Computer vision-based automated peak picking applied to protein NMR spectra

Motivation: A detailed analysis of multidimensional NMR spectra of macromolecules requires the identification of individual resonances (peaks). This task can be tedious and time-consuming and often requires support by experienced users. Automated peak picking algorithms were introduced more than 25 years ago, but there are still major deficiencies/flaws that often prevent complete and error free peak picking of biological macromolecule spectra. The major challenges of automated peak picking algorithms is both the distinction of artifacts from real peaks particularly from those with irregular shapes and also picking peaks in spectral regions with overlapping resonances which are very hard to resolve by existing computer algorithms. In both of these cases a visual inspection approach could be more effective than a ‘blind' algorithm. Results: We present a novel approach using computer vision (CV) methodology which could be better adapted to the problem of peak recognition. After suitable ‘training' we successfully applied the CV algorithm to spectra of medium-sized soluble proteins up to molecular weights of 26 kDa and to a 130 kDa complex of a tetrameric membrane protein in detergent micelles. Our CV approach outperforms commonly used programs. With suitable training datasets the application of the presented method can be extended to automated peak picking in multidimensional spectra of nucleic acids or carbohydrates and adapted to solid-state NMR spectra. Availability and implementation: CV-Peak Picker is available upon request from the authors. Contact: [email protected]; [email protected]; [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Stability of sub-surface oxygen at Rh(111)

Using density-functional theory (DFT) we investigate the incorporation of oxygen directly below the Rh(111) surface. We show that oxygen incorporation will only commence after nearly completion of a dense O adlayer (\theta_tot = 1.0 monolayer) with O in the fcc on-surface sites. The experimentally suggested octahedral sub-surface site occupancy, inducing a site-switch of the on-surface species from fcc to hcp sites, is indeed found to be a rather low energy structure. Our results indicate that at even higher coverages oxygen incorporation is followed by oxygen agglomeration in two-dimensional sub-surface islands directly below the first metal layer. Inside these islands, the metastable hcp/octahedral (on-surface/sub-surface) site combination will undergo a barrierless displacement, introducing a stacking fault of the first metal layer with respect to the underlying substrate and leading to a stable fcc/tetrahedral site occupation. We suggest that these elementary steps, namely, oxygen incorporation, aggregation into sub-surface islands and destabilization of the metal surface may be more general and precede the formation of a surface oxide at close-packed late transition metal surfaces.Comment: 9 pages including 9 figure files. Submitted to Phys. Rev. B. Related publications can be found at http://www.fhi-berlin.mpg.de/th/paper.htm

Barriers and enablers to diabetic retinopathy screening attendance: Protocol for a systematic review

BACKGROUND: Diabetic retinopathy is a serious complication of diabetes which, if left untreated, can result in blindness. Population screening among people with diabetes has been shown to be clinically effective; however, suboptimal attendance with wide demographic disparities has been reported. To develop quality improvement interventions to maximise attendance, it is important to understand the theoretical determinants (i.e. barriers and enablers) of screening behaviour. The aim of this systematic review is to identify and synthesise the modifiable barriers and enablers associated with diabetic retinopathy screening attendance. METHODS/DESIGN: Primary and secondary studies will be included if they report perceived barriers/enablers of diabetic retinopathy screening attendance, from the perspectives of people with diabetes and healthcare providers. There will be no restrictions on study design. Studies will be identified from published and grey literature through multiple sources. Bibliographic databases will be searched using synonyms in four search domains: diabetic retinopathy; screening; barriers/enablers; and theoretical constructs relating to behaviour. Search engines and established databases of grey literature will be searched to identify additional relevant studies. Extracted data will include: participant quotations from qualitative studies, statistical analyses from questionnaire and survey studies, and interpretive descriptions and summaries of results from reports. All extracted data will be coded into domains from the Theoretical Domains Framework (TDF) and (for organisational level data) the Consolidated Framework of Implementation Research (CFIR); with domains representing theoretical barriers/enablers proposed to mediate behaviour change. The potential role of each domain in influencing retinopathy screening attendance will be investigated through thematic analysis of the TDF/ CFIR coding. Domain importance will be identified using pre-specified criteria: "frequency" and "expressed importance". Variations in perceived barriers and enablers between demographic groups (e.g., socio-economic, ethnic) will be explored. DISCUSSION: This review will identify important barriers and enablers likely to influence attendance for diabetic retinopathy screening. The results will be used to assess the extent to which existing interventions targeting attendance address the theoretical determinants of attendance behaviour. Findings will inform recommendations for future intervention design. SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42016032990

Differential Photoelectron Holography: A New Approach for Three-Dimensional Atomic Imaging

We propose differential holography as a method to overcome the long-standing forward-scattering problem in photoelectron holography and related techniques for the three-dimensional imaging of atoms. Atomic images reconstructed from experimental and theoretical Cu 3p holograms from Cu(001) demonstrate that this method suppresses strong forward-scattering effects so as to yield more accurate three-dimensional images of side- and back-scattering atoms.Comment: revtex, 4 pages, 2 figure

Ex vivo propagation in a novel 3D high-throughput co-culture system for multiple myeloma

PURPOSE: Multiple myeloma (MM) remains an incurable hematologic malignancy which ultimately develops drug resistance and evades treatment. Despite substantial therapeutic advances over the past years, the clinical failure rate of preclinically promising anti-MM drugs remains substantial. More realistic in vitro models are thus required to better predict clinical efficacy of a preclinically active compound. METHODS: Here, we report on the establishment of a conical agarose 3D co-culture platform for the preclinical propagation of primary MM cells ex vivo. Cell growth was compared to yet established 2D and liquid overlay systems. MM cell lines (MMCL: RPMI-8226, U266, OPM-2) and primary patient specimens were tested. Drug sensitivity was examined by exploring the cytotoxic effect of bortezomib and the deubiquitinase inhibitor auranofin under various conditions. RESULTS: In contrast to 2D and liquid overlay, cell proliferation in the 3D array followed a sigmoidal curve characterized by an initial growth delay but more durable proliferation of MMCL over 12 days of culture. Primary MM specimens did not expand in ex vivo monoculture, but required co-culture support by a human stromal cell line (HS-5, MSP-1). HS-5 induced a \u3e fivefold increase in cluster volume and maintained long-term viability of primary MM cells for up to 21 days. Bortezomib and auranofin induced less cytotoxicity under 3D vs. 2D condition and in co- vs. monoculture, respectively. CONCLUSIONS: This study introduces a novel model that is capable of long-term propagation and drug testing of primary MM specimens ex vivo overcoming some of the pitfalls of currently available in vitro models

Pathways to professionalism? Quality improvement, care pathways, and the interplay of standardisation and clinical autonomy.

Care pathways are a prominent feature of efforts to improve healthcare quality, outcomes and accountability, but sociological studies of pathways often find professional resistance to standardisation. This qualitative study examined the adoption and adaptation of a novel pathway as part of a randomised controlled trial in an unusually complex, non-linear field - emergency general surgery - by teams of surgeons and physicians in six theoretically sampled sites in the UK. We find near-universal receptivity to the concept of a pathway as a means of improving peri-operative processes and outcomes, but concern about the impact on appropriate professional judgement. However, this concern translated not into resistance and implementation failure, but into a nuancing of the pathways-as-realised in each site, and their use as a means of enhancing professional decision-making and inter-professional collaboration. We discuss our findings in the context of recent literature on the interplay between managerialism and professionalism in healthcare, and highlight practical and theoretical implications

Study of a Swiss dopa-responsive dystonia family with a deletion in GCH1: redefining DYT14 as DYT5.

OBJECTIVE: To report the study of a multigenerational Swiss family with dopa-responsive dystonia (DRD). METHODS: Clinical investigation was made of available family members, including historical and chart reviews. Subject examinations were video recorded. Genetic analysis included a genome-wide linkage study with microsatellite markers (STR), GTP cyclohydrolase I (GCH1) gene sequencing, and dosage analysis. RESULTS: We evaluated 32 individuals, of whom 6 were clinically diagnosed with DRD, with childhood-onset progressive foot dystonia, later generalizing, followed by parkinsonism in the two older patients. The response to levodopa was very good. Two additional patients had late onset dopa-responsive parkinsonism. Three other subjects had DRD symptoms on historical grounds. We found suggestive linkage to the previously reported DYT14 locus, which excluded GCH1. However, further study with more stringent criteria for disease status attribution showed linkage to a larger region, which included GCH1. No mutation was found in GCH1 by gene sequencing but dosage methods identified a novel heterozygous deletion of exons 3 to 6 of GCH1. The mutation was found in seven subjects. One of the patients with dystonia represented a phenocopy. CONCLUSIONS: This study rules out the previously reported DYT14 locus as a cause of disease, as a novel multiexonic deletion was identified in GCH1. This work highlights the necessity of an accurate clinical diagnosis in linkage studies as well as the need for appropriate allele frequencies, penetrance, and phenocopy estimates. Comprehensive sequencing and dosage analysis of known genes is recommended prior to genome-wide linkage analysis

Administration of Intranasal Insulin During Cardiopulmonary Resuscitation Improves Neurological Outcomes After Cardiac Arrest

INTRODUCTION: Over 325,000 people die from cardiac arrest each year. Prognosis is poor and survivors typically experience persistent neurologic deficits. Currently, neuroprotective treatments to reduce brain injury in cardiac arrest survivors are limited and ineffective. This study evaluates the potential neuroprotection induced by high dose intranasal insulin (HD-IN-I) in a rodent model of asphyxial cardiac arrest. METHODS: Male Long Evans rats were block randomized to sham-operated controls or 8-minute asphyxial cardiac arrest treated with placebo or HD-IN-I at the onset of CPR. To investigate mechanism of action, hippocampi were collected 30 minutes post-ROSC and analyzed by Western blot for phosphorylation of Akt. To assess long-term functional outcomes, neurobehavioral evaluation was conducted using neurologic function scores daily and Barnes maze, Rotarod, and passive avoidance on days 7-10 post-ROSC. Histologic quantification of surviving hippocampal CA1 pyramidal neurons was also conducted. RESULTS: Hippocampal phospho-Akt/total Akt ratio increased 2-fold in the placebo group and 5.7-fold in HD-IN-I group relative to shams (p \u3c 0.05). Rats treated with HD-IN-I had significantly improved performance on Rotarod, Barnes maze, and passive avoidance (p \u3c 0.05). HD-IN-I had no significant effect on ROSC rate, 10-day survival, systemic glycemic response, or on the number of surviving CA1 pyramidal neurons compared to placebo treatment. DISCUSSION: This study is the first to demonstrate that HD-IN-I administered at the onset of CPR, causes phosphorylation of brain Akt and results in significant neuroprotection. This primary work strongly suggests that intranasal insulin could be the first highly effective neuroprotective treatment for cardiac arrest patients