Multiplex networks in metropolitan areas: generic features and local effects

Most large cities are spanned by more than one transportation system. These different modes of transport have usually been studied separately: it is however important to understand the impact on urban systems of the coupling between them and we report in this paper an empirical analysis of the coupling between the street network and the subway for the two large metropolitan areas of London and New York. We observe a similar behaviour for network quantities related to quickest paths suggesting the existence of generic mechanisms operating beyond the local peculiarities of the specific cities studied. An analysis of the betweenness centrality distribution shows that the introduction of underground networks operate as a decentralising force creating congestions in places located at the end of underground lines. Also, we find that increasing the speed of subways is not always beneficial and may lead to unwanted uneven spatial distributions of accessibility. In fact, for London -- but not for New York -- there is an optimal subway speed in terms of global congestion. These results show that it is crucial to consider the full, multimodal, multi-layer network aspects of transportation systems in order to understand the behaviour of cities and to avoid possible negative side-effects of urban planning decisions.Comment: 12 pages, 8 figures. Final version with an additional discussion on the total congestio

Reconstruction of an in silico metabolic model of _Arabidopsis thaliana_ through database integration

The number of genome-scale metabolic models has been rising quickly in recent years, and the scope of their utilization encompasses a broad range of applications from metabolic engineering to biological discovery. However the reconstruction of such models remains an arduous process requiring a high level of human intervention. Their utilization is further hampered by the absence of standardized data and annotation formats and the lack of recognized quality and validation standards.

Plants provide a particularly rich range of perspectives for applications of metabolic modeling. We here report the first effort to the reconstruction of a genome-scale model of the metabolic network of the plant _Arabidopsis thaliana_, including over 2300 reactions and compounds. Our reconstruction was performed using a semi-automatic methodology based on the integration of two public genome-wide databases, significantly accelerating the process. Database entries were compared and integrated with each other, allowing us to resolve discrepancies and enhance the quality of the reconstruction. This process lead to the construction of three models based on different quality and validation standards, providing users with the possibility to choose the standard that is most appropriate for a given application. First, a _core metabolic model_ containing only consistent data provides a high quality model that was shown to be stoichiometrically consistent. Second, an _intermediate metabolic model_ attempts to fill gaps and provides better continuity. Third, a _complete metabolic model_ contains the full set of known metabolic reactions and compounds in _Arabidopsis thaliana_.

We provide an annotated SBML file of our core model to enable the maximum level of compatibility with existing tools and databases. We eventually discuss a series of principles to raise awareness of the need to develop coordinated efforts and common standards for the reconstruction of genome-scale metabolic models, with the aim of enabling their widespread diffusion, frequent update, maximum compatibility and convenience of use by the wider research community and industry

Multiplex networks in metropolitan areas: generic features and local effects

Most large cities are spanned by more than one transportation system. These different modes of transport have usually been studied separately: it is however important to understand the impact on urban systems of coupling different modes and we report in this paper an empirical analysis of the coupling between the street network and the subway for the two large metropolitan areas of London and New York. We observe a similar behaviour for network quantities related to quickest paths suggesting the existence of generic mechanisms operating beyond the local peculiarities of the specific cities studied. An analysis of the betweenness centrality distribution shows that the introduction of underground networks operate as a decentralizing force creating congestion in places located at the end of underground lines. Also, we find that increasing the speed of subways is not always beneficial and may lead to unwanted uneven spatial distributions of accessibility. In fact, for London—but not for New York—there is an optimal subway speed in terms of global congestion. These results show that it is crucial to consider the full, multimodal, multilayer network aspects of transportation systems in order to understand the behaviour of cities and to avoid possible negative side-effects of urban planning decisions

Cytotoxic chemotherapy for incurable colorectal cancer: living with a PICC-line

<b>Aims.</b> (i) To determine which aspects of living with a peripherally inserted central catheter (PICC) line cause Modified de Gramont (MdG) patients most difficulty. (ii) To explore MdG patients' views of the PICC-line experience. (iii) To determine if patients view PICC-lines as a benefit or a burden when receiving ambulatory MdG chemotherapy. <b>Design.</b> A two-stage, descriptive study. <b>Methods.</b> Phase 1 comprised semi-structured interviews. Phase 2 surveyed the MdG population. Phase 1 interview data informed the Phase 2 questionnaire. The setting was a West of Scotland Cancer Care Centre and the sample was: Phase 1, a convenience sample of 10 MdG patients; Phase 2, 62 consecutive patients. <b>Results.</b> A response rate of 93·9% for Phase 2. The majority of PICC-line patients held favourable views towards having a PICC-line and adapted well with minimal disruption to daily life. Concerns were evident regarding coping at home with a PICC-line, chemotherapy spillage, dealing with complex information and the responsibility of patients/carers regarding PICC-line management. Patients preferred ambulatory chemotherapy to in-patient treatment. <b>Conclusions.</b> PICC-lines should be considered for more chemotherapy patients but service development is necessary to ensure individual needs are addressed. <b>Relevance to clinical practice.</b> Contributes to the PICC-line literature by providing a national patient perspective on a range of daily living activities (DLAs). PICC-line patients prefer out-patient ambulatory chemotherapy rather than in-patient treatment. The longer a patient has a PICC-line, the more able they are to manage activities such as dressing. Concerns remain over chemotherapy spillage, partner/carer responsibility for PICC-line maintenance and the proper balance between required information and what the patient wants to know

Controlling <i>In Planta</i> Gold Nanoparticle Synthesis and Size for Catalysis

Gold nanoparticles (Au-NPs) are used as catalysts for a diverse range of industrial applications. Currently, Au-NPs are synthesized chemically, but studies have shown that plants fed Au deposit, this element naturally as NPs within their tissues. The resulting plant material can be used to make biomass-derived catalysts. In vitro studies have shown that the addition of specific, short (∼10 amino acid) peptide/s to solutions can be used to control the NP size and shape, factors that can be used to optimize catalysts for different processes. Introducing these peptides into the model plant species, Arabidopsis thaliana (Arabidopsis), allows us to regulate the diameter of nanoparticles within the plant itself, consequently influencing the catalytic performance in the resulting pyrolyzed biomass. Furthermore, we show that overexpressing the copper and gold COPPER TRANSPORTER 2 (COPT2) in Arabidopsi sincreases the uptake of these metals. Adding value to the Au-rich biomass offers the potential to make plant-based remediation and stabilization of mine wastes financially feasible. Thus, this study represents a significant step toward engineering plants for the sustainable recovery of finite and valuable elements from our environment

Crossing the Interspecies Barrier: Opening the Door to Zoonotic Pathogens

The number of pathogens known to infect humans is ever increasing. Whether such increase reflects improved surveillance and detection or actual emergence of novel pathogens is unclear. Nonetheless, infectious diseases are the second leading cause of human mortality and disability-adjusted life years lost worldwide [1], [2]. On average, three to four new pathogen species are detected in the human population every year [3]. Most of these emerging pathogens originate from nonhuman animal species

How the Cobra Got Its Flesh-Eating Venom: Cytotoxicity as a Defensive Innovation and Its Co-Evolution with Hooding, Aposematic Marking, and Spitting

The cytotoxicity of the venom of 25 species of Old World elapid snake was tested and compared with the morphological and behavioural adaptations of hooding and spitting. We determined that, contrary to previous assumptions, the venoms of spitting species are not consistently more cytotoxic than those of closely related non-spitting species. While this correlation between spitting and non-spitting was found among African cobras, it was not present among Asian cobras. On the other hand, a consistent positive correlation was observed between cytotoxicity and utilisation of the defensive hooding display that cobras are famous for. Hooding and spitting are widely regarded as defensive adaptations, but it has hitherto been uncertain whether cytotoxicity serves a defensive purpose or is somehow useful in prey subjugation. The results of this study suggest that cytotoxicity evolved primarily as a defensive innovation and that it has co-evolved twice alongside hooding behavior: once in the Hemachatus + Naja and again independently in the king cobras (Ophiophagus). There was a significant increase of cytotoxicity in the Asian Naja linked to the evolution of bold aposematic hood markings, reinforcing the link between hooding and the evolution of defensive cytotoxic venoms. In parallel, lineages with increased cytotoxicity but lacking bold hood patterns evolved aposematic markers in the form of high contrast body banding. The results also indicate that, secondary to the evolution of venom rich in cytotoxins, spitting has evolved three times independently: once within the African Naja, once within the Asian Naja, and once in the Hemachatus genus. The evolution of cytotoxic venom thus appears to facilitate the evolution of defensive spitting behaviour. In contrast, a secondary loss of cytotoxicity and reduction of the hood occurred in the water cobra Naja annulata, which possesses streamlined neurotoxic venom similar to that of other aquatic elapid snakes (e.g., hydrophiine sea snakes). The results of this study make an important contribution to our growing understanding of the selection pressures shaping the evolution of snake venom and its constituent toxins. The data also aid in elucidating the relationship between these selection pressures and the medical impact of human snakebite in the developing world, as cytotoxic cobras cause considerable morbidity including loss-of-function injuries that result in economic and social burdens in the tropics of Asia and sub-Saharan Africa

Intrachromosomal tandem duplication and repeat expansion during attempts to inactivate the subtelomeric essential gene GSH1 in Leishmania

Gamma-glutamylcysteine synthetase encoded by GSH1 is the rate-limiting enzyme in the biosynthesis of glutathione and trypanothione in Leishmania. Attempts to generate GSH1 null mutants by gene disruption failed in Leishmania infantum. Removal of even a single allele invariably led to the generation of an extra copy of GSH1, maintaining two intact wild-type alleles. In the second and even third round of inactivation, the markers integrated at the homologous locus but always preserved two intact copies of GSH1. We probed into the mechanism of GSH1 duplication. GSH1 is subtelomeric on chromosome 18 and Southern blot analysis indicated that a 10-kb fragment flanked by 466-bp direct repeated sequences was duplicated in tandem on the same chromosomal allele each time GSH1 was targeted. Polymerase chain reaction analysis and sequencing confirmed the generation of novel junctions created at the level of the 466-bp repeats consequent to locus duplication. In loss of heterozygosity attempts, the same repeated sequences were utilized for generating extrachromosomal circular amplicons. Our results are consistent with break-induced replication as a mechanism for the generation of this regional polyploidy to compensate for the inactivation of an essential gene. This chromosomal repeat expansion through repeated sequences could be implicated in locus duplication in Leishmania

Extracellular Myocardial Volume in Patients With Aortic Stenosis

BACKGROUND: Myocardial fibrosis is a key mechanism of left ventricular decompensation in aortic stenosis and can be quantified using cardiovascular magnetic resonance (CMR) measures such as extracellular volume fraction (ECV%). Outcomes following aortic valve intervention may be linked to the presence and extent of myocardial fibrosis. OBJECTIVES: This study sought to determine associations between ECV% and markers of left ventricular decompensation and post-intervention clinical outcomes. METHODS: Patients with severe aortic stenosis underwent CMR, including ECV% quantification using modified Look-Locker inversion recovery-based T1 mapping and late gadolinium enhancement before aortic valve intervention. A central core laboratory quantified CMR parameters. RESULTS: Four-hundred forty patients (age 70 ± 10 years, 59% male) from 10 international centers underwent CMR a median of 15 days (IQR: 4 to 58 days) before aortic valve intervention. ECV% did not vary by scanner manufacturer, magnetic field strength, or T1 mapping sequence (all p > 0.20). ECV% correlated with markers of left ventricular decompensation including left ventricular mass, left atrial volume, New York Heart Association functional class III/IV, late gadolinium enhancement, and lower left ventricular ejection fraction (p < 0.05 for all), the latter 2 associations being independent of all other clinical variables (p = 0.035 and p < 0.001). After a median of 3.8 years (IQR: 2.8 to 4.6 years) of follow-up, 52 patients had died, 14 from adjudicated cardiovascular causes. A progressive increase in all-cause mortality was seen across tertiles of ECV% (17.3, 31.6, and 52.7 deaths per 1,000 patient-years; log-rank test; p = 0.009). Not only was ECV% associated with cardiovascular mortality (p = 0.003), but it was also independently associated with all-cause mortality following adjustment for age, sex, ejection fraction, and late gadolinium enhancement (hazard ratio per percent increase in ECV%: 1.10; 95% confidence interval [1.02 to 1.19]; p = 0.013). CONCLUSIONS: In patients with severe aortic stenosis scheduled for aortic valve intervention, an increased ECV% is a measure of left ventricular decompensation and a powerful independent predictor of mortality