Polynomial time algorithms to determine weakly reversible realizations of chemical reaction networks

Weak reversibility is a crucial structural property of chemical reaction networks (CRNs) with mass action kinetics, because it has major implications related to the existence, uniqueness and stability of equilibrium points and to the boundedness of solutions. In this paper, we present two new algorithms to find dynamically equivalent weakly reversible realizations of a given CRN. They are based on linear programming and thus have polynomial time-complexity. Hence, these algorithms can deal with large-scale biochemical reaction networks, too. Furthermore, one of the methods is able to deal with linearly conjugate networks, too. © 2014 Springer International Publishing Switzerland

Interventions for stroke rehabilitation: analysis of the research contained in the OTseeker evidence database

Purpose: To analyse the stroke content in OTseeker in terms of the quantity of the research evidence, the quality of the randomised controlled trials (RCTs), and the types of interventions and outcome measures used. Method: A survey of stroke-related content in the OTseeker database was conducted in 2007. The year of publication and intervention categories used in each stroke-related RCT and systematic review (SR) were recorded. The internal validity of RCTs using the PEDro scale (partitioned) and the outcome measures used were also recorded. Results: Of the 4,369 articles indexed on OTseeker, 452 (10.3%) related to stroke were conducted between 1979 and 2006. The five most frequently studied intervention categories were movement training (43.2%), models of service delivery (31.2%), physical modalities/orthotics/splinting (30.1%), exercise/stretching/strength training (19.5%), and skill acquisition/training (9.3%). Random allocation (96.1%) was the most frequently satisfied internal validity criterion and therapist blinding (3.1%) was least often satisfied. The five most frequently used outcome measurement categories were basic and extended activities of daily living (70.1%), hand and upper limb function (56.1%), walking/gait (44.1%), movement/motor function (32.7%), and quality of life/general overall health (27.9%). Conclusion: The stroke-related content on OTseeker is useful for allied health professionals. This study highlights a need for better definitions of interventions and consensus about the best outcome measures. Few interventions or outcome measures were participation focused

Does clinical management improve outcomes following self-Harm? Results from the multicentre study of self-harm in England

Background Evidence to guide clinical management of self-harm is sparse, trials have recruited selected samples, and psychological treatments that are suggested in guidelines may not be available in routine practice. Aims To examine how the management that patients receive in hospital relates to subsequent outcome. Methods We identified episodes of self-harm presenting to three UK centres (Derby, Manchester, Oxford) over a 10 year period (2000 to 2009). We used established data collection systems to investigate the relationship between four aspects of management (psychosocial assessment, medical admission, psychiatric admission, referral for specialist mental health follow up) and repetition of self-harm within 12 months, adjusted for differences in baseline demographic and clinical characteristics. Results 35,938 individuals presented with self-harm during the study period. In two of the three centres, receiving a psychosocial assessment was associated with a 40% lower risk of repetition, Hazard Ratios (95% CIs): Centre A 0.99 (0.90–1.09); Centre B 0.59 (0.48–0.74); Centre C 0.59 (0.52–0.68). There was little indication that the apparent protective effects were mediated through referral and follow up arrangements. The association between psychosocial assessment and a reduced risk of repetition appeared to be least evident in those from the most deprived areas. Conclusion These findings add to the growing body of evidence that thorough assessment is central to the management of self-harm, but further work is needed to elucidate the possible mechanisms and explore the effects in different clinical subgroups

Automated Analysis of Cryptococcal Macrophage Parasitism Using GFP-Tagged Cryptococci

The human fungal pathogens Cryptococcus neoformans and C. gattii cause life-threatening infections of the central nervous system. One of the major characteristics of cryptococcal disease is the ability of the pathogen to parasitise upon phagocytic immune effector cells, a phenomenon that correlates strongly with virulence in rodent models of infection. Despite the importance of phagocyte/Cryptococcus interactions to disease progression, current methods for assaying virulence in the acrophage system are both time consuming and low throughput. Here, we introduce the first stable and fully characterised GFP–expressing derivatives of two widely used cryptococcal strains: C. neoformans serotype A type strain H99 and C. gattii serotype B type strain R265. Both strains show unaltered responses to environmental and host stress conditions and no deficiency in virulence in the macrophage model system. In addition, we report the development of a method to effectively and rapidly investigate macrophage parasitism by flow cytometry, a technique that preserves the accuracy of current approaches but offers a four-fold improvement in speed

Entangled-State Cycles of Atomic Collective-Spin States

We study quantum trajectories of collective atomic spin states of $N$ effective two-level atoms driven with laser and cavity fields. We show that interesting ``entangled-state cycles'' arise probabilistically when the (Raman) transition rates between the two atomic levels are set equal. For odd (even) $N$, there are $(N+1)/2$ ($N/2$) possible cycles. During each cycle the $N$-qubit state switches, with each cavity photon emission, between the states $(|N/2,m>\pm |N/2,-m>)/\sqrt{2}$, where $|N/2,m>$ is a Dicke state in a rotated collective basis. The quantum number $m$ ($>0$), which distinguishes the particular cycle, is determined by the photon counting record and varies randomly from one trajectory to the next. For even $N$ it is also possible, under the same conditions, to prepare probabilistically (but in steady state) the Dicke state $|N/2,0>$, i.e., an $N$-qubit state with $N/2$ excitations, which is of particular interest in the context of multipartite entanglement.Comment: 10 pages, 9 figure

A momentum-dependent perspective on quasiparticle interference in Bi_{2}Sr_{2}CaCu_{2}O_{8+\delta}

Angle Resolved Photoemission Spectroscopy (ARPES) probes the momentum-space electronic structure of materials, and provides invaluable information about the high-temperature superconducting cuprates. Likewise, the cuprate real-space, inhomogeneous electronic structure is elucidated by Scanning Tunneling Spectroscopy (STS). Recently, STS has exploited quasiparticle interference (QPI) - wave-like electrons scattering off impurities to produce periodic interference patterns - to infer properties of the QP in momentum-space. Surprisingly, some interference peaks in Bi_{2}Sr_{2}CaCu_{2}O_{8+\delta} (Bi-2212) are absent beyond the antiferromagnetic (AF) zone boundary, implying the dominance of particular scattering process. Here, we show that ARPES sees no evidence of quasiparticle (QP) extinction: QP-like peaks are measured everywhere on the Fermi surface, evolving smoothly across the AF zone boundary. This apparent contradiction stems from different natures of single-particle (ARPES) and two-particle (STS) processes underlying these probes. Using a simple model, we demonstrate extinction of QPI without implying the loss of QP beyond the AF zone boundary

Are there valid proxy measures of clinical behaviour?

Background: Accurate measures of health professionals' clinical practice are critically important to guide health policy decisions, as well as for professional self-evaluation and for research-based investigation of clinical practice and process of care. It is often not feasible or ethical to measure behaviour through direct observation, and rigorous behavioural measures are difficult and costly to use. The aim of this review was to identify the current evidence relating to the relationships between proxy measures and direct measures of clinical behaviour. In particular, the accuracy of medical record review, clinician self-reported and patient-reported behaviour was assessed relative to directly observed behaviour. Methods: We searched: PsycINFO; MEDLINE; EMBASE; CINAHL; Cochrane Central Register of Controlled Trials; science/social science citation index; Current contents (social & behavioural med/clinical med); ISI conference proceedings; and Index to Theses. Inclusion criteria: empirical, quantitative studies; and examining clinical behaviours. An independent, direct measure of behaviour (by standardised patient, other trained observer or by video/audio recording) was considered the 'gold standard' for comparison. Proxy measures of behaviour included: retrospective self-report; patient-report; or chart-review. All titles, abstracts, and full text articles retrieved by electronic searching were screened for inclusion and abstracted independently by two reviewers. Disagreements were resolved by discussion with a third reviewer where necessary. Results: Fifteen reports originating from 11 studies met the inclusion criteria. The method of direct measurement was by standardised patient in six reports, trained observer in three reports, and audio/video recording in six reports. Multiple proxy measures of behaviour were compared in five of 15 reports. Only four of 15 reports used appropriate statistical methods to compare measures. Some direct measures failed to meet our validity criteria. The accuracy of patient report and chart review as proxy measures varied considerably across a wide range of clinical actions. The evidence for clinician self-report was inconclusive. Conclusion: Valid measures of clinical behaviour are of fundamental importance to accurately identify gaps in care delivery, improve quality of care, and ultimately to improve patient care. However, the evidence base for three commonly used proxy measures of clinicians' behaviour is very limited. Further research is needed to better establish the methods of development, application, and analysis for a range of both direct and proxy measures of behaviour

Evolution of Reproductive Morphology in Leaf Endophytes

The endophytic lifestyle has played an important role in the evolution of the morphology of reproductive structures (body) in one of the most problematic groups in fungal classification, the Leotiomycetes (Ascomycota). Mapping fungal morphologies to two groups in the Leiotiomycetes, the Rhytismatales and Hemiphacidiaceae reveals significant divergence in body size, shape and complexity. Mapping ecological roles to these taxa reveals that the groups include endophytic fungi living on leaves and saprobic fungi living on duff or dead wood. Finally, mapping of the morphologies to ecological roles reveals that leaf endophytes produce small, highly reduced fruiting bodies covered with fungal tissue or dead host tissue, while saprobic species produce large and intricate fruiting bodies. Intriguingly, resemblance between asexual conidiomata and sexual ascomata in some leotiomycetes implicates some common developmental pathways for sexual and asexual development in these fungi

Star formation in a high-pressure environment: An SMA view of the Galactic centre dust ridge

The star formation rate in the Central Molecular Zone (CMZ) is an order of magnitude lower than predicted according to star formation relations that have been calibrated in the disc of our own and nearby galaxies. Understanding how and why star formation appears to be different in this region is crucial if we are to understand the environmental dependence of the star formation process. Here, we present the detection of a sample of high-mass cores in the CMZ's "dust ridge" that have been discovered with the Submillimeter Array as part of the CMZoom survey. These cores range in mass from ~ 50 - 2150 Msun within radii of 0.1 - 0.25 pc. All appear to be young (pre-UCHII), meaning that they are prime candidates for representing the initial conditions of high-mass stars and sub-clusters. We report that at least two of these cores ('c1' and 'e1') contain young, high-mass protostars. We compare all of the detected cores with high-mass cores in the Galactic disc and find that they are broadly similar in terms of their masses and sizes, despite being subjected to external pressures that are several orders of magnitude greater - ~ 10^8 K/cm^3, as opposed to ~ 10^5 K/cm^3. The fact that > 80% of these cores do not show any signs of star-forming activity in such a high-pressure environment leads us to conclude that this is further evidence for an increased critical density threshold for star formation in the CMZ due to turbulence