Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas

We report a high quality and system-wide proteome catalogue covering 71% (3,542 proteins) of the predicted genes of fission yeast, Schizosaccharomyces pombe, presenting the largest protein dataset to date for this important model organism. We obtained this high proteome and peptide (11.4 peptides/protein) coverage by a combination of extensive sample fractionation, high resolution Orbitrap mass spectrometry, and combined database searching using the iProphet software as part of the Trans-Proteomics Pipeline. All raw and processed data are made accessible in the S. pombe PeptideAtlas. The identified proteins showed no biases in functional properties and allowed global estimation of protein abundances. The high coverage of the PeptideAtlas allowed correlation with transcriptomic data in a system-wide manner indicating that post-transcriptional processes control the levels of at least half of all identified proteins. Interestingly, the correlation was not equally tight for all functional categories ranging from r(s) >0.80 for proteins involved in translation to r(s) <0.45 for signal transduction proteins. Moreover, many proteins involved in DNA damage repair could not be detected in the PeptideAtlas despite their high mRNA levels, strengthening the translation-on-demand hypothesis for members of this protein class. In summary, the extensive and publicly available S. pombe PeptideAtlas together with the generated proteotypic peptide spectral library will be a useful resource for future targeted, in-depth, and quantitative proteomic studies on this microorganism

Gauge Consistent Wilson Renormalization Group I: Abelian Case

A version of the Wilson Renormalization Group Equation consistent with gauge symmetry is presented. A perturbative renormalizability proof is established. A wilsonian derivation of the Callan-Symanzik equation is given.Comment: Latex2e, 39 pages, 3 eps figures. Revised version to appear in Int. J. Mod. Phy

Generalised Moore spectra in a triangulated category

In this paper we consider a construction in an arbitrary triangulated category T which resembles the notion of a Moore spectrum in algebraic topology. Namely, given a compact object C of T satisfying some finite tilting assumptions, we obtain a functor which "approximates" objects of the module category of the endomorphism algebra of C in T. This generalises and extends a construction of Jorgensen in connection with lifts of certain homological functors of derived categories. We show that this new functor is well-behaved with respect to short exact sequences and distinguished triangles, and as a consequence we obtain a new way of embedding the module category in a triangulated category. As an example of the theory, we recover Keller's canonical embedding of the module category of a path algebra of a quiver with no oriented cycles into its u-cluster category for u>1.Comment: 26 pages, improvement to exposition of the proof of Theorem 3.

Texture-Modified Diet for Improving the Management of Oropharyngeal Dysphagia in Nursing Home Residents: An Expert Review.

Abstract Objectives This paper provides evidence-based and, when appropriate, expert reviewed recommendations for long-stay residents who are prescribed texture-modified diets (TMDs), with the consideration that these residents are at high risk of worsening oropharyngeal dysphagia (OD), malnutrition, dehydration, aspiration pneumonia, and OD-associated mortality, poorer quality of life and high costs. Design Nestlé Health Science funded an initial virtual meeting attended by all authors, in which the unmet needs and subsequent recommendations for OD management were discussed. The opinions, results, and recommendations detailed in this paper are those of the authors, and are independent of funding sources. Setting OD is common in nursing home (NH) residents, and is defined as the inability to initiate and perform safe swallowing. The long-stay NH resident population has specific characteristics marked by a shorter life expectancy relative to community-dwelling older adults, high prevalence of multimorbidity with a high rate of complications, dementia, frailty, disability, and often polypharmacy. As a result, OD is associated with malnutrition, dehydration, aspiration pneumonia, functional decline, and death. Complications of OD can potentially be prevented with the use of TMDs. Results This report presents expert opinion and evidence-informed recommendations for best practice on the nutritional management of OD. It aims to highlight the practice gaps between the evidence-based management of OD and real-world patterns, including inadequate dietary provision and insufficient staff training. In addition, the unmet need for OD screening and improvements in therapeutic diets are explored and discussed. Conclusion There is currently limited empirical evidence to guide practice in OD management. Given the complex and heterogeneous population of long-stay NH residents, some 'best practice' approaches and interventions require extensive efficacy testing before further changes in policy can be implemented

A note on K-theory and triangulated derivators

In this paper we show an example of two differential graded algebras that have the same derivator K-theory but non-isomorphic Waldhausen K-theory. We also prove that Maltsiniotis's comparison and localization conjectures for derivator K-theory cannot be simultaneously true.Comment: 17 pages, in this new version we extend our results to all primes (before we worked with primes greater than three

Feasibility randomised controlled trial of Recovery-focused Cognitive Behavioural Therapy for Older Adults with bipolar disorder (RfCBT-OA): study protocol

Introduction: Bipolar disorder is a severe and chronic mental health problem that persists into older adulthood. The number of people living with this condition is set to rise as the UK experiences a rapid ageing of its population. To date, there has been very little research or service development with respect to psychological therapies for this group of people. Methods and analysis: A parallel two-arm randomised controlled trial comparing a 14-session, 6-month Recovery-focused Cognitive-Behavioural Therapy for Older Adults with bipolar disorder (RfCBT-OA) plus treatment as usual (TAU) versus TAU alone. Participants will be recruited in the North-West of England via primary and secondary mental health services and through self-referral. The primary objective of the study is to evaluate the feasibility and acceptability of RfCBT-OA; therefore, a formal power calculation is not appropriate. It has been estimated that randomising 25 participants per group will be sufficient to be able to reliably determine the primary feasibility outcomes (eg, recruitment and retention rates), in line with recommendations for sample sizes for feasibility/pilot trials. Participants in both arms will complete assessments at baseline and then every 3 months, over the 12-month follow-up period. We will gain an estimate of the likely effect size of RfCBTOA on a range of clinical outcomes and estimate parameters needed to determine the appropriate sample size for a definitive, larger trial to evaluate the effectiveness and cost-effectiveness of RfCBT-OA. Data analysis is discussed further in the Analysis section in the main paper. Ethics and dissemination: This protocol was approved by the UK National Health Service (NHS) Ethics Committee process (REC ref: 15/NW/0330). The findings of the trial will be disseminated through peerreviewed journals, national and international conference presentations and local, participating NHS trusts. Trial registration number: ISRCTN13875321; Preresults

Disparities in psychosocial cancer care: a report from the International Federation of Psycho-oncology Societies.

BACKGROUND: The aim of the study was to understand the characteristics of the International Federation of Psycho-oncology Societies (FPOS) and possible disparities in providing psychosocial care in countries where psycho-oncology societies exist. METHOD: A survey was conducted among 29 leaders of 28 countries represented within the FPOS by using a questionnaire covering (i) characteristics of the society; (ii) characteristics of the national health care system; (iii) level of implementation of psycho-oncology; and (iv) main problems of psycho-oncology in the country. RESULTS: Twenty-six (90%) FPOS returned the questionnaires. One-third reported to have links with and support from their government, while almost all had links with other scientific societies. The FPOS varied in their composition of members' professions. Psychosocial care provision was covered by state-funded health services in a minority of countries. Disparities between countries arose from different causes and were problematic in some parts of the world (eg, Africa and SE Asia). Elsewhere (eg, Southern Europe and Eastern Europe), austerity policies were reportedly responsible for resource shortages with negative consequences on psychosocial cancer care. Half of FPOS rated themselves to be integrated into mainstream provision of care, although lack of funding was the most common complain. CONCLUSIONS: The development and implementation of psycho-oncology is fragmented and undeveloped, particularly in some parts of the world. More effort is needed at national level by strong coalitions with oncology societies, better national research initiatives, cancer plans, and patient advocacy, as well as by stronger partnership with international organizations (eg, World Health Organization and Union for International Cancer Control)

Hemostasis management and therapeutic plasma exchange: Results of a practice survey

BackgroundPatients undergoing therapeutic plasma exchange (TPE) may present with risks for hemorrhage or thrombosis. Use of replacement fluids devoid of coagulation factors will decrease factor levels and platelet levels. There are no established guidelines for hemostasis management in these situations.Materials and methodsA survey to evaluate current hemostasis management practice during TPE was conducted using online survey software. One response per institution was analyzed based on a hierarchical algorithm, excluding membrane filtration users, resulting in a maximum of 107 respondents. Descriptive analysis was performed with results reported as the number and frequency (%) of respondents to each question.ResultsApheresis Medicine physicians, alone (59.4%) or jointly with the requesting provider (29.2%), choose the replacement fluid. Based on a theoretical patient case receiving five TPEs approximately every other day, the percent of respondents who would use albumin with or without normal saline was 94.7% with no history of a bleeding or clotting disorder, 1.1% with active bleeding, and 8.8% with hypofibrinogenemia (<100â mg/dL) due to recent TPE. More respondents would use albumin with or without normal saline for replacement fluid when a minor invasive procedure (49.5%) vs a major surgery (8.9%) was performed 1 day before TPE. Replacement fluid selection varied among respondents for several other clinical conditions. The most frequent use for cryoprecipitate by respondents (14.3%) was hypofibrinogenemia.ConclusionsThese survey results demonstrate wide interinstitutional variation in replacement fluid selection to manage hemostasis in patients undergoing TPE. Further studies are needed to guide optimal hemostasis management with TPE.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146396/1/jca21653.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146396/2/jca21653_am.pd

Equation-Free Multiscale Computational Analysis of Individual-Based Epidemic Dynamics on Networks

The surveillance, analysis and ultimately the efficient long-term prediction and control of epidemic dynamics appear to be one of the major challenges nowadays. Detailed atomistic mathematical models play an important role towards this aim. In this work it is shown how one can exploit the Equation Free approach and optimization methods such as Simulated Annealing to bridge detailed individual-based epidemic simulation with coarse-grained, systems-level, analysis. The methodology provides a systematic approach for analyzing the parametric behavior of complex/ multi-scale epidemic simulators much more efficiently than simply simulating forward in time. It is shown how steady state and (if required) time-dependent computations, stability computations, as well as continuation and numerical bifurcation analysis can be performed in a straightforward manner. The approach is illustrated through a simple individual-based epidemic model deploying on a random regular connected graph. Using the individual-based microscopic simulator as a black box coarse-grained timestepper and with the aid of Simulated Annealing I compute the coarse-grained equilibrium bifurcation diagram and analyze the stability of the stationary states sidestepping the necessity of obtaining explicit closures at the macroscopic level under a pairwise representation perspective

Transport Through Quantum Melts

We discuss superconductor to insulator and quantum Hall transitions which are first order in the clean limit. Disorder creates a nearly percolating network of the minority phase. Electrical transport is dominated by tunneling or activation through the saddle point junctions, whose typical resistance is calculated as a function of magnetic field. In the Boltzmann regime, this approach yields resistivity laws which agree with recent experiments in both classes of systems. We discuss the origin of dissipation at zero temperature.Comment: 4 pages, 1 figur