julilili42/papers huggingface dataset:
Role of the Twin-Arginine Translocation Pathway in Staphylococcus
2009-07-25

ABSTRACT In Staphylococcus , the twin-arginine translocation (Tat) pathway is present only in some species and is composed of TatA and TatC. The tatAC operon is associated with the fepABC operon, which encodes homologs to an iron-binding lipoprotein, an iron-dependent peroxidase (FepB), and a high-affinity iron permease. The FepB protein has a typical twin-arginine (RR) signal peptide. The tat and fep operons constitute an entity that is not present in all staphylococcal species. Our analysis was focused on Staphylococcus aureus and S. carnosus strains. Tat deletion mutants ( ΔtatAC ) were unable to export active FepB, indicating that this enzyme is a Tat substrate. When the RR signal sequence from FepB was fused to prolipase and protein A, their export became Tat dependent. Since no other protein with a Tat signal could be detected, the fepABC - tatAC genes comprise not only a genetic but also a functional unit. We demonstrated that FepABC drives iron import, and in a mouse kidney abscess model, the bacterial loads of Δ tatAC and Δ tat - fep mutants were decreased. For the first time, we show that the Tat pathway in S. aureus is functional and serves to translocate the iron-dependent peroxidase FepB.
Channel‐like NH3 flux by ammonium transporter AtAMT2
2009-07-25

Prokaryotes, plants and animals control ammonium fluxes by the regulated expression of ammonium transporters (AMTs) and/or the related Rhesus (Rh) proteins. Plant AMTs were previously reported to mediate electrogenic transport. Functional analysis of AtAMT2 from Arabidopsis in yeast and oocytes suggests that is the recruited substrate, but the uncharged form NH 3 is conducted. AtAMT2 partially co‐localized with electrogenic AMTs and conducted methylamine with low affinity. This transport mechanism may apply to other plant ammonium transporters and explains the different capacities of AMTs to accumulate ammonium in the plant cell.
Biodistribution and Imaging of 1-(2-Deoxy-β-D-Ribofuranosyl)-2,4-Difluoro-5-[123/125I]Iodobenzene (dRF[123/125I]IB), A Nonpolar Thymidine-Mimetic Nucleoside, in Rats and Tumor-Bearing Mice
2009-07-25

1-(2-Deoxy-beta-D-ribofuranosyl)-2,4-difluoro-5-iodobenzene (dRFIB) is a putative bioisostere of iododeoxyuridine (IUdR). The advantages of dRFIB over IUdR for in vivo studies include resistance to both phosphorolytic cleavage of the nucleoside bond and de-iodination. dRFIB was radioiodinated (dRF(123/125)IB) by copper-catalyzed exchange using commercial sodium [(123/125)I]iodide. The in vivo biodistribution of dRF[(125)I]IB in BALBc mice and imaging of dRF[(123)I]IB in Sprague-Dawley rats are reported. In vivo data for rats show rapid clearance of radioactivity from blood (>95%ID in 15 minutes), extensive excretion in urine (56%ID/24 hours), concentration in the hepatobiliary-small intestine system and very little fecal excretion (approximately 3%ID/24 hours). Pharmacokinetic data for dRF[(125)I]IB (i.v. 48.7 ug/kg) in rats (t(1/2)[h] = 0.51 +/- 0.14, AUC(inf)[microg.min/mL] = 3.7 +/- 0.4, Cl[L/kg/h] = 0.75 +/- 0.12, Vss[L/kg] = 0.96 +/- 0.18) confirm previously reported dose-dependent pharmacokinetics. Scintigraphic images of rats dosed with dRF[(123)I]I were compatible with rapid soft-tissue clearance and extensive accumulation of radioactivity in bladder/urine and liver/small intestine. In tumor-bearing mice, thyroid and stomach radioactivity was indicative of moderate deiodination. An unidentified polar radioactive metabolite was detected in serum.
The wild west
2009-07-26

Embedded SW design can be compared to the lawless wild west. With no clear methodology and no standard multi core platform modeling environment every company has to improvise its own solution. The problems facing embedded software users are becoming more complex since:
Experimental and theoretical investigation of vibrational spectra of copper phthalocyanine: polarized single‐crystal Raman spectra, isotope effect and DFT calculations
2009-07-27

Abstract The IR‐ and Raman spectra of copper phthalocyanine (CuPc), as well as the isotopic wavenumber shifts upon 15 N substitution in CuPc, were investigated experimentally and theoretically. The symmetry of molecular vibrations was determined using polarized Raman spectra of an oriented CuPc single crystal. Density functional theory (DFT) calculations were used for the detailed assignment of different bands in the vibrational spectra of CuPc. Theoretically predicted geometry, wavenumbers and isotopic shifts are in a very good agreement with the experimental values. A comparison of experimentally obtained isotopic shifts with theoretical predictions allowed us to reveal some characteristic features of normal vibrations of CuPc molecule. Copyright © 2009 John Wiley &amp; Sons, Ltd.
KICK AND RUSH: PARADOXICAL KINESIA IN PARKINSON DISEASE
2009-07-27

A 68-year-old enthusiastic soccer player with idiopathic Parkinson disease (PD) had unpredictable, immobilizing freezing of gait, which did not respond even to high doses of dopaminergic medication. By kicking a tennis ball attached to a rubber band, he could reliably overcome ...
Mystery or Misery? Primary Group A Streptococcal Peritonitis in Women: Case Report
2009-07-27

Acute primary peritonitis in the absence of other comorbid conditions such as liver cirrhosis, immunosuppression, or nephrotic syndrome is a rare disorder in young adults. In women, ascending genital infections are thought to be a major pathogenic cause of this type of peritonitis. Pus was detected in the peritoneal cavity by abdominal paracentesis in a 27-year-old woman who had no predisposing features for severe peritonitis. Abdominal computed tomography showed perirectal edema. Laparotomy was performed, but no intra-abdominal focus of infection could be detected. The abdomen was irrigated via a subhepatic and retroperitoneal presacral approach, and broad-spectrum antibiotic therapy was started. Blood cultures revealed group A streptococci, usually a common cause of upper respiratory tract infections or erysipelas. Within a few days, the patient recovered completely and returned to normal life.
Propionate Analogues of Zearalenone Bind to Hsp90
2009-07-27

Abstract By replacement of an acetate with propionate through organic synthesis a range of zearalenone analogues were prepared. As key steps in the synthesis of the analogues we used the Noyori hydrogenation of methyl acetoacetate followed by Frater alkylation of the enantiomeric 3‐hydroxybutyrates. This converted the second acetate to a propionate. Through the derived alkyne, chain extension led to 3‐methylundec‐10‐en‐2‐ol derivatives. These were condensed with 2,4‐dimethoxy‐6‐vinylbenzoic acid. Ring‐closing metathesis of the obtained esters led to macrolactones, which were deproteced to give the zearalenone analogues. Several of the analogues showed cytotoxicity against the L929 mouse fibroblast cell line comparable to zearalenone (9 μ M ) itself. In the thermal‐shift assay, two analogues 35 and ent ‐ 35 displayed stronger binding than the natural product geldanamycin to the chaperone Hsp90.
Catheter Ablation of Recurrent Scar‐Related Ventricular Tachycardia Using Electroanatomical Mapping and Irrigated Ablation Technology: Results of the Prospective Multicenter Euro‐VT‐Study
2009-07-28

Catheter Ablation of Ventricular Tachycardia. Introduction: Ventricular tachycardia (VT) late after myocardial infarction is an important contributor to morbidity and mortality. This prospective multicenter study assessed the efficacy and safety of electroanatomical mapping in combination with open‐saline irrigated ablation technology for ablation of chronic recurrent mappable and unmappable VT in remote myocardial infarction. Methods and Results: In 8 European institutions, 63 patients (89% males) were enrolled in the study. All patients had remote myocardial infarction and presented with a median number of 17 (range 1–380) VTs in the preceding 6 months. Incessant VT was present in 14 patients (22%). Left ventricular ejection fraction measured 30 ± 13%. A mean of 3 VTs were targeted per patient and 22% of all patients had only unmappable VT. The mean follow‐up period was 12 ± 3 months. A total of 164 VTs were targeted during catheter ablation. Ablation was acutely successful in 51 patients (81%). One patient (1.5%) experienced a major complication with degeneration of VT into ventricular fibrillation necessitating cardiopulmonary resuscitation maneuvers. However, no death occurred acutely or within the first 30 days after catheter ablation. During the follow‐up, 19 of the initially successful ablated patients (37%) and 31 of all ablated patients (49%) developed some type of VT recurrence. Conclusions: The results of this multicenter study demonstrate the high acute success rate and a low complication rate of irrigated tip catheter ablation of all clinical relevant VTs in remote myocardial infarction. However, during the follow‐up a relevant number of recurrences occurred. (J Cardiovasc Electrophysiol, Vol. 21, pp. 47–53, January 2010)
Molecular Taxonomy of Phytopathogenic Fungi: A Case Study in Peronospora
2009-07-28

A corrected taxonomy is provided for all Peronospora ITS sequences contained in public databases. Clustering optimization appears to be broadly applicable in automated, sequence-based taxonomy. The method connects traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both traditional species concepts and genetic divergence.
Soft X‐ray spectromicroscopy of nickel sorption in a natural river biofilm
2009-07-28

Abstract Scanning transmission X‐ray microscopy (STXM) at the C 1s, O 1s, Ni 2p, Ca 2p, Mn 2p, Fe 2p, Mg 1s, Al 1s and Si 1s edges was used to study Ni sorption in a complex natural river biofilm. The 10‐week grown river biofilm was exposed to 10 mg L −1 Ni 2+ (as NiCl 2 ) for 24 h. The region of the biofilm examined was dominated by filamentous structures, which were interpreted as the discarded sheaths of filamentous bacteria, as well as a sparse distribution of rod‐shaped bacteria. The region also contained discrete particles with spectra similar to those of muscovite, SiO 2 and CaCO 3 . The Ni(II) ions were selectively adsorbed by the sheaths of the filamentous bacteria. The sheaths were observed to be metal rich with significant amounts of Ca, Fe and Mn, along with the Ni. In addition, the sheaths had a large silicate content but little organic material. The metal content of the rod‐shaped bacterial cells was much lower. The Fe on the sheath was mainly in the Fe(III) oxidation state. Mn was found in II, III and IV oxidation states. The Ni was likely sorbed to Mn–Fe minerals on the sheath. These STXM results have probed nano‐scale biogeochemistry associated with bacterial species in a complex, natural biofilm community. They have implications for selective Ni contamination of the food chain and for developing bioremediation strategies.
Neutrophil antimicrobial defense against Staphylococcus aureus is mediated by phagolysosomal but not extracellular trap-associated cathelicidin
2009-07-28

Abstract Study took advantage of the hyper-susceptible phenotype of S. aureus ΔdltA against cationic AMPs to investigate the impact of the murine cathelicidin CRAMP to identify its key site of action in neutrophils. Neutrophils kill invading pathogens by AMPs, including cathelicidins, ROS, and NETs. The human pathogen Staphylococcus aureus exhibits enhanced resistance to neutrophil AMPs, including the murine cathelicidin CRAMP, in part, as a result of alanylation of teichoic acids by the dlt operon. In this study, we took advantage of the hypersusceptible phenotype of S. aureus ΔdltA against cationic AMPs to study the impact of the murine cathelicidin CRAMP on staphylococcal killing and to identify its key site of action in murine neutrophils. We demonstrate that CRAMP remained intracellular during PMN exudation from blood and was secreted upon PMA stimulation. We show first evidence that CRAMP was recruited to phagolysosomes in infected neutrophils and exhibited intracellular activity against S. aureus. Later in infection, neutrophils produced NETs, and immunofluorescence revealed association of CRAMP with S. aureus in NETs, which similarly killed S. aureus wt and ΔdltA, indicating that CRAMP activity was reduced when associated with NETs. Indeed, the presence of DNA reduced the antimicrobial activity of CRAMP, and CRAMP localization in response to S. aureus was independent of the NADPH oxidase, whereas killing was partially dependent on a functional NADPH oxidase. Our study indicates that neutrophils use CRAMP in a timed and locally coordinated manner in defense against S. aureus.
New evidence and new methods to measure human capital inequality before and during the industrial revolution: France and the US in the seventeenth to nineteenth centuries
2009-07-29

We explore pre‐ and early industrial inequality of numeracy using the age heaping method and anthropometric strategies. For France, we map differential numeracy between the upper and lower segments of a sample population for 26 regions during the seventeenth century. For the US, inequality of numeracy is estimated for 25 states during the 19th century. Testing the hypothesis of a negative impact of inequality on welfare growth, we find evidence that lower inequality increased industrial development in the US, whereas for France such an effect was only evident in interactions with political variables such as proximity to central government.
Observing quantum gases in real time: Single-atom detection on a chip
2009-07-29

Single magnetically trapped atoms on an atom chip are detected with efficiency by three photon ionization and subsequent ion detection in a channel electron multiplier. State selective detection of single atoms and high-resolution optical spectroscopy on trapped atom clouds are demonstrated. The temperature and particle density of a trapped atomic gas is monitored in situ and in real time with negligible atom loss due to ionization below 5%.
Mobile Genetic Element-Encoded Cytolysin Connects Virulence to Methicillin Resistance in MRSA
2009-07-30

Bacterial virulence and antibiotic resistance have a significant influence on disease severity and treatment options during bacterial infections. Frequently, the underlying genetic determinants are encoded on mobile genetic elements (MGEs). In the leading human pathogen Staphylococcus aureus, MGEs that contain antibiotic resistance genes commonly do not contain genes for virulence determinants. The phenol-soluble modulins (PSMs) are staphylococcal cytolytic toxins with a crucial role in immune evasion. While all known PSMs are core genome-encoded, we here describe a previously unidentified psm gene, psm-mec, within the staphylococcal methicillin resistance-encoding MGE SCCmec. PSM-mec was strongly expressed in many strains and showed the physico-chemical, pro-inflammatory, and cytolytic characteristics typical of PSMs. Notably, in an S. aureus strain with low production of core genome-encoded PSMs, expression of PSM-mec had a significant impact on immune evasion and disease. In addition to providing high-level resistance to methicillin, acquisition of SCCmec elements encoding PSM-mec by horizontal gene transfer may therefore contribute to staphylococcal virulence by substituting for the lack of expression of core genome-encoded PSMs. Thus, our study reveals a previously unknown role of methicillin resistance clusters in staphylococcal pathogenesis and shows that important virulence and antibiotic resistance determinants may be combined in staphylococcal MGEs.
Catheter-Based Delivery of Fluid Paclitaxel for Prevention of Restenosis in Native Coronary Artery Lesions After Stent Implantation
2009-07-30

Background— Stents eluting antiproliferative drugs reduce the incidence of restenosis but delay healing of the vascular wall. We assessed the safety and efficacy of catheter-based local delivery of fluid paclitaxel in patients with coronary de novo stenoses after implantation of a bare metal stent. Methods and Results— We conducted a prospective, randomized trial comparing the local delivery of fluid paclitaxel after bare metal stent implantation (group I) with the implantation of a bare metal stent (group II) and the implantation of a paclitaxel-eluting stent (group III) in 204 patients. The primary end point was in-stent late lumen loss. Secondary end points included binary restenosis rate &gt;50%, minimal lumen diameter, diameter stenosis, and a composite clinical end point (major adverse cardiac events and revascularization of the target lesion) 6 months after intervention. At 6 months, angiography showed an in-stent late lumen loss of 0.61±0.44 mm in group I versus 0.99±0.72 mm in group II (I versus II, P =0.0006) and 0.44±0.48 mm in group III (noninferiority of I versus III, P =0.023). The 1-sided 95% CI for the true difference of the means of in-stent late lumen loss in groups I and III was −∞ to 0.3174188. The cumulative overall rate of major cardiac events was 13.4% in group I, 26.8% in group II, and 14.9% in group III. Target lesion revascularization rate was 13.4% (group I), 22.1% (group II), and 13.4% (group III). Conclusions— Additional antiproliferative treatment of de novo lesions in native coronary arteries with catheter-based delivery of fluid paclitaxel after bare metal stenting was safe and significantly reduced neointimal proliferation, restenosis, and clinical events compared with bare metal stent implantation alone.
The Role of Temporo-parietal Cortex in Subcortical Visual Extinction
2009-07-30

Abstract Visual extinction is an intriguing defect of awareness in stroke patients, referring to the unsuccessful perception of contralesional events under conditions of competition. Previous studies have investigated the cortical and subcortical brain structures that, when damaged or inactivated, provoke visual extinction. The present experiment asked how lesions of subcortical structures may contribute to the appearance of visual extinction. We investigated whether lesions centering on right basal ganglia may induce dysfunction in distant, structurally intact cortical structures. Normalized perfusion-weighted MRI was used to identify structurally intact but abnormally perfused brain tissue, that is, zones that are receiving enough blood supply to remain structurally intact but not enough to function normally. We compared patients with right basal ganglia lesions showing versus not showing visual extinction. In the extinction patients, the contrast revealed cortical malperfusion that clustered around the right TPJ. It seems as if malfunction of this area is a critical aspect in visual extinction not only after cortical lesion but also in the case of subcortical basal ganglia damage. Our results support the idea that a normally functioning TPJ area plays a decisive role for the attentional network involved in detecting of visual stimuli under conditions of competition.
Inhibition of Suicidal Erythrocyte Death by Xanthohumol
2009-07-30

Xanthohumol is a proapoptotic hop-derived beer component with anticancer and antimicrobial activities. Similar to nucleated cells, erythrocytes may undergo suicidal cell death or eryptosis, which is triggered by oxidative stress (tert-butylhydroperoxide, TBOOH) or energy depletion (removal of glucose). The triggers increase cytosolic Ca(2+) concentration, leading to activation of Ca(2+)-sensitive K(+) channels with subsequent cell shrinkage and to cell membrane scrambling with subsequent phosphatidylserine exposure at the erythrocyte surface. Eryptotic cells are cleared from the circulating blood, leading to anemia, and may adhere to the vascular wall, thus impeding microcirculation. The present experiments explored whether xanthohumol influences eryptosis using flow cytometry. Exposure of human erythrocytes to 0.3 mM TBOOH or incubation in glucose-free solution significantly increased Fluo3 fluorescence (Ca(2+) concentration) as well as annexin V-binding (cell membrane scrambling) and decreased forward scatter (cell volume), effects significantly blunted by xanthohumol. In conclusion, xanthohumol is a potent inhibitor of suicidal erythrocyte death in vitro.
NUMERICAL DISSIPATION IN RSPH SIMULATIONS OF ASTROPHYSICAL FLOWS WITH APPLICATION TO PROTOPLANETARY DISKS
2009-07-30

Smoothed Particle Hydrodynamics (SPH) is widely used for astrophysical applications, in particular problems of self-gravitational hydrodynamics. However, critics have argued that inherent accuracy problems with the method can be identified, in particular when it comes to describing shocks and dynamical instabilities. Regularized Smoothed Particle Hydrodynamics (RSPH) has previously been proposed as an extension to SPH. It is an attempt to increase the accuracy of the hydrodynamical description without having to abandon the Lagrangian formulation altogether. As the name implies, the method relies on a regularization technique where the solution at temporal intervals is mapped on to a new set of regularly placed particles. This technique allows us to reduce the numerical noise otherwise caused by highly irregular particle distributions and to take advantage of a more flexible approach to variable resolution. The cost of introducing the regularization scheme lies in increased methodical complexity, and in increased numerical dissipation. This paper investigates the numerical dissipation both qualitatively and quantitatively in the context of two-dimensional models relevant to the study of protoplanetary disks. Basic hydrodynamical tests highlight key properties of the RSPH approach. By comparison with an analytical solution, we are also able to quantify the dependence of the spurious viscosity on key numerical parameters. To put the theoretical discussion in perspective, we also present results from simulations of test problems involving disk–planet interactions. The results are compared to published results obtained with other codes.
Children’s Height and Parental Unemployment: A Large-Scale Anthropometric Study on Eastern Germany, 1994–2006
2009-07-31

Abstract The average height of children is an indicator of the quality of nutrition and healthcare. In this study, we assess the effect of unemployment and other factors on this variable. In the Eastern German Land of Brandenburg, a dataset of 253,050 preschool height measurements was compiled and complemented with information on parents’ schooling and employment status. Unemployment might have negative psychological effects, with an impact on parental care. Both a panel analysis of districts and an assessment at the individual level yield the result that increasing unemployment, net out-migration and fertility were in fact reducing height.
Synthesis and Crystal Structure of a Bixbyite‐Type Solid Solution Zr0.43Er0.57O1.07N0.43
2009-07-31

Abstract A powder of the composition 40 mol‐% Er 2 O 3 and 60 mol‐% ZrO 2 has been prepared. The anion deficient fluorite related compound Zr 3 Er 4 O 12 [ R \\bar{3} : a = 971.79(7) pm and c = 907.976(0) pm] was produced. This precursor was treated with gaseous ammonia at temperatures between 25 and 1200 °C. The reaction was followed in situ by X‐ray diffraction in a high temperature reaction chamber under a constant flow of ammonia. The nitridation of Zr 3 Er 4 O 12 led to a nitride oxide of the solid‐solution‐type with an apparent composition Zr 0.43 Er 0.57 O 1.07 N 0.43 The compound crystallizes isostructural to bixbyite due to vacancy ordering [ Ia \\bar{3} : a = 1036.37(4) pm]. The reoxidation of the nitride oxide was monitored in DTA/TG experiments exhibiting an almost complete reoxidation to the starting composition except for some inclusions of dinitrogen.
Spectrum of practice in the diagnosis of nosocomial pneumonia in patients requiring mechanical ventilation in European intensive care units
2009-08-01

Etiological diagnosis of nosocomial pneumonia in a large sample of European intensive care units was based mainly on noninvasive techniques. However, there was high variability in bronchoscopy use between the participating intensive care units.