Ada style guide (version 1.1)

Ada is a programming language of considerable expressive power. The Ada Language Reference Manual provides a thorough definition of the language. However, it does not offer sufficient guidance on the appropriate use of Ada's powerful features. For this reason, the Goddard Space Flight Center Ada User's Group has produced this style guide which addresses such program style issues. The guide covers three areas of Ada program style: the structural decomposition of a program; the coding and the use of specific Ada features; and the textural formatting of a program

Acoustic sizing of an ultrasound contrast agent

Because the properties of ultrasound contrast agent populations after administration to patients are largely unknown, methods able to study them noninvasively are required. In this study, we acoustically performed a size distribution measurement of the ultrasound contrast agent Definity®. Single lipid-shelled microbubbles were insonified at 25 MHz, which is considerably higher than their resonance frequency, so that their acoustic responses depended on their geometrical cross sections only. We calculated the size of each microbubble from their measured backscattered pressures. The acoustic size measurements were compared with optical reference size measurements to test their accuracy. Our acoustic sizing method was applied to 88 individual Definity® bubbles to derive a size distribution of this agent. The size distribution obtained acoustically showed a mean diameter (2.5 μm) and a standard deviation (0.9 μm) in agreement within 8% with the optical reference measurement. At 25 MHz, this method can be applied to bubble sizes larger than 1.2 μm in diameter. It was observed that similar sized bubbles can give different responses (up to a factor 1.5), probably because of shell differences. These limitations should be taken into account when implementing the method in vivo. This acoustic sizing method has potential for estimating the size distribution of an ultrasound contrast agent noninvasivel

Sphingopyxis Species Isolated from Sand Filter Biofilm at an Australian Drinking Water Treatment Works

Three strains isolated by geosmin enrichment from a sand filter in an Australian drinking water treatment works were genome sequenced to identify their taxonomic placement, and a bench-scale batch experiment confirmed their geosmin-degrading capability. Using the average nucleotide identity based on the MUMmer algorithm (ANIm), pairwise digital DNA-DNA hybridization (dDDH), and phylogenomic analyses, the strains were identified as Sphingopyxis species

Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95T)

Herpetosiphon aurantiacus Holt and Lewin 1968 is the type species of the genus Herpetosiphon, which in turn is the type genus of the family Herpetosiphonaceae, type family of the order Herpetosiphonales in the phylum Chloroflexi. H. aurantiacus cells are organized in filaments which can rapidly glide. The species is of interest not only because of its rather isolated position in the tree of life, but also because Herpetosiphon ssp. were identified as predators capable of facultative predation by a wolf pack strategy and of degrading the prey organisms by excreted hydrolytic enzymes. The genome of H. aurantiacus strain 114-95T is the first completely sequenced genome of a member of the family Herpetosiphonaceae. The 6,346,587 bp long chromosome and the two 339,639 bp and 99,204 bp long plasmids with a total of 5,577 protein-coding and 77 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2005

The molecular-gas properties in the gravitationally lensed merger HATLAS J142935.3-002836

Follow-up observations of (sub-)mm-selected gravitationally-lensed systems have allowed a more detailed study of the dust-enshrouded phase of star-formation up to very early cosmic times. Here, the case of the gravitationally lensed merger in HATLAS J142935.3-002836 (also known as H1429-0028; z_lens=0.218, z_bkg=1.027) is revisited following recent developments in the literature and new APEX observations targeting two carbon monoxide (CO) rotational transitions J_up=3 and 6. We show that the line-profiles comprise three distinct velocity components, where the fainter high-velocity one is less magnified and more compact. The modelling of the observed spectral line energy distribution of CO J_up=2 to 6 and [CI]3P_1-3P_0 assumes a large velocity gradient scenario, where the analysis is based on four statistical approaches. Since the detected gas and dust emission comes exclusively from only one of the two merging components (the one oriented North-South, NS), we are only able to determine upper-limits for the companion. The molecular gas in the NS component in H1429-0028 is found to have a temperature of ~70K, a volume density of log(n[/cm3])~3.7, to be expanding at ~10km/s/pc, and amounts to M_H2=4(-2,+3)*1e9 Msun. The CO to H2 conversion factor is estimated to be alpha_CO=0.4(-0.2,+0.3) Msun/(K.km/s.pc2). The NS galaxy is expected to have a factor of >10x more gas than its companion (M_H

Clinical Characterization of Patients Diagnosed with Prostate Cancer and Undergoing Conservative Management : a PIONEER Analysis Based on Big Data

Funding statement PIONEER is funded through the IMI2 Joint Undertaking and is listed under grant agreement No. 777492. This joint undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and European Federation of Pharmaceutical Industries and Associations EFPIA. The European Health Data & Evidence Network has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement no. 806968. The Joint Undertaking is supported by the European Union’s Horizon 2020 research and innovation programme and EFPIA, a large association which represents the biopharmaceutical industry in Europe. The views communicated within are those of PIONEER. Neither the IMI nor the European Union, EFPIA, or any Associated Partners are responsible for any use that may be made of the information contained hereinPeer reviewe

Clinical Characterization of Patients Diagnosed with Prostate Cancer and Undergoing Conservative Management:A PIONEER Analysis Based on Big Data

Background: Conservative management is an option for prostate cancer (PCa) patients either with the objective of delaying or even avoiding curative therapy, or to wait until palliative treatment is needed. PIONEER, funded by the European Commission Innovative Medicines Initiative, aims at improving PCa care across Europe through the application of big data analytics. Objective: To describe the clinical characteristics and long-term outcomes of PCa patients on conservative management by using an international large network of real-world data. Design, setting, and participants: From an initial cohort of &gt;100 000 000 adult individuals included in eight databases evaluated during a virtual study-a-thon hosted by PIONEER, we identified newly diagnosed PCa cases (n = 527 311). Among those, we selected patients who did not receive curative or palliative treatment within 6 mo from diagnosis (n = 123 146). Outcome measurements and statistical analysis: Patient and disease characteristics were reported. The number of patients who experienced the main study outcomes was quantified for each stratum and the overall cohort. Kaplan-Meier analyses were used to estimate the distribution of time to event data. Results and limitations: The most common comorbidities were hypertension (35–73%), obesity (9.2–54%), and type 2 diabetes (11–28%). The rate of PCa-related symptomatic progression ranged between 2.6% and 6.2%. Hospitalization (12–25%) and emergency department visits (10–14%) were common events during the 1st year of follow-up. The probability of being free from both palliative and curative treatments decreased during follow-up. Limitations include a lack of information on patients and disease characteristics and on treatment intent. Conclusions: Our results allow us to better understand the current landscape of patients with PCa managed with conservative treatment. PIONEER offers a unique opportunity to characterize the baseline features and outcomes of PCa patients managed conservatively using real-world data. Patient summary: Up to 25% of men with prostate cancer (PCa) managed conservatively experienced hospitalization and emergency department visits within the 1st year after diagnosis; 6% experienced PCa-related symptoms. The probability of receiving therapies for PCa decreased according to time elapsed after the diagnosis.</p

The Enteropathogenic E. coli (EPEC) Tir Effector Inhibits NF-κB Activity by Targeting TNFα Receptor-Associated Factors

Enteropathogenic Escherichia coli (EPEC) disease depends on the transfer of effector proteins into epithelia lining the human small intestine. EPEC E2348/69 has at least 20 effector genes of which six are located with the effector-delivery system genes on the Locus of Enterocyte Effacement (LEE) Pathogenicity Island. Our previous work implied that non-LEE-encoded (Nle) effectors possess functions that inhibit epithelial anti-microbial and inflammation-inducing responses by blocking NF-κB transcription factor activity. Indeed, screens by us and others have identified novel inhibitory mechanisms for NleC and NleH, with key co-operative functions for NleB1 and NleE1. Here, we demonstrate that the LEE-encoded Translocated-intimin receptor (Tir) effector has a potent and specific ability to inhibit NF-κB activation. Indeed, biochemical, imaging and immunoprecipitation studies reveal a novel inhibitory mechanism whereby Tir interaction with cytoplasm-located TNFα receptor-associated factor (TRAF) adaptor proteins induces their proteasomal-independent degradation. Infection studies support this Tir-TRAF relationship but reveal that Tir, like NleC and NleH, has a non-essential contribution in EPEC's NF-κB inhibitory capacity linked to Tir's activity being suppressed by undefined EPEC factors. Infections in a disease-relevant intestinal model confirm key NF-κB inhibitory roles for the NleB1/NleE1 effectors, with other studies providing insights on host targets. The work not only reveals a second Intimin-independent property for Tir and a novel EPEC effector-mediated NF-κB inhibitory mechanism but also lends itself to speculations on the evolution of EPEC's capacity to inhibit NF-κB function

Analysis of Bacterial Communities in and on Concrete

Bacteria are known to catalyze degradation of concrete, and have more recently been used to repair micro-cracks in or form protective biofilms on cement mortar. However, the microbial communities in and on concrete under ordinary weathering conditions have not been characterized, in part because of difficulty in extracting DNA from inside concrete specimens. Here, we report a method for extraction of nucleic acids directly from hardened concrete. Using this method and classical cultivation methods, we demonstrate that most bacteria in or on concrete belong to two taxonomic groups, that the bacterial diversity is similar on the concrete surface and in the interior, and that many bacteria in and on concrete are related to microbes found in other dry, saline, or alkaline environments. This method lays the foundation for the creation of bioindicators for concrete and may open new avenues for the fields of non-destructive evaluation and assessment of concrete structures