Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Functionally Important TonB-ExbD Periplasmic Domain Interactions In Vivo

ABSTRACT In Gram-negative bacteria, the cytoplasmic membrane proton-motive force energizes the active transport of TonB-dependent ligands through outer membrane TonB-gated transporters. In Escherichia coli, cytoplasmic membrane proteins ExbB and ExbD couple the proton-motive force to conformational changes in TonB, which are hypothesized to form the basis of energy transduction through direct contact with the transporters. While the role of ExbB is not well understood, contact between periplasmic domains of TonB and ExbD is required, with the conformational response of TonB to presence or absence of proton motive force being modulated through ExbD. A region (residues 92 to 121) within the ExbD periplasmic domain was previously identified as being important for TonB interaction. Here, the specific sites of periplasmic domain interactions between that region and the TonB carboxy terminus were identified by examining 270 combinations of 45 TonB and 6 ExbD individual cysteine substitutions for disulfide-linked heterodimer formation. ExbD residues A92C, K97C, and T109C interacted with multiple TonB substitutions in four regions of the TonB carboxy terminus. Two regions were on each side of the TonB residues known to interact with the TonB box of TonB-gated transporters, suggesting that ExbD positions TonB for correct interaction at that site. A third region contained a functionally important glycine residue, and the fourth region involved a highly conserved predicted amphipathic helix. Three ExbD substitutions, F103C, L115C, and T121C, were nonreactive with any TonB cysteine substitutions. ExbD D25, a candidate to be on a proton translocation pathway, was important to support efficient TonB-ExbD heterodimerization at these specific regions.
Octopine and nopaline oxidases from Ti plasmids of Agrobacterium tumefaciens: molecular analysis, relationship, and functional characterization

The occ and noc regions of pTiAch5 (octopine) and pTiC58 (nopaline) Ti plasmids are responsible for the catabolic utilization of octopine and nopaline in Agrobacterium spp. The first enzymatic step is the oxidative cleavage into L-arginine and pyruvate or 2-ketoglutarate, respectively, by membrane-bound opine oxidases requiring two polypeptides (subunits B and A) for function. The DNA sequences showed that the subunits of pTiAch5 and pTiC58 are related, but none of the proteins revealed significant similarities to the biosynthetic enzymes expressed in transformed plant cells. The four proteins had no extensive overall similarity to other proteins, but the 35 N-terminal amino acids contained motifs found in many enzymes utilizing flavin adenine dinucleotide, flavin mononucleotide, or NAD(P)+ as cofactors. However, the activities were completely independent of added cofactors, and the nature of the electron acceptor remained unclear. Membrane solubilization led to complete loss of enzyme activity. The nopaline oxidase accepted nopaline and octopine (Vmax ratio, 5:1) with similar Km values (1.1 mM). The octopine oxidase had high activity with octopine (Km = 1 mM) and barely detectable activity with nopaline. The subunits from the occ and the noc regions were exchangeable. The combinations ooxB-noxA and noxB-ooxA both produced active enzymes which oxidized octopine and nopaline at similar rates, suggesting that both subunits contributed to the substrate specificity. These experiments also showed that the formation of functional enzyme required close proximity of the subunit genes on the same plasmid and that even a reversal of the gene order (A-B instead of B-A) led to reduced activity.
Flow-Sensitive Sub-Zero Control-Flow Analysis in Linear-Log Time

Traditional control-flow analysis (CFA) for higher-order languages is too expensive to be used as an every-day analysis in an otherwise fast compiler that is often called upon to compile large programs. It is even more expensive when flow sensitivity is added to handle optimizations like type recovery. In particular, the fastest known algorithms for 0CFA, the least expensive of the popular kCFA family of analyses, run in cubic time and are not flow-sensitive. A less precise form of control-flow analysis, sub-0CFA, runs in linear time, but is also not flow-sensitive. This paper presents a flow-sensitive sub-0CFA algorithm that runs in linear-log time. The algorithm has been used to perform a type recovery analysis that justifies the removal of over half of the run-time checks that would otherwise be necessary to ensure type safety in the latently typed language Scheme.
Symbiosis: Sharing mobile resources for stream processing

Nowadays, the overwhelming amount of data generated on Internet have boosted the development of new solutions to process data on time windows closer to real time. Such solutions are known as Distributed Stream Processing Engines (DSPEs). DSPEs were specially designed to process data streams over cluster infrastructure, however the great massification of mobile devices opens new opportunities to process data closer to the source in order to reduce latency and traffic over the network. In this paper we propose Symbiosis, an architecture oriented to process data streams over mobile clients such as tablets and smartphones. Symbiosis model aims to exploit mobile devices resources to pre-process data streams generated on neighbors clients. Implementing data processing on mobile nodes is challenging due to their mobility and the limited battery power. In order to cope with such a requirements, Symbiosis proposes a data processing method based on checkpoints which consider both mobility and available energy in the device.
Significance of CD 105 expression for tumour angiogenesis and prognosis in endometrial carcinomas

Angiogenesis is a key process in tumour growth and metastasis, and Factor‐VIII microvascular density has been found to influence prognosis among endometrial carcinoma patients. The CD105/endoglin antibody has been reported to preferentially bind to activated endothelial cells in tissues participating in angiogenesis, and we therefore wanted to compare the prognostic significance of CD105/endoglin to that of Factor‐VIII. In a population‐based endometrial carcinoma study with long (median 11.5 years) and complete patient follow‐up, mean intratumour microvascular density (MVD) assessed using CD105/endoglin was investigated and compared with previous data for MVD assessed using Factor‐VIII. MVD by CD105/endoglin was significantly correlated with MVD by Factor‐VIII (p=0.001). However, tumours within the two groups defined by the upper and lower quartiles for CD105/endoglin‐MVD were both significantly more often metastatic (FIGO‐stage III/IV; p=0.03), with high tumour cell proliferation by Ki67 (p=0.007) and with reduced survival (p=0.036) as compared with the intermediate groups. In Cox regression analysis, CD105/endoglin‐MVD showed independent prognostic influence when analysed together with patient age, FIGO stage, histologic subtype, histologic grade and Factor‐VIII‐MVD, while the latter lost its prognostic impact when CD105/endoglin was included. In the subgroup with high MVD, there was a tendency towards improved response to radiation therapy. In conclusion, CD105/endoglin‐MVD is significantly associated with FIGO stage, tumour proliferation and prognosis in endometrial carcinoma, indicating that this is a better angiogenic marker in these tumours.
Effects of Saporin-Induced Lesions of Three Arousal Populations on Daily Levels of Sleep and Wake

The hypocretin (HCRT) neurons are located only in the perifornical area of the lateral hypothalamus and heavily innervate the cholinergic neurons in the basal forebrain (BF), histamine neurons in the tuberomammillary nucleus (TMN), and the noradrenergic locus ceruleus (LC) neurons, three neuronal populations that have traditionally been implicated in regulating arousal. Based on the innervation, HCRT neurons may regulate arousal by driving these downstream arousal neurons. Here, we directly test this hypothesis by a simultaneous triple lesion of these neurons using three saporin-conjugated neurotoxins. Three weeks after lesion, the daily levels of wake were not changed in rats with double or triple lesions, although rats with triple lesions were asleep more during the light-to-dark transition period. The double- and triple-lesioned rats also had more stable sleep architecture compared with nonlesioned saline rats. These results suggest that the cholinergic BF, TMN, and LC neurons jointly modulate arousal at a specific circadian time, but they are not essential links in the circuitry responsible for daily levels of wake, as traditionally hypothesized.
The Use of &bgr;-Blockers to Decrease Adverse Perioperative Cardiac Events

As the population ages, more surgeries are performed on patients with increased risk factors. Many of these surgeries will result in complications and mortality. Myocardial ischemia is often associated with cardiac complications in the perioperative patient. Unfortunately, an episode of myocardial ischemia will result in a 70% mortality rate. Perioperative patients are complex because of their atypical presentation, incisional pain, and the effects of analgesia. The critical care nurse must be able to determine a patient's risk factors and surgical risks and then take measures to ensure that the patient receives adequate treatment both before and after surgery. &bgr;-Blockers may decrease a patient's risk of developing myocardial ischemia, yet they are often underused. A multidisciplinary approach is needed to ensure the proper use of &bgr;-blockers in an effort to reduce cardiac complications in the perioperative elderly patient.
Right Ventricular Changes after Left‐Sided Lesions: Underlying Cardiac Mechanics

This issue contains an important report by Doctors Li and Cheung who analyzed changes in right ventricular (RV) motion in adolescents and young adults after correction of coarctation of the aorta by either surgical approaches or by balloon angioplasty. Their contribution focuses upon the biventricular long-term effects of these interventions. They employed speckle tracking echocardiography (STE) to document changes in RV systolic and diastolic parameters, and observed increased thickness of the left ventricle (LV), septum, and RV-free wall. Their studies demonstrate adverse changes in RV isovolumic contraction, impaired descent of tricuspid annular velocity, and diminished RV longitudinal strain. This spectrum of movement observations confirms unfavorable changes in RV motion following correction of coarctation of the aorta, a left-sided lesion. The presence of these adverse RV motions introduces two questions. First, what is the myocardial structural reason for impaired RV dynamics following relief of aortic obstruction by either surgical of catheter-based approaches? Second, does this abnormality of RV motion reflect the natural history of surgical or angioplasty procedures used in these patients, or could it have been avoided by adopting other approaches to remedy aortic narrowing by coarctation?
A low complexity pilot aided channel estimation method for WCDMA communication systems

This letter deals with the performance evaluation of a pilot aided method for estimating channel parameters in wideband code division multiple access (WCDMA) communication systems. Unlike previous approaches, a successive interference cancellation algorithm is used to reduce multipath and multiuser interference caused by pilot signal replicas on the channel parameter estimation, and on the detection of the information bearing signals. Comparisons with the ideal case of perfect knowledge of the channel parameters and the classical channel parameter estimation algorithm have highlighted the good performance of the proposed approach.
Bürgerinitiativen: Ihre Funktion aus Sicht der Bevölkerung und ihre kommunikativen Aktivitäten

Der Kurzbericht gibt eine aktuelle Bestandsaufnahme des Engagements von Burgern in „Burgerinitiative“. Dazu werden Daten einer reprasentativen Umfrage der deutschen Bevolkerung aus dem Jahr 2008 herangezogen. Zunachst wird anhand der Daten die Frage nach der Akzeptanz von Burgerinitiativen in der Bevolkerung beantwortet. In einem zweiten Schritt wird ein Blick „in“ die Burgerinitiativen gerichtet: Welche Themen bearbeiten sie? Welche Medien werden eingesetzt? Welche Aktions- und Handlungsformen uberwiegen und welche Rolle spielt Onlinekommunikation dabei?
Identification and Sequence Analysis of a 27-Kilobase Chromosomal Fragment Containing a Salmonella Pathogenicity Island Located at 92 Minutes on the Chromosome Map of Salmonella enterica Serovar Typhimurium LT2

ABSTRACT Using a genomic approach, we have identified a newSalmonella pathogenicity island, SPI-4, which is the fourthSalmonella pathogenicity island to be identified. SPI-4 was located at 92 min on the chromosome map and was flanked by thessb and soxSR loci. The DNA sequence covering the entire SPI-4 and both boundaries was determined. The size of SPI-4 was about 25 kb and it contains 18 putative open reading frames (ORFs). Three of these ORFs encode proteins that have significant homology with proteins involved in toxin secretion. Another five ORFs encode proteins that have significant homology with hypothetical proteins fromSynechocystis sp. strain PCC6803 or Acinetobacter calcoaceticus. The rest of the ORFs encode novel proteins, one of which has five membrane-spanning domains. SPI-4 is likely to carry a type I secretion system involved in toxin secretion. Furthermore, a previously identified locus (ims98), which is required for intramacrophage survival, was also mapped within the SPI-4 region. These findings suggested that SPI-4 is needed for intramacrophage survival.
Far-Ultraviolet Astronomy on the Astro-1 Space Shuttle Mission

The Astro-1 mission obtained observations related to a wide variety of current problems in astronomy during a 9-day flight of the space shuttle Columbia. Early results from one of the instruments, the Hopkins Ultraviolet Telescope, are reviewed here. Among these are new insights concerning the origin of the ultraviolet light from the old stellar population in elliptical galaxies, new evidence for a hot, gaseous corona surrounding the Milky Way, improved views of the physical conditions in active galactic nuclei, and a measurement of the ionization state of the local interstellar medium.
Current and future approaches to treat graft failure after allogeneic hematopoietic stem cell transplantation

Introduction: One significant obstacle to the success of allogeneic hematopoietic stem cell transplantation (HSCT) is represented by graft failure, defined as either lack of initial engraftment of donor cells (primary graft failure) or loss of donor cells after initial engraftment (secondary graft failure). Graft failure mediated by host immune cells attacking donor stem cells is named graft rejection. Factors associated with graft failure include HLA disparity in the donor/recipient pair, underlying disease, viral infections, type of conditioning regimen and stem cell source employed. Areas covered: In this article, the experts summarize current approaches to treat graft failure/rejection after HSCT, and they discuss new strategies of graft manipulation and immune therapy of particular interest for preventing/treating this complication. Expert opinion: A limited array of options is available to treat graft failure. The experts believe that re-transplantation from another donor or the same donor (if there is no evidence of immunologically mediated graft failure) is the treatment of choice for patients with primary graft failure or acute graft rejection. The experts think that strategies based on innovative approaches of graft manipulation, new agents or cellular therapies could render in the future graft failure a much less relevant problem for HSCT recipients.
Age-dependency of sevoflurane-induced electroencephalogram dynamics in children.

BACKGROUND General anaesthesia induces highly structured oscillations in the electroencephalogram (EEG) in adults, but the anaesthesia-induced EEG in paediatric patients is less understood. Neural circuits undergo structural and functional transformations during development that might be reflected in anaesthesia-induced EEG oscillations. We therefore investigated age-related changes in the EEG during sevoflurane general anaesthesia in paediatric patients. METHODS We analysed the EEG recorded during routine care of patients between 0 and 28 yr of age (n=54), using power spectral and coherence methods. The power spectrum quantifies the energy in the EEG at each frequency, while the coherence measures the frequency-dependent correlation or synchronization between EEG signals at different scalp locations. We characterized the EEG as a function of age and within 5 age groups: <1 yr old (n=4), 1-6 yr old (n=12), >6-14 yr old (n=14), >14-21 yr old (n=11), >21-28 yr old (n=13). RESULTS EEG power significantly increased from infancy through ∼6 yr, subsequently declining to a plateau at approximately 21 yr. Alpha (8-13 Hz) coherence, a prominent EEG feature associated with sevoflurane-induced unconsciousness in adults, is absent in patients <1 yr. CONCLUSIONS Sevoflurane-induced EEG dynamics in children vary significantly as a function of age. These age-related dynamics likely reflect ongoing development within brain circuits that are modulated by sevoflurane. These readily observed paediatric-specific EEG signatures could be used to improve brain state monitoring in children receiving general anaesthesia.
Public Perception of Physical Risks: Effect of the Experience of Repeated Explosion Accidents at a Chemical Plant

To explore the influence of experiencing accidental explosions, a questionnaire-based survey was conducted. This paper compares the risk perception characteristics of inhabitants living near a chemical plant at which accidental explosions occurred (group A) and of those living near a plant where no serious accidents have occurred (group B). The survey forms contain the following items: demographics, knowledge about causes of accidental explosion, dread, frequency, and risk rating variables. In addition, participants of group A are asked about their level of participation in physical risk communication. The survey reveals that 1) participants of group A have a greater sense of dread than those of group B; 2) participants of group A are more likely to perceive accidental explosions in chemical plants that occur more frequently; 3) risk rating of physical risks is independent of that of health risks; 4) the “frequency” variable is a key factor that influences decision making whether they participate in physical risk communication or not.
Social signals and the ENR index - noise of searches on SNs with keyword-based logic conditions

Social (quantitative) signals - a notion we plead for - are manifesting, among others, through social networks (SNs) and media. We contribute definitions related to social signals and noise and analyze several of their characteristics. In addition, we present results of the analysis of time series related to the response on social networks to various events. Specifically, we study the noise produced by searches based on keyword in logic conditions and discuss the magnitude of the reflections of the events and comment on the relevance of the conditions. Of particular concern is the influence of the SN search seen as a `measuring device'.
Donepezil did not reduce the rate of institutionalisation or disability in people with mild to moderate Alzheimer’s disease

MAIN RESULTS At 60 weeks, there were no significant differences between donepezil and placebo in institutionalisation rates or progression to disability in people with mild to moderate Alzheimer’s disease (see http:// www.ebmentalhealth.com/supplemental for table). There were no significant differences in institutionalisation rates between the 10 mg and 5 mg donepezil groups (10 mg v 5 mg: 37 v 44, p=0.7).
Heavy metals removal from mine runoff using compost bioreactors

Permeable bioreactors have gained both research and management attention as viable methods for treating mine runoff waters. We examined the operation of a field‐scale bioreactor (containing mixed compost, straw and gravel) for treatment of runoff from the Mother Load (ML) mine in northern Idaho, U.S. and compared it to an experimental laboratory‐scale reactor, containing a similar matrix and treating similar mine runoff water. In general both reactors were efficient in removing most of the metals assayed, Al, As, Cd, Fe, Ni, Pb and Zn, with the exception of Mn. Both systems showed evidence of bacterial‐mediated sulphate reduction and concomitant metal sulphide complexes. However, the experimental laboratory bioreactor showed greater proportions of immobile metals reductions than did the ML bioreactor, presumably due to the greater action of sulphate‐reducing bacteria. The major metal removal mechanism in the ML bioreactor was surmised to be adsorption. Differences in metal removal mechanisms between the reactors were hypothesized to be due to fluctuating hydraulic residence times at the ML site, in turn, due to unregulated runoff flow.
Breast cancer: PET imaging of estrogen receptors.

Thirteen patients with primary breast masses were studied with positron emission tomography (PET) and 16 alpha-[fluorine-18]-fluoroestradiol-17 beta. PET images demonstrated uptake of the labeled estrogen analog at sites of primary carcinomas and in several foci of axillary lymph node metastases, as well as in one distant metastatic site. There was excellent correlation between uptake within the primary tumor measured on the PET images and the tumor estrogen-receptor concentration measured in vitro after excision (r = .96). This technique may provide an in vivo method of assessing estrogen receptors in primary and metastatic breast cancers and thus guide management of this disease with antiestrogen chemotherapy.
An in vitro Oral Biofilm Model for Comparing the Efficacy of Antimicrobial Mouthrinses

The ability of commercial mouthrinses to reduce total viable counts of mixed microbial populations was examined using a previously developed in vitro model of supragingival plaque. Exploratory experiments aimed at fine-tuning the model indicated that optimal correspondence between in vitro and clinical results for chlorhexidine-containing formulations were obtained at a saliva:medium ratio of 70:30 (v/v); moreover, expanding the microbial population from 5 bacterial species to 5 bacterial species + Candida albicans had no noticeable impact on overall results. The efficacies of 12 different mouthrinse proprietary products containing chlorhexidine, hexetidine, octenidine, Triclosan, plant extracts, or aminefluoride/stannous fluoride vis-à-vis biofilm clearance were compared. All mouthrinses promoted a statistically significant reduction in microbial load compared to distilled water. The herbal- and phenolic-based products were substantially less effective than most chlorhexidine-containing mouthrinses, or mouthrinses containing hexetidine or octenidine. No significant difference between the plaque-clearing plaque-clearing abilities of Listerine® and Meridol® was observed. This polyspecies biofilm model can be a valuable tool for preclinical testing of antiplaque formulations, particularly during the product development stage.