the end of the night indicated a shift from carbohydrates to organic acids as the main substrates for respiration in the wild type, while MEm plants use more reduced compounds, like fatty acids and proteins, to fuel respiration. It is concluded that the alterations observed in sd MEm plants are a consequence of impairment in the supply of carbon skeletons during a long dark period. This carbon starvation phenotype observed at the end of the night demonstrates a physiological role of the C4 acids, which may be a constitutive function in plants.
A neglected lineage of North American turtles fills a major gap in the fossil record
2010-01-27

Abstract: The fossil record of the two primary subclades of softshell turtles (Trionychidae) is exceedingly asymmetric, as a result of a ghost range of total clade Cyclanorbinae that is estimated at 80 Ma. Herein, we present the first phylogenetic analysis of Trionychidae that includes a representative of the poorly studied taxon Plastomenidae, which is known from the Campanian to Eocene of North America. The analysis reveals that plastomenids are stem cyclanorbines, thus significantly reducing the apparent ghost range of total group Cyclanorbinae to approximately 30 Ma. Plastomenids are either an early branching clade of stem Cyclanorbinae, or they represent a paraphyletic grade that gave rise to modern cyclanorbines. Although abundant, the fossil record is still too poorly understood to distinguish between these two primary hypotheses. The previously persistent extremely long ghost range of total clade Cyclanorbinae appears to have been the result of a research bias.
Solar Cell Blends: High‐Resolution Spectroscopic Mapping of the Chemical Contrast from Nanometer Domains in P3HT:PCBM Organic Blend Films for Solar‐Cell Applications (Adv. Funct. Mater. 3/2010)
2010-01-27

The inside cover image presents a near-field spectroscopic map of a P3HT:PCBM solar cell blend film obtaining using a parabolic-mirror-assisted optical microscope. This technique allows for simultaneous recording of both morphological and spectroscopic information, and on page 492 Xiao Wang et al. use it to investigate local molecular distribution, photoluminescence quenching efficiency, and other key properties of the P3HT:PCBM blend film.
Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison
2010-01-28

The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). While enabling the taxonomist, in principle, to obtain an estimate of the overall similarity between the genomes of two strains, this technique is tedious and error-prone and cannot be used to incrementally build up a comparative database. Recent technological progress in the area of genome sequencing calls for bioinformatics methods to replace the wet-lab DDH by in-silico genome-to-genome comparison. Here we investigate state-of-the-art methods for inferring whole-genome distances in their ability to mimic DDH. Algorithms to efficiently determine high-scoring segment pairs or maximally unique matches perform well as a basis of inferring intergenomic distances. The examined distance functions, which are able to cope with heavily reduced genomes and repetitive sequence regions, outperform previously described ones regarding the correlation with and error ratios in emulating DDH. Simulation of incompletely sequenced genomes indicates that some distance formulas are very robust against missing fractions of genomic information. Digitally derived genome-to-genome distances show a better correlation with 16S rRNA gene sequence distances than DDH values. The future perspectives of genome-informed taxonomy are discussed, and the investigated methods are made available as a web service for genome-based species delineation.
Decorrelated Neuronal Firing in Cortical Microcircuits
2010-01-28

Columns, Connections, and Correlations What is the nature of interactions between neurons in neural circuits? The prevalent hypothesis suggests that dense local connectivity causes nearby cortical neurons to receive substantial amounts of common input, which in turn leads to strong correlations between them. Now two studies challenge this view, which impacts our fundamental understanding of coding in the cortex. Ecker et al. (p. 584 ) investigated the statistics of correlated firing in pairs of neurons from area V1 of awake macaque monkeys. In contrast to previous studies, correlations turned out to be very low, irrespective of the stimulus being shown to the animals, the distances of the recording sites, and the similarity of the neuron's receptive fields or response properties. In an accompanying modeling and recording paper, Renart et al. (p. 587 ) demonstrate how it is possible to have zero noise correlation, even among cells with common input.
Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs
2010-01-28

DNA-DNA hybridization (DDH) is a widely applied wet-lab technique to obtain an estimate of the overall similarity between the genomes of two organisms. To base the species concept for prokaryotes ultimately on DDH was chosen by microbiologists as a pragmatic approach for deciding about the recognition of novel species, but also allowed a relatively high degree of standardization compared to other areas of taxonomy. However, DDH is tedious and error-prone and first and foremost cannot be used to incrementally establish a comparative database. Recent studies have shown that in-silico methods for the comparison of genome sequences can be used to replace DDH. Considering the ongoing rapid technological progress of sequencing methods, genome-based prokaryote taxonomy is coming into reach. However, calculating distances between genomes is dependent on multiple choices for software and program settings. We here provide an overview over the modifications that can be applied to distance methods based in high-scoring segment pairs (HSPs) or maximally unique matches (MUMs) and that need to be documented. General recommendations on determining HSPs using BLAST or other algorithms are also provided. As a reference implementation, we introduce the GGDC web server (http://ggdc.gbdp.org).